From 9561c0f029df9c87608c8c084344ad347641a4fd Mon Sep 17 00:00:00 2001 From: Lily Wang Date: Thu, 18 Jun 2020 23:37:08 +1000 Subject: [PATCH 01/18] updated dependencies, available readers, wildcard selections --- doc/source/contributing_code.rst | 36 ++++----- doc/source/formats/coordinate_readers.txt | 7 ++ doc/source/formats/format_overview.txt | 8 ++ .../formats/reference/classes/CONFIG.txt | 1 + doc/source/formats/reference/classes/CRD.txt | 1 + doc/source/formats/reference/classes/DATA.txt | 1 + doc/source/formats/reference/classes/DCD.txt | 1 + doc/source/formats/reference/classes/DMS.txt | 1 + doc/source/formats/reference/classes/GMS.txt | 1 + doc/source/formats/reference/classes/GRO.txt | 1 + doc/source/formats/reference/classes/GSD.txt | 1 + .../formats/reference/classes/HISTORY.txt | 1 + .../formats/reference/classes/INPCRD.txt | 1 + doc/source/formats/reference/classes/ITP.txt | 1 + .../formats/reference/classes/LAMMPS.txt | 1 + .../formats/reference/classes/LAMMPSDUMP.txt | 1 + doc/source/formats/reference/classes/MMTF.txt | 1 + doc/source/formats/reference/classes/MOL2.txt | 1 + doc/source/formats/reference/classes/NCDF.txt | 1 + doc/source/formats/reference/classes/PDB.txt | 1 + .../formats/reference/classes/PDBQT.txt | 1 + doc/source/formats/reference/classes/PQR.txt | 1 + doc/source/formats/reference/classes/PSF.txt | 1 + doc/source/formats/reference/classes/TOP.txt | 1 + doc/source/formats/reference/classes/TPR.txt | 1 + doc/source/formats/reference/classes/TRJ.txt | 1 + doc/source/formats/reference/classes/TRR.txt | 1 + doc/source/formats/reference/classes/TRZ.txt | 1 + doc/source/formats/reference/classes/TXYZ.txt | 1 + doc/source/formats/reference/classes/XML.txt | 1 + doc/source/formats/reference/classes/XPDB.txt | 1 + doc/source/formats/reference/classes/XTC.txt | 1 + doc/source/formats/reference/classes/XYZ.txt | 1 + .../formats/selection_exporter_formats.txt | 1 + doc/source/formats/topology_parsers.txt | 3 +- doc/source/generated/selections/base.txt | 1 + doc/source/generated/selections/nucleic.txt | 1 + .../generated/selections/nucleic_backbone.txt | 1 + .../generated/selections/nucleic_sugar.txt | 1 + doc/source/generated/selections/protein.txt | 1 + .../generated/selections/protein_backbone.txt | 1 + .../generated/topology/connectivityattrs.txt | 1 + doc/source/generated/topology/defaults.txt | 75 +++++++++++-------- .../generated/topology/groupmethods.txt | 1 + .../generated/topology/topologyattrs.txt | 63 +++++++++------- doc/source/installation.rst | 5 +- doc/source/scripts/core.py | 6 ++ doc/source/selections.rst | 17 +++-- 48 files changed, 169 insertions(+), 90 deletions(-) diff --git a/doc/source/contributing_code.rst b/doc/source/contributing_code.rst index 7c63450d4..506341bb9 100644 --- a/doc/source/contributing_code.rst +++ b/doc/source/contributing_code.rst @@ -209,11 +209,12 @@ and activated your virtual environment. First we need to install dependencies: # if using conda conda install -c biobuilds -c conda-forge \ - pip cython numpy mmtf-python mock six biopython \ - networkx cython matplotlib scipy griddataformats \ - hypothesis gsd codecov "seaborn>=0.7.0,<=0.9" \ - clustalw=2.1 netcdf4 scikit-learn "joblib>=0.12"\ - psutil pytest + biopython chemfiles clustalw==2.1 codecov cython \ + griddataformats gsd hypothesis joblib>=0.12 \ + matplotlib mmtf-python mock netcdf4 networkx \ + numpy>=1.17.3 psutil pytest scikit-learn scipy \ + seaborn>=0.7.0,<0.9 sphinx==1.8.5 tidynamics>=1.0.0 \ + tqdm>=4.43.0 # if using conda with python 3.7 or 3.8, also run conda install -c conda-forge parmed @@ -221,13 +222,18 @@ and activated your virtual environment. First we need to install dependencies: # if using conda with other versions of python, also run pip install parmed + # documentation dependencies + pip install sphinx-sitemap sphinx_rtd_theme msmb_theme==1.2.0 + .. code-block:: bash # if using pip and virtualenv - pip install cython numpy mmtf-python mock six biopython \ - networkx cython matplotlib scipy griddataformats \ - hypothesis gsd codecov "seaborn>=0.7.0,<=0.9" \ - netcdf4 scikit-learn "joblib>=0.12" parmed psutil pytest + pip install biopython chemfiles codecov cython \ + griddataformats gsd hypothesis joblib>=0.12 matplotlib \ + msmb_theme==1.2.0 netcdf4 networkx numpy>=1.17.3 \ + parmed psutil pytest scikit-learn scipy seaborn>=0.7.0,<0.9 \ + sphinx==1.8.5 sphinx_rtd_theme tidynamics>=1.0.0 \ + tqdm>=4.43.0 Ensure that you have a working C/C++ compiler (e.g. gcc or clang). You will also need Python ≥ 3.4. We will now install MDAnalysis. @@ -555,17 +561,7 @@ Building the documentation The online documentation is generated from the pages in ``mdanalysis/package/doc/sphinx/source/documentation_pages``. The documentation for the current release are hosted at www.mdanalysis.org/docs, while the development version is at www.mdanalysis.org/mdanalysis/. -In order to build the documentation, you must first :ref:`clone the main MDAnalysis repo `. :ref:`Set up a virtual environment ` in the same way as you would for the code (you can use the same environment as you do for the code). You will need to install several packages for the docs. - - .. code-block:: bash - - pip install sphinx sphinx-sitemap sphinx_rtd_theme - -In addition, build the development version of MDAnalysis (if you haven't done this already): - - .. code-block:: bash - - pip install -e . +In order to build the documentation, you must first :ref:`clone the main MDAnalysis repo `. :ref:`Set up a virtual environment ` in the same way as you would for the code (you should typically use the same environment as you do for the code). Build the development version of MDAnalysis. Then, generate the docs with: diff --git a/doc/source/formats/coordinate_readers.txt b/doc/source/formats/coordinate_readers.txt index b9e2c922e..14de31399 100644 --- a/doc/source/formats/coordinate_readers.txt +++ b/doc/source/formats/coordinate_readers.txt @@ -1,26 +1,33 @@ +.. Generated by gen_format_overview_classes.py ===================================== ========================================= ============ ======== File type Description Velocities Forces ===================================== ========================================= ============ ======== :ref:`ARC ` Tinker file +:ref:`CHEMFILES ` chemfiles object :ref:`CONFIG ` DL_Poly CONFIG file ✓ +:ref:`COOR ` NAMDBIN file :ref:`CRD ` CHARMM CARD file :ref:`CRDBOX ` AMBER ASCII trajectories :ref:`DATA ` LAMMPS data file ✓ :ref:`DCD ` CHARMM, NAMD, or LAMMPS binary trajectory :ref:`DMS ` DESRES Molecular Structure file ✓ :ref:`ENT ` Standard PDB file +:ref:`FHIAIMS ` FHIAIMS file ✓ :ref:`GMS ` GAMESS file :ref:`GRO ` GROMACS structure file ✓ :ref:`GSD ` HOOMD GSD file :ref:`HISTORY ` DL_Poly HISTORY file ✓ +:ref:`IN ` FHIAIMS file ✓ :ref:`INPCRD ` AMBER restart file :ref:`LAMMPS ` a LAMMPS DCD trajectory :ref:`LAMMPSDUMP ` LAMMPS ascii dump file :ref:`MDCRD ` AMBER ASCII trajectories :ref:`MMTF ` MMTF file :ref:`MOL2 ` Tripos MOL2 file +:ref:`NAMDBIN ` NAMDBIN file :ref:`NC ` AMBER NETCDF format ✓ ✓ :ref:`NCDF ` AMBER NETCDF format ✓ ✓ +:ref:`PARMED ` parmed Structure :ref:`PDB ` Standard PDB file :ref:`PDBQT ` PDBQT file :ref:`PQR ` PQR file diff --git a/doc/source/formats/format_overview.txt b/doc/source/formats/format_overview.txt index eed1ef3b7..15ccb97c9 100644 --- a/doc/source/formats/format_overview.txt +++ b/doc/source/formats/format_overview.txt @@ -1,27 +1,35 @@ +.. Generated by gen_format_overview_classes.py ===================================== ========================================= ========== ============= ====== ======= File type Description Topology Coordinates Read Write ===================================== ========================================= ========== ============= ====== ======= :ref:`ARC ` Tinker file ✓ ✓ ✓ +:ref:`CHEMFILES ` chemfiles object ✓ ✓ ✓ :ref:`CONFIG ` DL_Poly CONFIG file ✓ ✓ ✓ +:ref:`COOR ` NAMDBIN file ✓ ✓ ✓ :ref:`CRD ` CHARMM CARD file ✓ ✓ ✓ ✓ :ref:`CRDBOX ` AMBER ASCII trajectories ✓ ✓ :ref:`DATA ` LAMMPS data file ✓ ✓ ✓ ✓ :ref:`DCD ` CHARMM, NAMD, or LAMMPS binary trajectory ✓ ✓ ✓ :ref:`DMS ` DESRES Molecular Structure file ✓ ✓ ✓ :ref:`ENT ` Standard PDB file ✓ ✓ ✓ ✓ +:ref:`FHIAIMS ` FHIAIMS file ✓ ✓ ✓ ✓ :ref:`GMS ` GAMESS file ✓ ✓ ✓ :ref:`GRO ` GROMACS structure file ✓ ✓ ✓ ✓ :ref:`GSD ` HOOMD GSD file ✓ ✓ ✓ :ref:`HISTORY ` DL_Poly HISTORY file ✓ ✓ ✓ +:ref:`IN ` FHIAIMS file ✓ ✓ ✓ ✓ :ref:`INPCRD ` AMBER restart file ✓ ✓ +:ref:`ITP ` GROMACS portable topology file ✓ ✓ :ref:`LAMMPS ` a LAMMPS DCD trajectory ✓ ✓ ✓ :ref:`LAMMPSDUMP ` LAMMPS ascii dump file ✓ ✓ ✓ :ref:`MDCRD ` AMBER ASCII trajectories ✓ ✓ :ref:`MMTF ` MMTF file ✓ ✓ ✓ :ref:`MOL2 ` Tripos MOL2 file ✓ ✓ ✓ ✓ +:ref:`NAMDBIN ` NAMDBIN file ✓ ✓ ✓ :ref:`NC ` AMBER NETCDF format ✓ ✓ :ref:`NCDF ` AMBER NETCDF format ✓ ✓ ✓ :ref:`PARM7 ` AMBER topology file ✓ ✓ +:ref:`PARMED ` parmed Structure ✓ ✓ ✓ :ref:`PDB ` Standard PDB file ✓ ✓ ✓ ✓ :ref:`PDBQT ` PDBQT file ✓ ✓ ✓ ✓ :ref:`PQR ` PQR file ✓ ✓ ✓ ✓ diff --git a/doc/source/formats/reference/classes/CONFIG.txt b/doc/source/formats/reference/classes/CONFIG.txt index 1b872455e..19ff9db02 100644 --- a/doc/source/formats/reference/classes/CONFIG.txt +++ b/doc/source/formats/reference/classes/CONFIG.txt @@ -1,3 +1,4 @@ +.. Generated by gen_format_overview_classes.py ===================== ====================================================== **Coordinate reader** :class:`MDAnalysis.coordinates.DLPoly.ConfigReader` **Topology parser** :class:`MDAnalysis.topology.DLPolyParser.ConfigParser` diff --git a/doc/source/formats/reference/classes/CRD.txt b/doc/source/formats/reference/classes/CRD.txt index 950c764a2..0b78ab332 100644 --- a/doc/source/formats/reference/classes/CRD.txt +++ b/doc/source/formats/reference/classes/CRD.txt @@ -1,3 +1,4 @@ +.. Generated by gen_format_overview_classes.py ===================== ================================================ **Coordinate reader** :class:`MDAnalysis.coordinates.CRD.CRDReader` **Coordinate writer** :class:`MDAnalysis.coordinates.CRD.CRDWriter` diff --git a/doc/source/formats/reference/classes/DATA.txt b/doc/source/formats/reference/classes/DATA.txt index d7aed82d3..ff985f95a 100644 --- a/doc/source/formats/reference/classes/DATA.txt +++ b/doc/source/formats/reference/classes/DATA.txt @@ -1,3 +1,4 @@ +.. Generated by gen_format_overview_classes.py ===================== ==================================================== **Coordinate reader** :class:`MDAnalysis.coordinates.LAMMPS.DATAReader` **Coordinate writer** :class:`MDAnalysis.coordinates.LAMMPS.DATAWriter` diff --git a/doc/source/formats/reference/classes/DCD.txt b/doc/source/formats/reference/classes/DCD.txt index c9877ca85..584e7d53d 100644 --- a/doc/source/formats/reference/classes/DCD.txt +++ b/doc/source/formats/reference/classes/DCD.txt @@ -1,3 +1,4 @@ +.. Generated by gen_format_overview_classes.py ===================== ============================================= **Coordinate reader** :class:`MDAnalysis.coordinates.DCD.DCDReader` **Coordinate writer** :class:`MDAnalysis.coordinates.DCD.DCDWriter` diff --git a/doc/source/formats/reference/classes/DMS.txt b/doc/source/formats/reference/classes/DMS.txt index f913a4b33..c4662fb9a 100644 --- a/doc/source/formats/reference/classes/DMS.txt +++ b/doc/source/formats/reference/classes/DMS.txt @@ -1,3 +1,4 @@ +.. Generated by gen_format_overview_classes.py ===================== ================================================ **Coordinate reader** :class:`MDAnalysis.coordinates.DMS.DMSReader` **Topology parser** :class:`MDAnalysis.topology.DMSParser.DMSParser` diff --git a/doc/source/formats/reference/classes/GMS.txt b/doc/source/formats/reference/classes/GMS.txt index 230ca2437..d9c038d82 100644 --- a/doc/source/formats/reference/classes/GMS.txt +++ b/doc/source/formats/reference/classes/GMS.txt @@ -1,3 +1,4 @@ +.. Generated by gen_format_overview_classes.py ===================== ================================================ **Coordinate reader** :class:`MDAnalysis.coordinates.GMS.GMSReader` **Topology parser** :class:`MDAnalysis.topology.GMSParser.GMSParser` diff --git a/doc/source/formats/reference/classes/GRO.txt b/doc/source/formats/reference/classes/GRO.txt index e592d2e5c..b446e22a3 100644 --- a/doc/source/formats/reference/classes/GRO.txt +++ b/doc/source/formats/reference/classes/GRO.txt @@ -1,3 +1,4 @@ +.. Generated by gen_format_overview_classes.py ===================== ================================================ **Coordinate reader** :class:`MDAnalysis.coordinates.GRO.GROReader` **Coordinate writer** :class:`MDAnalysis.coordinates.GRO.GROWriter` diff --git a/doc/source/formats/reference/classes/GSD.txt b/doc/source/formats/reference/classes/GSD.txt index 1337593e0..e2047045c 100644 --- a/doc/source/formats/reference/classes/GSD.txt +++ b/doc/source/formats/reference/classes/GSD.txt @@ -1,3 +1,4 @@ +.. Generated by gen_format_overview_classes.py ===================== ================================================ **Coordinate reader** :class:`MDAnalysis.coordinates.GSD.GSDReader` **Topology parser** :class:`MDAnalysis.topology.GSDParser.GSDParser` diff --git a/doc/source/formats/reference/classes/HISTORY.txt b/doc/source/formats/reference/classes/HISTORY.txt index 4c3ac24f5..64b0822d1 100644 --- a/doc/source/formats/reference/classes/HISTORY.txt +++ b/doc/source/formats/reference/classes/HISTORY.txt @@ -1,3 +1,4 @@ +.. Generated by gen_format_overview_classes.py ===================== ======================================================= **Coordinate reader** :class:`MDAnalysis.coordinates.DLPoly.HistoryReader` **Topology parser** :class:`MDAnalysis.topology.DLPolyParser.HistoryParser` diff --git a/doc/source/formats/reference/classes/INPCRD.txt b/doc/source/formats/reference/classes/INPCRD.txt index 874a4a7ca..964f73564 100644 --- a/doc/source/formats/reference/classes/INPCRD.txt +++ b/doc/source/formats/reference/classes/INPCRD.txt @@ -1,3 +1,4 @@ +.. Generated by gen_format_overview_classes.py ===================== ================================================ **Coordinate reader** :class:`MDAnalysis.coordinates.INPCRD.INPReader` ===================== ================================================ diff --git a/doc/source/formats/reference/classes/ITP.txt b/doc/source/formats/reference/classes/ITP.txt index f4073e3fb..d6699ce76 100644 --- a/doc/source/formats/reference/classes/ITP.txt +++ b/doc/source/formats/reference/classes/ITP.txt @@ -1,3 +1,4 @@ +.. Generated by gen_format_overview_classes.py =================== ================================================ **Topology parser** :class:`MDAnalysis.topology.ITPParser.ITPParser` =================== ================================================ diff --git a/doc/source/formats/reference/classes/LAMMPS.txt b/doc/source/formats/reference/classes/LAMMPS.txt index 4879b1251..878d58c7b 100644 --- a/doc/source/formats/reference/classes/LAMMPS.txt +++ b/doc/source/formats/reference/classes/LAMMPS.txt @@ -1,3 +1,4 @@ +.. Generated by gen_format_overview_classes.py ===================== ================================================ **Coordinate reader** :class:`MDAnalysis.coordinates.LAMMPS.DCDReader` **Coordinate writer** :class:`MDAnalysis.coordinates.LAMMPS.DCDWriter` diff --git a/doc/source/formats/reference/classes/LAMMPSDUMP.txt b/doc/source/formats/reference/classes/LAMMPSDUMP.txt index dc5fdb9d8..266d5ec17 100644 --- a/doc/source/formats/reference/classes/LAMMPSDUMP.txt +++ b/doc/source/formats/reference/classes/LAMMPSDUMP.txt @@ -1,3 +1,4 @@ +.. Generated by gen_format_overview_classes.py ===================== ========================================================== **Coordinate reader** :class:`MDAnalysis.coordinates.LAMMPS.DumpReader` **Topology parser** :class:`MDAnalysis.topology.LAMMPSParser.LammpsDumpParser` diff --git a/doc/source/formats/reference/classes/MMTF.txt b/doc/source/formats/reference/classes/MMTF.txt index a3b725b24..5a7f75fef 100644 --- a/doc/source/formats/reference/classes/MMTF.txt +++ b/doc/source/formats/reference/classes/MMTF.txt @@ -1,3 +1,4 @@ +.. Generated by gen_format_overview_classes.py ===================== ================================================== **Coordinate reader** :class:`MDAnalysis.coordinates.MMTF.MMTFReader` **Topology parser** :class:`MDAnalysis.topology.MMTFParser.MMTFParser` diff --git a/doc/source/formats/reference/classes/MOL2.txt b/doc/source/formats/reference/classes/MOL2.txt index 36c9f5563..bc58cc86a 100644 --- a/doc/source/formats/reference/classes/MOL2.txt +++ b/doc/source/formats/reference/classes/MOL2.txt @@ -1,3 +1,4 @@ +.. Generated by gen_format_overview_classes.py ===================== ================================================== **Coordinate reader** :class:`MDAnalysis.coordinates.MOL2.MOL2Reader` **Coordinate writer** :class:`MDAnalysis.coordinates.MOL2.MOL2Writer` diff --git a/doc/source/formats/reference/classes/NCDF.txt b/doc/source/formats/reference/classes/NCDF.txt index e297dd7c7..2c709ce1c 100644 --- a/doc/source/formats/reference/classes/NCDF.txt +++ b/doc/source/formats/reference/classes/NCDF.txt @@ -1,3 +1,4 @@ +.. Generated by gen_format_overview_classes.py ===================== ============================================== **Coordinate reader** :class:`MDAnalysis.coordinates.TRJ.NCDFReader` **Coordinate writer** :class:`MDAnalysis.coordinates.TRJ.NCDFWriter` diff --git a/doc/source/formats/reference/classes/PDB.txt b/doc/source/formats/reference/classes/PDB.txt index 67824dec7..53f6306b1 100644 --- a/doc/source/formats/reference/classes/PDB.txt +++ b/doc/source/formats/reference/classes/PDB.txt @@ -1,3 +1,4 @@ +.. Generated by gen_format_overview_classes.py ===================== ================================================ **Coordinate reader** :class:`MDAnalysis.coordinates.PDB.PDBReader` **Coordinate writer** :class:`MDAnalysis.coordinates.PDB.PDBWriter` diff --git a/doc/source/formats/reference/classes/PDBQT.txt b/doc/source/formats/reference/classes/PDBQT.txt index b5e2cc01e..25c6e4d71 100644 --- a/doc/source/formats/reference/classes/PDBQT.txt +++ b/doc/source/formats/reference/classes/PDBQT.txt @@ -1,3 +1,4 @@ +.. Generated by gen_format_overview_classes.py ===================== ==================================================== **Coordinate reader** :class:`MDAnalysis.coordinates.PDBQT.PDBQTReader` **Coordinate writer** :class:`MDAnalysis.coordinates.PDBQT.PDBQTWriter` diff --git a/doc/source/formats/reference/classes/PQR.txt b/doc/source/formats/reference/classes/PQR.txt index 716ec423b..20e1d84f8 100644 --- a/doc/source/formats/reference/classes/PQR.txt +++ b/doc/source/formats/reference/classes/PQR.txt @@ -1,3 +1,4 @@ +.. Generated by gen_format_overview_classes.py ===================== ================================================ **Coordinate reader** :class:`MDAnalysis.coordinates.PQR.PQRReader` **Coordinate writer** :class:`MDAnalysis.coordinates.PQR.PQRWriter` diff --git a/doc/source/formats/reference/classes/PSF.txt b/doc/source/formats/reference/classes/PSF.txt index 977aae370..205d38765 100644 --- a/doc/source/formats/reference/classes/PSF.txt +++ b/doc/source/formats/reference/classes/PSF.txt @@ -1,3 +1,4 @@ +.. Generated by gen_format_overview_classes.py =================== ================================================ **Topology parser** :class:`MDAnalysis.topology.PSFParser.PSFParser` =================== ================================================ diff --git a/doc/source/formats/reference/classes/TOP.txt b/doc/source/formats/reference/classes/TOP.txt index d2066311c..e2447df62 100644 --- a/doc/source/formats/reference/classes/TOP.txt +++ b/doc/source/formats/reference/classes/TOP.txt @@ -1,3 +1,4 @@ +.. Generated by gen_format_overview_classes.py =================== ================================================ **Topology parser** :class:`MDAnalysis.topology.TOPParser.TOPParser` =================== ================================================ diff --git a/doc/source/formats/reference/classes/TPR.txt b/doc/source/formats/reference/classes/TPR.txt index a55166dc0..665127221 100644 --- a/doc/source/formats/reference/classes/TPR.txt +++ b/doc/source/formats/reference/classes/TPR.txt @@ -1,3 +1,4 @@ +.. Generated by gen_format_overview_classes.py =================== ================================================ **Topology parser** :class:`MDAnalysis.topology.TPRParser.TPRParser` =================== ================================================ diff --git a/doc/source/formats/reference/classes/TRJ.txt b/doc/source/formats/reference/classes/TRJ.txt index e9f645992..5398eddcf 100644 --- a/doc/source/formats/reference/classes/TRJ.txt +++ b/doc/source/formats/reference/classes/TRJ.txt @@ -1,3 +1,4 @@ +.. Generated by gen_format_overview_classes.py ===================== ============================================= **Coordinate reader** :class:`MDAnalysis.coordinates.TRJ.TRJReader` ===================== ============================================= diff --git a/doc/source/formats/reference/classes/TRR.txt b/doc/source/formats/reference/classes/TRR.txt index 7351c6d92..d40232874 100644 --- a/doc/source/formats/reference/classes/TRR.txt +++ b/doc/source/formats/reference/classes/TRR.txt @@ -1,3 +1,4 @@ +.. Generated by gen_format_overview_classes.py ===================== ============================================= **Coordinate reader** :class:`MDAnalysis.coordinates.TRR.TRRReader` **Coordinate writer** :class:`MDAnalysis.coordinates.TRR.TRRWriter` diff --git a/doc/source/formats/reference/classes/TRZ.txt b/doc/source/formats/reference/classes/TRZ.txt index 7de36e58a..289b548c4 100644 --- a/doc/source/formats/reference/classes/TRZ.txt +++ b/doc/source/formats/reference/classes/TRZ.txt @@ -1,3 +1,4 @@ +.. Generated by gen_format_overview_classes.py ===================== ============================================= **Coordinate reader** :class:`MDAnalysis.coordinates.TRZ.TRZReader` **Coordinate writer** :class:`MDAnalysis.coordinates.TRZ.TRZWriter` diff --git a/doc/source/formats/reference/classes/TXYZ.txt b/doc/source/formats/reference/classes/TXYZ.txt index 032b00031..7d0c0d398 100644 --- a/doc/source/formats/reference/classes/TXYZ.txt +++ b/doc/source/formats/reference/classes/TXYZ.txt @@ -1,3 +1,4 @@ +.. Generated by gen_format_overview_classes.py ===================== ================================================== **Coordinate reader** :class:`MDAnalysis.coordinates.TXYZ.TXYZReader` **Topology parser** :class:`MDAnalysis.topology.TXYZParser.TXYZParser` diff --git a/doc/source/formats/reference/classes/XML.txt b/doc/source/formats/reference/classes/XML.txt index 5cb676f63..3022e5b66 100644 --- a/doc/source/formats/reference/classes/XML.txt +++ b/doc/source/formats/reference/classes/XML.txt @@ -1,3 +1,4 @@ +.. Generated by gen_format_overview_classes.py =================== ========================================================== **Topology parser** :class:`MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser` =================== ========================================================== diff --git a/doc/source/formats/reference/classes/XPDB.txt b/doc/source/formats/reference/classes/XPDB.txt index 371c5dd99..028e15a99 100644 --- a/doc/source/formats/reference/classes/XPDB.txt +++ b/doc/source/formats/reference/classes/XPDB.txt @@ -1,3 +1,4 @@ +.. Generated by gen_format_overview_classes.py ===================== ================================================================ **Coordinate reader** :class:`MDAnalysis.coordinates.PDB.ExtendedPDBReader` **Topology parser** :class:`MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser` diff --git a/doc/source/formats/reference/classes/XTC.txt b/doc/source/formats/reference/classes/XTC.txt index bdba2ee82..9a3cae368 100644 --- a/doc/source/formats/reference/classes/XTC.txt +++ b/doc/source/formats/reference/classes/XTC.txt @@ -1,3 +1,4 @@ +.. Generated by gen_format_overview_classes.py ===================== ============================================= **Coordinate reader** :class:`MDAnalysis.coordinates.XTC.XTCReader` **Coordinate writer** :class:`MDAnalysis.coordinates.XTC.XTCWriter` diff --git a/doc/source/formats/reference/classes/XYZ.txt b/doc/source/formats/reference/classes/XYZ.txt index 5199cfd50..cbdd317fa 100644 --- a/doc/source/formats/reference/classes/XYZ.txt +++ b/doc/source/formats/reference/classes/XYZ.txt @@ -1,3 +1,4 @@ +.. Generated by gen_format_overview_classes.py ===================== ================================================ **Coordinate reader** :class:`MDAnalysis.coordinates.XYZ.XYZReader` **Coordinate writer** :class:`MDAnalysis.coordinates.XYZ.XYZWriter` diff --git a/doc/source/formats/selection_exporter_formats.txt b/doc/source/formats/selection_exporter_formats.txt index 9d8f3f00f..21acdfef1 100644 --- a/doc/source/formats/selection_exporter_formats.txt +++ b/doc/source/formats/selection_exporter_formats.txt @@ -1,3 +1,4 @@ +.. Generated by gen_selection_exporters.py ========== =========== ======================================== ====================================================== Program Extension Description Class ========== =========== ======================================== ====================================================== diff --git a/doc/source/formats/topology_parsers.txt b/doc/source/formats/topology_parsers.txt index 720cabff3..2f597e826 100644 --- a/doc/source/formats/topology_parsers.txt +++ b/doc/source/formats/topology_parsers.txt @@ -1,3 +1,4 @@ +.. Generated by gen_topologyparser_attrs.py ====================================== =============================== ========================================================================================= ==================== Format Description Attributes read Attributes guessed ====================================== =============================== ========================================================================================= ==================== @@ -21,5 +22,5 @@ Format Description Attribu :ref:`TXYZ, ARC ` Tinker file bonds, names masses :ref:`XML ` HOOMD XML file angles, bonds, charges, dihedrals, impropers, radii :ref:`XPDB ` Extended PDB file altLocs, bonds, chainIDs, icodes, names, occupancies, record_types, resnames, tempfactors masses, types -:ref:`XYZ ` XYZ file names masses, types +:ref:`XYZ ` XYZ file elements, names masses, types ====================================== =============================== ========================================================================================= ==================== diff --git a/doc/source/generated/selections/base.txt b/doc/source/generated/selections/base.txt index 7778e9564..959b0336c 100644 --- a/doc/source/generated/selections/base.txt +++ b/doc/source/generated/selections/base.txt @@ -1,3 +1,4 @@ +.. Generated by gen_standard_selections.py == == == == == == == === N9 N7 C8 C5 C4 N3 C2 N1 C6 O6 N2 N6 O2 N4 O4 C5M diff --git a/doc/source/generated/selections/nucleic.txt b/doc/source/generated/selections/nucleic.txt index 85f7a6299..c3e7618ab 100644 --- a/doc/source/generated/selections/nucleic.txt +++ b/doc/source/generated/selections/nucleic.txt @@ -1,3 +1,4 @@ +.. Generated by gen_standard_selections.py === === === === === === === === ADE URA CYT GUA THY DA DC DG DT RA RU RG RC A T U diff --git a/doc/source/generated/selections/nucleic_backbone.txt b/doc/source/generated/selections/nucleic_backbone.txt index 66590ec1c..ac2e4290b 100644 --- a/doc/source/generated/selections/nucleic_backbone.txt +++ b/doc/source/generated/selections/nucleic_backbone.txt @@ -1,3 +1,4 @@ +.. Generated by gen_standard_selections.py = === === === === P C5' C3' O3' O5' = === === === === diff --git a/doc/source/generated/selections/nucleic_sugar.txt b/doc/source/generated/selections/nucleic_sugar.txt index f112bed13..9dd4be470 100644 --- a/doc/source/generated/selections/nucleic_sugar.txt +++ b/doc/source/generated/selections/nucleic_sugar.txt @@ -1,3 +1,4 @@ +.. Generated by gen_standard_selections.py === === === === === C1' C2' C3' C4' O4' === === === === === diff --git a/doc/source/generated/selections/protein.txt b/doc/source/generated/selections/protein.txt index 80cbd0c56..505da9cd0 100644 --- a/doc/source/generated/selections/protein.txt +++ b/doc/source/generated/selections/protein.txt @@ -1,3 +1,4 @@ +.. Generated by gen_standard_selections.py ==== ==== ==== ==== ==== ==== ==== ==== ACE ALA ALAD ARG ARGN ASF ASH ASN ASN1 ASP ASPH CALA CARG CASF CASN CASP diff --git a/doc/source/generated/selections/protein_backbone.txt b/doc/source/generated/selections/protein_backbone.txt index 88371d41c..eb5b1de1e 100644 --- a/doc/source/generated/selections/protein_backbone.txt +++ b/doc/source/generated/selections/protein_backbone.txt @@ -1,3 +1,4 @@ +.. Generated by gen_standard_selections.py = == = = N CA C O = == = = diff --git a/doc/source/generated/topology/connectivityattrs.txt b/doc/source/generated/topology/connectivityattrs.txt index 55cecbcba..e2f6ca2d7 100644 --- a/doc/source/generated/topology/connectivityattrs.txt +++ b/doc/source/generated/topology/connectivityattrs.txt @@ -1,3 +1,4 @@ +.. Generated by gen_topologyparser_attrs.py ========= =========== ============================================================================================================================================================================================================================================================================================================================================= Atom AtomGroup Supported formats ========= =========== ============================================================================================================================================================================================================================================================================================================================================= diff --git a/doc/source/generated/topology/defaults.txt b/doc/source/generated/topology/defaults.txt index 48d7c58c8..204728b46 100644 --- a/doc/source/generated/topology/defaults.txt +++ b/doc/source/generated/topology/defaults.txt @@ -1,32 +1,43 @@ -============= ============ ======================================== ======= ======================= -Atom AtomGroup default level type -============= ============ ======================================== ======= ======================= -altLocs altLoc '' atom -angles angles No default values atom -atomiccharges atomiccharge No default values atom -atomnums atomnum No default values atom -bfactors bfactor 0.0 atom -bonds bonds No default values atom -chainIDs chainID '' atom -charges charge 0.0 atom -dihedrals dihedrals No default values atom -elements element '' atom -icodes icode '' residue -ids id continuous sequence from 1 to n_atoms atom -impropers impropers No default values atom -masses mass 0.0 atom -models model No default values segment -molnums molnum No default values residue -moltypes moltype No default values residue -names name '' atom -occupancies occupancy 0.0 atom -radii radius 0.0 atom -record_types record_type 'ATOM' atom -resids resid continuous sequence from 1 to n_residues residue -resnames resname '' residue -resnums resnum continuous sequence from 1 to n_residues residue -segids segid '' segment -tempfactors tempfactor 0.0 atom -type_indices type_index No default values atom -types type '' atom -============= ============ ======================================== ======= ======================= +.. Generated by gen_topologyattr_defaults.py +============= ============= ======================================== ======= ======================= +Atom AtomGroup default level type +============= ============= ======================================== ======= ======================= +altLocs altLoc '' atom +angles angles No default values atom +atomiccharges atomiccharge No default values atom +atomnums atomnum No default values atom +bfactors bfactor 0.0 atom +bonds bonds No default values atom +chainIDs chainID '' atom +chargegroups chargegroup No default values atom +charges charge 0.0 atom +cmaps cmaps No default values atom +dihedrals dihedrals No default values atom +elements element '' atom +epsilon14s epsilon14 0.0 atom +epsilons epsilon 0.0 atom +gbscreens gbscreen 0.0 atom +icodes icode '' residue +ids id continuous sequence from 1 to n_atoms atom +impropers impropers No default values atom +masses mass 0.0 atom +models model No default values segment +molnums molnum No default values residue +moltypes moltype No default values residue +names name '' atom +nbindices nbindex 0 atom +occupancies occupancy 0.0 atom +radii radius 0.0 atom +record_types record_type 'ATOM' atom +resids resid continuous sequence from 1 to n_residues residue +resnames resname '' residue +resnums resnum continuous sequence from 1 to n_residues residue +rmin14s rmin14 0.0 atom +rmins rmin 0.0 atom +segids segid '' segment +solventradii solventradius 0.0 atom +tempfactors tempfactor 0.0 atom +type_indices type_index No default values atom +types type '' atom +ureybradleys ureybradleys No default values atom +============= ============= ======================================== ======= ======================= diff --git a/doc/source/generated/topology/groupmethods.txt b/doc/source/generated/topology/groupmethods.txt index 1880560ad..59c8d4f61 100644 --- a/doc/source/generated/topology/groupmethods.txt +++ b/doc/source/generated/topology/groupmethods.txt @@ -1,3 +1,4 @@ +.. Generated by gen_topology_groupmethods.py ================================================================== ====================================================================== ========== Method Description Requires ================================================================== ====================================================================== ========== diff --git a/doc/source/generated/topology/topologyattrs.txt b/doc/source/generated/topology/topologyattrs.txt index 7f47cd4e1..85588dcee 100644 --- a/doc/source/generated/topology/topologyattrs.txt +++ b/doc/source/generated/topology/topologyattrs.txt @@ -1,26 +1,37 @@ -============ ============= ================================== =================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== -Atom AtomGroup Description Supported formats -============ ============= ================================== =================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== -altLoc altLocs Alternate location :ref:`MMTF `, :ref:`PDB, ENT `, :ref:`PDBQT `, :ref:`XPDB ` -angles angles :ref:`DATA `, :ref:`GSD `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`XML ` -atomiccharge atomiccharges Atomic number :ref:`GMS ` -atomnum atomnums ? :ref:`DMS ` -bfactor bfactors alias of tempfactor :ref:`MMTF ` -bonds bonds :ref:`DATA `, :ref:`DMS `, :ref:`GSD `, :ref:`MMTF `, :ref:`MOL2 `, :ref:`PDB, ENT `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`TXYZ, ARC `, :ref:`XML `, :ref:`XPDB ` -chainID chainIDs chain ID :ref:`DMS `, :ref:`PDB, ENT `, :ref:`XPDB ` -charge charges partial atomic charge :ref:`DATA `, :ref:`DMS `, :ref:`GSD `, :ref:`MMTF `, :ref:`MOL2 `, :ref:`PDBQT `, :ref:`PQR `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`XML ` -dihedrals dihedrals :ref:`DATA `, :ref:`GSD `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`XML ` -element elements atom element :ref:`TOP, PRMTOP, PARM7 ` -icode icodes atom insertion code :ref:`MMTF `, :ref:`PDB, ENT `, :ref:`PDBQT `, :ref:`PQR `, :ref:`XPDB ` -impropers impropers :ref:`DATA `, :ref:`GSD `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`XML ` -model models model number (from 0) :ref:`MMTF ` -molnum molnums [molecules] number (from 0) :ref:`TPR ` -moltype moltypes [moleculetype] name :ref:`TPR ` -name names atom names :ref:`CONFIG `, :ref:`CRD `, :ref:`DMS `, :ref:`GMS `, :ref:`GRO `, :ref:`GSD `, :ref:`HISTORY `, :ref:`MMTF `, :ref:`MOL2 `, :ref:`PDB, ENT `, :ref:`PDBQT `, :ref:`PQR `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`TXYZ, ARC `, :ref:`XPDB `, :ref:`XYZ ` -occupancy occupancies atom occupancy :ref:`MMTF `, :ref:`PDB, ENT `, :ref:`PDBQT `, :ref:`XPDB ` -radius radii atomic radius :ref:`GSD `, :ref:`PQR `, :ref:`XML ` -record_type record_types ATOM / HETATM :ref:`PDB, ENT `, :ref:`PDBQT `, :ref:`PQR `, :ref:`XPDB ` -resname resnames residue name (except GSD has ints) :ref:`CRD `, :ref:`DMS `, :ref:`GRO `, :ref:`GSD `, :ref:`MMTF `, :ref:`MOL2 `, :ref:`PDB, ENT `, :ref:`PDBQT `, :ref:`PQR `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`XPDB ` -tempfactor tempfactors B-factor :ref:`CRD `, :ref:`PDB, ENT `, :ref:`PDBQT `, :ref:`XPDB ` -type_index type_indices amber atom type number :ref:`TOP, PRMTOP, PARM7 ` -============ ============= ================================== =================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== +.. Generated by gen_topologyparser_attrs.py +============= ============= ================================== =================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== +Atom AtomGroup Description Supported formats +============= ============= ================================== =================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== +altLoc altLocs Alternate location :ref:`MMTF `, :ref:`PDB, ENT `, :ref:`PDBQT `, :ref:`XPDB ` +angles angles :ref:`DATA `, :ref:`GSD `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`XML ` +atomiccharge atomiccharges Atomic number :ref:`GMS ` +atomnum atomnums ? :ref:`DMS ` +bfactor bfactors alias of tempfactor :ref:`MMTF ` +bonds bonds :ref:`DATA `, :ref:`DMS `, :ref:`GSD `, :ref:`MMTF `, :ref:`MOL2 `, :ref:`PDB, ENT `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`TXYZ, ARC `, :ref:`XML `, :ref:`XPDB ` +chainID chainIDs chain ID :ref:`DMS `, :ref:`PDB, ENT `, :ref:`XPDB ` +charge charges partial atomic charge :ref:`DATA `, :ref:`DMS `, :ref:`GSD `, :ref:`MMTF `, :ref:`MOL2 `, :ref:`PDBQT `, :ref:`PQR `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`XML ` +chargegroup chargegroups +cmaps cmaps +dihedrals dihedrals :ref:`DATA `, :ref:`GSD `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`XML ` +element elements atom element :ref:`TOP, PRMTOP, PARM7 `, :ref:`XYZ ` +epsilon epsilons +epsilon14 epsilon14s +gbscreen gbscreens +icode icodes atom insertion code :ref:`MMTF `, :ref:`PDB, ENT `, :ref:`PDBQT `, :ref:`PQR `, :ref:`XPDB ` +impropers impropers :ref:`DATA `, :ref:`GSD `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`XML ` +model models model number (from 0) :ref:`MMTF ` +molnum molnums [molecules] number (from 0) :ref:`TPR ` +moltype moltypes [moleculetype] name :ref:`TPR ` +name names atom names :ref:`CONFIG `, :ref:`CRD `, :ref:`DMS `, :ref:`GMS `, :ref:`GRO `, :ref:`GSD `, :ref:`HISTORY `, :ref:`MMTF `, :ref:`MOL2 `, :ref:`PDB, ENT `, :ref:`PDBQT `, :ref:`PQR `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`TXYZ, ARC `, :ref:`XPDB `, :ref:`XYZ ` +nbindex nbindices +occupancy occupancies atom occupancy :ref:`MMTF `, :ref:`PDB, ENT `, :ref:`PDBQT `, :ref:`XPDB ` +radius radii atomic radius :ref:`GSD `, :ref:`PQR `, :ref:`XML ` +record_type record_types ATOM / HETATM :ref:`PDB, ENT `, :ref:`PDBQT `, :ref:`PQR `, :ref:`XPDB ` +resname resnames residue name (except GSD has ints) :ref:`CRD `, :ref:`DMS `, :ref:`GRO `, :ref:`GSD `, :ref:`MMTF `, :ref:`MOL2 `, :ref:`PDB, ENT `, :ref:`PDBQT `, :ref:`PQR `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`XPDB ` +rmin rmins +rmin14 rmin14s +solventradius solventradii +tempfactor tempfactors B-factor :ref:`CRD `, :ref:`PDB, ENT `, :ref:`PDBQT `, :ref:`XPDB ` +type_index type_indices amber atom type number :ref:`TOP, PRMTOP, PARM7 ` +ureybradleys ureybradleys +============= ============= ================================== =================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== diff --git a/doc/source/installation.rst b/doc/source/installation.rst index c761aeabe..dc2da1c51 100644 --- a/doc/source/installation.rst +++ b/doc/source/installation.rst @@ -59,16 +59,15 @@ To install/upgrade tests: Development versions ==================== -To install development versions of MDAnalysis, you can compile it from source. +To install development versions of MDAnalysis, you can compile it from source. In order to install from source, you will need ``numpy`` and ``cython``. See :ref:`create-virtual-environment` for instructions on how to create a full development environment. .. code-block:: bash git clone https://github.com/MDAnalysis/mdanalysis cd mdanalysis + # assuming you have already installed required dependencies pip install -e . -In order to install from source, you will need ``numpy`` and ``cython``. See :ref:`create-virtual-environment` for instructions on how to create a full development environment. - Testing ------- diff --git a/doc/source/scripts/core.py b/doc/source/scripts/core.py index 0c5fe84be..74c40eaee 100644 --- a/doc/source/scripts/core.py +++ b/doc/source/scripts/core.py @@ -6,12 +6,16 @@ # ====== TOPOLOGY ====== # DESCRIPTIONS = { + 'CHEMFILES': 'chemfiles object', + 'PARMED': 'parmed Structure', 'CRD': 'CHARMM CARD file', 'CONFIG': 'DL_Poly CONFIG file', + 'COOR': 'NAMDBIN file', 'DCD': 'CHARMM, NAMD, or LAMMPS binary trajectory', 'HISTORY': 'DL_Poly HISTORY file', 'DMS': 'DESRES Molecular Structure file', 'XPDB': 'Extended PDB file', + 'FHIAIMS': 'FHIAIMS file', 'GMS': 'GAMESS file', 'GRO': 'GROMACS structure file', 'GSD': 'HOOMD GSD file', @@ -19,9 +23,11 @@ 'DATA': 'LAMMPS data file', 'INPCRD': 'AMBER restart file', 'ITP': 'GROMACS portable topology file', + 'IN': 'FHIAIMS file', 'LAMMPS': 'a LAMMPS DCD trajectory', 'LAMMPSDUMP': 'LAMMPS ascii dump file', 'MMTF' : 'MMTF file', + 'NAMDBIN': 'NAMDBIN file', 'NCDF': 'AMBER NETCDF format', 'MOL2': 'Tripos MOL2 file', 'PDB': 'Standard PDB file', diff --git a/doc/source/selections.rst b/doc/source/selections.rst index 3ea6ac61b..236704ba5 100644 --- a/doc/source/selections.rst +++ b/doc/source/selections.rst @@ -68,14 +68,15 @@ selection parser. The following applies to all selections: u.select_atoms("segid DMPC and not (name H* or type OW)") -* Currently, wildcards are implemented as a form of pattern - matching: Using the ``*`` character in a string such as ``GL*`` selects - all strings that start with "GL" such as "GLU", "GLY", "GLX29", "GLN". Only terminal wildcards (i.e. matching the last part of a name) are currently supported. - -.. note:: - - Up until version 1.0.0, MDAnalysis will ignore everything after the ``*``. ``u.select_atoms("resname *E")`` will not select atoms whose residue name ends in E, but instead select every atom. - +* String selections such as names and residue names can be + matched with Unix shell-style wildcards. Using ``*`` + in a string matches any number of any characters; ``?`` + matches any single character; ``[seq]`` matches any character in *seq*; + and ``[!seq]`` matches any character not in *seq*. For example, + the string ``GL*`` selects all strings that start with "GL", + such as "GLU", "GLY", "GLX29", "GLN". ``GL[YN]`` will select all "GLY" and + "GLN" strings. Any number of patterns can be included in the search. + For more information on pattern matching, see the :mod:`fnmatch` documentation. Simple selections ----------------- From 48db63f086b638bccb5895e4dabc2c861ef26ec8 Mon Sep 17 00:00:00 2001 From: Lily Wang Date: Thu, 18 Jun 2020 23:56:42 +1000 Subject: [PATCH 02/18] add rtd --- .readthedocs.yml | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 .readthedocs.yml diff --git a/.readthedocs.yml b/.readthedocs.yml new file mode 100644 index 000000000..aefe6f5b0 --- /dev/null +++ b/.readthedocs.yml @@ -0,0 +1,22 @@ +# .readthedocs.yml +# Read the Docs configuration file +# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details + +# Required +version: 2 + +# Build documentation in the docs/ directory with Sphinx +sphinx: + configuration: doc/source/conf.py + +# Build documentation with MkDocs +#mkdocs: +# configuration: mkdocs.yml + + +# Optionally set the version of Python and requirements required to build your docs +python: + version: 3.7 + +conda: + environment: environment.yml \ No newline at end of file From 0b80f64ee4db97ea709ec384cfa593d0d433e288 Mon Sep 17 00:00:00 2001 From: Lily Wang Date: Fri, 19 Jun 2020 01:12:04 +1000 Subject: [PATCH 03/18] add info on parmed and chemfiles --- doc/source/formats/coordinate_readers.txt | 11 ++++++----- doc/source/formats/format_overview.txt | 13 +++++++------ doc/source/formats/reference/chemfiles.rst | 12 ++++++++++++ doc/source/formats/reference/classes/CONFIG.txt | 3 ++- doc/source/formats/reference/classes/CRD.txt | 3 ++- doc/source/formats/reference/classes/DATA.txt | 3 ++- doc/source/formats/reference/classes/DCD.txt | 3 ++- doc/source/formats/reference/classes/DMS.txt | 3 ++- doc/source/formats/reference/classes/GMS.txt | 3 ++- doc/source/formats/reference/classes/GRO.txt | 3 ++- doc/source/formats/reference/classes/GSD.txt | 3 ++- doc/source/formats/reference/classes/HISTORY.txt | 3 ++- doc/source/formats/reference/classes/INPCRD.txt | 3 ++- doc/source/formats/reference/classes/ITP.txt | 3 ++- doc/source/formats/reference/classes/LAMMPS.txt | 3 ++- doc/source/formats/reference/classes/LAMMPSDUMP.txt | 3 ++- doc/source/formats/reference/classes/MMTF.txt | 3 ++- doc/source/formats/reference/classes/MOL2.txt | 3 ++- doc/source/formats/reference/classes/NCDF.txt | 3 ++- doc/source/formats/reference/classes/PDB.txt | 3 ++- doc/source/formats/reference/classes/PDBQT.txt | 3 ++- doc/source/formats/reference/classes/PQR.txt | 3 ++- doc/source/formats/reference/classes/PSF.txt | 3 ++- doc/source/formats/reference/classes/TOP.txt | 3 ++- doc/source/formats/reference/classes/TPR.txt | 3 ++- doc/source/formats/reference/classes/TRJ.txt | 3 ++- doc/source/formats/reference/classes/TRR.txt | 3 ++- doc/source/formats/reference/classes/TRZ.txt | 3 ++- doc/source/formats/reference/classes/TXYZ.txt | 3 ++- doc/source/formats/reference/classes/XML.txt | 3 ++- doc/source/formats/reference/classes/XPDB.txt | 3 ++- doc/source/formats/reference/classes/XTC.txt | 3 ++- doc/source/formats/reference/classes/XYZ.txt | 3 ++- doc/source/formats/reference/coor.rst | 8 ++++++++ doc/source/formats/reference/in.rst | 8 ++++++++ doc/source/formats/reference/parmed.rst | 12 ++++++++++++ doc/source/formats/selection_exporter_formats.txt | 3 ++- doc/source/formats/topology_parsers.txt | 5 +++-- doc/source/generated/selections/base.txt | 3 ++- doc/source/generated/selections/nucleic.txt | 3 ++- .../generated/selections/nucleic_backbone.txt | 3 ++- doc/source/generated/selections/nucleic_sugar.txt | 3 ++- doc/source/generated/selections/protein.txt | 3 ++- .../generated/selections/protein_backbone.txt | 3 ++- doc/source/generated/topology/connectivityattrs.txt | 3 ++- doc/source/generated/topology/defaults.txt | 3 ++- doc/source/generated/topology/groupmethods.txt | 3 ++- doc/source/generated/topology/topologyattrs.txt | 5 +++-- doc/source/scripts/base.py | 2 +- doc/source/scripts/core.py | 6 ++---- doc/source/scripts/gen_format_overview_classes.py | 7 +++++-- 51 files changed, 147 insertions(+), 62 deletions(-) create mode 100644 doc/source/formats/reference/chemfiles.rst create mode 100644 doc/source/formats/reference/coor.rst create mode 100644 doc/source/formats/reference/in.rst create mode 100644 doc/source/formats/reference/parmed.rst diff --git a/doc/source/formats/coordinate_readers.txt b/doc/source/formats/coordinate_readers.txt index 14de31399..b7c26f7e3 100644 --- a/doc/source/formats/coordinate_readers.txt +++ b/doc/source/formats/coordinate_readers.txt @@ -1,30 +1,29 @@ -.. Generated by gen_format_overview_classes.py ===================================== ========================================= ============ ======== File type Description Velocities Forces ===================================== ========================================= ============ ======== :ref:`ARC ` Tinker file :ref:`CHEMFILES ` chemfiles object :ref:`CONFIG ` DL_Poly CONFIG file ✓ -:ref:`COOR ` NAMDBIN file +:ref:`COOR ` NAMD binary restart file :ref:`CRD ` CHARMM CARD file :ref:`CRDBOX ` AMBER ASCII trajectories :ref:`DATA ` LAMMPS data file ✓ :ref:`DCD ` CHARMM, NAMD, or LAMMPS binary trajectory :ref:`DMS ` DESRES Molecular Structure file ✓ :ref:`ENT ` Standard PDB file -:ref:`FHIAIMS ` FHIAIMS file ✓ +:ref:`FHIAIMS ` FHI-aims input file ✓ :ref:`GMS ` GAMESS file :ref:`GRO ` GROMACS structure file ✓ :ref:`GSD ` HOOMD GSD file :ref:`HISTORY ` DL_Poly HISTORY file ✓ -:ref:`IN ` FHIAIMS file ✓ +:ref:`IN ` FHI-aims input file ✓ :ref:`INPCRD ` AMBER restart file :ref:`LAMMPS ` a LAMMPS DCD trajectory :ref:`LAMMPSDUMP ` LAMMPS ascii dump file :ref:`MDCRD ` AMBER ASCII trajectories :ref:`MMTF ` MMTF file :ref:`MOL2 ` Tripos MOL2 file -:ref:`NAMDBIN ` NAMDBIN file +:ref:`NAMDBIN ` NAMD binary restart file :ref:`NC ` AMBER NETCDF format ✓ ✓ :ref:`NCDF ` AMBER NETCDF format ✓ ✓ :ref:`PARMED ` parmed Structure @@ -40,3 +39,5 @@ File type Description :ref:`XTC ` GROMACS compressed trajectory :ref:`XYZ ` XYZ file ===================================== ========================================= ============ ======== + +.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/format_overview.txt b/doc/source/formats/format_overview.txt index 15ccb97c9..71c301772 100644 --- a/doc/source/formats/format_overview.txt +++ b/doc/source/formats/format_overview.txt @@ -1,23 +1,22 @@ -.. Generated by gen_format_overview_classes.py ===================================== ========================================= ========== ============= ====== ======= File type Description Topology Coordinates Read Write ===================================== ========================================= ========== ============= ====== ======= :ref:`ARC ` Tinker file ✓ ✓ ✓ :ref:`CHEMFILES ` chemfiles object ✓ ✓ ✓ :ref:`CONFIG ` DL_Poly CONFIG file ✓ ✓ ✓ -:ref:`COOR ` NAMDBIN file ✓ ✓ ✓ +:ref:`COOR ` NAMD binary restart file ✓ ✓ ✓ :ref:`CRD ` CHARMM CARD file ✓ ✓ ✓ ✓ :ref:`CRDBOX ` AMBER ASCII trajectories ✓ ✓ :ref:`DATA ` LAMMPS data file ✓ ✓ ✓ ✓ :ref:`DCD ` CHARMM, NAMD, or LAMMPS binary trajectory ✓ ✓ ✓ :ref:`DMS ` DESRES Molecular Structure file ✓ ✓ ✓ :ref:`ENT ` Standard PDB file ✓ ✓ ✓ ✓ -:ref:`FHIAIMS ` FHIAIMS file ✓ ✓ ✓ ✓ +:ref:`FHIAIMS ` FHI-aims input file ✓ ✓ ✓ ✓ :ref:`GMS ` GAMESS file ✓ ✓ ✓ :ref:`GRO ` GROMACS structure file ✓ ✓ ✓ ✓ :ref:`GSD ` HOOMD GSD file ✓ ✓ ✓ :ref:`HISTORY ` DL_Poly HISTORY file ✓ ✓ ✓ -:ref:`IN ` FHIAIMS file ✓ ✓ ✓ ✓ +:ref:`IN ` FHI-aims input file ✓ ✓ ✓ ✓ :ref:`INPCRD ` AMBER restart file ✓ ✓ :ref:`ITP ` GROMACS portable topology file ✓ ✓ :ref:`LAMMPS ` a LAMMPS DCD trajectory ✓ ✓ ✓ @@ -25,11 +24,11 @@ File type Description :ref:`MDCRD ` AMBER ASCII trajectories ✓ ✓ :ref:`MMTF ` MMTF file ✓ ✓ ✓ :ref:`MOL2 ` Tripos MOL2 file ✓ ✓ ✓ ✓ -:ref:`NAMDBIN ` NAMDBIN file ✓ ✓ ✓ +:ref:`NAMDBIN ` NAMD binary restart file ✓ ✓ ✓ :ref:`NC ` AMBER NETCDF format ✓ ✓ :ref:`NCDF ` AMBER NETCDF format ✓ ✓ ✓ :ref:`PARM7 ` AMBER topology file ✓ ✓ -:ref:`PARMED ` parmed Structure ✓ ✓ ✓ +:ref:`PARMED ` parmed Structure ✓ ✓ ✓ ✓ :ref:`PDB ` Standard PDB file ✓ ✓ ✓ ✓ :ref:`PDBQT ` PDBQT file ✓ ✓ ✓ ✓ :ref:`PQR ` PQR file ✓ ✓ ✓ ✓ @@ -47,3 +46,5 @@ File type Description :ref:`XTC ` GROMACS compressed trajectory ✓ ✓ ✓ :ref:`XYZ ` XYZ file ✓ ✓ ✓ ✓ ===================================== ========================================= ========== ============= ====== ======= + +.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/reference/chemfiles.rst b/doc/source/formats/reference/chemfiles.rst new file mode 100644 index 000000000..9e1e07800 --- /dev/null +++ b/doc/source/formats/reference/chemfiles.rst @@ -0,0 +1,12 @@ +.. -*- coding: utf-8 -*- +.. _CHEMFILES-format: + +======================================== +CHEMFILES (chemfiles Trajectory or file) +======================================== + +.. include:: classes/CHEMFILES.txt + +The chemfiles_ library provides a C++ implementation of readers and writers for multiple formats. Pass in either a :class:`chemfiles.Trajectory` to be converted into an MDAnalysis Universe, or pass in files to this format with the keyword ``format='CHEMFILES'`` to read the information with the chemfiles implementation. You can also write the MDAnalysis Universe back into a chemfiles object for further work. + +.. _chemfiles: https://chemfiles.org/ \ No newline at end of file diff --git a/doc/source/formats/reference/classes/CONFIG.txt b/doc/source/formats/reference/classes/CONFIG.txt index 19ff9db02..4ebe03bff 100644 --- a/doc/source/formats/reference/classes/CONFIG.txt +++ b/doc/source/formats/reference/classes/CONFIG.txt @@ -1,5 +1,6 @@ -.. Generated by gen_format_overview_classes.py ===================== ====================================================== **Coordinate reader** :class:`MDAnalysis.coordinates.DLPoly.ConfigReader` **Topology parser** :class:`MDAnalysis.topology.DLPolyParser.ConfigParser` ===================== ====================================================== + +.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/reference/classes/CRD.txt b/doc/source/formats/reference/classes/CRD.txt index 0b78ab332..9398e443f 100644 --- a/doc/source/formats/reference/classes/CRD.txt +++ b/doc/source/formats/reference/classes/CRD.txt @@ -1,6 +1,7 @@ -.. Generated by gen_format_overview_classes.py ===================== ================================================ **Coordinate reader** :class:`MDAnalysis.coordinates.CRD.CRDReader` **Coordinate writer** :class:`MDAnalysis.coordinates.CRD.CRDWriter` **Topology parser** :class:`MDAnalysis.topology.CRDParser.CRDParser` ===================== ================================================ + +.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/reference/classes/DATA.txt b/doc/source/formats/reference/classes/DATA.txt index ff985f95a..cdbf5c258 100644 --- a/doc/source/formats/reference/classes/DATA.txt +++ b/doc/source/formats/reference/classes/DATA.txt @@ -1,6 +1,7 @@ -.. Generated by gen_format_overview_classes.py ===================== ==================================================== **Coordinate reader** :class:`MDAnalysis.coordinates.LAMMPS.DATAReader` **Coordinate writer** :class:`MDAnalysis.coordinates.LAMMPS.DATAWriter` **Topology parser** :class:`MDAnalysis.topology.LAMMPSParser.DATAParser` ===================== ==================================================== + +.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/reference/classes/DCD.txt b/doc/source/formats/reference/classes/DCD.txt index 584e7d53d..2af18a428 100644 --- a/doc/source/formats/reference/classes/DCD.txt +++ b/doc/source/formats/reference/classes/DCD.txt @@ -1,5 +1,6 @@ -.. Generated by gen_format_overview_classes.py ===================== ============================================= **Coordinate reader** :class:`MDAnalysis.coordinates.DCD.DCDReader` **Coordinate writer** :class:`MDAnalysis.coordinates.DCD.DCDWriter` ===================== ============================================= + +.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/reference/classes/DMS.txt b/doc/source/formats/reference/classes/DMS.txt index c4662fb9a..94b31935f 100644 --- a/doc/source/formats/reference/classes/DMS.txt +++ b/doc/source/formats/reference/classes/DMS.txt @@ -1,5 +1,6 @@ -.. Generated by gen_format_overview_classes.py ===================== ================================================ **Coordinate reader** :class:`MDAnalysis.coordinates.DMS.DMSReader` **Topology parser** :class:`MDAnalysis.topology.DMSParser.DMSParser` ===================== ================================================ + +.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/reference/classes/GMS.txt b/doc/source/formats/reference/classes/GMS.txt index d9c038d82..d7523fe47 100644 --- a/doc/source/formats/reference/classes/GMS.txt +++ b/doc/source/formats/reference/classes/GMS.txt @@ -1,5 +1,6 @@ -.. Generated by gen_format_overview_classes.py ===================== ================================================ **Coordinate reader** :class:`MDAnalysis.coordinates.GMS.GMSReader` **Topology parser** :class:`MDAnalysis.topology.GMSParser.GMSParser` ===================== ================================================ + +.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/reference/classes/GRO.txt b/doc/source/formats/reference/classes/GRO.txt index b446e22a3..b93fb12f6 100644 --- a/doc/source/formats/reference/classes/GRO.txt +++ b/doc/source/formats/reference/classes/GRO.txt @@ -1,6 +1,7 @@ -.. Generated by gen_format_overview_classes.py ===================== ================================================ **Coordinate reader** :class:`MDAnalysis.coordinates.GRO.GROReader` **Coordinate writer** :class:`MDAnalysis.coordinates.GRO.GROWriter` **Topology parser** :class:`MDAnalysis.topology.GROParser.GROParser` ===================== ================================================ + +.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/reference/classes/GSD.txt b/doc/source/formats/reference/classes/GSD.txt index e2047045c..8fb952e61 100644 --- a/doc/source/formats/reference/classes/GSD.txt +++ b/doc/source/formats/reference/classes/GSD.txt @@ -1,5 +1,6 @@ -.. Generated by gen_format_overview_classes.py ===================== ================================================ **Coordinate reader** :class:`MDAnalysis.coordinates.GSD.GSDReader` **Topology parser** :class:`MDAnalysis.topology.GSDParser.GSDParser` ===================== ================================================ + +.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/reference/classes/HISTORY.txt b/doc/source/formats/reference/classes/HISTORY.txt index 64b0822d1..01e3d9372 100644 --- a/doc/source/formats/reference/classes/HISTORY.txt +++ b/doc/source/formats/reference/classes/HISTORY.txt @@ -1,5 +1,6 @@ -.. Generated by gen_format_overview_classes.py ===================== ======================================================= **Coordinate reader** :class:`MDAnalysis.coordinates.DLPoly.HistoryReader` **Topology parser** :class:`MDAnalysis.topology.DLPolyParser.HistoryParser` ===================== ======================================================= + +.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/reference/classes/INPCRD.txt b/doc/source/formats/reference/classes/INPCRD.txt index 964f73564..26c847a25 100644 --- a/doc/source/formats/reference/classes/INPCRD.txt +++ b/doc/source/formats/reference/classes/INPCRD.txt @@ -1,4 +1,5 @@ -.. Generated by gen_format_overview_classes.py ===================== ================================================ **Coordinate reader** :class:`MDAnalysis.coordinates.INPCRD.INPReader` ===================== ================================================ + +.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/reference/classes/ITP.txt b/doc/source/formats/reference/classes/ITP.txt index d6699ce76..628dab03f 100644 --- a/doc/source/formats/reference/classes/ITP.txt +++ b/doc/source/formats/reference/classes/ITP.txt @@ -1,4 +1,5 @@ -.. Generated by gen_format_overview_classes.py =================== ================================================ **Topology parser** :class:`MDAnalysis.topology.ITPParser.ITPParser` =================== ================================================ + +.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/reference/classes/LAMMPS.txt b/doc/source/formats/reference/classes/LAMMPS.txt index 878d58c7b..b69d20df8 100644 --- a/doc/source/formats/reference/classes/LAMMPS.txt +++ b/doc/source/formats/reference/classes/LAMMPS.txt @@ -1,5 +1,6 @@ -.. Generated by gen_format_overview_classes.py ===================== ================================================ **Coordinate reader** :class:`MDAnalysis.coordinates.LAMMPS.DCDReader` **Coordinate writer** :class:`MDAnalysis.coordinates.LAMMPS.DCDWriter` ===================== ================================================ + +.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/reference/classes/LAMMPSDUMP.txt b/doc/source/formats/reference/classes/LAMMPSDUMP.txt index 266d5ec17..cdcea3918 100644 --- a/doc/source/formats/reference/classes/LAMMPSDUMP.txt +++ b/doc/source/formats/reference/classes/LAMMPSDUMP.txt @@ -1,5 +1,6 @@ -.. Generated by gen_format_overview_classes.py ===================== ========================================================== **Coordinate reader** :class:`MDAnalysis.coordinates.LAMMPS.DumpReader` **Topology parser** :class:`MDAnalysis.topology.LAMMPSParser.LammpsDumpParser` ===================== ========================================================== + +.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/reference/classes/MMTF.txt b/doc/source/formats/reference/classes/MMTF.txt index 5a7f75fef..c942e5944 100644 --- a/doc/source/formats/reference/classes/MMTF.txt +++ b/doc/source/formats/reference/classes/MMTF.txt @@ -1,5 +1,6 @@ -.. Generated by gen_format_overview_classes.py ===================== ================================================== **Coordinate reader** :class:`MDAnalysis.coordinates.MMTF.MMTFReader` **Topology parser** :class:`MDAnalysis.topology.MMTFParser.MMTFParser` ===================== ================================================== + +.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/reference/classes/MOL2.txt b/doc/source/formats/reference/classes/MOL2.txt index bc58cc86a..c7ac1fae3 100644 --- a/doc/source/formats/reference/classes/MOL2.txt +++ b/doc/source/formats/reference/classes/MOL2.txt @@ -1,6 +1,7 @@ -.. Generated by gen_format_overview_classes.py ===================== ================================================== **Coordinate reader** :class:`MDAnalysis.coordinates.MOL2.MOL2Reader` **Coordinate writer** :class:`MDAnalysis.coordinates.MOL2.MOL2Writer` **Topology parser** :class:`MDAnalysis.topology.MOL2Parser.MOL2Parser` ===================== ================================================== + +.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/reference/classes/NCDF.txt b/doc/source/formats/reference/classes/NCDF.txt index 2c709ce1c..7b3c1132d 100644 --- a/doc/source/formats/reference/classes/NCDF.txt +++ b/doc/source/formats/reference/classes/NCDF.txt @@ -1,5 +1,6 @@ -.. Generated by gen_format_overview_classes.py ===================== ============================================== **Coordinate reader** :class:`MDAnalysis.coordinates.TRJ.NCDFReader` **Coordinate writer** :class:`MDAnalysis.coordinates.TRJ.NCDFWriter` ===================== ============================================== + +.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/reference/classes/PDB.txt b/doc/source/formats/reference/classes/PDB.txt index 53f6306b1..69c22eeeb 100644 --- a/doc/source/formats/reference/classes/PDB.txt +++ b/doc/source/formats/reference/classes/PDB.txt @@ -1,6 +1,7 @@ -.. Generated by gen_format_overview_classes.py ===================== ================================================ **Coordinate reader** :class:`MDAnalysis.coordinates.PDB.PDBReader` **Coordinate writer** :class:`MDAnalysis.coordinates.PDB.PDBWriter` **Topology parser** :class:`MDAnalysis.topology.PDBParser.PDBParser` ===================== ================================================ + +.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/reference/classes/PDBQT.txt b/doc/source/formats/reference/classes/PDBQT.txt index 25c6e4d71..28aeb3eef 100644 --- a/doc/source/formats/reference/classes/PDBQT.txt +++ b/doc/source/formats/reference/classes/PDBQT.txt @@ -1,6 +1,7 @@ -.. Generated by gen_format_overview_classes.py ===================== ==================================================== **Coordinate reader** :class:`MDAnalysis.coordinates.PDBQT.PDBQTReader` **Coordinate writer** :class:`MDAnalysis.coordinates.PDBQT.PDBQTWriter` **Topology parser** :class:`MDAnalysis.topology.PDBQTParser.PDBQTParser` ===================== ==================================================== + +.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/reference/classes/PQR.txt b/doc/source/formats/reference/classes/PQR.txt index 20e1d84f8..f125a732e 100644 --- a/doc/source/formats/reference/classes/PQR.txt +++ b/doc/source/formats/reference/classes/PQR.txt @@ -1,6 +1,7 @@ -.. Generated by gen_format_overview_classes.py ===================== ================================================ **Coordinate reader** :class:`MDAnalysis.coordinates.PQR.PQRReader` **Coordinate writer** :class:`MDAnalysis.coordinates.PQR.PQRWriter` **Topology parser** :class:`MDAnalysis.topology.PQRParser.PQRParser` ===================== ================================================ + +.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/reference/classes/PSF.txt b/doc/source/formats/reference/classes/PSF.txt index 205d38765..fac2d1cdb 100644 --- a/doc/source/formats/reference/classes/PSF.txt +++ b/doc/source/formats/reference/classes/PSF.txt @@ -1,4 +1,5 @@ -.. Generated by gen_format_overview_classes.py =================== ================================================ **Topology parser** :class:`MDAnalysis.topology.PSFParser.PSFParser` =================== ================================================ + +.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/reference/classes/TOP.txt b/doc/source/formats/reference/classes/TOP.txt index e2447df62..737ab8deb 100644 --- a/doc/source/formats/reference/classes/TOP.txt +++ b/doc/source/formats/reference/classes/TOP.txt @@ -1,4 +1,5 @@ -.. Generated by gen_format_overview_classes.py =================== ================================================ **Topology parser** :class:`MDAnalysis.topology.TOPParser.TOPParser` =================== ================================================ + +.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/reference/classes/TPR.txt b/doc/source/formats/reference/classes/TPR.txt index 665127221..5dbd9fbb8 100644 --- a/doc/source/formats/reference/classes/TPR.txt +++ b/doc/source/formats/reference/classes/TPR.txt @@ -1,4 +1,5 @@ -.. Generated by gen_format_overview_classes.py =================== ================================================ **Topology parser** :class:`MDAnalysis.topology.TPRParser.TPRParser` =================== ================================================ + +.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/reference/classes/TRJ.txt b/doc/source/formats/reference/classes/TRJ.txt index 5398eddcf..e69fe67f0 100644 --- a/doc/source/formats/reference/classes/TRJ.txt +++ b/doc/source/formats/reference/classes/TRJ.txt @@ -1,4 +1,5 @@ -.. Generated by gen_format_overview_classes.py ===================== ============================================= **Coordinate reader** :class:`MDAnalysis.coordinates.TRJ.TRJReader` ===================== ============================================= + +.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/reference/classes/TRR.txt b/doc/source/formats/reference/classes/TRR.txt index d40232874..d5ba9aa59 100644 --- a/doc/source/formats/reference/classes/TRR.txt +++ b/doc/source/formats/reference/classes/TRR.txt @@ -1,5 +1,6 @@ -.. Generated by gen_format_overview_classes.py ===================== ============================================= **Coordinate reader** :class:`MDAnalysis.coordinates.TRR.TRRReader` **Coordinate writer** :class:`MDAnalysis.coordinates.TRR.TRRWriter` ===================== ============================================= + +.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/reference/classes/TRZ.txt b/doc/source/formats/reference/classes/TRZ.txt index 289b548c4..325812478 100644 --- a/doc/source/formats/reference/classes/TRZ.txt +++ b/doc/source/formats/reference/classes/TRZ.txt @@ -1,5 +1,6 @@ -.. Generated by gen_format_overview_classes.py ===================== ============================================= **Coordinate reader** :class:`MDAnalysis.coordinates.TRZ.TRZReader` **Coordinate writer** :class:`MDAnalysis.coordinates.TRZ.TRZWriter` ===================== ============================================= + +.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/reference/classes/TXYZ.txt b/doc/source/formats/reference/classes/TXYZ.txt index 7d0c0d398..5e48068eb 100644 --- a/doc/source/formats/reference/classes/TXYZ.txt +++ b/doc/source/formats/reference/classes/TXYZ.txt @@ -1,5 +1,6 @@ -.. Generated by gen_format_overview_classes.py ===================== ================================================== **Coordinate reader** :class:`MDAnalysis.coordinates.TXYZ.TXYZReader` **Topology parser** :class:`MDAnalysis.topology.TXYZParser.TXYZParser` ===================== ================================================== + +.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/reference/classes/XML.txt b/doc/source/formats/reference/classes/XML.txt index 3022e5b66..52dcade0f 100644 --- a/doc/source/formats/reference/classes/XML.txt +++ b/doc/source/formats/reference/classes/XML.txt @@ -1,4 +1,5 @@ -.. Generated by gen_format_overview_classes.py =================== ========================================================== **Topology parser** :class:`MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser` =================== ========================================================== + +.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/reference/classes/XPDB.txt b/doc/source/formats/reference/classes/XPDB.txt index 028e15a99..a127ff459 100644 --- a/doc/source/formats/reference/classes/XPDB.txt +++ b/doc/source/formats/reference/classes/XPDB.txt @@ -1,5 +1,6 @@ -.. Generated by gen_format_overview_classes.py ===================== ================================================================ **Coordinate reader** :class:`MDAnalysis.coordinates.PDB.ExtendedPDBReader` **Topology parser** :class:`MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser` ===================== ================================================================ + +.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/reference/classes/XTC.txt b/doc/source/formats/reference/classes/XTC.txt index 9a3cae368..a1d46845b 100644 --- a/doc/source/formats/reference/classes/XTC.txt +++ b/doc/source/formats/reference/classes/XTC.txt @@ -1,5 +1,6 @@ -.. Generated by gen_format_overview_classes.py ===================== ============================================= **Coordinate reader** :class:`MDAnalysis.coordinates.XTC.XTCReader` **Coordinate writer** :class:`MDAnalysis.coordinates.XTC.XTCWriter` ===================== ============================================= + +.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/reference/classes/XYZ.txt b/doc/source/formats/reference/classes/XYZ.txt index cbdd317fa..3c6174b13 100644 --- a/doc/source/formats/reference/classes/XYZ.txt +++ b/doc/source/formats/reference/classes/XYZ.txt @@ -1,6 +1,7 @@ -.. Generated by gen_format_overview_classes.py ===================== ================================================ **Coordinate reader** :class:`MDAnalysis.coordinates.XYZ.XYZReader` **Coordinate writer** :class:`MDAnalysis.coordinates.XYZ.XYZWriter` **Topology parser** :class:`MDAnalysis.topology.XYZParser.XYZParser` ===================== ================================================ + +.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/reference/coor.rst b/doc/source/formats/reference/coor.rst new file mode 100644 index 000000000..d64f696ab --- /dev/null +++ b/doc/source/formats/reference/coor.rst @@ -0,0 +1,8 @@ +.. -*- coding: utf-8 -*- +.. _COOR-format: + +======================================= +COOR (NAMD binary restart files) +======================================= + +.. include:: classes/COOR.txt \ No newline at end of file diff --git a/doc/source/formats/reference/in.rst b/doc/source/formats/reference/in.rst new file mode 100644 index 000000000..60513364d --- /dev/null +++ b/doc/source/formats/reference/in.rst @@ -0,0 +1,8 @@ +.. -*- coding: utf-8 -*- +.. _IN-format: + +======================================= +IN (FHI-aims input files) +======================================= + +.. include:: classes/IN.txt \ No newline at end of file diff --git a/doc/source/formats/reference/parmed.rst b/doc/source/formats/reference/parmed.rst new file mode 100644 index 000000000..c8955f9d6 --- /dev/null +++ b/doc/source/formats/reference/parmed.rst @@ -0,0 +1,12 @@ +.. -*- coding: utf-8 -*- +.. _PARMED-format: + +========================= +PARMED (ParmEd Structure) +========================= + +.. include:: classes/PARMED.txt + +The ParmEd_ library is a general tool for molecular modelling, often used to manipulate system topologies or convert between file formats. You can pass in a :class:`parmed.Structure` to be converted into an MDAnalysis Universe, and convert it back using a :class:`~MDAnalysis.coordinates.ParmEd.ParmEdConverter`. While you can convert Universes created by other means (e.g. by reading files) into a ParmEd structure, MDAnalysis does not read or generate details such the "type" of a bond (i.e. bondtype), or information such as ``ureybradley`` terms. + +.. _ParmEd: https://parmed.github.io/ParmEd/html/index.html \ No newline at end of file diff --git a/doc/source/formats/selection_exporter_formats.txt b/doc/source/formats/selection_exporter_formats.txt index 21acdfef1..c5aa63901 100644 --- a/doc/source/formats/selection_exporter_formats.txt +++ b/doc/source/formats/selection_exporter_formats.txt @@ -1,4 +1,3 @@ -.. Generated by gen_selection_exporters.py ========== =========== ======================================== ====================================================== Program Extension Description Class ========== =========== ======================================== ====================================================== @@ -8,3 +7,5 @@ Program Extension Description Class `PyMol`_ pml PyMOL selection string :class:`MDAnalysis.selections.pymol.SelectionWriter` `VMD`_ vmd VMD macros, available in Representations :class:`MDAnalysis.selections.vmd.SelectionWriter` ========== =========== ======================================== ====================================================== + +.. Generated by gen_selection_exporters.py \ No newline at end of file diff --git a/doc/source/formats/topology_parsers.txt b/doc/source/formats/topology_parsers.txt index 2f597e826..a619b27d3 100644 --- a/doc/source/formats/topology_parsers.txt +++ b/doc/source/formats/topology_parsers.txt @@ -1,4 +1,3 @@ -.. Generated by gen_topologyparser_attrs.py ====================================== =============================== ========================================================================================= ==================== Format Description Attributes read Attributes guessed ====================================== =============================== ========================================================================================= ==================== @@ -17,10 +16,12 @@ Format Description Attribu :ref:`PDBQT ` PDBQT file altLocs, charges, icodes, names, occupancies, record_types, resnames, tempfactors masses :ref:`PQR ` PQR file charges, icodes, names, radii, record_types, resnames masses, types :ref:`PSF ` CHARMM, NAMD, or XPLOR PSF file angles, bonds, charges, dihedrals, impropers, names, resnames -:ref:`TOP, PRMTOP, PARM7 ` AMBER topology file angles, bonds, charges, dihedrals, impropers, names, resnames, type_indices elements +:ref:`TOP, PRMTOP, PARM7 ` AMBER topology file angles, bonds, charges, dihedrals, impropers, names, resnames, type_indices :ref:`TPR ` GROMACS run topology file angles, bonds, charges, dihedrals, impropers, molnums, moltypes, names, resnames :ref:`TXYZ, ARC ` Tinker file bonds, names masses :ref:`XML ` HOOMD XML file angles, bonds, charges, dihedrals, impropers, radii :ref:`XPDB ` Extended PDB file altLocs, bonds, chainIDs, icodes, names, occupancies, record_types, resnames, tempfactors masses, types :ref:`XYZ ` XYZ file elements, names masses, types ====================================== =============================== ========================================================================================= ==================== + +.. Generated by gen_topologyparser_attrs.py \ No newline at end of file diff --git a/doc/source/generated/selections/base.txt b/doc/source/generated/selections/base.txt index 959b0336c..cd322970a 100644 --- a/doc/source/generated/selections/base.txt +++ b/doc/source/generated/selections/base.txt @@ -1,5 +1,6 @@ -.. Generated by gen_standard_selections.py == == == == == == == === N9 N7 C8 C5 C4 N3 C2 N1 C6 O6 N2 N6 O2 N4 O4 C5M == == == == == == == === + +.. Generated by gen_standard_selections.py \ No newline at end of file diff --git a/doc/source/generated/selections/nucleic.txt b/doc/source/generated/selections/nucleic.txt index c3e7618ab..2e23d9073 100644 --- a/doc/source/generated/selections/nucleic.txt +++ b/doc/source/generated/selections/nucleic.txt @@ -1,4 +1,3 @@ -.. Generated by gen_standard_selections.py === === === === === === === === ADE URA CYT GUA THY DA DC DG DT RA RU RG RC A T U @@ -6,3 +5,5 @@ C G DA5 DC5 DG5 DT5 DA3 DC3 DG3 DT3 RA5 RU5 RG5 RC5 RA3 RU3 RG3 RC3 === === === === === === === === + +.. Generated by gen_standard_selections.py \ No newline at end of file diff --git a/doc/source/generated/selections/nucleic_backbone.txt b/doc/source/generated/selections/nucleic_backbone.txt index ac2e4290b..d553d0908 100644 --- a/doc/source/generated/selections/nucleic_backbone.txt +++ b/doc/source/generated/selections/nucleic_backbone.txt @@ -1,4 +1,5 @@ -.. Generated by gen_standard_selections.py = === === === === P C5' C3' O3' O5' = === === === === + +.. Generated by gen_standard_selections.py \ No newline at end of file diff --git a/doc/source/generated/selections/nucleic_sugar.txt b/doc/source/generated/selections/nucleic_sugar.txt index 9dd4be470..abd07604b 100644 --- a/doc/source/generated/selections/nucleic_sugar.txt +++ b/doc/source/generated/selections/nucleic_sugar.txt @@ -1,4 +1,5 @@ -.. Generated by gen_standard_selections.py === === === === === C1' C2' C3' C4' O4' === === === === === + +.. Generated by gen_standard_selections.py \ No newline at end of file diff --git a/doc/source/generated/selections/protein.txt b/doc/source/generated/selections/protein.txt index 505da9cd0..d7363f2b8 100644 --- a/doc/source/generated/selections/protein.txt +++ b/doc/source/generated/selections/protein.txt @@ -1,4 +1,3 @@ -.. Generated by gen_standard_selections.py ==== ==== ==== ==== ==== ==== ==== ==== ACE ALA ALAD ARG ARGN ASF ASH ASN ASN1 ASP ASPH CALA CARG CASF CASN CASP @@ -14,3 +13,5 @@ NHIE NHIP NILE NLEU NLYS NME NMET NPHE NPRO NSER NTHR NTRP NTYR NVAL ORN PGLU PHE PRO QLN SER THR TRP TYR VAL ==== ==== ==== ==== ==== ==== ==== ==== + +.. Generated by gen_standard_selections.py \ No newline at end of file diff --git a/doc/source/generated/selections/protein_backbone.txt b/doc/source/generated/selections/protein_backbone.txt index eb5b1de1e..d302b3b1f 100644 --- a/doc/source/generated/selections/protein_backbone.txt +++ b/doc/source/generated/selections/protein_backbone.txt @@ -1,4 +1,5 @@ -.. Generated by gen_standard_selections.py = == = = N CA C O = == = = + +.. Generated by gen_standard_selections.py \ No newline at end of file diff --git a/doc/source/generated/topology/connectivityattrs.txt b/doc/source/generated/topology/connectivityattrs.txt index e2f6ca2d7..db3ee840e 100644 --- a/doc/source/generated/topology/connectivityattrs.txt +++ b/doc/source/generated/topology/connectivityattrs.txt @@ -1,4 +1,3 @@ -.. Generated by gen_topologyparser_attrs.py ========= =========== ============================================================================================================================================================================================================================================================================================================================================= Atom AtomGroup Supported formats ========= =========== ============================================================================================================================================================================================================================================================================================================================================= @@ -7,3 +6,5 @@ bonds bonds :ref:`DATA `, :ref:`DMS `, :ref dihedrals dihedrals :ref:`DATA `, :ref:`GSD `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`XML ` impropers impropers :ref:`DATA `, :ref:`GSD `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`XML ` ========= =========== ============================================================================================================================================================================================================================================================================================================================================= + +.. Generated by gen_topologyparser_attrs.py \ No newline at end of file diff --git a/doc/source/generated/topology/defaults.txt b/doc/source/generated/topology/defaults.txt index 204728b46..bc423b584 100644 --- a/doc/source/generated/topology/defaults.txt +++ b/doc/source/generated/topology/defaults.txt @@ -1,4 +1,3 @@ -.. Generated by gen_topologyattr_defaults.py ============= ============= ======================================== ======= ======================= Atom AtomGroup default level type ============= ============= ======================================== ======= ======================= @@ -41,3 +40,5 @@ type_indices type_index No default values atom types type '' atom ureybradleys ureybradleys No default values atom ============= ============= ======================================== ======= ======================= + +.. Generated by gen_topologyattr_defaults.py \ No newline at end of file diff --git a/doc/source/generated/topology/groupmethods.txt b/doc/source/generated/topology/groupmethods.txt index 59c8d4f61..c994bde09 100644 --- a/doc/source/generated/topology/groupmethods.txt +++ b/doc/source/generated/topology/groupmethods.txt @@ -1,4 +1,3 @@ -.. Generated by gen_topology_groupmethods.py ================================================================== ====================================================================== ========== Method Description Requires ================================================================== ====================================================================== ========== @@ -12,3 +11,5 @@ Method Description :meth:`~MDAnalysis.core.topologyattrs.Masses.shape_parameter` Shape parameter masses :meth:`~MDAnalysis.core.topologyattrs.Masses.total_mass` Total mass of (compounds of) the group masses ================================================================== ====================================================================== ========== + +.. Generated by gen_topology_groupmethods.py \ No newline at end of file diff --git a/doc/source/generated/topology/topologyattrs.txt b/doc/source/generated/topology/topologyattrs.txt index 85588dcee..2ad489811 100644 --- a/doc/source/generated/topology/topologyattrs.txt +++ b/doc/source/generated/topology/topologyattrs.txt @@ -1,4 +1,3 @@ -.. Generated by gen_topologyparser_attrs.py ============= ============= ================================== =================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== Atom AtomGroup Description Supported formats ============= ============= ================================== =================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -13,7 +12,7 @@ charge charges partial atomic charge :ref:`DATA `, :ref:`GSD `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`XML ` -element elements atom element :ref:`TOP, PRMTOP, PARM7 `, :ref:`XYZ ` +element elements atom element :ref:`XYZ ` epsilon epsilons epsilon14 epsilon14s gbscreen gbscreens @@ -35,3 +34,5 @@ tempfactor tempfactors B-factor :ref:`CRD ` ureybradleys ureybradleys ============= ============= ================================== =================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== + +.. Generated by gen_topologyparser_attrs.py \ No newline at end of file diff --git a/doc/source/scripts/base.py b/doc/source/scripts/base.py index e733dcc9a..5c24d9b06 100644 --- a/doc/source/scripts/base.py +++ b/doc/source/scripts/base.py @@ -68,11 +68,11 @@ def get_line(self, *args): def write_table(self): with open(self.path, 'w') as f: - f.write('.. Generated by {}\n'.format(sys.argv[0])) print(tabulate.tabulate(self.lines, headers=self.headings, tablefmt='rst'), file=f) + f.write('\n.. Generated by {}'.format(sys.argv[0])) print('Wrote ', self.filename) # ==== HELPER FUNCTIONS ==== # diff --git a/doc/source/scripts/core.py b/doc/source/scripts/core.py index 74c40eaee..639f2afc5 100644 --- a/doc/source/scripts/core.py +++ b/doc/source/scripts/core.py @@ -10,12 +10,11 @@ 'PARMED': 'parmed Structure', 'CRD': 'CHARMM CARD file', 'CONFIG': 'DL_Poly CONFIG file', - 'COOR': 'NAMDBIN file', + 'COOR': 'NAMD binary restart file', 'DCD': 'CHARMM, NAMD, or LAMMPS binary trajectory', 'HISTORY': 'DL_Poly HISTORY file', 'DMS': 'DESRES Molecular Structure file', 'XPDB': 'Extended PDB file', - 'FHIAIMS': 'FHIAIMS file', 'GMS': 'GAMESS file', 'GRO': 'GROMACS structure file', 'GSD': 'HOOMD GSD file', @@ -23,11 +22,10 @@ 'DATA': 'LAMMPS data file', 'INPCRD': 'AMBER restart file', 'ITP': 'GROMACS portable topology file', - 'IN': 'FHIAIMS file', + 'IN': 'FHI-aims input file', 'LAMMPS': 'a LAMMPS DCD trajectory', 'LAMMPSDUMP': 'LAMMPS ascii dump file', 'MMTF' : 'MMTF file', - 'NAMDBIN': 'NAMDBIN file', 'NCDF': 'AMBER NETCDF format', 'MOL2': 'Tripos MOL2 file', 'PDB': 'Standard PDB file', diff --git a/doc/source/scripts/gen_format_overview_classes.py b/doc/source/scripts/gen_format_overview_classes.py index bdd1c9a63..65b7dc872 100644 --- a/doc/source/scripts/gen_format_overview_classes.py +++ b/doc/source/scripts/gen_format_overview_classes.py @@ -8,7 +8,7 @@ from collections import defaultdict -from MDAnalysis import _READERS, _SINGLEFRAME_WRITERS, _PARSERS +from MDAnalysis import _READERS, _SINGLEFRAME_WRITERS, _PARSERS, _CONVERTERS from base import TableWriter from core import DESCRIPTIONS @@ -16,7 +16,8 @@ for clstype, dct in (('Coordinate reader', _READERS), ('Coordinate writer', _SINGLEFRAME_WRITERS), - ('Topology parser', _PARSERS)): + ('Topology parser', _PARSERS), + ('Converter', _CONVERTERS)): for fmt, klass in dct.items(): if fmt in ('CHAIN', 'MEMORY', 'MINIMAL', 'NULL'): continue # get their own pages @@ -68,6 +69,8 @@ def _read(self, fmt, handlers): def _write(self, fmt, handlers): if 'Coordinate writer' in handlers: return SUCCESS + if 'Converter' in handlers: + return SUCCESS return FAIL class CoordinateReaders(FormatOverview): From e25b5d5f719699f44d0e85d7391a79148ba2c171 Mon Sep 17 00:00:00 2001 From: Lily Wang Date: Fri, 19 Jun 2020 10:11:01 +1000 Subject: [PATCH 04/18] auto-generate tables --- .gitignore | 2 +- doc/source/conf.py | 5 +- doc/source/formats/coordinate_readers.txt | 6 +-- doc/source/formats/coordinates.rst | 4 +- doc/source/formats/format_overview.txt | 6 +-- doc/source/formats/index.rst | 4 +- .../formats/reference/classes/CONFIG.txt | 4 +- doc/source/formats/reference/classes/CRD.txt | 4 +- doc/source/formats/reference/classes/DATA.txt | 4 +- doc/source/formats/reference/classes/DCD.txt | 4 +- doc/source/formats/reference/classes/DMS.txt | 4 +- doc/source/formats/reference/classes/GMS.txt | 4 +- doc/source/formats/reference/classes/GRO.txt | 4 +- doc/source/formats/reference/classes/GSD.txt | 4 +- .../formats/reference/classes/HISTORY.txt | 4 +- .../formats/reference/classes/INPCRD.txt | 4 +- doc/source/formats/reference/classes/ITP.txt | 4 +- .../formats/reference/classes/LAMMPS.txt | 4 +- .../formats/reference/classes/LAMMPSDUMP.txt | 4 +- doc/source/formats/reference/classes/MMTF.txt | 4 +- doc/source/formats/reference/classes/MOL2.txt | 4 +- doc/source/formats/reference/classes/NCDF.txt | 4 +- doc/source/formats/reference/classes/PDB.txt | 4 +- .../formats/reference/classes/PDBQT.txt | 4 +- doc/source/formats/reference/classes/PQR.txt | 4 +- doc/source/formats/reference/classes/PSF.txt | 4 +- doc/source/formats/reference/classes/TOP.txt | 4 +- doc/source/formats/reference/classes/TPR.txt | 4 +- doc/source/formats/reference/classes/TRJ.txt | 4 +- doc/source/formats/reference/classes/TRR.txt | 4 +- doc/source/formats/reference/classes/TRZ.txt | 4 +- doc/source/formats/reference/classes/TXYZ.txt | 4 +- doc/source/formats/reference/classes/XML.txt | 4 +- doc/source/formats/reference/classes/XPDB.txt | 4 +- doc/source/formats/reference/classes/XTC.txt | 4 +- doc/source/formats/reference/classes/XYZ.txt | 4 +- .../formats/selection_exporter_formats.txt | 6 +-- doc/source/formats/selection_exporters.rst | 4 +- doc/source/formats/topology.rst | 4 +- doc/source/formats/topology_parsers.txt | 46 ++++++++-------- doc/source/generated/selections/base.txt | 4 +- doc/source/generated/selections/nucleic.txt | 4 +- .../generated/selections/nucleic_backbone.txt | 4 +- .../generated/selections/nucleic_sugar.txt | 4 +- doc/source/generated/selections/protein.txt | 4 +- .../generated/selections/protein_backbone.txt | 4 +- .../generated/topology/connectivityattrs.txt | 18 +++---- doc/source/generated/topology/defaults.txt | 4 +- .../generated/topology/groupmethods.txt | 4 +- .../generated/topology/topologyattrs.txt | 52 +++++++++---------- doc/source/scripts/base.py | 5 +- .../scripts/gen_format_overview_classes.py | 2 + doc/source/scripts/gen_selection_exporters.py | 1 + .../scripts/gen_topologyparser_attrs.py | 6 ++- 54 files changed, 163 insertions(+), 160 deletions(-) diff --git a/.gitignore b/.gitignore index eb6d47f52..dcd3de159 100644 --- a/.gitignore +++ b/.gitignore @@ -22,7 +22,7 @@ doc/build *.so # Ignore generated docs -# *.txt +*.txt # ignore generated files *.vmd diff --git a/doc/source/conf.py b/doc/source/conf.py index 62f2d0c6b..7876ab9d0 100644 --- a/doc/source/conf.py +++ b/doc/source/conf.py @@ -16,7 +16,7 @@ import datetime from collections import OrderedDict import MDAnalysis as mda -# import subprocess +import subprocess import sphinx_rtd_theme from ipywidgets.embed import DEFAULT_EMBED_REQUIREJS_URL @@ -54,13 +54,12 @@ def sort_authors(filename): # -- Scripts ----------------------------------------------- # Get Travis to regenerate txt tables by re-running scripts # before deploying docs. -# Turned off for now as 0.21.0 not released yet. # This allows us to gitignore .txt files as well as # auto-recreate tables for each deployment. # Turn off if using sphinx_autobuild as this will autobuild # to infinity. # -# subprocess.call('./scripts/generate_all.sh') +subprocess.call('./scripts/generate_all.sh') # -- General configuration --------------------------------------------------- diff --git a/doc/source/formats/coordinate_readers.txt b/doc/source/formats/coordinate_readers.txt index b7c26f7e3..1111abb5f 100644 --- a/doc/source/formats/coordinate_readers.txt +++ b/doc/source/formats/coordinate_readers.txt @@ -1,4 +1,6 @@ -===================================== ========================================= ============ ======== +.. Generated by gen_format_overview_classes.py + +.. table:: {self.include_table}===================================== ========================================= ============ ======== File type Description Velocities Forces ===================================== ========================================= ============ ======== :ref:`ARC ` Tinker file @@ -39,5 +41,3 @@ File type Description :ref:`XTC ` GROMACS compressed trajectory :ref:`XYZ ` XYZ file ===================================== ========================================= ============ ======== - -.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/coordinates.rst b/doc/source/formats/coordinates.rst index b2ac0f04b..9ddeebcf4 100644 --- a/doc/source/formats/coordinates.rst +++ b/doc/source/formats/coordinates.rst @@ -3,6 +3,4 @@ Coordinates =========== -.. table:: Table of supported coordinate readers and the information read - - .. include:: coordinate_readers.txt +.. include:: coordinate_readers.txt diff --git a/doc/source/formats/format_overview.txt b/doc/source/formats/format_overview.txt index 71c301772..773af95fa 100644 --- a/doc/source/formats/format_overview.txt +++ b/doc/source/formats/format_overview.txt @@ -1,4 +1,6 @@ -===================================== ========================================= ========== ============= ====== ======= +.. Generated by gen_format_overview_classes.py + +.. table:: {self.include_table}===================================== ========================================= ========== ============= ====== ======= File type Description Topology Coordinates Read Write ===================================== ========================================= ========== ============= ====== ======= :ref:`ARC ` Tinker file ✓ ✓ ✓ @@ -46,5 +48,3 @@ File type Description :ref:`XTC ` GROMACS compressed trajectory ✓ ✓ ✓ :ref:`XYZ ` XYZ file ✓ ✓ ✓ ✓ ===================================== ========================================= ========== ============= ====== ======= - -.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/index.rst b/doc/source/formats/index.rst index 80588fa4a..77511989a 100644 --- a/doc/source/formats/index.rst +++ b/doc/source/formats/index.rst @@ -25,9 +25,7 @@ If a trajectory is loaded without time information, MDAnalysis will set a defaul .. _format-overview: -.. table:: Table of all supported formats in MDAnalysis - - .. include:: format_overview.txt +.. include:: format_overview.txt .. _topology-parsers: diff --git a/doc/source/formats/reference/classes/CONFIG.txt b/doc/source/formats/reference/classes/CONFIG.txt index 4ebe03bff..abbdd8caf 100644 --- a/doc/source/formats/reference/classes/CONFIG.txt +++ b/doc/source/formats/reference/classes/CONFIG.txt @@ -1,6 +1,6 @@ +.. Generated by gen_format_overview_classes.py + ===================== ====================================================== **Coordinate reader** :class:`MDAnalysis.coordinates.DLPoly.ConfigReader` **Topology parser** :class:`MDAnalysis.topology.DLPolyParser.ConfigParser` ===================== ====================================================== - -.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/reference/classes/CRD.txt b/doc/source/formats/reference/classes/CRD.txt index 9398e443f..08a61080c 100644 --- a/doc/source/formats/reference/classes/CRD.txt +++ b/doc/source/formats/reference/classes/CRD.txt @@ -1,7 +1,7 @@ +.. Generated by gen_format_overview_classes.py + ===================== ================================================ **Coordinate reader** :class:`MDAnalysis.coordinates.CRD.CRDReader` **Coordinate writer** :class:`MDAnalysis.coordinates.CRD.CRDWriter` **Topology parser** :class:`MDAnalysis.topology.CRDParser.CRDParser` ===================== ================================================ - -.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/reference/classes/DATA.txt b/doc/source/formats/reference/classes/DATA.txt index cdbf5c258..f76bcd70a 100644 --- a/doc/source/formats/reference/classes/DATA.txt +++ b/doc/source/formats/reference/classes/DATA.txt @@ -1,7 +1,7 @@ +.. Generated by gen_format_overview_classes.py + ===================== ==================================================== **Coordinate reader** :class:`MDAnalysis.coordinates.LAMMPS.DATAReader` **Coordinate writer** :class:`MDAnalysis.coordinates.LAMMPS.DATAWriter` **Topology parser** :class:`MDAnalysis.topology.LAMMPSParser.DATAParser` ===================== ==================================================== - -.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/reference/classes/DCD.txt b/doc/source/formats/reference/classes/DCD.txt index 2af18a428..c175f4d89 100644 --- a/doc/source/formats/reference/classes/DCD.txt +++ b/doc/source/formats/reference/classes/DCD.txt @@ -1,6 +1,6 @@ +.. Generated by gen_format_overview_classes.py + ===================== ============================================= **Coordinate reader** :class:`MDAnalysis.coordinates.DCD.DCDReader` **Coordinate writer** :class:`MDAnalysis.coordinates.DCD.DCDWriter` ===================== ============================================= - -.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/reference/classes/DMS.txt b/doc/source/formats/reference/classes/DMS.txt index 94b31935f..9f408f01d 100644 --- a/doc/source/formats/reference/classes/DMS.txt +++ b/doc/source/formats/reference/classes/DMS.txt @@ -1,6 +1,6 @@ +.. Generated by gen_format_overview_classes.py + ===================== ================================================ **Coordinate reader** :class:`MDAnalysis.coordinates.DMS.DMSReader` **Topology parser** :class:`MDAnalysis.topology.DMSParser.DMSParser` ===================== ================================================ - -.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/reference/classes/GMS.txt b/doc/source/formats/reference/classes/GMS.txt index d7523fe47..c9dcab87f 100644 --- a/doc/source/formats/reference/classes/GMS.txt +++ b/doc/source/formats/reference/classes/GMS.txt @@ -1,6 +1,6 @@ +.. Generated by gen_format_overview_classes.py + ===================== ================================================ **Coordinate reader** :class:`MDAnalysis.coordinates.GMS.GMSReader` **Topology parser** :class:`MDAnalysis.topology.GMSParser.GMSParser` ===================== ================================================ - -.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/reference/classes/GRO.txt b/doc/source/formats/reference/classes/GRO.txt index b93fb12f6..a2b27d3c4 100644 --- a/doc/source/formats/reference/classes/GRO.txt +++ b/doc/source/formats/reference/classes/GRO.txt @@ -1,7 +1,7 @@ +.. Generated by gen_format_overview_classes.py + ===================== ================================================ **Coordinate reader** :class:`MDAnalysis.coordinates.GRO.GROReader` **Coordinate writer** :class:`MDAnalysis.coordinates.GRO.GROWriter` **Topology parser** :class:`MDAnalysis.topology.GROParser.GROParser` ===================== ================================================ - -.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/reference/classes/GSD.txt b/doc/source/formats/reference/classes/GSD.txt index 8fb952e61..b108969a0 100644 --- a/doc/source/formats/reference/classes/GSD.txt +++ b/doc/source/formats/reference/classes/GSD.txt @@ -1,6 +1,6 @@ +.. Generated by gen_format_overview_classes.py + ===================== ================================================ **Coordinate reader** :class:`MDAnalysis.coordinates.GSD.GSDReader` **Topology parser** :class:`MDAnalysis.topology.GSDParser.GSDParser` ===================== ================================================ - -.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/reference/classes/HISTORY.txt b/doc/source/formats/reference/classes/HISTORY.txt index 01e3d9372..6e683f3b8 100644 --- a/doc/source/formats/reference/classes/HISTORY.txt +++ b/doc/source/formats/reference/classes/HISTORY.txt @@ -1,6 +1,6 @@ +.. Generated by gen_format_overview_classes.py + ===================== ======================================================= **Coordinate reader** :class:`MDAnalysis.coordinates.DLPoly.HistoryReader` **Topology parser** :class:`MDAnalysis.topology.DLPolyParser.HistoryParser` ===================== ======================================================= - -.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/reference/classes/INPCRD.txt b/doc/source/formats/reference/classes/INPCRD.txt index 26c847a25..90bdcbde8 100644 --- a/doc/source/formats/reference/classes/INPCRD.txt +++ b/doc/source/formats/reference/classes/INPCRD.txt @@ -1,5 +1,5 @@ +.. Generated by gen_format_overview_classes.py + ===================== ================================================ **Coordinate reader** :class:`MDAnalysis.coordinates.INPCRD.INPReader` ===================== ================================================ - -.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/reference/classes/ITP.txt b/doc/source/formats/reference/classes/ITP.txt index 628dab03f..12d2c6a0a 100644 --- a/doc/source/formats/reference/classes/ITP.txt +++ b/doc/source/formats/reference/classes/ITP.txt @@ -1,5 +1,5 @@ +.. Generated by gen_format_overview_classes.py + =================== ================================================ **Topology parser** :class:`MDAnalysis.topology.ITPParser.ITPParser` =================== ================================================ - -.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/reference/classes/LAMMPS.txt b/doc/source/formats/reference/classes/LAMMPS.txt index b69d20df8..227416982 100644 --- a/doc/source/formats/reference/classes/LAMMPS.txt +++ b/doc/source/formats/reference/classes/LAMMPS.txt @@ -1,6 +1,6 @@ +.. Generated by gen_format_overview_classes.py + ===================== ================================================ **Coordinate reader** :class:`MDAnalysis.coordinates.LAMMPS.DCDReader` **Coordinate writer** :class:`MDAnalysis.coordinates.LAMMPS.DCDWriter` ===================== ================================================ - -.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/reference/classes/LAMMPSDUMP.txt b/doc/source/formats/reference/classes/LAMMPSDUMP.txt index cdcea3918..c302a7671 100644 --- a/doc/source/formats/reference/classes/LAMMPSDUMP.txt +++ b/doc/source/formats/reference/classes/LAMMPSDUMP.txt @@ -1,6 +1,6 @@ +.. Generated by gen_format_overview_classes.py + ===================== ========================================================== **Coordinate reader** :class:`MDAnalysis.coordinates.LAMMPS.DumpReader` **Topology parser** :class:`MDAnalysis.topology.LAMMPSParser.LammpsDumpParser` ===================== ========================================================== - -.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/reference/classes/MMTF.txt b/doc/source/formats/reference/classes/MMTF.txt index c942e5944..a2bc60ea3 100644 --- a/doc/source/formats/reference/classes/MMTF.txt +++ b/doc/source/formats/reference/classes/MMTF.txt @@ -1,6 +1,6 @@ +.. Generated by gen_format_overview_classes.py + ===================== ================================================== **Coordinate reader** :class:`MDAnalysis.coordinates.MMTF.MMTFReader` **Topology parser** :class:`MDAnalysis.topology.MMTFParser.MMTFParser` ===================== ================================================== - -.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/reference/classes/MOL2.txt b/doc/source/formats/reference/classes/MOL2.txt index c7ac1fae3..b22bfa8ab 100644 --- a/doc/source/formats/reference/classes/MOL2.txt +++ b/doc/source/formats/reference/classes/MOL2.txt @@ -1,7 +1,7 @@ +.. Generated by gen_format_overview_classes.py + ===================== ================================================== **Coordinate reader** :class:`MDAnalysis.coordinates.MOL2.MOL2Reader` **Coordinate writer** :class:`MDAnalysis.coordinates.MOL2.MOL2Writer` **Topology parser** :class:`MDAnalysis.topology.MOL2Parser.MOL2Parser` ===================== ================================================== - -.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/reference/classes/NCDF.txt b/doc/source/formats/reference/classes/NCDF.txt index 7b3c1132d..92fd74f79 100644 --- a/doc/source/formats/reference/classes/NCDF.txt +++ b/doc/source/formats/reference/classes/NCDF.txt @@ -1,6 +1,6 @@ +.. Generated by gen_format_overview_classes.py + ===================== ============================================== **Coordinate reader** :class:`MDAnalysis.coordinates.TRJ.NCDFReader` **Coordinate writer** :class:`MDAnalysis.coordinates.TRJ.NCDFWriter` ===================== ============================================== - -.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/reference/classes/PDB.txt b/doc/source/formats/reference/classes/PDB.txt index 69c22eeeb..c3b0ead5d 100644 --- a/doc/source/formats/reference/classes/PDB.txt +++ b/doc/source/formats/reference/classes/PDB.txt @@ -1,7 +1,7 @@ +.. Generated by gen_format_overview_classes.py + ===================== ================================================ **Coordinate reader** :class:`MDAnalysis.coordinates.PDB.PDBReader` **Coordinate writer** :class:`MDAnalysis.coordinates.PDB.PDBWriter` **Topology parser** :class:`MDAnalysis.topology.PDBParser.PDBParser` ===================== ================================================ - -.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/reference/classes/PDBQT.txt b/doc/source/formats/reference/classes/PDBQT.txt index 28aeb3eef..4c43c0f88 100644 --- a/doc/source/formats/reference/classes/PDBQT.txt +++ b/doc/source/formats/reference/classes/PDBQT.txt @@ -1,7 +1,7 @@ +.. Generated by gen_format_overview_classes.py + ===================== ==================================================== **Coordinate reader** :class:`MDAnalysis.coordinates.PDBQT.PDBQTReader` **Coordinate writer** :class:`MDAnalysis.coordinates.PDBQT.PDBQTWriter` **Topology parser** :class:`MDAnalysis.topology.PDBQTParser.PDBQTParser` ===================== ==================================================== - -.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/reference/classes/PQR.txt b/doc/source/formats/reference/classes/PQR.txt index f125a732e..0c9a8b305 100644 --- a/doc/source/formats/reference/classes/PQR.txt +++ b/doc/source/formats/reference/classes/PQR.txt @@ -1,7 +1,7 @@ +.. Generated by gen_format_overview_classes.py + ===================== ================================================ **Coordinate reader** :class:`MDAnalysis.coordinates.PQR.PQRReader` **Coordinate writer** :class:`MDAnalysis.coordinates.PQR.PQRWriter` **Topology parser** :class:`MDAnalysis.topology.PQRParser.PQRParser` ===================== ================================================ - -.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/reference/classes/PSF.txt b/doc/source/formats/reference/classes/PSF.txt index fac2d1cdb..1d0308116 100644 --- a/doc/source/formats/reference/classes/PSF.txt +++ b/doc/source/formats/reference/classes/PSF.txt @@ -1,5 +1,5 @@ +.. Generated by gen_format_overview_classes.py + =================== ================================================ **Topology parser** :class:`MDAnalysis.topology.PSFParser.PSFParser` =================== ================================================ - -.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/reference/classes/TOP.txt b/doc/source/formats/reference/classes/TOP.txt index 737ab8deb..37f18d608 100644 --- a/doc/source/formats/reference/classes/TOP.txt +++ b/doc/source/formats/reference/classes/TOP.txt @@ -1,5 +1,5 @@ +.. Generated by gen_format_overview_classes.py + =================== ================================================ **Topology parser** :class:`MDAnalysis.topology.TOPParser.TOPParser` =================== ================================================ - -.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/reference/classes/TPR.txt b/doc/source/formats/reference/classes/TPR.txt index 5dbd9fbb8..68042547d 100644 --- a/doc/source/formats/reference/classes/TPR.txt +++ b/doc/source/formats/reference/classes/TPR.txt @@ -1,5 +1,5 @@ +.. Generated by gen_format_overview_classes.py + =================== ================================================ **Topology parser** :class:`MDAnalysis.topology.TPRParser.TPRParser` =================== ================================================ - -.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/reference/classes/TRJ.txt b/doc/source/formats/reference/classes/TRJ.txt index e69fe67f0..0d964f6c6 100644 --- a/doc/source/formats/reference/classes/TRJ.txt +++ b/doc/source/formats/reference/classes/TRJ.txt @@ -1,5 +1,5 @@ +.. Generated by gen_format_overview_classes.py + ===================== ============================================= **Coordinate reader** :class:`MDAnalysis.coordinates.TRJ.TRJReader` ===================== ============================================= - -.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/reference/classes/TRR.txt b/doc/source/formats/reference/classes/TRR.txt index d5ba9aa59..529ccfe42 100644 --- a/doc/source/formats/reference/classes/TRR.txt +++ b/doc/source/formats/reference/classes/TRR.txt @@ -1,6 +1,6 @@ +.. Generated by gen_format_overview_classes.py + ===================== ============================================= **Coordinate reader** :class:`MDAnalysis.coordinates.TRR.TRRReader` **Coordinate writer** :class:`MDAnalysis.coordinates.TRR.TRRWriter` ===================== ============================================= - -.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/reference/classes/TRZ.txt b/doc/source/formats/reference/classes/TRZ.txt index 325812478..df39f9a87 100644 --- a/doc/source/formats/reference/classes/TRZ.txt +++ b/doc/source/formats/reference/classes/TRZ.txt @@ -1,6 +1,6 @@ +.. Generated by gen_format_overview_classes.py + ===================== ============================================= **Coordinate reader** :class:`MDAnalysis.coordinates.TRZ.TRZReader` **Coordinate writer** :class:`MDAnalysis.coordinates.TRZ.TRZWriter` ===================== ============================================= - -.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/reference/classes/TXYZ.txt b/doc/source/formats/reference/classes/TXYZ.txt index 5e48068eb..15bd735db 100644 --- a/doc/source/formats/reference/classes/TXYZ.txt +++ b/doc/source/formats/reference/classes/TXYZ.txt @@ -1,6 +1,6 @@ +.. Generated by gen_format_overview_classes.py + ===================== ================================================== **Coordinate reader** :class:`MDAnalysis.coordinates.TXYZ.TXYZReader` **Topology parser** :class:`MDAnalysis.topology.TXYZParser.TXYZParser` ===================== ================================================== - -.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/reference/classes/XML.txt b/doc/source/formats/reference/classes/XML.txt index 52dcade0f..63b829649 100644 --- a/doc/source/formats/reference/classes/XML.txt +++ b/doc/source/formats/reference/classes/XML.txt @@ -1,5 +1,5 @@ +.. Generated by gen_format_overview_classes.py + =================== ========================================================== **Topology parser** :class:`MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser` =================== ========================================================== - -.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/reference/classes/XPDB.txt b/doc/source/formats/reference/classes/XPDB.txt index a127ff459..3fda83ef9 100644 --- a/doc/source/formats/reference/classes/XPDB.txt +++ b/doc/source/formats/reference/classes/XPDB.txt @@ -1,6 +1,6 @@ +.. Generated by gen_format_overview_classes.py + ===================== ================================================================ **Coordinate reader** :class:`MDAnalysis.coordinates.PDB.ExtendedPDBReader` **Topology parser** :class:`MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser` ===================== ================================================================ - -.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/reference/classes/XTC.txt b/doc/source/formats/reference/classes/XTC.txt index a1d46845b..29a1fa1d4 100644 --- a/doc/source/formats/reference/classes/XTC.txt +++ b/doc/source/formats/reference/classes/XTC.txt @@ -1,6 +1,6 @@ +.. Generated by gen_format_overview_classes.py + ===================== ============================================= **Coordinate reader** :class:`MDAnalysis.coordinates.XTC.XTCReader` **Coordinate writer** :class:`MDAnalysis.coordinates.XTC.XTCWriter` ===================== ============================================= - -.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/reference/classes/XYZ.txt b/doc/source/formats/reference/classes/XYZ.txt index 3c6174b13..73230d44e 100644 --- a/doc/source/formats/reference/classes/XYZ.txt +++ b/doc/source/formats/reference/classes/XYZ.txt @@ -1,7 +1,7 @@ +.. Generated by gen_format_overview_classes.py + ===================== ================================================ **Coordinate reader** :class:`MDAnalysis.coordinates.XYZ.XYZReader` **Coordinate writer** :class:`MDAnalysis.coordinates.XYZ.XYZWriter` **Topology parser** :class:`MDAnalysis.topology.XYZParser.XYZParser` ===================== ================================================ - -.. Generated by gen_format_overview_classes.py \ No newline at end of file diff --git a/doc/source/formats/selection_exporter_formats.txt b/doc/source/formats/selection_exporter_formats.txt index c5aa63901..59dbd153d 100644 --- a/doc/source/formats/selection_exporter_formats.txt +++ b/doc/source/formats/selection_exporter_formats.txt @@ -1,4 +1,6 @@ -========== =========== ======================================== ====================================================== +.. Generated by gen_selection_exporters.py + +.. table:: {self.include_table}========== =========== ======================================== ====================================================== Program Extension Description Class ========== =========== ======================================== ====================================================== `CHARMM`_ str CHARMM selection of individual atoms :class:`MDAnalysis.selections.charmm.SelectionWriter` @@ -7,5 +9,3 @@ Program Extension Description Class `PyMol`_ pml PyMOL selection string :class:`MDAnalysis.selections.pymol.SelectionWriter` `VMD`_ vmd VMD macros, available in Representations :class:`MDAnalysis.selections.vmd.SelectionWriter` ========== =========== ======================================== ====================================================== - -.. Generated by gen_selection_exporters.py \ No newline at end of file diff --git a/doc/source/formats/selection_exporters.rst b/doc/source/formats/selection_exporters.rst index 90b45f821..ad1cbd3bb 100644 --- a/doc/source/formats/selection_exporters.rst +++ b/doc/source/formats/selection_exporters.rst @@ -8,9 +8,7 @@ Selection exporters Selection exporters allow you to write a selection of atoms to a file that can be read by another program. -.. table:: Supported selection exporters - - .. include:: selection_exporter_formats.txt +.. include:: selection_exporter_formats.txt Writing selections ================== diff --git a/doc/source/formats/topology.rst b/doc/source/formats/topology.rst index c2bf6ffda..e9cb25c50 100644 --- a/doc/source/formats/topology.rst +++ b/doc/source/formats/topology.rst @@ -2,6 +2,4 @@ Topology ======== -.. table:: Table of supported topology parsers and the attributes read - - .. include:: topology_parsers.txt \ No newline at end of file +.. include:: topology_parsers.txt \ No newline at end of file diff --git a/doc/source/formats/topology_parsers.txt b/doc/source/formats/topology_parsers.txt index a619b27d3..d172d593c 100644 --- a/doc/source/formats/topology_parsers.txt +++ b/doc/source/formats/topology_parsers.txt @@ -1,27 +1,29 @@ -====================================== =============================== ========================================================================================= ==================== -Format Description Attributes read Attributes guessed -====================================== =============================== ========================================================================================= ==================== -:ref:`CONFIG ` DL_Poly CONFIG file names masses, types -:ref:`CRD ` CHARMM CARD file names, resnames, tempfactors masses, types +.. Generated by gen_topologyparser_attrs.py + +.. table:: {self.include_table}====================================== =============================== =================================================================================================================================================================================================================== ==================== +Format Description Attributes read Attributes guessed +====================================== =============================== =================================================================================================================================================================================================================== ==================== +:ref:`CONFIG ` DL_Poly CONFIG file names masses, types +:ref:`CRD ` CHARMM CARD file names, resnames, tempfactors masses, types :ref:`DATA ` LAMMPS data file angles, bonds, charges, dihedrals, impropers -:ref:`DMS ` DESRES Molecular Structure file atomnums, bonds, chainIDs, charges, names, resnames types -:ref:`GMS ` GAMESS file atomiccharges, names masses, types -:ref:`GRO ` GROMACS structure file names, resnames masses, types +:ref:`DMS ` DESRES Molecular Structure file atomnums, bonds, chainIDs, charges, names, resnames types +:ref:`GMS ` GAMESS file atomiccharges, names masses, types +:ref:`GRO ` GROMACS structure file names, resnames masses, types :ref:`GSD ` HOOMD GSD file angles, bonds, charges, dihedrals, impropers, names, radii, resnames -:ref:`HISTORY ` DL_Poly HISTORY file names masses, types -:ref:`LAMMPSDUMP ` LAMMPS ascii dump file masses -:ref:`MMTF ` MMTF file altLocs, bfactors, bonds, charges, icodes, models, names, occupancies, resnames masses -:ref:`MOL2 ` Tripos MOL2 file bonds, charges, names, resnames masses -:ref:`PDB, ENT ` Standard PDB file altLocs, bonds, chainIDs, icodes, names, occupancies, record_types, resnames, tempfactors masses, types -:ref:`PDBQT ` PDBQT file altLocs, charges, icodes, names, occupancies, record_types, resnames, tempfactors masses -:ref:`PQR ` PQR file charges, icodes, names, radii, record_types, resnames masses, types +:ref:`HISTORY ` DL_Poly HISTORY file names masses, types +:ref:`IN, FHIAIMS ` FHI-aims input file elements, names masses, types +:ref:`LAMMPSDUMP ` LAMMPS ascii dump file masses +:ref:`MMTF ` MMTF file altLocs, bfactors, bonds, charges, icodes, models, names, occupancies, resnames masses +:ref:`MOL2 ` Tripos MOL2 file bonds, charges, names, resnames masses +:ref:`PARMED ` parmed Structure altLocs, angles, bonds, chainIDs, charges, cmaps, dihedrals, elements, epsilon14s, epsilons, gbscreens, impropers, names, nbindices, occupancies, resnames, rmin14s, rmins, solventradii, tempfactors, ureybradleys +:ref:`PDB, ENT ` Standard PDB file altLocs, bonds, chainIDs, icodes, names, occupancies, record_types, resnames, tempfactors masses, types +:ref:`PDBQT ` PDBQT file altLocs, charges, icodes, names, occupancies, record_types, resnames, tempfactors masses +:ref:`PQR ` PQR file charges, icodes, names, radii, record_types, resnames masses, types :ref:`PSF ` CHARMM, NAMD, or XPLOR PSF file angles, bonds, charges, dihedrals, impropers, names, resnames -:ref:`TOP, PRMTOP, PARM7 ` AMBER topology file angles, bonds, charges, dihedrals, impropers, names, resnames, type_indices +:ref:`TOP, PRMTOP, PARM7 ` AMBER topology file angles, bonds, charges, dihedrals, impropers, names, resnames, type_indices elements :ref:`TPR ` GROMACS run topology file angles, bonds, charges, dihedrals, impropers, molnums, moltypes, names, resnames -:ref:`TXYZ, ARC ` Tinker file bonds, names masses +:ref:`TXYZ, ARC ` Tinker file bonds, names masses :ref:`XML ` HOOMD XML file angles, bonds, charges, dihedrals, impropers, radii -:ref:`XPDB ` Extended PDB file altLocs, bonds, chainIDs, icodes, names, occupancies, record_types, resnames, tempfactors masses, types -:ref:`XYZ ` XYZ file elements, names masses, types -====================================== =============================== ========================================================================================= ==================== - -.. Generated by gen_topologyparser_attrs.py \ No newline at end of file +:ref:`XPDB ` Extended PDB file altLocs, bonds, chainIDs, icodes, names, occupancies, record_types, resnames, tempfactors masses, types +:ref:`XYZ ` XYZ file elements, names masses, types +====================================== =============================== =================================================================================================================================================================================================================== ==================== diff --git a/doc/source/generated/selections/base.txt b/doc/source/generated/selections/base.txt index cd322970a..15f6b1bc1 100644 --- a/doc/source/generated/selections/base.txt +++ b/doc/source/generated/selections/base.txt @@ -1,6 +1,6 @@ +.. Generated by gen_standard_selections.py + == == == == == == == === N9 N7 C8 C5 C4 N3 C2 N1 C6 O6 N2 N6 O2 N4 O4 C5M == == == == == == == === - -.. Generated by gen_standard_selections.py \ No newline at end of file diff --git a/doc/source/generated/selections/nucleic.txt b/doc/source/generated/selections/nucleic.txt index 2e23d9073..85b69582f 100644 --- a/doc/source/generated/selections/nucleic.txt +++ b/doc/source/generated/selections/nucleic.txt @@ -1,3 +1,5 @@ +.. Generated by gen_standard_selections.py + === === === === === === === === ADE URA CYT GUA THY DA DC DG DT RA RU RG RC A T U @@ -5,5 +7,3 @@ C G DA5 DC5 DG5 DT5 DA3 DC3 DG3 DT3 RA5 RU5 RG5 RC5 RA3 RU3 RG3 RC3 === === === === === === === === - -.. Generated by gen_standard_selections.py \ No newline at end of file diff --git a/doc/source/generated/selections/nucleic_backbone.txt b/doc/source/generated/selections/nucleic_backbone.txt index d553d0908..c877c13c7 100644 --- a/doc/source/generated/selections/nucleic_backbone.txt +++ b/doc/source/generated/selections/nucleic_backbone.txt @@ -1,5 +1,5 @@ +.. Generated by gen_standard_selections.py + = === === === === P C5' C3' O3' O5' = === === === === - -.. Generated by gen_standard_selections.py \ No newline at end of file diff --git a/doc/source/generated/selections/nucleic_sugar.txt b/doc/source/generated/selections/nucleic_sugar.txt index abd07604b..765831f56 100644 --- a/doc/source/generated/selections/nucleic_sugar.txt +++ b/doc/source/generated/selections/nucleic_sugar.txt @@ -1,5 +1,5 @@ +.. Generated by gen_standard_selections.py + === === === === === C1' C2' C3' C4' O4' === === === === === - -.. Generated by gen_standard_selections.py \ No newline at end of file diff --git a/doc/source/generated/selections/protein.txt b/doc/source/generated/selections/protein.txt index d7363f2b8..e62f595a2 100644 --- a/doc/source/generated/selections/protein.txt +++ b/doc/source/generated/selections/protein.txt @@ -1,3 +1,5 @@ +.. Generated by gen_standard_selections.py + ==== ==== ==== ==== ==== ==== ==== ==== ACE ALA ALAD ARG ARGN ASF ASH ASN ASN1 ASP ASPH CALA CARG CASF CASN CASP @@ -13,5 +15,3 @@ NHIE NHIP NILE NLEU NLYS NME NMET NPHE NPRO NSER NTHR NTRP NTYR NVAL ORN PGLU PHE PRO QLN SER THR TRP TYR VAL ==== ==== ==== ==== ==== ==== ==== ==== - -.. Generated by gen_standard_selections.py \ No newline at end of file diff --git a/doc/source/generated/selections/protein_backbone.txt b/doc/source/generated/selections/protein_backbone.txt index d302b3b1f..4ca709b5e 100644 --- a/doc/source/generated/selections/protein_backbone.txt +++ b/doc/source/generated/selections/protein_backbone.txt @@ -1,5 +1,5 @@ +.. Generated by gen_standard_selections.py + = == = = N CA C O = == = = - -.. Generated by gen_standard_selections.py \ No newline at end of file diff --git a/doc/source/generated/topology/connectivityattrs.txt b/doc/source/generated/topology/connectivityattrs.txt index db3ee840e..413550c37 100644 --- a/doc/source/generated/topology/connectivityattrs.txt +++ b/doc/source/generated/topology/connectivityattrs.txt @@ -1,10 +1,10 @@ -========= =========== ============================================================================================================================================================================================================================================================================================================================================= -Atom AtomGroup Supported formats -========= =========== ============================================================================================================================================================================================================================================================================================================================================= -angles angles :ref:`DATA `, :ref:`GSD `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`XML ` -bonds bonds :ref:`DATA `, :ref:`DMS `, :ref:`GSD `, :ref:`MMTF `, :ref:`MOL2 `, :ref:`PDB, ENT `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`TXYZ, ARC `, :ref:`XML `, :ref:`XPDB ` -dihedrals dihedrals :ref:`DATA `, :ref:`GSD `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`XML ` -impropers impropers :ref:`DATA `, :ref:`GSD `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`XML ` -========= =========== ============================================================================================================================================================================================================================================================================================================================================= +.. Generated by gen_topologyparser_attrs.py -.. Generated by gen_topologyparser_attrs.py \ No newline at end of file +========= =========== ============================================================================================================================================================================================================================================================================================================================================================================ +Atom AtomGroup Supported formats +========= =========== ============================================================================================================================================================================================================================================================================================================================================================================ +angles angles :ref:`DATA `, :ref:`GSD `, :ref:`PARMED `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`XML ` +bonds bonds :ref:`DATA `, :ref:`DMS `, :ref:`GSD `, :ref:`MMTF `, :ref:`MOL2 `, :ref:`PARMED `, :ref:`PDB, ENT `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`TXYZ, ARC `, :ref:`XML `, :ref:`XPDB ` +dihedrals dihedrals :ref:`DATA `, :ref:`GSD `, :ref:`PARMED `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`XML ` +impropers impropers :ref:`DATA `, :ref:`GSD `, :ref:`PARMED `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`XML ` +========= =========== ============================================================================================================================================================================================================================================================================================================================================================================ diff --git a/doc/source/generated/topology/defaults.txt b/doc/source/generated/topology/defaults.txt index bc423b584..d73b38ddd 100644 --- a/doc/source/generated/topology/defaults.txt +++ b/doc/source/generated/topology/defaults.txt @@ -1,3 +1,5 @@ +.. Generated by gen_topologyattr_defaults.py + ============= ============= ======================================== ======= ======================= Atom AtomGroup default level type ============= ============= ======================================== ======= ======================= @@ -40,5 +42,3 @@ type_indices type_index No default values atom types type '' atom ureybradleys ureybradleys No default values atom ============= ============= ======================================== ======= ======================= - -.. Generated by gen_topologyattr_defaults.py \ No newline at end of file diff --git a/doc/source/generated/topology/groupmethods.txt b/doc/source/generated/topology/groupmethods.txt index c994bde09..e1f1f2835 100644 --- a/doc/source/generated/topology/groupmethods.txt +++ b/doc/source/generated/topology/groupmethods.txt @@ -1,3 +1,5 @@ +.. Generated by gen_topology_groupmethods.py + ================================================================== ====================================================================== ========== Method Description Requires ================================================================== ====================================================================== ========== @@ -11,5 +13,3 @@ Method Description :meth:`~MDAnalysis.core.topologyattrs.Masses.shape_parameter` Shape parameter masses :meth:`~MDAnalysis.core.topologyattrs.Masses.total_mass` Total mass of (compounds of) the group masses ================================================================== ====================================================================== ========== - -.. Generated by gen_topology_groupmethods.py \ No newline at end of file diff --git a/doc/source/generated/topology/topologyattrs.txt b/doc/source/generated/topology/topologyattrs.txt index 2ad489811..75a6e7a0f 100644 --- a/doc/source/generated/topology/topologyattrs.txt +++ b/doc/source/generated/topology/topologyattrs.txt @@ -1,38 +1,38 @@ -============= ============= ================================== =================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== +.. Generated by gen_topologyparser_attrs.py + +============= ============= ================================== ================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== Atom AtomGroup Description Supported formats -============= ============= ================================== =================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== -altLoc altLocs Alternate location :ref:`MMTF `, :ref:`PDB, ENT `, :ref:`PDBQT `, :ref:`XPDB ` -angles angles :ref:`DATA `, :ref:`GSD `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`XML ` +============= ============= ================================== ================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== +altLoc altLocs Alternate location :ref:`MMTF `, :ref:`PARMED `, :ref:`PDB, ENT `, :ref:`PDBQT `, :ref:`XPDB ` +angles angles :ref:`DATA `, :ref:`GSD `, :ref:`PARMED `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`XML ` atomiccharge atomiccharges Atomic number :ref:`GMS ` atomnum atomnums ? :ref:`DMS ` bfactor bfactors alias of tempfactor :ref:`MMTF ` -bonds bonds :ref:`DATA `, :ref:`DMS `, :ref:`GSD `, :ref:`MMTF `, :ref:`MOL2 `, :ref:`PDB, ENT `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`TXYZ, ARC `, :ref:`XML `, :ref:`XPDB ` -chainID chainIDs chain ID :ref:`DMS `, :ref:`PDB, ENT `, :ref:`XPDB ` -charge charges partial atomic charge :ref:`DATA `, :ref:`DMS `, :ref:`GSD `, :ref:`MMTF `, :ref:`MOL2 `, :ref:`PDBQT `, :ref:`PQR `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`XML ` +bonds bonds :ref:`DATA `, :ref:`DMS `, :ref:`GSD `, :ref:`MMTF `, :ref:`MOL2 `, :ref:`PARMED `, :ref:`PDB, ENT `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`TXYZ, ARC `, :ref:`XML `, :ref:`XPDB ` +chainID chainIDs chain ID :ref:`DMS `, :ref:`PARMED `, :ref:`PDB, ENT `, :ref:`XPDB ` +charge charges partial atomic charge :ref:`DATA `, :ref:`DMS `, :ref:`GSD `, :ref:`MMTF `, :ref:`MOL2 `, :ref:`PARMED `, :ref:`PDBQT `, :ref:`PQR `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`XML ` chargegroup chargegroups -cmaps cmaps -dihedrals dihedrals :ref:`DATA `, :ref:`GSD `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`XML ` -element elements atom element :ref:`XYZ ` -epsilon epsilons -epsilon14 epsilon14s -gbscreen gbscreens +cmaps cmaps :ref:`PARMED ` +dihedrals dihedrals :ref:`DATA `, :ref:`GSD `, :ref:`PARMED `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`XML ` +element elements atom element :ref:`IN, FHIAIMS `, :ref:`PARMED `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`XYZ ` +epsilon epsilons :ref:`PARMED ` +epsilon14 epsilon14s :ref:`PARMED ` +gbscreen gbscreens :ref:`PARMED ` icode icodes atom insertion code :ref:`MMTF `, :ref:`PDB, ENT `, :ref:`PDBQT `, :ref:`PQR `, :ref:`XPDB ` -impropers impropers :ref:`DATA `, :ref:`GSD `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`XML ` +impropers impropers :ref:`DATA `, :ref:`GSD `, :ref:`PARMED `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`XML ` model models model number (from 0) :ref:`MMTF ` molnum molnums [molecules] number (from 0) :ref:`TPR ` moltype moltypes [moleculetype] name :ref:`TPR ` -name names atom names :ref:`CONFIG `, :ref:`CRD `, :ref:`DMS `, :ref:`GMS `, :ref:`GRO `, :ref:`GSD `, :ref:`HISTORY `, :ref:`MMTF `, :ref:`MOL2 `, :ref:`PDB, ENT `, :ref:`PDBQT `, :ref:`PQR `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`TXYZ, ARC `, :ref:`XPDB `, :ref:`XYZ ` -nbindex nbindices -occupancy occupancies atom occupancy :ref:`MMTF `, :ref:`PDB, ENT `, :ref:`PDBQT `, :ref:`XPDB ` +name names atom names :ref:`CONFIG `, :ref:`CRD `, :ref:`DMS `, :ref:`GMS `, :ref:`GRO `, :ref:`GSD `, :ref:`HISTORY `, :ref:`IN, FHIAIMS `, :ref:`MMTF `, :ref:`MOL2 `, :ref:`PARMED `, :ref:`PDB, ENT `, :ref:`PDBQT `, :ref:`PQR `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`TXYZ, ARC `, :ref:`XPDB `, :ref:`XYZ ` +nbindex nbindices :ref:`PARMED ` +occupancy occupancies atom occupancy :ref:`MMTF `, :ref:`PARMED `, :ref:`PDB, ENT `, :ref:`PDBQT `, :ref:`XPDB ` radius radii atomic radius :ref:`GSD `, :ref:`PQR `, :ref:`XML ` record_type record_types ATOM / HETATM :ref:`PDB, ENT `, :ref:`PDBQT `, :ref:`PQR `, :ref:`XPDB ` -resname resnames residue name (except GSD has ints) :ref:`CRD `, :ref:`DMS `, :ref:`GRO `, :ref:`GSD `, :ref:`MMTF `, :ref:`MOL2 `, :ref:`PDB, ENT `, :ref:`PDBQT `, :ref:`PQR `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`XPDB ` -rmin rmins -rmin14 rmin14s -solventradius solventradii -tempfactor tempfactors B-factor :ref:`CRD `, :ref:`PDB, ENT `, :ref:`PDBQT `, :ref:`XPDB ` +resname resnames residue name (except GSD has ints) :ref:`CRD `, :ref:`DMS `, :ref:`GRO `, :ref:`GSD `, :ref:`MMTF `, :ref:`MOL2 `, :ref:`PARMED `, :ref:`PDB, ENT `, :ref:`PDBQT `, :ref:`PQR `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`XPDB ` +rmin rmins :ref:`PARMED ` +rmin14 rmin14s :ref:`PARMED ` +solventradius solventradii :ref:`PARMED ` +tempfactor tempfactors B-factor :ref:`CRD `, :ref:`PARMED `, :ref:`PDB, ENT `, :ref:`PDBQT `, :ref:`XPDB ` type_index type_indices amber atom type number :ref:`TOP, PRMTOP, PARM7 ` -ureybradleys ureybradleys -============= ============= ================================== =================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== - -.. Generated by gen_topologyparser_attrs.py \ No newline at end of file +ureybradleys ureybradleys :ref:`PARMED ` +============= ============= ================================== ================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== diff --git a/doc/source/scripts/base.py b/doc/source/scripts/base.py index 5c24d9b06..14fd4f0e9 100644 --- a/doc/source/scripts/base.py +++ b/doc/source/scripts/base.py @@ -16,6 +16,7 @@ class TableWriter(object): """ filename = '' + include_table = False headings = [] preprocess = [] postprocess = [] @@ -68,11 +69,13 @@ def get_line(self, *args): def write_table(self): with open(self.path, 'w') as f: + f.write(f'.. Generated by {sys.argv[0]}\n\n') + if self.include_table: + f.write('.. table:: {self.include_table}') print(tabulate.tabulate(self.lines, headers=self.headings, tablefmt='rst'), file=f) - f.write('\n.. Generated by {}'.format(sys.argv[0])) print('Wrote ', self.filename) # ==== HELPER FUNCTIONS ==== # diff --git a/doc/source/scripts/gen_format_overview_classes.py b/doc/source/scripts/gen_format_overview_classes.py index 65b7dc872..ace247eab 100644 --- a/doc/source/scripts/gen_format_overview_classes.py +++ b/doc/source/scripts/gen_format_overview_classes.py @@ -30,6 +30,7 @@ class FormatOverview(TableWriter): filename = 'formats/format_overview.txt' + include_table = 'Table of all supported formats in MDAnalysis' preprocess = ['keys'] headings = ['File type', 'Description', 'Topology', 'Coordinates', 'Read', 'Write'] @@ -75,6 +76,7 @@ def _write(self, fmt, handlers): class CoordinateReaders(FormatOverview): filename = 'formats/coordinate_readers.txt' + include_table = 'Table of supported coordinate readers and the information read' headings = ['File type', 'Description', 'Velocities', 'Forces'] def _set_up_input(self): diff --git a/doc/source/scripts/gen_selection_exporters.py b/doc/source/scripts/gen_selection_exporters.py index d617bc8a5..4cd082aae 100644 --- a/doc/source/scripts/gen_selection_exporters.py +++ b/doc/source/scripts/gen_selection_exporters.py @@ -18,6 +18,7 @@ class SelectionExporterWriter(TableWriter): headings = ['Program', 'Extension', 'Description', 'Class'] filename = 'formats/selection_exporter_formats.txt' + include_table = 'Supported selection exporters' sort = True def _set_up_input(self): diff --git a/doc/source/scripts/gen_topologyparser_attrs.py b/doc/source/scripts/gen_topologyparser_attrs.py index 8af63a92d..cba83ee8c 100755 --- a/doc/source/scripts/gen_topologyparser_attrs.py +++ b/doc/source/scripts/gen_topologyparser_attrs.py @@ -17,6 +17,7 @@ from MDAnalysisTests.topology.test_crd import TestCRDParser from MDAnalysisTests.topology.test_dlpoly import TestDLPHistoryParser, TestDLPConfigParser from MDAnalysisTests.topology.test_dms import TestDMSParser +from MDAnalysisTests.topology.test_fhiaims import TestFHIAIMS from MDAnalysisTests.topology.test_gms import GMSBase from MDAnalysisTests.topology.test_gro import TestGROParser from MDAnalysisTests.topology.test_gsd import TestGSDParser @@ -24,6 +25,7 @@ from MDAnalysisTests.topology.test_lammpsdata import LammpsBase, TestDumpParser from MDAnalysisTests.topology.test_mmtf import TestMMTFParser from MDAnalysisTests.topology.test_mol2 import TestMOL2Base +from MDAnalysisTests.topology.test_parmed import BaseTestParmedParser from MDAnalysisTests.topology.test_pdb import TestPDBParser from MDAnalysisTests.topology.test_pdbqt import TestPDBQT from MDAnalysisTests.topology.test_pqr import TestPQRParser @@ -35,9 +37,10 @@ from MDAnalysisTests.topology.test_xyz import XYZBase PARSER_TESTS = (TestCRDParser, TestDLPHistoryParser, TestDLPConfigParser, - TestDMSParser, GMSBase, + TestDMSParser, TestFHIAIMS, GMSBase, TestGROParser, TestGSDParser, TestHoomdXMLParser, LammpsBase, TestMMTFParser, TestMOL2Base, + BaseTestParmedParser, TestPDBParser, TestPDBQT, TestPQRParser, PSFBase, TestPRMParser, TPRAttrs, TestTXYZParser, TestXPDBParser, XYZBase, TestDumpParser) @@ -54,6 +57,7 @@ class TopologyParsers(TableWriter): headings = ['Format', 'Description', 'Attributes read', 'Attributes guessed'] preprocess = ['keys'] filename = 'formats/topology_parsers.txt' + include_table = 'Table of supported topology parsers and the attributes read' sort = True def __init__(self): From 1094f2da60ba0799f7230590a763f2a1c3188825 Mon Sep 17 00:00:00 2001 From: Lily Wang Date: Fri, 19 Jun 2020 10:27:25 +1000 Subject: [PATCH 05/18] get script path --- doc/source/scripts/base.py | 2 +- doc/source/scripts/generate_all.sh | 14 ++++++++------ 2 files changed, 9 insertions(+), 7 deletions(-) diff --git a/doc/source/scripts/base.py b/doc/source/scripts/base.py index 14fd4f0e9..233af91ef 100644 --- a/doc/source/scripts/base.py +++ b/doc/source/scripts/base.py @@ -71,7 +71,7 @@ def write_table(self): with open(self.path, 'w') as f: f.write(f'.. Generated by {sys.argv[0]}\n\n') if self.include_table: - f.write('.. table:: {self.include_table}') + f.write(f'.. table:: {self.include_table}\n\n') print(tabulate.tabulate(self.lines, headers=self.headings, tablefmt='rst'), diff --git a/doc/source/scripts/generate_all.sh b/doc/source/scripts/generate_all.sh index 1928ba2dc..9e1a852b4 100755 --- a/doc/source/scripts/generate_all.sh +++ b/doc/source/scripts/generate_all.sh @@ -1,8 +1,10 @@ #!/usr/bin/env bash -python gen_format_overview_classes.py -python gen_selection_exporters.py -python gen_standard_selections.py -python gen_topology_groupmethods.py -python gen_topologyattr_defaults.py -python gen_topologyparser_attrs.py \ No newline at end of file +GENPATH=$(echo $(cd $(dirname $0) && pwd -P)) + +python $GENPATH/gen_format_overview_classes.py +python $GENPATH/gen_selection_exporters.py +python $GENPATH/gen_standard_selections.py +python $GENPATH/gen_topology_groupmethods.py +python $GENPATH/gen_topologyattr_defaults.py +python $GENPATH/gen_topologyparser_attrs.py \ No newline at end of file From b2b3773758915c9f73cbfa62c6874aea841c1e1b Mon Sep 17 00:00:00 2001 From: Lily Wang Date: Fri, 19 Jun 2020 10:49:31 +1000 Subject: [PATCH 06/18] hack script to add elements for PDB --- doc/source/formats/topology_parsers.txt | 8 +++++--- doc/source/generated/topology/topologyattrs.txt | 2 +- doc/source/scripts/gen_topologyparser_attrs.py | 4 ++++ 3 files changed, 10 insertions(+), 4 deletions(-) diff --git a/doc/source/formats/topology_parsers.txt b/doc/source/formats/topology_parsers.txt index d172d593c..7263fec0e 100644 --- a/doc/source/formats/topology_parsers.txt +++ b/doc/source/formats/topology_parsers.txt @@ -1,6 +1,8 @@ .. Generated by gen_topologyparser_attrs.py -.. table:: {self.include_table}====================================== =============================== =================================================================================================================================================================================================================== ==================== +.. table:: Table of supported topology parsers and the attributes read + +====================================== =============================== =================================================================================================================================================================================================================== ==================== Format Description Attributes read Attributes guessed ====================================== =============================== =================================================================================================================================================================================================================== ==================== :ref:`CONFIG ` DL_Poly CONFIG file names masses, types @@ -16,11 +18,11 @@ Format Description Attribu :ref:`MMTF ` MMTF file altLocs, bfactors, bonds, charges, icodes, models, names, occupancies, resnames masses :ref:`MOL2 ` Tripos MOL2 file bonds, charges, names, resnames masses :ref:`PARMED ` parmed Structure altLocs, angles, bonds, chainIDs, charges, cmaps, dihedrals, elements, epsilon14s, epsilons, gbscreens, impropers, names, nbindices, occupancies, resnames, rmin14s, rmins, solventradii, tempfactors, ureybradleys -:ref:`PDB, ENT ` Standard PDB file altLocs, bonds, chainIDs, icodes, names, occupancies, record_types, resnames, tempfactors masses, types +:ref:`PDB, ENT ` Standard PDB file altLocs, bonds, chainIDs, elements, icodes, names, occupancies, record_types, resnames, tempfactors masses, types :ref:`PDBQT ` PDBQT file altLocs, charges, icodes, names, occupancies, record_types, resnames, tempfactors masses :ref:`PQR ` PQR file charges, icodes, names, radii, record_types, resnames masses, types :ref:`PSF ` CHARMM, NAMD, or XPLOR PSF file angles, bonds, charges, dihedrals, impropers, names, resnames -:ref:`TOP, PRMTOP, PARM7 ` AMBER topology file angles, bonds, charges, dihedrals, impropers, names, resnames, type_indices elements +:ref:`TOP, PRMTOP, PARM7 ` AMBER topology file angles, bonds, charges, dihedrals, impropers, names, resnames, type_indices :ref:`TPR ` GROMACS run topology file angles, bonds, charges, dihedrals, impropers, molnums, moltypes, names, resnames :ref:`TXYZ, ARC ` Tinker file bonds, names masses :ref:`XML ` HOOMD XML file angles, bonds, charges, dihedrals, impropers, radii diff --git a/doc/source/generated/topology/topologyattrs.txt b/doc/source/generated/topology/topologyattrs.txt index 75a6e7a0f..b07428e5a 100644 --- a/doc/source/generated/topology/topologyattrs.txt +++ b/doc/source/generated/topology/topologyattrs.txt @@ -14,7 +14,7 @@ charge charges partial atomic charge :ref:`DATA ` dihedrals dihedrals :ref:`DATA `, :ref:`GSD `, :ref:`PARMED `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`XML ` -element elements atom element :ref:`IN, FHIAIMS `, :ref:`PARMED `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`XYZ ` +element elements atom element :ref:`IN, FHIAIMS `, :ref:`PARMED `, :ref:`PDB, ENT `, :ref:`XYZ ` epsilon epsilons :ref:`PARMED ` epsilon14 epsilon14s :ref:`PARMED ` gbscreen gbscreens :ref:`PARMED ` diff --git a/doc/source/scripts/gen_topologyparser_attrs.py b/doc/source/scripts/gen_topologyparser_attrs.py index cba83ee8c..6129300e8 100755 --- a/doc/source/scripts/gen_topologyparser_attrs.py +++ b/doc/source/scripts/gen_topologyparser_attrs.py @@ -51,7 +51,11 @@ for p in PARSER_TESTS: e, g = set(p.expected_attrs)-MANDATORY_ATTRS, set(p.guessed_attrs) + # clunky hack for PDB + if p is TestPDBParser: + e.add('elements') parser_attrs[p.parser] = (e, g) + class TopologyParsers(TableWriter): headings = ['Format', 'Description', 'Attributes read', 'Attributes guessed'] From b17ea1ceb7683935f42b1a6a4594c19fdf543279 Mon Sep 17 00:00:00 2001 From: Lily Wang Date: Fri, 19 Jun 2020 10:55:11 +1000 Subject: [PATCH 07/18] update comment --- doc/source/formats/coordinate_readers.txt | 6 ++++-- doc/source/formats/format_overview.txt | 6 ++++-- doc/source/formats/reference/classes/CONFIG.txt | 2 +- doc/source/formats/reference/classes/CRD.txt | 2 +- doc/source/formats/reference/classes/DATA.txt | 2 +- doc/source/formats/reference/classes/DCD.txt | 2 +- doc/source/formats/reference/classes/DMS.txt | 2 +- doc/source/formats/reference/classes/GMS.txt | 2 +- doc/source/formats/reference/classes/GRO.txt | 2 +- doc/source/formats/reference/classes/GSD.txt | 2 +- doc/source/formats/reference/classes/HISTORY.txt | 2 +- doc/source/formats/reference/classes/INPCRD.txt | 2 +- doc/source/formats/reference/classes/ITP.txt | 2 +- doc/source/formats/reference/classes/LAMMPS.txt | 2 +- doc/source/formats/reference/classes/LAMMPSDUMP.txt | 2 +- doc/source/formats/reference/classes/MMTF.txt | 2 +- doc/source/formats/reference/classes/MOL2.txt | 2 +- doc/source/formats/reference/classes/NCDF.txt | 2 +- doc/source/formats/reference/classes/PDB.txt | 2 +- doc/source/formats/reference/classes/PDBQT.txt | 2 +- doc/source/formats/reference/classes/PQR.txt | 2 +- doc/source/formats/reference/classes/PSF.txt | 2 +- doc/source/formats/reference/classes/TOP.txt | 2 +- doc/source/formats/reference/classes/TPR.txt | 2 +- doc/source/formats/reference/classes/TRJ.txt | 2 +- doc/source/formats/reference/classes/TRR.txt | 2 +- doc/source/formats/reference/classes/TRZ.txt | 2 +- doc/source/formats/reference/classes/TXYZ.txt | 2 +- doc/source/formats/reference/classes/XML.txt | 2 +- doc/source/formats/reference/classes/XPDB.txt | 2 +- doc/source/formats/reference/classes/XTC.txt | 2 +- doc/source/formats/reference/classes/XYZ.txt | 2 +- doc/source/formats/selection_exporter_formats.txt | 6 ++++-- doc/source/formats/topology_parsers.txt | 2 +- doc/source/generated/selections/base.txt | 2 +- doc/source/generated/selections/nucleic.txt | 2 +- doc/source/generated/selections/nucleic_backbone.txt | 2 +- doc/source/generated/selections/nucleic_sugar.txt | 2 +- doc/source/generated/selections/protein.txt | 2 +- doc/source/generated/selections/protein_backbone.txt | 2 +- doc/source/generated/topology/connectivityattrs.txt | 2 +- doc/source/generated/topology/defaults.txt | 2 +- doc/source/generated/topology/groupmethods.txt | 2 +- doc/source/generated/topology/topologyattrs.txt | 2 +- doc/source/scripts/base.py | 2 +- 45 files changed, 54 insertions(+), 48 deletions(-) diff --git a/doc/source/formats/coordinate_readers.txt b/doc/source/formats/coordinate_readers.txt index 1111abb5f..9660b39a4 100644 --- a/doc/source/formats/coordinate_readers.txt +++ b/doc/source/formats/coordinate_readers.txt @@ -1,6 +1,8 @@ -.. Generated by gen_format_overview_classes.py +.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py -.. table:: {self.include_table}===================================== ========================================= ============ ======== +.. table:: Table of supported coordinate readers and the information read + +===================================== ========================================= ============ ======== File type Description Velocities Forces ===================================== ========================================= ============ ======== :ref:`ARC ` Tinker file diff --git a/doc/source/formats/format_overview.txt b/doc/source/formats/format_overview.txt index 773af95fa..7739c381c 100644 --- a/doc/source/formats/format_overview.txt +++ b/doc/source/formats/format_overview.txt @@ -1,6 +1,8 @@ -.. Generated by gen_format_overview_classes.py +.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py -.. table:: {self.include_table}===================================== ========================================= ========== ============= ====== ======= +.. table:: Table of all supported formats in MDAnalysis + +===================================== ========================================= ========== ============= ====== ======= File type Description Topology Coordinates Read Write ===================================== ========================================= ========== ============= ====== ======= :ref:`ARC ` Tinker file ✓ ✓ ✓ diff --git a/doc/source/formats/reference/classes/CONFIG.txt b/doc/source/formats/reference/classes/CONFIG.txt index abbdd8caf..46d02a477 100644 --- a/doc/source/formats/reference/classes/CONFIG.txt +++ b/doc/source/formats/reference/classes/CONFIG.txt @@ -1,4 +1,4 @@ -.. Generated by gen_format_overview_classes.py +.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py ===================== ====================================================== **Coordinate reader** :class:`MDAnalysis.coordinates.DLPoly.ConfigReader` diff --git a/doc/source/formats/reference/classes/CRD.txt b/doc/source/formats/reference/classes/CRD.txt index 08a61080c..70053079b 100644 --- a/doc/source/formats/reference/classes/CRD.txt +++ b/doc/source/formats/reference/classes/CRD.txt @@ -1,4 +1,4 @@ -.. Generated by gen_format_overview_classes.py +.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py ===================== ================================================ **Coordinate reader** :class:`MDAnalysis.coordinates.CRD.CRDReader` diff --git a/doc/source/formats/reference/classes/DATA.txt b/doc/source/formats/reference/classes/DATA.txt index f76bcd70a..f0b973ac8 100644 --- a/doc/source/formats/reference/classes/DATA.txt +++ b/doc/source/formats/reference/classes/DATA.txt @@ -1,4 +1,4 @@ -.. Generated by gen_format_overview_classes.py +.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py ===================== ==================================================== **Coordinate reader** :class:`MDAnalysis.coordinates.LAMMPS.DATAReader` diff --git a/doc/source/formats/reference/classes/DCD.txt b/doc/source/formats/reference/classes/DCD.txt index c175f4d89..46848d3f4 100644 --- a/doc/source/formats/reference/classes/DCD.txt +++ b/doc/source/formats/reference/classes/DCD.txt @@ -1,4 +1,4 @@ -.. Generated by gen_format_overview_classes.py +.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py ===================== ============================================= **Coordinate reader** :class:`MDAnalysis.coordinates.DCD.DCDReader` diff --git a/doc/source/formats/reference/classes/DMS.txt b/doc/source/formats/reference/classes/DMS.txt index 9f408f01d..54d692e4e 100644 --- a/doc/source/formats/reference/classes/DMS.txt +++ b/doc/source/formats/reference/classes/DMS.txt @@ -1,4 +1,4 @@ -.. Generated by gen_format_overview_classes.py +.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py ===================== ================================================ **Coordinate reader** :class:`MDAnalysis.coordinates.DMS.DMSReader` diff --git a/doc/source/formats/reference/classes/GMS.txt b/doc/source/formats/reference/classes/GMS.txt index c9dcab87f..a7914f4c1 100644 --- a/doc/source/formats/reference/classes/GMS.txt +++ b/doc/source/formats/reference/classes/GMS.txt @@ -1,4 +1,4 @@ -.. Generated by gen_format_overview_classes.py +.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py ===================== ================================================ **Coordinate reader** :class:`MDAnalysis.coordinates.GMS.GMSReader` diff --git a/doc/source/formats/reference/classes/GRO.txt b/doc/source/formats/reference/classes/GRO.txt index a2b27d3c4..13594aba9 100644 --- a/doc/source/formats/reference/classes/GRO.txt +++ b/doc/source/formats/reference/classes/GRO.txt @@ -1,4 +1,4 @@ -.. Generated by gen_format_overview_classes.py +.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py ===================== ================================================ **Coordinate reader** :class:`MDAnalysis.coordinates.GRO.GROReader` diff --git a/doc/source/formats/reference/classes/GSD.txt b/doc/source/formats/reference/classes/GSD.txt index b108969a0..8ea8862a3 100644 --- a/doc/source/formats/reference/classes/GSD.txt +++ b/doc/source/formats/reference/classes/GSD.txt @@ -1,4 +1,4 @@ -.. Generated by gen_format_overview_classes.py +.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py ===================== ================================================ **Coordinate reader** :class:`MDAnalysis.coordinates.GSD.GSDReader` diff --git a/doc/source/formats/reference/classes/HISTORY.txt b/doc/source/formats/reference/classes/HISTORY.txt index 6e683f3b8..743f1280f 100644 --- a/doc/source/formats/reference/classes/HISTORY.txt +++ b/doc/source/formats/reference/classes/HISTORY.txt @@ -1,4 +1,4 @@ -.. Generated by gen_format_overview_classes.py +.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py ===================== ======================================================= **Coordinate reader** :class:`MDAnalysis.coordinates.DLPoly.HistoryReader` diff --git a/doc/source/formats/reference/classes/INPCRD.txt b/doc/source/formats/reference/classes/INPCRD.txt index 90bdcbde8..b4b0e61cf 100644 --- a/doc/source/formats/reference/classes/INPCRD.txt +++ b/doc/source/formats/reference/classes/INPCRD.txt @@ -1,4 +1,4 @@ -.. Generated by gen_format_overview_classes.py +.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py ===================== ================================================ **Coordinate reader** :class:`MDAnalysis.coordinates.INPCRD.INPReader` diff --git a/doc/source/formats/reference/classes/ITP.txt b/doc/source/formats/reference/classes/ITP.txt index 12d2c6a0a..5f2c0810e 100644 --- a/doc/source/formats/reference/classes/ITP.txt +++ b/doc/source/formats/reference/classes/ITP.txt @@ -1,4 +1,4 @@ -.. Generated by gen_format_overview_classes.py +.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py =================== ================================================ **Topology parser** :class:`MDAnalysis.topology.ITPParser.ITPParser` diff --git a/doc/source/formats/reference/classes/LAMMPS.txt b/doc/source/formats/reference/classes/LAMMPS.txt index 227416982..102ac8294 100644 --- a/doc/source/formats/reference/classes/LAMMPS.txt +++ b/doc/source/formats/reference/classes/LAMMPS.txt @@ -1,4 +1,4 @@ -.. Generated by gen_format_overview_classes.py +.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py ===================== ================================================ **Coordinate reader** :class:`MDAnalysis.coordinates.LAMMPS.DCDReader` diff --git a/doc/source/formats/reference/classes/LAMMPSDUMP.txt b/doc/source/formats/reference/classes/LAMMPSDUMP.txt index c302a7671..529d1e0a9 100644 --- a/doc/source/formats/reference/classes/LAMMPSDUMP.txt +++ b/doc/source/formats/reference/classes/LAMMPSDUMP.txt @@ -1,4 +1,4 @@ -.. Generated by gen_format_overview_classes.py +.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py ===================== ========================================================== **Coordinate reader** :class:`MDAnalysis.coordinates.LAMMPS.DumpReader` diff --git a/doc/source/formats/reference/classes/MMTF.txt b/doc/source/formats/reference/classes/MMTF.txt index a2bc60ea3..168cb34bf 100644 --- a/doc/source/formats/reference/classes/MMTF.txt +++ b/doc/source/formats/reference/classes/MMTF.txt @@ -1,4 +1,4 @@ -.. Generated by gen_format_overview_classes.py +.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py ===================== ================================================== **Coordinate reader** :class:`MDAnalysis.coordinates.MMTF.MMTFReader` diff --git a/doc/source/formats/reference/classes/MOL2.txt b/doc/source/formats/reference/classes/MOL2.txt index b22bfa8ab..9df227c11 100644 --- a/doc/source/formats/reference/classes/MOL2.txt +++ b/doc/source/formats/reference/classes/MOL2.txt @@ -1,4 +1,4 @@ -.. Generated by gen_format_overview_classes.py +.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py ===================== ================================================== **Coordinate reader** :class:`MDAnalysis.coordinates.MOL2.MOL2Reader` diff --git a/doc/source/formats/reference/classes/NCDF.txt b/doc/source/formats/reference/classes/NCDF.txt index 92fd74f79..1967038b9 100644 --- a/doc/source/formats/reference/classes/NCDF.txt +++ b/doc/source/formats/reference/classes/NCDF.txt @@ -1,4 +1,4 @@ -.. Generated by gen_format_overview_classes.py +.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py ===================== ============================================== **Coordinate reader** :class:`MDAnalysis.coordinates.TRJ.NCDFReader` diff --git a/doc/source/formats/reference/classes/PDB.txt b/doc/source/formats/reference/classes/PDB.txt index c3b0ead5d..df98fffd7 100644 --- a/doc/source/formats/reference/classes/PDB.txt +++ b/doc/source/formats/reference/classes/PDB.txt @@ -1,4 +1,4 @@ -.. Generated by gen_format_overview_classes.py +.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py ===================== ================================================ **Coordinate reader** :class:`MDAnalysis.coordinates.PDB.PDBReader` diff --git a/doc/source/formats/reference/classes/PDBQT.txt b/doc/source/formats/reference/classes/PDBQT.txt index 4c43c0f88..6699839d7 100644 --- a/doc/source/formats/reference/classes/PDBQT.txt +++ b/doc/source/formats/reference/classes/PDBQT.txt @@ -1,4 +1,4 @@ -.. Generated by gen_format_overview_classes.py +.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py ===================== ==================================================== **Coordinate reader** :class:`MDAnalysis.coordinates.PDBQT.PDBQTReader` diff --git a/doc/source/formats/reference/classes/PQR.txt b/doc/source/formats/reference/classes/PQR.txt index 0c9a8b305..0b9248585 100644 --- a/doc/source/formats/reference/classes/PQR.txt +++ b/doc/source/formats/reference/classes/PQR.txt @@ -1,4 +1,4 @@ -.. Generated by gen_format_overview_classes.py +.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py ===================== ================================================ **Coordinate reader** :class:`MDAnalysis.coordinates.PQR.PQRReader` diff --git a/doc/source/formats/reference/classes/PSF.txt b/doc/source/formats/reference/classes/PSF.txt index 1d0308116..9fc8cb054 100644 --- a/doc/source/formats/reference/classes/PSF.txt +++ b/doc/source/formats/reference/classes/PSF.txt @@ -1,4 +1,4 @@ -.. Generated by gen_format_overview_classes.py +.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py =================== ================================================ **Topology parser** :class:`MDAnalysis.topology.PSFParser.PSFParser` diff --git a/doc/source/formats/reference/classes/TOP.txt b/doc/source/formats/reference/classes/TOP.txt index 37f18d608..d2c583952 100644 --- a/doc/source/formats/reference/classes/TOP.txt +++ b/doc/source/formats/reference/classes/TOP.txt @@ -1,4 +1,4 @@ -.. Generated by gen_format_overview_classes.py +.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py =================== ================================================ **Topology parser** :class:`MDAnalysis.topology.TOPParser.TOPParser` diff --git a/doc/source/formats/reference/classes/TPR.txt b/doc/source/formats/reference/classes/TPR.txt index 68042547d..f0fe1a0f4 100644 --- a/doc/source/formats/reference/classes/TPR.txt +++ b/doc/source/formats/reference/classes/TPR.txt @@ -1,4 +1,4 @@ -.. Generated by gen_format_overview_classes.py +.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py =================== ================================================ **Topology parser** :class:`MDAnalysis.topology.TPRParser.TPRParser` diff --git a/doc/source/formats/reference/classes/TRJ.txt b/doc/source/formats/reference/classes/TRJ.txt index 0d964f6c6..baf15d26e 100644 --- a/doc/source/formats/reference/classes/TRJ.txt +++ b/doc/source/formats/reference/classes/TRJ.txt @@ -1,4 +1,4 @@ -.. Generated by gen_format_overview_classes.py +.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py ===================== ============================================= **Coordinate reader** :class:`MDAnalysis.coordinates.TRJ.TRJReader` diff --git a/doc/source/formats/reference/classes/TRR.txt b/doc/source/formats/reference/classes/TRR.txt index 529ccfe42..7c86cd5b0 100644 --- a/doc/source/formats/reference/classes/TRR.txt +++ b/doc/source/formats/reference/classes/TRR.txt @@ -1,4 +1,4 @@ -.. Generated by gen_format_overview_classes.py +.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py ===================== ============================================= **Coordinate reader** :class:`MDAnalysis.coordinates.TRR.TRRReader` diff --git a/doc/source/formats/reference/classes/TRZ.txt b/doc/source/formats/reference/classes/TRZ.txt index df39f9a87..eb6945d0a 100644 --- a/doc/source/formats/reference/classes/TRZ.txt +++ b/doc/source/formats/reference/classes/TRZ.txt @@ -1,4 +1,4 @@ -.. Generated by gen_format_overview_classes.py +.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py ===================== ============================================= **Coordinate reader** :class:`MDAnalysis.coordinates.TRZ.TRZReader` diff --git a/doc/source/formats/reference/classes/TXYZ.txt b/doc/source/formats/reference/classes/TXYZ.txt index 15bd735db..cd1c40b14 100644 --- a/doc/source/formats/reference/classes/TXYZ.txt +++ b/doc/source/formats/reference/classes/TXYZ.txt @@ -1,4 +1,4 @@ -.. Generated by gen_format_overview_classes.py +.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py ===================== ================================================== **Coordinate reader** :class:`MDAnalysis.coordinates.TXYZ.TXYZReader` diff --git a/doc/source/formats/reference/classes/XML.txt b/doc/source/formats/reference/classes/XML.txt index 63b829649..a7da04728 100644 --- a/doc/source/formats/reference/classes/XML.txt +++ b/doc/source/formats/reference/classes/XML.txt @@ -1,4 +1,4 @@ -.. Generated by gen_format_overview_classes.py +.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py =================== ========================================================== **Topology parser** :class:`MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser` diff --git a/doc/source/formats/reference/classes/XPDB.txt b/doc/source/formats/reference/classes/XPDB.txt index 3fda83ef9..0cc810519 100644 --- a/doc/source/formats/reference/classes/XPDB.txt +++ b/doc/source/formats/reference/classes/XPDB.txt @@ -1,4 +1,4 @@ -.. Generated by gen_format_overview_classes.py +.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py ===================== ================================================================ **Coordinate reader** :class:`MDAnalysis.coordinates.PDB.ExtendedPDBReader` diff --git a/doc/source/formats/reference/classes/XTC.txt b/doc/source/formats/reference/classes/XTC.txt index 29a1fa1d4..e8536a99c 100644 --- a/doc/source/formats/reference/classes/XTC.txt +++ b/doc/source/formats/reference/classes/XTC.txt @@ -1,4 +1,4 @@ -.. Generated by gen_format_overview_classes.py +.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py ===================== ============================================= **Coordinate reader** :class:`MDAnalysis.coordinates.XTC.XTCReader` diff --git a/doc/source/formats/reference/classes/XYZ.txt b/doc/source/formats/reference/classes/XYZ.txt index 73230d44e..0e0dbb257 100644 --- a/doc/source/formats/reference/classes/XYZ.txt +++ b/doc/source/formats/reference/classes/XYZ.txt @@ -1,4 +1,4 @@ -.. Generated by gen_format_overview_classes.py +.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py ===================== ================================================ **Coordinate reader** :class:`MDAnalysis.coordinates.XYZ.XYZReader` diff --git a/doc/source/formats/selection_exporter_formats.txt b/doc/source/formats/selection_exporter_formats.txt index 59dbd153d..191e861d8 100644 --- a/doc/source/formats/selection_exporter_formats.txt +++ b/doc/source/formats/selection_exporter_formats.txt @@ -1,6 +1,8 @@ -.. Generated by gen_selection_exporters.py +.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_selection_exporters.py -.. table:: {self.include_table}========== =========== ======================================== ====================================================== +.. table:: Supported selection exporters + +========== =========== ======================================== ====================================================== Program Extension Description Class ========== =========== ======================================== ====================================================== `CHARMM`_ str CHARMM selection of individual atoms :class:`MDAnalysis.selections.charmm.SelectionWriter` diff --git a/doc/source/formats/topology_parsers.txt b/doc/source/formats/topology_parsers.txt index 7263fec0e..b56b0f212 100644 --- a/doc/source/formats/topology_parsers.txt +++ b/doc/source/formats/topology_parsers.txt @@ -1,4 +1,4 @@ -.. Generated by gen_topologyparser_attrs.py +.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_topologyparser_attrs.py .. table:: Table of supported topology parsers and the attributes read diff --git a/doc/source/generated/selections/base.txt b/doc/source/generated/selections/base.txt index 15f6b1bc1..60fb8b8ee 100644 --- a/doc/source/generated/selections/base.txt +++ b/doc/source/generated/selections/base.txt @@ -1,4 +1,4 @@ -.. Generated by gen_standard_selections.py +.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_standard_selections.py == == == == == == == === N9 N7 C8 C5 C4 N3 C2 N1 diff --git a/doc/source/generated/selections/nucleic.txt b/doc/source/generated/selections/nucleic.txt index 85b69582f..197404872 100644 --- a/doc/source/generated/selections/nucleic.txt +++ b/doc/source/generated/selections/nucleic.txt @@ -1,4 +1,4 @@ -.. Generated by gen_standard_selections.py +.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_standard_selections.py === === === === === === === === ADE URA CYT GUA THY DA DC DG diff --git a/doc/source/generated/selections/nucleic_backbone.txt b/doc/source/generated/selections/nucleic_backbone.txt index c877c13c7..d4f67d6c5 100644 --- a/doc/source/generated/selections/nucleic_backbone.txt +++ b/doc/source/generated/selections/nucleic_backbone.txt @@ -1,4 +1,4 @@ -.. Generated by gen_standard_selections.py +.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_standard_selections.py = === === === === P C5' C3' O3' O5' diff --git a/doc/source/generated/selections/nucleic_sugar.txt b/doc/source/generated/selections/nucleic_sugar.txt index 765831f56..ce9469f04 100644 --- a/doc/source/generated/selections/nucleic_sugar.txt +++ b/doc/source/generated/selections/nucleic_sugar.txt @@ -1,4 +1,4 @@ -.. Generated by gen_standard_selections.py +.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_standard_selections.py === === === === === C1' C2' C3' C4' O4' diff --git a/doc/source/generated/selections/protein.txt b/doc/source/generated/selections/protein.txt index e62f595a2..3d9982ffd 100644 --- a/doc/source/generated/selections/protein.txt +++ b/doc/source/generated/selections/protein.txt @@ -1,4 +1,4 @@ -.. Generated by gen_standard_selections.py +.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_standard_selections.py ==== ==== ==== ==== ==== ==== ==== ==== ACE ALA ALAD ARG ARGN ASF ASH ASN diff --git a/doc/source/generated/selections/protein_backbone.txt b/doc/source/generated/selections/protein_backbone.txt index 4ca709b5e..cc4da9119 100644 --- a/doc/source/generated/selections/protein_backbone.txt +++ b/doc/source/generated/selections/protein_backbone.txt @@ -1,4 +1,4 @@ -.. Generated by gen_standard_selections.py +.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_standard_selections.py = == = = N CA C O diff --git a/doc/source/generated/topology/connectivityattrs.txt b/doc/source/generated/topology/connectivityattrs.txt index 413550c37..62584c063 100644 --- a/doc/source/generated/topology/connectivityattrs.txt +++ b/doc/source/generated/topology/connectivityattrs.txt @@ -1,4 +1,4 @@ -.. Generated by gen_topologyparser_attrs.py +.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_topologyparser_attrs.py ========= =========== ============================================================================================================================================================================================================================================================================================================================================================================ Atom AtomGroup Supported formats diff --git a/doc/source/generated/topology/defaults.txt b/doc/source/generated/topology/defaults.txt index d73b38ddd..ce72900cc 100644 --- a/doc/source/generated/topology/defaults.txt +++ b/doc/source/generated/topology/defaults.txt @@ -1,4 +1,4 @@ -.. Generated by gen_topologyattr_defaults.py +.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_topologyattr_defaults.py ============= ============= ======================================== ======= ======================= Atom AtomGroup default level type diff --git a/doc/source/generated/topology/groupmethods.txt b/doc/source/generated/topology/groupmethods.txt index e1f1f2835..d78548b75 100644 --- a/doc/source/generated/topology/groupmethods.txt +++ b/doc/source/generated/topology/groupmethods.txt @@ -1,4 +1,4 @@ -.. Generated by gen_topology_groupmethods.py +.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_topology_groupmethods.py ================================================================== ====================================================================== ========== Method Description Requires diff --git a/doc/source/generated/topology/topologyattrs.txt b/doc/source/generated/topology/topologyattrs.txt index b07428e5a..e81d1b59e 100644 --- a/doc/source/generated/topology/topologyattrs.txt +++ b/doc/source/generated/topology/topologyattrs.txt @@ -1,4 +1,4 @@ -.. Generated by gen_topologyparser_attrs.py +.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_topologyparser_attrs.py ============= ============= ================================== ================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== Atom AtomGroup Description Supported formats diff --git a/doc/source/scripts/base.py b/doc/source/scripts/base.py index 233af91ef..d40b1c8ec 100644 --- a/doc/source/scripts/base.py +++ b/doc/source/scripts/base.py @@ -69,7 +69,7 @@ def get_line(self, *args): def write_table(self): with open(self.path, 'w') as f: - f.write(f'.. Generated by {sys.argv[0]}\n\n') + f.write(f'..\n Generated by {sys.argv[0].split('/')[-1]}\n\n') if self.include_table: f.write(f'.. table:: {self.include_table}\n\n') print(tabulate.tabulate(self.lines, From c6e4b83bfcbe58070572cdd69f31b74e1bdd338a Mon Sep 17 00:00:00 2001 From: Lily Wang Date: Fri, 19 Jun 2020 11:07:16 +1000 Subject: [PATCH 08/18] indent table --- doc/source/formats/reference/classes/.gitignore | 3 --- doc/source/scripts/base.py | 11 ++++++----- 2 files changed, 6 insertions(+), 8 deletions(-) diff --git a/doc/source/formats/reference/classes/.gitignore b/doc/source/formats/reference/classes/.gitignore index eeb90c660..e69de29bb 100644 --- a/doc/source/formats/reference/classes/.gitignore +++ b/doc/source/formats/reference/classes/.gitignore @@ -1,3 +0,0 @@ -# Ignore everything here -* -!.gitignore diff --git a/doc/source/scripts/base.py b/doc/source/scripts/base.py index d40b1c8ec..170a8f3bd 100644 --- a/doc/source/scripts/base.py +++ b/doc/source/scripts/base.py @@ -3,6 +3,7 @@ import sys import os import tabulate +import textwrap from collections import defaultdict @@ -69,13 +70,13 @@ def get_line(self, *args): def write_table(self): with open(self.path, 'w') as f: - f.write(f'..\n Generated by {sys.argv[0].split('/')[-1]}\n\n') + f.write(f'..\n Generated by {sys.argv[0].split("/")[-1]}\n\n') if self.include_table: f.write(f'.. table:: {self.include_table}\n\n') - print(tabulate.tabulate(self.lines, - headers=self.headings, - tablefmt='rst'), - file=f) + tabled = tabulate.tabulate(self.lines, + headers=self.headings, + tablefmt='rst') + f.write(textwrap.indent(tabled, ' ')) print('Wrote ', self.filename) # ==== HELPER FUNCTIONS ==== # From 889d29ac9e5f7b2f061488b4927a507a39342c6f Mon Sep 17 00:00:00 2001 From: Lily Wang Date: Fri, 19 Jun 2020 11:09:47 +1000 Subject: [PATCH 09/18] rm txt files --- .gitignore | 3 +- doc/source/formats/coordinate_readers.txt | 45 ---------------- doc/source/formats/format_overview.txt | 52 ------------------- .../formats/reference/classes/CONFIG.txt | 6 --- doc/source/formats/reference/classes/CRD.txt | 7 --- doc/source/formats/reference/classes/DATA.txt | 7 --- doc/source/formats/reference/classes/DCD.txt | 6 --- doc/source/formats/reference/classes/DMS.txt | 6 --- doc/source/formats/reference/classes/GMS.txt | 6 --- doc/source/formats/reference/classes/GRO.txt | 7 --- doc/source/formats/reference/classes/GSD.txt | 6 --- .../formats/reference/classes/HISTORY.txt | 6 --- .../formats/reference/classes/INPCRD.txt | 5 -- doc/source/formats/reference/classes/ITP.txt | 5 -- .../formats/reference/classes/LAMMPS.txt | 6 --- .../formats/reference/classes/LAMMPSDUMP.txt | 6 --- doc/source/formats/reference/classes/MMTF.txt | 6 --- doc/source/formats/reference/classes/MOL2.txt | 7 --- doc/source/formats/reference/classes/NCDF.txt | 6 --- doc/source/formats/reference/classes/PDB.txt | 7 --- .../formats/reference/classes/PDBQT.txt | 7 --- doc/source/formats/reference/classes/PQR.txt | 7 --- doc/source/formats/reference/classes/PSF.txt | 5 -- doc/source/formats/reference/classes/TOP.txt | 5 -- doc/source/formats/reference/classes/TPR.txt | 5 -- doc/source/formats/reference/classes/TRJ.txt | 5 -- doc/source/formats/reference/classes/TRR.txt | 6 --- doc/source/formats/reference/classes/TRZ.txt | 6 --- doc/source/formats/reference/classes/TXYZ.txt | 6 --- doc/source/formats/reference/classes/XML.txt | 5 -- doc/source/formats/reference/classes/XPDB.txt | 6 --- doc/source/formats/reference/classes/XTC.txt | 6 --- doc/source/formats/reference/classes/XYZ.txt | 7 --- .../formats/selection_exporter_formats.txt | 13 ----- doc/source/formats/topology_parsers.txt | 31 ----------- doc/source/generated/selections/base.txt | 6 --- doc/source/generated/selections/nucleic.txt | 9 ---- .../generated/selections/nucleic_backbone.txt | 5 -- .../generated/selections/nucleic_sugar.txt | 5 -- doc/source/generated/selections/protein.txt | 17 ------ .../generated/selections/protein_backbone.txt | 5 -- .../generated/topology/connectivityattrs.txt | 10 ---- doc/source/generated/topology/defaults.txt | 44 ---------------- .../generated/topology/groupmethods.txt | 15 ------ .../generated/topology/topologyattrs.txt | 38 -------------- 45 files changed, 2 insertions(+), 477 deletions(-) delete mode 100644 doc/source/formats/coordinate_readers.txt delete mode 100644 doc/source/formats/format_overview.txt delete mode 100644 doc/source/formats/reference/classes/CONFIG.txt delete mode 100644 doc/source/formats/reference/classes/CRD.txt delete mode 100644 doc/source/formats/reference/classes/DATA.txt delete mode 100644 doc/source/formats/reference/classes/DCD.txt delete mode 100644 doc/source/formats/reference/classes/DMS.txt delete mode 100644 doc/source/formats/reference/classes/GMS.txt delete mode 100644 doc/source/formats/reference/classes/GRO.txt delete mode 100644 doc/source/formats/reference/classes/GSD.txt delete mode 100644 doc/source/formats/reference/classes/HISTORY.txt delete mode 100644 doc/source/formats/reference/classes/INPCRD.txt delete mode 100644 doc/source/formats/reference/classes/ITP.txt delete mode 100644 doc/source/formats/reference/classes/LAMMPS.txt delete mode 100644 doc/source/formats/reference/classes/LAMMPSDUMP.txt delete mode 100644 doc/source/formats/reference/classes/MMTF.txt delete mode 100644 doc/source/formats/reference/classes/MOL2.txt delete mode 100644 doc/source/formats/reference/classes/NCDF.txt delete mode 100644 doc/source/formats/reference/classes/PDB.txt delete mode 100644 doc/source/formats/reference/classes/PDBQT.txt delete mode 100644 doc/source/formats/reference/classes/PQR.txt delete mode 100644 doc/source/formats/reference/classes/PSF.txt delete mode 100644 doc/source/formats/reference/classes/TOP.txt delete mode 100644 doc/source/formats/reference/classes/TPR.txt delete mode 100644 doc/source/formats/reference/classes/TRJ.txt delete mode 100644 doc/source/formats/reference/classes/TRR.txt delete mode 100644 doc/source/formats/reference/classes/TRZ.txt delete mode 100644 doc/source/formats/reference/classes/TXYZ.txt delete mode 100644 doc/source/formats/reference/classes/XML.txt delete mode 100644 doc/source/formats/reference/classes/XPDB.txt delete mode 100644 doc/source/formats/reference/classes/XTC.txt delete mode 100644 doc/source/formats/reference/classes/XYZ.txt delete mode 100644 doc/source/formats/selection_exporter_formats.txt delete mode 100644 doc/source/formats/topology_parsers.txt delete mode 100644 doc/source/generated/selections/base.txt delete mode 100644 doc/source/generated/selections/nucleic.txt delete mode 100644 doc/source/generated/selections/nucleic_backbone.txt delete mode 100644 doc/source/generated/selections/nucleic_sugar.txt delete mode 100644 doc/source/generated/selections/protein.txt delete mode 100644 doc/source/generated/selections/protein_backbone.txt delete mode 100644 doc/source/generated/topology/connectivityattrs.txt delete mode 100644 doc/source/generated/topology/defaults.txt delete mode 100644 doc/source/generated/topology/groupmethods.txt delete mode 100644 doc/source/generated/topology/topologyattrs.txt diff --git a/.gitignore b/.gitignore index dcd3de159..bf92abc3e 100644 --- a/.gitignore +++ b/.gitignore @@ -22,7 +22,8 @@ doc/build *.so # Ignore generated docs -*.txt +*/**/*.txt +!requirements.txt # ignore generated files *.vmd diff --git a/doc/source/formats/coordinate_readers.txt b/doc/source/formats/coordinate_readers.txt deleted file mode 100644 index 9660b39a4..000000000 --- a/doc/source/formats/coordinate_readers.txt +++ /dev/null @@ -1,45 +0,0 @@ -.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py - -.. table:: Table of supported coordinate readers and the information read - -===================================== ========================================= ============ ======== -File type Description Velocities Forces -===================================== ========================================= ============ ======== -:ref:`ARC ` Tinker file -:ref:`CHEMFILES ` chemfiles object -:ref:`CONFIG ` DL_Poly CONFIG file ✓ -:ref:`COOR ` NAMD binary restart file -:ref:`CRD ` CHARMM CARD file -:ref:`CRDBOX ` AMBER ASCII trajectories -:ref:`DATA ` LAMMPS data file ✓ -:ref:`DCD ` CHARMM, NAMD, or LAMMPS binary trajectory -:ref:`DMS ` DESRES Molecular Structure file ✓ -:ref:`ENT ` Standard PDB file -:ref:`FHIAIMS ` FHI-aims input file ✓ -:ref:`GMS ` GAMESS file -:ref:`GRO ` GROMACS structure file ✓ -:ref:`GSD ` HOOMD GSD file -:ref:`HISTORY ` DL_Poly HISTORY file ✓ -:ref:`IN ` FHI-aims input file ✓ -:ref:`INPCRD ` AMBER restart file -:ref:`LAMMPS ` a LAMMPS DCD trajectory -:ref:`LAMMPSDUMP ` LAMMPS ascii dump file -:ref:`MDCRD ` AMBER ASCII trajectories -:ref:`MMTF ` MMTF file -:ref:`MOL2 ` Tripos MOL2 file -:ref:`NAMDBIN ` NAMD binary restart file -:ref:`NC ` AMBER NETCDF format ✓ ✓ -:ref:`NCDF ` AMBER NETCDF format ✓ ✓ -:ref:`PARMED ` parmed Structure -:ref:`PDB ` Standard PDB file -:ref:`PDBQT ` PDBQT file -:ref:`PQR ` PQR file -:ref:`RESTRT ` AMBER restart file -:ref:`TRJ ` AMBER ASCII trajectories -:ref:`TRR ` GROMACS TRR trajectory ✓ ✓ -:ref:`TRZ ` IBIsCO or YASP binary trajectory ✓ -:ref:`TXYZ ` Tinker file -:ref:`XPDB ` Extended PDB file -:ref:`XTC ` GROMACS compressed trajectory -:ref:`XYZ ` XYZ file -===================================== ========================================= ============ ======== diff --git a/doc/source/formats/format_overview.txt b/doc/source/formats/format_overview.txt deleted file mode 100644 index 7739c381c..000000000 --- a/doc/source/formats/format_overview.txt +++ /dev/null @@ -1,52 +0,0 @@ -.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py - -.. table:: Table of all supported formats in MDAnalysis - -===================================== ========================================= ========== ============= ====== ======= -File type Description Topology Coordinates Read Write -===================================== ========================================= ========== ============= ====== ======= -:ref:`ARC ` Tinker file ✓ ✓ ✓ -:ref:`CHEMFILES ` chemfiles object ✓ ✓ ✓ -:ref:`CONFIG ` DL_Poly CONFIG file ✓ ✓ ✓ -:ref:`COOR ` NAMD binary restart file ✓ ✓ ✓ -:ref:`CRD ` CHARMM CARD file ✓ ✓ ✓ ✓ -:ref:`CRDBOX ` AMBER ASCII trajectories ✓ ✓ -:ref:`DATA ` LAMMPS data file ✓ ✓ ✓ ✓ -:ref:`DCD ` CHARMM, NAMD, or LAMMPS binary trajectory ✓ ✓ ✓ -:ref:`DMS ` DESRES Molecular Structure file ✓ ✓ ✓ -:ref:`ENT ` Standard PDB file ✓ ✓ ✓ ✓ -:ref:`FHIAIMS ` FHI-aims input file ✓ ✓ ✓ ✓ -:ref:`GMS ` GAMESS file ✓ ✓ ✓ -:ref:`GRO ` GROMACS structure file ✓ ✓ ✓ ✓ -:ref:`GSD ` HOOMD GSD file ✓ ✓ ✓ -:ref:`HISTORY ` DL_Poly HISTORY file ✓ ✓ ✓ -:ref:`IN ` FHI-aims input file ✓ ✓ ✓ ✓ -:ref:`INPCRD ` AMBER restart file ✓ ✓ -:ref:`ITP ` GROMACS portable topology file ✓ ✓ -:ref:`LAMMPS ` a LAMMPS DCD trajectory ✓ ✓ ✓ -:ref:`LAMMPSDUMP ` LAMMPS ascii dump file ✓ ✓ ✓ -:ref:`MDCRD ` AMBER ASCII trajectories ✓ ✓ -:ref:`MMTF ` MMTF file ✓ ✓ ✓ -:ref:`MOL2 ` Tripos MOL2 file ✓ ✓ ✓ ✓ -:ref:`NAMDBIN ` NAMD binary restart file ✓ ✓ ✓ -:ref:`NC ` AMBER NETCDF format ✓ ✓ -:ref:`NCDF ` AMBER NETCDF format ✓ ✓ ✓ -:ref:`PARM7 ` AMBER topology file ✓ ✓ -:ref:`PARMED ` parmed Structure ✓ ✓ ✓ ✓ -:ref:`PDB ` Standard PDB file ✓ ✓ ✓ ✓ -:ref:`PDBQT ` PDBQT file ✓ ✓ ✓ ✓ -:ref:`PQR ` PQR file ✓ ✓ ✓ ✓ -:ref:`PRMTOP ` AMBER topology file ✓ ✓ -:ref:`PSF ` CHARMM, NAMD, or XPLOR PSF file ✓ ✓ -:ref:`RESTRT ` AMBER restart file ✓ ✓ -:ref:`TOP ` AMBER topology file ✓ ✓ -:ref:`TPR ` GROMACS run topology file ✓ ✓ -:ref:`TRJ ` AMBER ASCII trajectories ✓ ✓ -:ref:`TRR ` GROMACS TRR trajectory ✓ ✓ ✓ -:ref:`TRZ ` IBIsCO or YASP binary trajectory ✓ ✓ ✓ -:ref:`TXYZ ` Tinker file ✓ ✓ ✓ -:ref:`XML ` HOOMD XML file ✓ ✓ -:ref:`XPDB ` Extended PDB file ✓ ✓ ✓ -:ref:`XTC ` GROMACS compressed trajectory ✓ ✓ ✓ -:ref:`XYZ ` XYZ file ✓ ✓ ✓ ✓ -===================================== ========================================= ========== ============= ====== ======= diff --git a/doc/source/formats/reference/classes/CONFIG.txt b/doc/source/formats/reference/classes/CONFIG.txt deleted file mode 100644 index 46d02a477..000000000 --- a/doc/source/formats/reference/classes/CONFIG.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py - -===================== ====================================================== -**Coordinate reader** :class:`MDAnalysis.coordinates.DLPoly.ConfigReader` -**Topology parser** :class:`MDAnalysis.topology.DLPolyParser.ConfigParser` -===================== ====================================================== diff --git a/doc/source/formats/reference/classes/CRD.txt b/doc/source/formats/reference/classes/CRD.txt deleted file mode 100644 index 70053079b..000000000 --- a/doc/source/formats/reference/classes/CRD.txt +++ /dev/null @@ -1,7 +0,0 @@ -.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py - -===================== ================================================ -**Coordinate reader** :class:`MDAnalysis.coordinates.CRD.CRDReader` -**Coordinate writer** :class:`MDAnalysis.coordinates.CRD.CRDWriter` -**Topology parser** :class:`MDAnalysis.topology.CRDParser.CRDParser` -===================== ================================================ diff --git a/doc/source/formats/reference/classes/DATA.txt b/doc/source/formats/reference/classes/DATA.txt deleted file mode 100644 index f0b973ac8..000000000 --- a/doc/source/formats/reference/classes/DATA.txt +++ /dev/null @@ -1,7 +0,0 @@ -.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py - -===================== ==================================================== -**Coordinate reader** :class:`MDAnalysis.coordinates.LAMMPS.DATAReader` -**Coordinate writer** :class:`MDAnalysis.coordinates.LAMMPS.DATAWriter` -**Topology parser** :class:`MDAnalysis.topology.LAMMPSParser.DATAParser` -===================== ==================================================== diff --git a/doc/source/formats/reference/classes/DCD.txt b/doc/source/formats/reference/classes/DCD.txt deleted file mode 100644 index 46848d3f4..000000000 --- a/doc/source/formats/reference/classes/DCD.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py - -===================== ============================================= -**Coordinate reader** :class:`MDAnalysis.coordinates.DCD.DCDReader` -**Coordinate writer** :class:`MDAnalysis.coordinates.DCD.DCDWriter` -===================== ============================================= diff --git a/doc/source/formats/reference/classes/DMS.txt b/doc/source/formats/reference/classes/DMS.txt deleted file mode 100644 index 54d692e4e..000000000 --- a/doc/source/formats/reference/classes/DMS.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py - -===================== ================================================ -**Coordinate reader** :class:`MDAnalysis.coordinates.DMS.DMSReader` -**Topology parser** :class:`MDAnalysis.topology.DMSParser.DMSParser` -===================== ================================================ diff --git a/doc/source/formats/reference/classes/GMS.txt b/doc/source/formats/reference/classes/GMS.txt deleted file mode 100644 index a7914f4c1..000000000 --- a/doc/source/formats/reference/classes/GMS.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py - -===================== ================================================ -**Coordinate reader** :class:`MDAnalysis.coordinates.GMS.GMSReader` -**Topology parser** :class:`MDAnalysis.topology.GMSParser.GMSParser` -===================== ================================================ diff --git a/doc/source/formats/reference/classes/GRO.txt b/doc/source/formats/reference/classes/GRO.txt deleted file mode 100644 index 13594aba9..000000000 --- a/doc/source/formats/reference/classes/GRO.txt +++ /dev/null @@ -1,7 +0,0 @@ -.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py - -===================== ================================================ -**Coordinate reader** :class:`MDAnalysis.coordinates.GRO.GROReader` -**Coordinate writer** :class:`MDAnalysis.coordinates.GRO.GROWriter` -**Topology parser** :class:`MDAnalysis.topology.GROParser.GROParser` -===================== ================================================ diff --git a/doc/source/formats/reference/classes/GSD.txt b/doc/source/formats/reference/classes/GSD.txt deleted file mode 100644 index 8ea8862a3..000000000 --- a/doc/source/formats/reference/classes/GSD.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py - -===================== ================================================ -**Coordinate reader** :class:`MDAnalysis.coordinates.GSD.GSDReader` -**Topology parser** :class:`MDAnalysis.topology.GSDParser.GSDParser` -===================== ================================================ diff --git a/doc/source/formats/reference/classes/HISTORY.txt b/doc/source/formats/reference/classes/HISTORY.txt deleted file mode 100644 index 743f1280f..000000000 --- a/doc/source/formats/reference/classes/HISTORY.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py - -===================== ======================================================= -**Coordinate reader** :class:`MDAnalysis.coordinates.DLPoly.HistoryReader` -**Topology parser** :class:`MDAnalysis.topology.DLPolyParser.HistoryParser` -===================== ======================================================= diff --git a/doc/source/formats/reference/classes/INPCRD.txt b/doc/source/formats/reference/classes/INPCRD.txt deleted file mode 100644 index b4b0e61cf..000000000 --- a/doc/source/formats/reference/classes/INPCRD.txt +++ /dev/null @@ -1,5 +0,0 @@ -.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py - -===================== ================================================ -**Coordinate reader** :class:`MDAnalysis.coordinates.INPCRD.INPReader` -===================== ================================================ diff --git a/doc/source/formats/reference/classes/ITP.txt b/doc/source/formats/reference/classes/ITP.txt deleted file mode 100644 index 5f2c0810e..000000000 --- a/doc/source/formats/reference/classes/ITP.txt +++ /dev/null @@ -1,5 +0,0 @@ -.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py - -=================== ================================================ -**Topology parser** :class:`MDAnalysis.topology.ITPParser.ITPParser` -=================== ================================================ diff --git a/doc/source/formats/reference/classes/LAMMPS.txt b/doc/source/formats/reference/classes/LAMMPS.txt deleted file mode 100644 index 102ac8294..000000000 --- a/doc/source/formats/reference/classes/LAMMPS.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py - -===================== ================================================ -**Coordinate reader** :class:`MDAnalysis.coordinates.LAMMPS.DCDReader` -**Coordinate writer** :class:`MDAnalysis.coordinates.LAMMPS.DCDWriter` -===================== ================================================ diff --git a/doc/source/formats/reference/classes/LAMMPSDUMP.txt b/doc/source/formats/reference/classes/LAMMPSDUMP.txt deleted file mode 100644 index 529d1e0a9..000000000 --- a/doc/source/formats/reference/classes/LAMMPSDUMP.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py - -===================== ========================================================== -**Coordinate reader** :class:`MDAnalysis.coordinates.LAMMPS.DumpReader` -**Topology parser** :class:`MDAnalysis.topology.LAMMPSParser.LammpsDumpParser` -===================== ========================================================== diff --git a/doc/source/formats/reference/classes/MMTF.txt b/doc/source/formats/reference/classes/MMTF.txt deleted file mode 100644 index 168cb34bf..000000000 --- a/doc/source/formats/reference/classes/MMTF.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py - -===================== ================================================== -**Coordinate reader** :class:`MDAnalysis.coordinates.MMTF.MMTFReader` -**Topology parser** :class:`MDAnalysis.topology.MMTFParser.MMTFParser` -===================== ================================================== diff --git a/doc/source/formats/reference/classes/MOL2.txt b/doc/source/formats/reference/classes/MOL2.txt deleted file mode 100644 index 9df227c11..000000000 --- a/doc/source/formats/reference/classes/MOL2.txt +++ /dev/null @@ -1,7 +0,0 @@ -.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py - -===================== ================================================== -**Coordinate reader** :class:`MDAnalysis.coordinates.MOL2.MOL2Reader` -**Coordinate writer** :class:`MDAnalysis.coordinates.MOL2.MOL2Writer` -**Topology parser** :class:`MDAnalysis.topology.MOL2Parser.MOL2Parser` -===================== ================================================== diff --git a/doc/source/formats/reference/classes/NCDF.txt b/doc/source/formats/reference/classes/NCDF.txt deleted file mode 100644 index 1967038b9..000000000 --- a/doc/source/formats/reference/classes/NCDF.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py - -===================== ============================================== -**Coordinate reader** :class:`MDAnalysis.coordinates.TRJ.NCDFReader` -**Coordinate writer** :class:`MDAnalysis.coordinates.TRJ.NCDFWriter` -===================== ============================================== diff --git a/doc/source/formats/reference/classes/PDB.txt b/doc/source/formats/reference/classes/PDB.txt deleted file mode 100644 index df98fffd7..000000000 --- a/doc/source/formats/reference/classes/PDB.txt +++ /dev/null @@ -1,7 +0,0 @@ -.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py - -===================== ================================================ -**Coordinate reader** :class:`MDAnalysis.coordinates.PDB.PDBReader` -**Coordinate writer** :class:`MDAnalysis.coordinates.PDB.PDBWriter` -**Topology parser** :class:`MDAnalysis.topology.PDBParser.PDBParser` -===================== ================================================ diff --git a/doc/source/formats/reference/classes/PDBQT.txt b/doc/source/formats/reference/classes/PDBQT.txt deleted file mode 100644 index 6699839d7..000000000 --- a/doc/source/formats/reference/classes/PDBQT.txt +++ /dev/null @@ -1,7 +0,0 @@ -.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py - -===================== ==================================================== -**Coordinate reader** :class:`MDAnalysis.coordinates.PDBQT.PDBQTReader` -**Coordinate writer** :class:`MDAnalysis.coordinates.PDBQT.PDBQTWriter` -**Topology parser** :class:`MDAnalysis.topology.PDBQTParser.PDBQTParser` -===================== ==================================================== diff --git a/doc/source/formats/reference/classes/PQR.txt b/doc/source/formats/reference/classes/PQR.txt deleted file mode 100644 index 0b9248585..000000000 --- a/doc/source/formats/reference/classes/PQR.txt +++ /dev/null @@ -1,7 +0,0 @@ -.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py - -===================== ================================================ -**Coordinate reader** :class:`MDAnalysis.coordinates.PQR.PQRReader` -**Coordinate writer** :class:`MDAnalysis.coordinates.PQR.PQRWriter` -**Topology parser** :class:`MDAnalysis.topology.PQRParser.PQRParser` -===================== ================================================ diff --git a/doc/source/formats/reference/classes/PSF.txt b/doc/source/formats/reference/classes/PSF.txt deleted file mode 100644 index 9fc8cb054..000000000 --- a/doc/source/formats/reference/classes/PSF.txt +++ /dev/null @@ -1,5 +0,0 @@ -.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py - -=================== ================================================ -**Topology parser** :class:`MDAnalysis.topology.PSFParser.PSFParser` -=================== ================================================ diff --git a/doc/source/formats/reference/classes/TOP.txt b/doc/source/formats/reference/classes/TOP.txt deleted file mode 100644 index d2c583952..000000000 --- a/doc/source/formats/reference/classes/TOP.txt +++ /dev/null @@ -1,5 +0,0 @@ -.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py - -=================== ================================================ -**Topology parser** :class:`MDAnalysis.topology.TOPParser.TOPParser` -=================== ================================================ diff --git a/doc/source/formats/reference/classes/TPR.txt b/doc/source/formats/reference/classes/TPR.txt deleted file mode 100644 index f0fe1a0f4..000000000 --- a/doc/source/formats/reference/classes/TPR.txt +++ /dev/null @@ -1,5 +0,0 @@ -.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py - -=================== ================================================ -**Topology parser** :class:`MDAnalysis.topology.TPRParser.TPRParser` -=================== ================================================ diff --git a/doc/source/formats/reference/classes/TRJ.txt b/doc/source/formats/reference/classes/TRJ.txt deleted file mode 100644 index baf15d26e..000000000 --- a/doc/source/formats/reference/classes/TRJ.txt +++ /dev/null @@ -1,5 +0,0 @@ -.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py - -===================== ============================================= -**Coordinate reader** :class:`MDAnalysis.coordinates.TRJ.TRJReader` -===================== ============================================= diff --git a/doc/source/formats/reference/classes/TRR.txt b/doc/source/formats/reference/classes/TRR.txt deleted file mode 100644 index 7c86cd5b0..000000000 --- a/doc/source/formats/reference/classes/TRR.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py - -===================== ============================================= -**Coordinate reader** :class:`MDAnalysis.coordinates.TRR.TRRReader` -**Coordinate writer** :class:`MDAnalysis.coordinates.TRR.TRRWriter` -===================== ============================================= diff --git a/doc/source/formats/reference/classes/TRZ.txt b/doc/source/formats/reference/classes/TRZ.txt deleted file mode 100644 index eb6945d0a..000000000 --- a/doc/source/formats/reference/classes/TRZ.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py - -===================== ============================================= -**Coordinate reader** :class:`MDAnalysis.coordinates.TRZ.TRZReader` -**Coordinate writer** :class:`MDAnalysis.coordinates.TRZ.TRZWriter` -===================== ============================================= diff --git a/doc/source/formats/reference/classes/TXYZ.txt b/doc/source/formats/reference/classes/TXYZ.txt deleted file mode 100644 index cd1c40b14..000000000 --- a/doc/source/formats/reference/classes/TXYZ.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py - -===================== ================================================== -**Coordinate reader** :class:`MDAnalysis.coordinates.TXYZ.TXYZReader` -**Topology parser** :class:`MDAnalysis.topology.TXYZParser.TXYZParser` -===================== ================================================== diff --git a/doc/source/formats/reference/classes/XML.txt b/doc/source/formats/reference/classes/XML.txt deleted file mode 100644 index a7da04728..000000000 --- a/doc/source/formats/reference/classes/XML.txt +++ /dev/null @@ -1,5 +0,0 @@ -.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py - -=================== ========================================================== -**Topology parser** :class:`MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser` -=================== ========================================================== diff --git a/doc/source/formats/reference/classes/XPDB.txt b/doc/source/formats/reference/classes/XPDB.txt deleted file mode 100644 index 0cc810519..000000000 --- a/doc/source/formats/reference/classes/XPDB.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py - -===================== ================================================================ -**Coordinate reader** :class:`MDAnalysis.coordinates.PDB.ExtendedPDBReader` -**Topology parser** :class:`MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser` -===================== ================================================================ diff --git a/doc/source/formats/reference/classes/XTC.txt b/doc/source/formats/reference/classes/XTC.txt deleted file mode 100644 index e8536a99c..000000000 --- a/doc/source/formats/reference/classes/XTC.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py - -===================== ============================================= -**Coordinate reader** :class:`MDAnalysis.coordinates.XTC.XTCReader` -**Coordinate writer** :class:`MDAnalysis.coordinates.XTC.XTCWriter` -===================== ============================================= diff --git a/doc/source/formats/reference/classes/XYZ.txt b/doc/source/formats/reference/classes/XYZ.txt deleted file mode 100644 index 0e0dbb257..000000000 --- a/doc/source/formats/reference/classes/XYZ.txt +++ /dev/null @@ -1,7 +0,0 @@ -.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_format_overview_classes.py - -===================== ================================================ -**Coordinate reader** :class:`MDAnalysis.coordinates.XYZ.XYZReader` -**Coordinate writer** :class:`MDAnalysis.coordinates.XYZ.XYZWriter` -**Topology parser** :class:`MDAnalysis.topology.XYZParser.XYZParser` -===================== ================================================ diff --git a/doc/source/formats/selection_exporter_formats.txt b/doc/source/formats/selection_exporter_formats.txt deleted file mode 100644 index 191e861d8..000000000 --- a/doc/source/formats/selection_exporter_formats.txt +++ /dev/null @@ -1,13 +0,0 @@ -.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_selection_exporters.py - -.. table:: Supported selection exporters - -========== =========== ======================================== ====================================================== -Program Extension Description Class -========== =========== ======================================== ====================================================== -`CHARMM`_ str CHARMM selection of individual atoms :class:`MDAnalysis.selections.charmm.SelectionWriter` -`Gromacs`_ ndx GROMACS index file :class:`MDAnalysis.selections.gromacs.SelectionWriter` -`Jmol`_ spt Jmol selection commands :class:`MDAnalysis.selections.jmol.SelectionWriter` -`PyMol`_ pml PyMOL selection string :class:`MDAnalysis.selections.pymol.SelectionWriter` -`VMD`_ vmd VMD macros, available in Representations :class:`MDAnalysis.selections.vmd.SelectionWriter` -========== =========== ======================================== ====================================================== diff --git a/doc/source/formats/topology_parsers.txt b/doc/source/formats/topology_parsers.txt deleted file mode 100644 index b56b0f212..000000000 --- a/doc/source/formats/topology_parsers.txt +++ /dev/null @@ -1,31 +0,0 @@ -.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_topologyparser_attrs.py - -.. table:: Table of supported topology parsers and the attributes read - -====================================== =============================== =================================================================================================================================================================================================================== ==================== -Format Description Attributes read Attributes guessed -====================================== =============================== =================================================================================================================================================================================================================== ==================== -:ref:`CONFIG ` DL_Poly CONFIG file names masses, types -:ref:`CRD ` CHARMM CARD file names, resnames, tempfactors masses, types -:ref:`DATA ` LAMMPS data file angles, bonds, charges, dihedrals, impropers -:ref:`DMS ` DESRES Molecular Structure file atomnums, bonds, chainIDs, charges, names, resnames types -:ref:`GMS ` GAMESS file atomiccharges, names masses, types -:ref:`GRO ` GROMACS structure file names, resnames masses, types -:ref:`GSD ` HOOMD GSD file angles, bonds, charges, dihedrals, impropers, names, radii, resnames -:ref:`HISTORY ` DL_Poly HISTORY file names masses, types -:ref:`IN, FHIAIMS ` FHI-aims input file elements, names masses, types -:ref:`LAMMPSDUMP ` LAMMPS ascii dump file masses -:ref:`MMTF ` MMTF file altLocs, bfactors, bonds, charges, icodes, models, names, occupancies, resnames masses -:ref:`MOL2 ` Tripos MOL2 file bonds, charges, names, resnames masses -:ref:`PARMED ` parmed Structure altLocs, angles, bonds, chainIDs, charges, cmaps, dihedrals, elements, epsilon14s, epsilons, gbscreens, impropers, names, nbindices, occupancies, resnames, rmin14s, rmins, solventradii, tempfactors, ureybradleys -:ref:`PDB, ENT ` Standard PDB file altLocs, bonds, chainIDs, elements, icodes, names, occupancies, record_types, resnames, tempfactors masses, types -:ref:`PDBQT ` PDBQT file altLocs, charges, icodes, names, occupancies, record_types, resnames, tempfactors masses -:ref:`PQR ` PQR file charges, icodes, names, radii, record_types, resnames masses, types -:ref:`PSF ` CHARMM, NAMD, or XPLOR PSF file angles, bonds, charges, dihedrals, impropers, names, resnames -:ref:`TOP, PRMTOP, PARM7 ` AMBER topology file angles, bonds, charges, dihedrals, impropers, names, resnames, type_indices -:ref:`TPR ` GROMACS run topology file angles, bonds, charges, dihedrals, impropers, molnums, moltypes, names, resnames -:ref:`TXYZ, ARC ` Tinker file bonds, names masses -:ref:`XML ` HOOMD XML file angles, bonds, charges, dihedrals, impropers, radii -:ref:`XPDB ` Extended PDB file altLocs, bonds, chainIDs, icodes, names, occupancies, record_types, resnames, tempfactors masses, types -:ref:`XYZ ` XYZ file elements, names masses, types -====================================== =============================== =================================================================================================================================================================================================================== ==================== diff --git a/doc/source/generated/selections/base.txt b/doc/source/generated/selections/base.txt deleted file mode 100644 index 60fb8b8ee..000000000 --- a/doc/source/generated/selections/base.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_standard_selections.py - -== == == == == == == === -N9 N7 C8 C5 C4 N3 C2 N1 -C6 O6 N2 N6 O2 N4 O4 C5M -== == == == == == == === diff --git a/doc/source/generated/selections/nucleic.txt b/doc/source/generated/selections/nucleic.txt deleted file mode 100644 index 197404872..000000000 --- a/doc/source/generated/selections/nucleic.txt +++ /dev/null @@ -1,9 +0,0 @@ -.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_standard_selections.py - -=== === === === === === === === -ADE URA CYT GUA THY DA DC DG -DT RA RU RG RC A T U -C G DA5 DC5 DG5 DT5 DA3 DC3 -DG3 DT3 RA5 RU5 RG5 RC5 RA3 RU3 -RG3 RC3 -=== === === === === === === === diff --git a/doc/source/generated/selections/nucleic_backbone.txt b/doc/source/generated/selections/nucleic_backbone.txt deleted file mode 100644 index d4f67d6c5..000000000 --- a/doc/source/generated/selections/nucleic_backbone.txt +++ /dev/null @@ -1,5 +0,0 @@ -.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_standard_selections.py - -= === === === === -P C5' C3' O3' O5' -= === === === === diff --git a/doc/source/generated/selections/nucleic_sugar.txt b/doc/source/generated/selections/nucleic_sugar.txt deleted file mode 100644 index ce9469f04..000000000 --- a/doc/source/generated/selections/nucleic_sugar.txt +++ /dev/null @@ -1,5 +0,0 @@ -.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_standard_selections.py - -=== === === === === -C1' C2' C3' C4' O4' -=== === === === === diff --git a/doc/source/generated/selections/protein.txt b/doc/source/generated/selections/protein.txt deleted file mode 100644 index 3d9982ffd..000000000 --- a/doc/source/generated/selections/protein.txt +++ /dev/null @@ -1,17 +0,0 @@ -.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_standard_selections.py - -==== ==== ==== ==== ==== ==== ==== ==== -ACE ALA ALAD ARG ARGN ASF ASH ASN -ASN1 ASP ASPH CALA CARG CASF CASN CASP -CCYS CCYX CGLN CGLU CGLY CHID CHIE CHIP -CILE CLEU CLYS CME CMET CPHE CPRO CSER -CTHR CTRP CTYR CVAL CYM CYS CYS1 CYS2 -CYSH CYX DAB GLH GLN GLU GLUH GLY -HID HIE HIP HIS HIS1 HIS2 HISA HISB -HISD HISE HISH HSD HSE HSP HYP ILE -LEU LYN LYS LYSH MET MSE NALA NARG -NASN NASP NCYS NCYX NGLN NGLU NGLY NHID -NHIE NHIP NILE NLEU NLYS NME NMET NPHE -NPRO NSER NTHR NTRP NTYR NVAL ORN PGLU -PHE PRO QLN SER THR TRP TYR VAL -==== ==== ==== ==== ==== ==== ==== ==== diff --git a/doc/source/generated/selections/protein_backbone.txt b/doc/source/generated/selections/protein_backbone.txt deleted file mode 100644 index cc4da9119..000000000 --- a/doc/source/generated/selections/protein_backbone.txt +++ /dev/null @@ -1,5 +0,0 @@ -.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_standard_selections.py - -= == = = -N CA C O -= == = = diff --git a/doc/source/generated/topology/connectivityattrs.txt b/doc/source/generated/topology/connectivityattrs.txt deleted file mode 100644 index 62584c063..000000000 --- a/doc/source/generated/topology/connectivityattrs.txt +++ /dev/null @@ -1,10 +0,0 @@ -.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_topologyparser_attrs.py - -========= =========== ============================================================================================================================================================================================================================================================================================================================================================================ -Atom AtomGroup Supported formats -========= =========== ============================================================================================================================================================================================================================================================================================================================================================================ -angles angles :ref:`DATA `, :ref:`GSD `, :ref:`PARMED `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`XML ` -bonds bonds :ref:`DATA `, :ref:`DMS `, :ref:`GSD `, :ref:`MMTF `, :ref:`MOL2 `, :ref:`PARMED `, :ref:`PDB, ENT `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`TXYZ, ARC `, :ref:`XML `, :ref:`XPDB ` -dihedrals dihedrals :ref:`DATA `, :ref:`GSD `, :ref:`PARMED `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`XML ` -impropers impropers :ref:`DATA `, :ref:`GSD `, :ref:`PARMED `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`XML ` -========= =========== ============================================================================================================================================================================================================================================================================================================================================================================ diff --git a/doc/source/generated/topology/defaults.txt b/doc/source/generated/topology/defaults.txt deleted file mode 100644 index ce72900cc..000000000 --- a/doc/source/generated/topology/defaults.txt +++ /dev/null @@ -1,44 +0,0 @@ -.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_topologyattr_defaults.py - -============= ============= ======================================== ======= ======================= -Atom AtomGroup default level type -============= ============= ======================================== ======= ======================= -altLocs altLoc '' atom -angles angles No default values atom -atomiccharges atomiccharge No default values atom -atomnums atomnum No default values atom -bfactors bfactor 0.0 atom -bonds bonds No default values atom -chainIDs chainID '' atom -chargegroups chargegroup No default values atom -charges charge 0.0 atom -cmaps cmaps No default values atom -dihedrals dihedrals No default values atom -elements element '' atom -epsilon14s epsilon14 0.0 atom -epsilons epsilon 0.0 atom -gbscreens gbscreen 0.0 atom -icodes icode '' residue -ids id continuous sequence from 1 to n_atoms atom -impropers impropers No default values atom -masses mass 0.0 atom -models model No default values segment -molnums molnum No default values residue -moltypes moltype No default values residue -names name '' atom -nbindices nbindex 0 atom -occupancies occupancy 0.0 atom -radii radius 0.0 atom -record_types record_type 'ATOM' atom -resids resid continuous sequence from 1 to n_residues residue -resnames resname '' residue -resnums resnum continuous sequence from 1 to n_residues residue -rmin14s rmin14 0.0 atom -rmins rmin 0.0 atom -segids segid '' segment -solventradii solventradius 0.0 atom -tempfactors tempfactor 0.0 atom -type_indices type_index No default values atom -types type '' atom -ureybradleys ureybradleys No default values atom -============= ============= ======================================== ======= ======================= diff --git a/doc/source/generated/topology/groupmethods.txt b/doc/source/generated/topology/groupmethods.txt deleted file mode 100644 index d78548b75..000000000 --- a/doc/source/generated/topology/groupmethods.txt +++ /dev/null @@ -1,15 +0,0 @@ -.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_topology_groupmethods.py - -================================================================== ====================================================================== ========== -Method Description Requires -================================================================== ====================================================================== ========== -:meth:`~MDAnalysis.core.topologyattrs.Charges.total_charge` Total charge of (compounds of) the group charges -:meth:`~MDAnalysis.core.topologyattrs.Masses.align_principal_axis` Align principal axis with index `axis` with `vector` masses -:meth:`~MDAnalysis.core.topologyattrs.Masses.asphericity` Asphericity masses -:meth:`~MDAnalysis.core.topologyattrs.Masses.center_of_mass` Center of mass of (compounds of) the group masses -:meth:`~MDAnalysis.core.topologyattrs.Masses.moment_of_inertia` Tensor moment of inertia relative to center of mass as 3x3 numpy array masses -:meth:`~MDAnalysis.core.topologyattrs.Masses.principal_axes` Calculate the principal axes from the moment of inertia masses -:meth:`~MDAnalysis.core.topologyattrs.Masses.radius_of_gyration` Radius of gyration masses -:meth:`~MDAnalysis.core.topologyattrs.Masses.shape_parameter` Shape parameter masses -:meth:`~MDAnalysis.core.topologyattrs.Masses.total_mass` Total mass of (compounds of) the group masses -================================================================== ====================================================================== ========== diff --git a/doc/source/generated/topology/topologyattrs.txt b/doc/source/generated/topology/topologyattrs.txt deleted file mode 100644 index e81d1b59e..000000000 --- a/doc/source/generated/topology/topologyattrs.txt +++ /dev/null @@ -1,38 +0,0 @@ -.. Generated by /Users/lily/pydev/UserGuide/doc/source/scripts/gen_topologyparser_attrs.py - -============= ============= ================================== ================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== -Atom AtomGroup Description Supported formats -============= ============= ================================== ================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== -altLoc altLocs Alternate location :ref:`MMTF `, :ref:`PARMED `, :ref:`PDB, ENT `, :ref:`PDBQT `, :ref:`XPDB ` -angles angles :ref:`DATA `, :ref:`GSD `, :ref:`PARMED `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`XML ` -atomiccharge atomiccharges Atomic number :ref:`GMS ` -atomnum atomnums ? :ref:`DMS ` -bfactor bfactors alias of tempfactor :ref:`MMTF ` -bonds bonds :ref:`DATA `, :ref:`DMS `, :ref:`GSD `, :ref:`MMTF `, :ref:`MOL2 `, :ref:`PARMED `, :ref:`PDB, ENT `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`TXYZ, ARC `, :ref:`XML `, :ref:`XPDB ` -chainID chainIDs chain ID :ref:`DMS `, :ref:`PARMED `, :ref:`PDB, ENT `, :ref:`XPDB ` -charge charges partial atomic charge :ref:`DATA `, :ref:`DMS `, :ref:`GSD `, :ref:`MMTF `, :ref:`MOL2 `, :ref:`PARMED `, :ref:`PDBQT `, :ref:`PQR `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`XML ` -chargegroup chargegroups -cmaps cmaps :ref:`PARMED ` -dihedrals dihedrals :ref:`DATA `, :ref:`GSD `, :ref:`PARMED `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`XML ` -element elements atom element :ref:`IN, FHIAIMS `, :ref:`PARMED `, :ref:`PDB, ENT `, :ref:`XYZ ` -epsilon epsilons :ref:`PARMED ` -epsilon14 epsilon14s :ref:`PARMED ` -gbscreen gbscreens :ref:`PARMED ` -icode icodes atom insertion code :ref:`MMTF `, :ref:`PDB, ENT `, :ref:`PDBQT `, :ref:`PQR `, :ref:`XPDB ` -impropers impropers :ref:`DATA `, :ref:`GSD `, :ref:`PARMED `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`XML ` -model models model number (from 0) :ref:`MMTF ` -molnum molnums [molecules] number (from 0) :ref:`TPR ` -moltype moltypes [moleculetype] name :ref:`TPR ` -name names atom names :ref:`CONFIG `, :ref:`CRD `, :ref:`DMS `, :ref:`GMS `, :ref:`GRO `, :ref:`GSD `, :ref:`HISTORY `, :ref:`IN, FHIAIMS `, :ref:`MMTF `, :ref:`MOL2 `, :ref:`PARMED `, :ref:`PDB, ENT `, :ref:`PDBQT `, :ref:`PQR `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`TXYZ, ARC `, :ref:`XPDB `, :ref:`XYZ ` -nbindex nbindices :ref:`PARMED ` -occupancy occupancies atom occupancy :ref:`MMTF `, :ref:`PARMED `, :ref:`PDB, ENT `, :ref:`PDBQT `, :ref:`XPDB ` -radius radii atomic radius :ref:`GSD `, :ref:`PQR `, :ref:`XML ` -record_type record_types ATOM / HETATM :ref:`PDB, ENT `, :ref:`PDBQT `, :ref:`PQR `, :ref:`XPDB ` -resname resnames residue name (except GSD has ints) :ref:`CRD `, :ref:`DMS `, :ref:`GRO `, :ref:`GSD `, :ref:`MMTF `, :ref:`MOL2 `, :ref:`PARMED `, :ref:`PDB, ENT `, :ref:`PDBQT `, :ref:`PQR `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`XPDB ` -rmin rmins :ref:`PARMED ` -rmin14 rmin14s :ref:`PARMED ` -solventradius solventradii :ref:`PARMED ` -tempfactor tempfactors B-factor :ref:`CRD `, :ref:`PARMED `, :ref:`PDB, ENT `, :ref:`PDBQT `, :ref:`XPDB ` -type_index type_indices amber atom type number :ref:`TOP, PRMTOP, PARM7 ` -ureybradleys ureybradleys :ref:`PARMED ` -============= ============= ================================== ================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== From 7ec5cfc7965d403559d1059e80ec1abbfc2b72ad Mon Sep 17 00:00:00 2001 From: Lily Wang Date: Fri, 19 Jun 2020 11:44:39 +1000 Subject: [PATCH 10/18] turn off auto-script run --- .gitignore | 4 +- doc/source/conf.py | 6 ++- doc/source/formats/coordinate_readers.txt | 46 ++++++++++++++++ doc/source/formats/format_overview.txt | 53 +++++++++++++++++++ .../formats/reference/classes/CHEMFILES.txt | 7 +++ .../formats/reference/classes/CONFIG.txt | 7 +++ doc/source/formats/reference/classes/COOR.txt | 7 +++ doc/source/formats/reference/classes/CRD.txt | 8 +++ doc/source/formats/reference/classes/DATA.txt | 8 +++ doc/source/formats/reference/classes/DCD.txt | 7 +++ doc/source/formats/reference/classes/DMS.txt | 7 +++ doc/source/formats/reference/classes/GMS.txt | 7 +++ doc/source/formats/reference/classes/GRO.txt | 8 +++ doc/source/formats/reference/classes/GSD.txt | 7 +++ .../formats/reference/classes/HISTORY.txt | 7 +++ doc/source/formats/reference/classes/IN.txt | 8 +++ .../formats/reference/classes/INPCRD.txt | 6 +++ doc/source/formats/reference/classes/ITP.txt | 6 +++ .../formats/reference/classes/LAMMPS.txt | 7 +++ .../formats/reference/classes/LAMMPSDUMP.txt | 7 +++ doc/source/formats/reference/classes/MMTF.txt | 7 +++ doc/source/formats/reference/classes/MOL2.txt | 8 +++ doc/source/formats/reference/classes/NCDF.txt | 7 +++ .../formats/reference/classes/PARMED.txt | 8 +++ doc/source/formats/reference/classes/PDB.txt | 8 +++ .../formats/reference/classes/PDBQT.txt | 8 +++ doc/source/formats/reference/classes/PQR.txt | 8 +++ doc/source/formats/reference/classes/PSF.txt | 6 +++ doc/source/formats/reference/classes/TOP.txt | 6 +++ doc/source/formats/reference/classes/TPR.txt | 6 +++ doc/source/formats/reference/classes/TRJ.txt | 6 +++ doc/source/formats/reference/classes/TRR.txt | 7 +++ doc/source/formats/reference/classes/TRZ.txt | 7 +++ doc/source/formats/reference/classes/TXYZ.txt | 7 +++ doc/source/formats/reference/classes/XML.txt | 6 +++ doc/source/formats/reference/classes/XPDB.txt | 7 +++ doc/source/formats/reference/classes/XTC.txt | 7 +++ doc/source/formats/reference/classes/XYZ.txt | 8 +++ .../formats/selection_exporter_formats.txt | 14 +++++ doc/source/formats/topology_parsers.txt | 32 +++++++++++ requirements.txt | 1 + 41 files changed, 393 insertions(+), 4 deletions(-) create mode 100644 doc/source/formats/coordinate_readers.txt create mode 100644 doc/source/formats/format_overview.txt create mode 100644 doc/source/formats/reference/classes/CHEMFILES.txt create mode 100644 doc/source/formats/reference/classes/CONFIG.txt create mode 100644 doc/source/formats/reference/classes/COOR.txt create mode 100644 doc/source/formats/reference/classes/CRD.txt create mode 100644 doc/source/formats/reference/classes/DATA.txt create mode 100644 doc/source/formats/reference/classes/DCD.txt create mode 100644 doc/source/formats/reference/classes/DMS.txt create mode 100644 doc/source/formats/reference/classes/GMS.txt create mode 100644 doc/source/formats/reference/classes/GRO.txt create mode 100644 doc/source/formats/reference/classes/GSD.txt create mode 100644 doc/source/formats/reference/classes/HISTORY.txt create mode 100644 doc/source/formats/reference/classes/IN.txt create mode 100644 doc/source/formats/reference/classes/INPCRD.txt create mode 100644 doc/source/formats/reference/classes/ITP.txt create mode 100644 doc/source/formats/reference/classes/LAMMPS.txt create mode 100644 doc/source/formats/reference/classes/LAMMPSDUMP.txt create mode 100644 doc/source/formats/reference/classes/MMTF.txt create mode 100644 doc/source/formats/reference/classes/MOL2.txt create mode 100644 doc/source/formats/reference/classes/NCDF.txt create mode 100644 doc/source/formats/reference/classes/PARMED.txt create mode 100644 doc/source/formats/reference/classes/PDB.txt create mode 100644 doc/source/formats/reference/classes/PDBQT.txt create mode 100644 doc/source/formats/reference/classes/PQR.txt create mode 100644 doc/source/formats/reference/classes/PSF.txt create mode 100644 doc/source/formats/reference/classes/TOP.txt create mode 100644 doc/source/formats/reference/classes/TPR.txt create mode 100644 doc/source/formats/reference/classes/TRJ.txt create mode 100644 doc/source/formats/reference/classes/TRR.txt create mode 100644 doc/source/formats/reference/classes/TRZ.txt create mode 100644 doc/source/formats/reference/classes/TXYZ.txt create mode 100644 doc/source/formats/reference/classes/XML.txt create mode 100644 doc/source/formats/reference/classes/XPDB.txt create mode 100644 doc/source/formats/reference/classes/XTC.txt create mode 100644 doc/source/formats/reference/classes/XYZ.txt create mode 100644 doc/source/formats/selection_exporter_formats.txt create mode 100644 doc/source/formats/topology_parsers.txt diff --git a/.gitignore b/.gitignore index bf92abc3e..7e5518a41 100644 --- a/.gitignore +++ b/.gitignore @@ -22,8 +22,8 @@ doc/build *.so # Ignore generated docs -*/**/*.txt -!requirements.txt +# */**/*.txt +# !requirements.txt # ignore generated files *.vmd diff --git a/doc/source/conf.py b/doc/source/conf.py index 7876ab9d0..b1113584b 100644 --- a/doc/source/conf.py +++ b/doc/source/conf.py @@ -16,7 +16,7 @@ import datetime from collections import OrderedDict import MDAnalysis as mda -import subprocess +# import subprocess import sphinx_rtd_theme from ipywidgets.embed import DEFAULT_EMBED_REQUIREJS_URL @@ -58,8 +58,10 @@ def sort_authors(filename): # auto-recreate tables for each deployment. # Turn off if using sphinx_autobuild as this will autobuild # to infinity. +# TURNED OFF FOR NOW until we sort out how versioned docs +# work and how we will install MDAnalysis + dependencies # -subprocess.call('./scripts/generate_all.sh') +# subprocess.call('./scripts/generate_all.sh') # -- General configuration --------------------------------------------------- diff --git a/doc/source/formats/coordinate_readers.txt b/doc/source/formats/coordinate_readers.txt new file mode 100644 index 000000000..030a5055e --- /dev/null +++ b/doc/source/formats/coordinate_readers.txt @@ -0,0 +1,46 @@ +.. + Generated by gen_format_overview_classes.py + +.. table:: Table of supported coordinate readers and the information read + + ===================================== ========================================= ============ ======== + File type Description Velocities Forces + ===================================== ========================================= ============ ======== + :ref:`ARC ` Tinker file + :ref:`CHEMFILES ` chemfiles object + :ref:`CONFIG ` DL_Poly CONFIG file ✓ + :ref:`COOR ` NAMD binary restart file + :ref:`CRD ` CHARMM CARD file + :ref:`CRDBOX ` AMBER ASCII trajectories + :ref:`DATA ` LAMMPS data file ✓ + :ref:`DCD ` CHARMM, NAMD, or LAMMPS binary trajectory + :ref:`DMS ` DESRES Molecular Structure file ✓ + :ref:`ENT ` Standard PDB file + :ref:`FHIAIMS ` FHI-aims input file ✓ + :ref:`GMS ` GAMESS file + :ref:`GRO ` GROMACS structure file ✓ + :ref:`GSD ` HOOMD GSD file + :ref:`HISTORY ` DL_Poly HISTORY file ✓ + :ref:`IN ` FHI-aims input file ✓ + :ref:`INPCRD ` AMBER restart file + :ref:`LAMMPS ` a LAMMPS DCD trajectory + :ref:`LAMMPSDUMP ` LAMMPS ascii dump file + :ref:`MDCRD ` AMBER ASCII trajectories + :ref:`MMTF ` MMTF file + :ref:`MOL2 ` Tripos MOL2 file + :ref:`NAMDBIN ` NAMD binary restart file + :ref:`NC ` AMBER NETCDF format ✓ ✓ + :ref:`NCDF ` AMBER NETCDF format ✓ ✓ + :ref:`PARMED ` parmed Structure + :ref:`PDB ` Standard PDB file + :ref:`PDBQT ` PDBQT file + :ref:`PQR ` PQR file + :ref:`RESTRT ` AMBER restart file + :ref:`TRJ ` AMBER ASCII trajectories + :ref:`TRR ` GROMACS TRR trajectory ✓ ✓ + :ref:`TRZ ` IBIsCO or YASP binary trajectory ✓ + :ref:`TXYZ ` Tinker file + :ref:`XPDB ` Extended PDB file + :ref:`XTC ` GROMACS compressed trajectory + :ref:`XYZ ` XYZ file + ===================================== ========================================= ============ ======== \ No newline at end of file diff --git a/doc/source/formats/format_overview.txt b/doc/source/formats/format_overview.txt new file mode 100644 index 000000000..00cd534a7 --- /dev/null +++ b/doc/source/formats/format_overview.txt @@ -0,0 +1,53 @@ +.. + Generated by gen_format_overview_classes.py + +.. table:: Table of all supported formats in MDAnalysis + + ===================================== ========================================= ========== ============= ====== ======= + File type Description Topology Coordinates Read Write + ===================================== ========================================= ========== ============= ====== ======= + :ref:`ARC ` Tinker file ✓ ✓ ✓ + :ref:`CHEMFILES ` chemfiles object ✓ ✓ ✓ + :ref:`CONFIG ` DL_Poly CONFIG file ✓ ✓ ✓ + :ref:`COOR ` NAMD binary restart file ✓ ✓ ✓ + :ref:`CRD ` CHARMM CARD file ✓ ✓ ✓ ✓ + :ref:`CRDBOX ` AMBER ASCII trajectories ✓ ✓ + :ref:`DATA ` LAMMPS data file ✓ ✓ ✓ ✓ + :ref:`DCD ` CHARMM, NAMD, or LAMMPS binary trajectory ✓ ✓ ✓ + :ref:`DMS ` DESRES Molecular Structure file ✓ ✓ ✓ + :ref:`ENT ` Standard PDB file ✓ ✓ ✓ ✓ + :ref:`FHIAIMS ` FHI-aims input file ✓ ✓ ✓ ✓ + :ref:`GMS ` GAMESS file ✓ ✓ ✓ + :ref:`GRO ` GROMACS structure file ✓ ✓ ✓ ✓ + :ref:`GSD ` HOOMD GSD file ✓ ✓ ✓ + :ref:`HISTORY ` DL_Poly HISTORY file ✓ ✓ ✓ + :ref:`IN ` FHI-aims input file ✓ ✓ ✓ ✓ + :ref:`INPCRD ` AMBER restart file ✓ ✓ + :ref:`ITP ` GROMACS portable topology file ✓ ✓ + :ref:`LAMMPS ` a LAMMPS DCD trajectory ✓ ✓ ✓ + :ref:`LAMMPSDUMP ` LAMMPS ascii dump file ✓ ✓ ✓ + :ref:`MDCRD ` AMBER ASCII trajectories ✓ ✓ + :ref:`MMTF ` MMTF file ✓ ✓ ✓ + :ref:`MOL2 ` Tripos MOL2 file ✓ ✓ ✓ ✓ + :ref:`NAMDBIN ` NAMD binary restart file ✓ ✓ ✓ + :ref:`NC ` AMBER NETCDF format ✓ ✓ + :ref:`NCDF ` AMBER NETCDF format ✓ ✓ ✓ + :ref:`PARM7 ` AMBER topology file ✓ ✓ + :ref:`PARMED ` parmed Structure ✓ ✓ ✓ ✓ + :ref:`PDB ` Standard PDB file ✓ ✓ ✓ ✓ + :ref:`PDBQT ` PDBQT file ✓ ✓ ✓ ✓ + :ref:`PQR ` PQR file ✓ ✓ ✓ ✓ + :ref:`PRMTOP ` AMBER topology file ✓ ✓ + :ref:`PSF ` CHARMM, NAMD, or XPLOR PSF file ✓ ✓ + :ref:`RESTRT ` AMBER restart file ✓ ✓ + :ref:`TOP ` AMBER topology file ✓ ✓ + :ref:`TPR ` GROMACS run topology file ✓ ✓ + :ref:`TRJ ` AMBER ASCII trajectories ✓ ✓ + :ref:`TRR ` GROMACS TRR trajectory ✓ ✓ ✓ + :ref:`TRZ ` IBIsCO or YASP binary trajectory ✓ ✓ ✓ + :ref:`TXYZ ` Tinker file ✓ ✓ ✓ + :ref:`XML ` HOOMD XML file ✓ ✓ + :ref:`XPDB ` Extended PDB file ✓ ✓ ✓ + :ref:`XTC ` GROMACS compressed trajectory ✓ ✓ ✓ + :ref:`XYZ ` XYZ file ✓ ✓ ✓ ✓ + ===================================== ========================================= ========== ============= ====== ======= \ No newline at end of file diff --git a/doc/source/formats/reference/classes/CHEMFILES.txt b/doc/source/formats/reference/classes/CHEMFILES.txt new file mode 100644 index 000000000..c0953963c --- /dev/null +++ b/doc/source/formats/reference/classes/CHEMFILES.txt @@ -0,0 +1,7 @@ +.. + Generated by gen_format_overview_classes.py + + ===================== ========================================================= + **Coordinate reader** :class:`MDAnalysis.coordinates.chemfiles.ChemfilesReader` + **Coordinate writer** :class:`MDAnalysis.coordinates.chemfiles.ChemfilesWriter` + ===================== ========================================================= \ No newline at end of file diff --git a/doc/source/formats/reference/classes/CONFIG.txt b/doc/source/formats/reference/classes/CONFIG.txt new file mode 100644 index 000000000..2be82f5c1 --- /dev/null +++ b/doc/source/formats/reference/classes/CONFIG.txt @@ -0,0 +1,7 @@ +.. + Generated by gen_format_overview_classes.py + + ===================== ====================================================== + **Coordinate reader** :class:`MDAnalysis.coordinates.DLPoly.ConfigReader` + **Topology parser** :class:`MDAnalysis.topology.DLPolyParser.ConfigParser` + ===================== ====================================================== \ No newline at end of file diff --git a/doc/source/formats/reference/classes/COOR.txt b/doc/source/formats/reference/classes/COOR.txt new file mode 100644 index 000000000..69f96e117 --- /dev/null +++ b/doc/source/formats/reference/classes/COOR.txt @@ -0,0 +1,7 @@ +.. + Generated by gen_format_overview_classes.py + + ===================== ===================================================== + **Coordinate reader** :class:`MDAnalysis.coordinates.NAMDBIN.NAMDBINReader` + **Coordinate writer** :class:`MDAnalysis.coordinates.NAMDBIN.NAMDBINWriter` + ===================== ===================================================== \ No newline at end of file diff --git a/doc/source/formats/reference/classes/CRD.txt b/doc/source/formats/reference/classes/CRD.txt new file mode 100644 index 000000000..60c623e98 --- /dev/null +++ b/doc/source/formats/reference/classes/CRD.txt @@ -0,0 +1,8 @@ +.. + Generated by gen_format_overview_classes.py + + ===================== ================================================ + **Coordinate reader** :class:`MDAnalysis.coordinates.CRD.CRDReader` + **Coordinate writer** :class:`MDAnalysis.coordinates.CRD.CRDWriter` + **Topology parser** :class:`MDAnalysis.topology.CRDParser.CRDParser` + ===================== ================================================ \ No newline at end of file diff --git a/doc/source/formats/reference/classes/DATA.txt b/doc/source/formats/reference/classes/DATA.txt new file mode 100644 index 000000000..66b2ec690 --- /dev/null +++ b/doc/source/formats/reference/classes/DATA.txt @@ -0,0 +1,8 @@ +.. + Generated by gen_format_overview_classes.py + + ===================== ==================================================== + **Coordinate reader** :class:`MDAnalysis.coordinates.LAMMPS.DATAReader` + **Coordinate writer** :class:`MDAnalysis.coordinates.LAMMPS.DATAWriter` + **Topology parser** :class:`MDAnalysis.topology.LAMMPSParser.DATAParser` + ===================== ==================================================== \ No newline at end of file diff --git a/doc/source/formats/reference/classes/DCD.txt b/doc/source/formats/reference/classes/DCD.txt new file mode 100644 index 000000000..22581106b --- /dev/null +++ b/doc/source/formats/reference/classes/DCD.txt @@ -0,0 +1,7 @@ +.. + Generated by gen_format_overview_classes.py + + ===================== ============================================= + **Coordinate reader** :class:`MDAnalysis.coordinates.DCD.DCDReader` + **Coordinate writer** :class:`MDAnalysis.coordinates.DCD.DCDWriter` + ===================== ============================================= \ No newline at end of file diff --git a/doc/source/formats/reference/classes/DMS.txt b/doc/source/formats/reference/classes/DMS.txt new file mode 100644 index 000000000..1b5162dd4 --- /dev/null +++ b/doc/source/formats/reference/classes/DMS.txt @@ -0,0 +1,7 @@ +.. + Generated by gen_format_overview_classes.py + + ===================== ================================================ + **Coordinate reader** :class:`MDAnalysis.coordinates.DMS.DMSReader` + **Topology parser** :class:`MDAnalysis.topology.DMSParser.DMSParser` + ===================== ================================================ \ No newline at end of file diff --git a/doc/source/formats/reference/classes/GMS.txt b/doc/source/formats/reference/classes/GMS.txt new file mode 100644 index 000000000..3416014d7 --- /dev/null +++ b/doc/source/formats/reference/classes/GMS.txt @@ -0,0 +1,7 @@ +.. + Generated by gen_format_overview_classes.py + + ===================== ================================================ + **Coordinate reader** :class:`MDAnalysis.coordinates.GMS.GMSReader` + **Topology parser** :class:`MDAnalysis.topology.GMSParser.GMSParser` + ===================== ================================================ \ No newline at end of file diff --git a/doc/source/formats/reference/classes/GRO.txt b/doc/source/formats/reference/classes/GRO.txt new file mode 100644 index 000000000..be5aeb55f --- /dev/null +++ b/doc/source/formats/reference/classes/GRO.txt @@ -0,0 +1,8 @@ +.. + Generated by gen_format_overview_classes.py + + ===================== ================================================ + **Coordinate reader** :class:`MDAnalysis.coordinates.GRO.GROReader` + **Coordinate writer** :class:`MDAnalysis.coordinates.GRO.GROWriter` + **Topology parser** :class:`MDAnalysis.topology.GROParser.GROParser` + ===================== ================================================ \ No newline at end of file diff --git a/doc/source/formats/reference/classes/GSD.txt b/doc/source/formats/reference/classes/GSD.txt new file mode 100644 index 000000000..5ef110d28 --- /dev/null +++ b/doc/source/formats/reference/classes/GSD.txt @@ -0,0 +1,7 @@ +.. + Generated by gen_format_overview_classes.py + + ===================== ================================================ + **Coordinate reader** :class:`MDAnalysis.coordinates.GSD.GSDReader` + **Topology parser** :class:`MDAnalysis.topology.GSDParser.GSDParser` + ===================== ================================================ \ No newline at end of file diff --git a/doc/source/formats/reference/classes/HISTORY.txt b/doc/source/formats/reference/classes/HISTORY.txt new file mode 100644 index 000000000..2bd2e6852 --- /dev/null +++ b/doc/source/formats/reference/classes/HISTORY.txt @@ -0,0 +1,7 @@ +.. + Generated by gen_format_overview_classes.py + + ===================== ======================================================= + **Coordinate reader** :class:`MDAnalysis.coordinates.DLPoly.HistoryReader` + **Topology parser** :class:`MDAnalysis.topology.DLPolyParser.HistoryParser` + ===================== ======================================================= \ No newline at end of file diff --git a/doc/source/formats/reference/classes/IN.txt b/doc/source/formats/reference/classes/IN.txt new file mode 100644 index 000000000..cde49a08e --- /dev/null +++ b/doc/source/formats/reference/classes/IN.txt @@ -0,0 +1,8 @@ +.. + Generated by gen_format_overview_classes.py + + ===================== ======================================================== + **Coordinate reader** :class:`MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader` + **Coordinate writer** :class:`MDAnalysis.coordinates.FHIAIMS.FHIAIMSWriter` + **Topology parser** :class:`MDAnalysis.topology.FHIAIMSParser.FHIAIMSParser` + ===================== ======================================================== \ No newline at end of file diff --git a/doc/source/formats/reference/classes/INPCRD.txt b/doc/source/formats/reference/classes/INPCRD.txt new file mode 100644 index 000000000..9f9d41f0a --- /dev/null +++ b/doc/source/formats/reference/classes/INPCRD.txt @@ -0,0 +1,6 @@ +.. + Generated by gen_format_overview_classes.py + + ===================== ================================================ + **Coordinate reader** :class:`MDAnalysis.coordinates.INPCRD.INPReader` + ===================== ================================================ \ No newline at end of file diff --git a/doc/source/formats/reference/classes/ITP.txt b/doc/source/formats/reference/classes/ITP.txt new file mode 100644 index 000000000..678d355b7 --- /dev/null +++ b/doc/source/formats/reference/classes/ITP.txt @@ -0,0 +1,6 @@ +.. + Generated by gen_format_overview_classes.py + + =================== ================================================ + **Topology parser** :class:`MDAnalysis.topology.ITPParser.ITPParser` + =================== ================================================ \ No newline at end of file diff --git a/doc/source/formats/reference/classes/LAMMPS.txt b/doc/source/formats/reference/classes/LAMMPS.txt new file mode 100644 index 000000000..df423bf4b --- /dev/null +++ b/doc/source/formats/reference/classes/LAMMPS.txt @@ -0,0 +1,7 @@ +.. + Generated by gen_format_overview_classes.py + + ===================== ================================================ + **Coordinate reader** :class:`MDAnalysis.coordinates.LAMMPS.DCDReader` + **Coordinate writer** :class:`MDAnalysis.coordinates.LAMMPS.DCDWriter` + ===================== ================================================ \ No newline at end of file diff --git a/doc/source/formats/reference/classes/LAMMPSDUMP.txt b/doc/source/formats/reference/classes/LAMMPSDUMP.txt new file mode 100644 index 000000000..69a50f02f --- /dev/null +++ b/doc/source/formats/reference/classes/LAMMPSDUMP.txt @@ -0,0 +1,7 @@ +.. + Generated by gen_format_overview_classes.py + + ===================== ========================================================== + **Coordinate reader** :class:`MDAnalysis.coordinates.LAMMPS.DumpReader` + **Topology parser** :class:`MDAnalysis.topology.LAMMPSParser.LammpsDumpParser` + ===================== ========================================================== \ No newline at end of file diff --git a/doc/source/formats/reference/classes/MMTF.txt b/doc/source/formats/reference/classes/MMTF.txt new file mode 100644 index 000000000..665ada298 --- /dev/null +++ b/doc/source/formats/reference/classes/MMTF.txt @@ -0,0 +1,7 @@ +.. + Generated by gen_format_overview_classes.py + + ===================== ================================================== + **Coordinate reader** :class:`MDAnalysis.coordinates.MMTF.MMTFReader` + **Topology parser** :class:`MDAnalysis.topology.MMTFParser.MMTFParser` + ===================== ================================================== \ No newline at end of file diff --git a/doc/source/formats/reference/classes/MOL2.txt b/doc/source/formats/reference/classes/MOL2.txt new file mode 100644 index 000000000..8b67c7c30 --- /dev/null +++ b/doc/source/formats/reference/classes/MOL2.txt @@ -0,0 +1,8 @@ +.. + Generated by gen_format_overview_classes.py + + ===================== ================================================== + **Coordinate reader** :class:`MDAnalysis.coordinates.MOL2.MOL2Reader` + **Coordinate writer** :class:`MDAnalysis.coordinates.MOL2.MOL2Writer` + **Topology parser** :class:`MDAnalysis.topology.MOL2Parser.MOL2Parser` + ===================== ================================================== \ No newline at end of file diff --git a/doc/source/formats/reference/classes/NCDF.txt b/doc/source/formats/reference/classes/NCDF.txt new file mode 100644 index 000000000..3007edbe1 --- /dev/null +++ b/doc/source/formats/reference/classes/NCDF.txt @@ -0,0 +1,7 @@ +.. + Generated by gen_format_overview_classes.py + + ===================== ============================================== + **Coordinate reader** :class:`MDAnalysis.coordinates.TRJ.NCDFReader` + **Coordinate writer** :class:`MDAnalysis.coordinates.TRJ.NCDFWriter` + ===================== ============================================== \ No newline at end of file diff --git a/doc/source/formats/reference/classes/PARMED.txt b/doc/source/formats/reference/classes/PARMED.txt new file mode 100644 index 000000000..720080d5f --- /dev/null +++ b/doc/source/formats/reference/classes/PARMED.txt @@ -0,0 +1,8 @@ +.. + Generated by gen_format_overview_classes.py + + ===================== ====================================================== + **Converter** :class:`MDAnalysis.coordinates.ParmEd.ParmEdConverter` + **Coordinate reader** :class:`MDAnalysis.coordinates.ParmEd.ParmEdReader` + **Topology parser** :class:`MDAnalysis.topology.ParmEdParser.ParmEdParser` + ===================== ====================================================== \ No newline at end of file diff --git a/doc/source/formats/reference/classes/PDB.txt b/doc/source/formats/reference/classes/PDB.txt new file mode 100644 index 000000000..83f9d4790 --- /dev/null +++ b/doc/source/formats/reference/classes/PDB.txt @@ -0,0 +1,8 @@ +.. + Generated by gen_format_overview_classes.py + + ===================== ================================================ + **Coordinate reader** :class:`MDAnalysis.coordinates.PDB.PDBReader` + **Coordinate writer** :class:`MDAnalysis.coordinates.PDB.PDBWriter` + **Topology parser** :class:`MDAnalysis.topology.PDBParser.PDBParser` + ===================== ================================================ \ No newline at end of file diff --git a/doc/source/formats/reference/classes/PDBQT.txt b/doc/source/formats/reference/classes/PDBQT.txt new file mode 100644 index 000000000..a44fac7e5 --- /dev/null +++ b/doc/source/formats/reference/classes/PDBQT.txt @@ -0,0 +1,8 @@ +.. + Generated by gen_format_overview_classes.py + + ===================== ==================================================== + **Coordinate reader** :class:`MDAnalysis.coordinates.PDBQT.PDBQTReader` + **Coordinate writer** :class:`MDAnalysis.coordinates.PDBQT.PDBQTWriter` + **Topology parser** :class:`MDAnalysis.topology.PDBQTParser.PDBQTParser` + ===================== ==================================================== \ No newline at end of file diff --git a/doc/source/formats/reference/classes/PQR.txt b/doc/source/formats/reference/classes/PQR.txt new file mode 100644 index 000000000..2bc1dc60e --- /dev/null +++ b/doc/source/formats/reference/classes/PQR.txt @@ -0,0 +1,8 @@ +.. + Generated by gen_format_overview_classes.py + + ===================== ================================================ + **Coordinate reader** :class:`MDAnalysis.coordinates.PQR.PQRReader` + **Coordinate writer** :class:`MDAnalysis.coordinates.PQR.PQRWriter` + **Topology parser** :class:`MDAnalysis.topology.PQRParser.PQRParser` + ===================== ================================================ \ No newline at end of file diff --git a/doc/source/formats/reference/classes/PSF.txt b/doc/source/formats/reference/classes/PSF.txt new file mode 100644 index 000000000..b0f1f438c --- /dev/null +++ b/doc/source/formats/reference/classes/PSF.txt @@ -0,0 +1,6 @@ +.. + Generated by gen_format_overview_classes.py + + =================== ================================================ + **Topology parser** :class:`MDAnalysis.topology.PSFParser.PSFParser` + =================== ================================================ \ No newline at end of file diff --git a/doc/source/formats/reference/classes/TOP.txt b/doc/source/formats/reference/classes/TOP.txt new file mode 100644 index 000000000..1389beab1 --- /dev/null +++ b/doc/source/formats/reference/classes/TOP.txt @@ -0,0 +1,6 @@ +.. + Generated by gen_format_overview_classes.py + + =================== ================================================ + **Topology parser** :class:`MDAnalysis.topology.TOPParser.TOPParser` + =================== ================================================ \ No newline at end of file diff --git a/doc/source/formats/reference/classes/TPR.txt b/doc/source/formats/reference/classes/TPR.txt new file mode 100644 index 000000000..30ae011af --- /dev/null +++ b/doc/source/formats/reference/classes/TPR.txt @@ -0,0 +1,6 @@ +.. + Generated by gen_format_overview_classes.py + + =================== ================================================ + **Topology parser** :class:`MDAnalysis.topology.TPRParser.TPRParser` + =================== ================================================ \ No newline at end of file diff --git a/doc/source/formats/reference/classes/TRJ.txt b/doc/source/formats/reference/classes/TRJ.txt new file mode 100644 index 000000000..28681453f --- /dev/null +++ b/doc/source/formats/reference/classes/TRJ.txt @@ -0,0 +1,6 @@ +.. + Generated by gen_format_overview_classes.py + + ===================== ============================================= + **Coordinate reader** :class:`MDAnalysis.coordinates.TRJ.TRJReader` + ===================== ============================================= \ No newline at end of file diff --git a/doc/source/formats/reference/classes/TRR.txt b/doc/source/formats/reference/classes/TRR.txt new file mode 100644 index 000000000..8cd1f3b42 --- /dev/null +++ b/doc/source/formats/reference/classes/TRR.txt @@ -0,0 +1,7 @@ +.. + Generated by gen_format_overview_classes.py + + ===================== ============================================= + **Coordinate reader** :class:`MDAnalysis.coordinates.TRR.TRRReader` + **Coordinate writer** :class:`MDAnalysis.coordinates.TRR.TRRWriter` + ===================== ============================================= \ No newline at end of file diff --git a/doc/source/formats/reference/classes/TRZ.txt b/doc/source/formats/reference/classes/TRZ.txt new file mode 100644 index 000000000..6d57845f5 --- /dev/null +++ b/doc/source/formats/reference/classes/TRZ.txt @@ -0,0 +1,7 @@ +.. + Generated by gen_format_overview_classes.py + + ===================== ============================================= + **Coordinate reader** :class:`MDAnalysis.coordinates.TRZ.TRZReader` + **Coordinate writer** :class:`MDAnalysis.coordinates.TRZ.TRZWriter` + ===================== ============================================= \ No newline at end of file diff --git a/doc/source/formats/reference/classes/TXYZ.txt b/doc/source/formats/reference/classes/TXYZ.txt new file mode 100644 index 000000000..b4d458724 --- /dev/null +++ b/doc/source/formats/reference/classes/TXYZ.txt @@ -0,0 +1,7 @@ +.. + Generated by gen_format_overview_classes.py + + ===================== ================================================== + **Coordinate reader** :class:`MDAnalysis.coordinates.TXYZ.TXYZReader` + **Topology parser** :class:`MDAnalysis.topology.TXYZParser.TXYZParser` + ===================== ================================================== \ No newline at end of file diff --git a/doc/source/formats/reference/classes/XML.txt b/doc/source/formats/reference/classes/XML.txt new file mode 100644 index 000000000..03de05b2d --- /dev/null +++ b/doc/source/formats/reference/classes/XML.txt @@ -0,0 +1,6 @@ +.. + Generated by gen_format_overview_classes.py + + =================== ========================================================== + **Topology parser** :class:`MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser` + =================== ========================================================== \ No newline at end of file diff --git a/doc/source/formats/reference/classes/XPDB.txt b/doc/source/formats/reference/classes/XPDB.txt new file mode 100644 index 000000000..003cd6d9d --- /dev/null +++ b/doc/source/formats/reference/classes/XPDB.txt @@ -0,0 +1,7 @@ +.. + Generated by gen_format_overview_classes.py + + ===================== ================================================================ + **Coordinate reader** :class:`MDAnalysis.coordinates.PDB.ExtendedPDBReader` + **Topology parser** :class:`MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser` + ===================== ================================================================ \ No newline at end of file diff --git a/doc/source/formats/reference/classes/XTC.txt b/doc/source/formats/reference/classes/XTC.txt new file mode 100644 index 000000000..ea898c8ba --- /dev/null +++ b/doc/source/formats/reference/classes/XTC.txt @@ -0,0 +1,7 @@ +.. + Generated by gen_format_overview_classes.py + + ===================== ============================================= + **Coordinate reader** :class:`MDAnalysis.coordinates.XTC.XTCReader` + **Coordinate writer** :class:`MDAnalysis.coordinates.XTC.XTCWriter` + ===================== ============================================= \ No newline at end of file diff --git a/doc/source/formats/reference/classes/XYZ.txt b/doc/source/formats/reference/classes/XYZ.txt new file mode 100644 index 000000000..b8cd1e8af --- /dev/null +++ b/doc/source/formats/reference/classes/XYZ.txt @@ -0,0 +1,8 @@ +.. + Generated by gen_format_overview_classes.py + + ===================== ================================================ + **Coordinate reader** :class:`MDAnalysis.coordinates.XYZ.XYZReader` + **Coordinate writer** :class:`MDAnalysis.coordinates.XYZ.XYZWriter` + **Topology parser** :class:`MDAnalysis.topology.XYZParser.XYZParser` + ===================== ================================================ \ No newline at end of file diff --git a/doc/source/formats/selection_exporter_formats.txt b/doc/source/formats/selection_exporter_formats.txt new file mode 100644 index 000000000..6fe94d789 --- /dev/null +++ b/doc/source/formats/selection_exporter_formats.txt @@ -0,0 +1,14 @@ +.. + Generated by gen_selection_exporters.py + +.. table:: Supported selection exporters + + ========== =========== ======================================== ====================================================== + Program Extension Description Class + ========== =========== ======================================== ====================================================== + `CHARMM`_ str CHARMM selection of individual atoms :class:`MDAnalysis.selections.charmm.SelectionWriter` + `Gromacs`_ ndx GROMACS index file :class:`MDAnalysis.selections.gromacs.SelectionWriter` + `Jmol`_ spt Jmol selection commands :class:`MDAnalysis.selections.jmol.SelectionWriter` + `PyMol`_ pml PyMOL selection string :class:`MDAnalysis.selections.pymol.SelectionWriter` + `VMD`_ vmd VMD macros, available in Representations :class:`MDAnalysis.selections.vmd.SelectionWriter` + ========== =========== ======================================== ====================================================== \ No newline at end of file diff --git a/doc/source/formats/topology_parsers.txt b/doc/source/formats/topology_parsers.txt new file mode 100644 index 000000000..deb18f3a7 --- /dev/null +++ b/doc/source/formats/topology_parsers.txt @@ -0,0 +1,32 @@ +.. + Generated by gen_topologyparser_attrs.py + +.. table:: Table of supported topology parsers and the attributes read + + ====================================== =============================== =================================================================================================================================================================================================================== ==================== + Format Description Attributes read Attributes guessed + ====================================== =============================== =================================================================================================================================================================================================================== ==================== + :ref:`CONFIG ` DL_Poly CONFIG file names masses, types + :ref:`CRD ` CHARMM CARD file names, resnames, tempfactors masses, types + :ref:`DATA ` LAMMPS data file angles, bonds, charges, dihedrals, impropers + :ref:`DMS ` DESRES Molecular Structure file atomnums, bonds, chainIDs, charges, names, resnames types + :ref:`GMS ` GAMESS file atomiccharges, names masses, types + :ref:`GRO ` GROMACS structure file names, resnames masses, types + :ref:`GSD ` HOOMD GSD file angles, bonds, charges, dihedrals, impropers, names, radii, resnames + :ref:`HISTORY ` DL_Poly HISTORY file names masses, types + :ref:`IN, FHIAIMS ` FHI-aims input file elements, names masses, types + :ref:`LAMMPSDUMP ` LAMMPS ascii dump file masses + :ref:`MMTF ` MMTF file altLocs, bfactors, bonds, charges, icodes, models, names, occupancies, resnames masses + :ref:`MOL2 ` Tripos MOL2 file bonds, charges, names, resnames masses + :ref:`PARMED ` parmed Structure altLocs, angles, bonds, chainIDs, charges, cmaps, dihedrals, elements, epsilon14s, epsilons, gbscreens, impropers, names, nbindices, occupancies, resnames, rmin14s, rmins, solventradii, tempfactors, ureybradleys + :ref:`PDB, ENT ` Standard PDB file altLocs, bonds, chainIDs, elements, icodes, names, occupancies, record_types, resnames, tempfactors masses, types + :ref:`PDBQT ` PDBQT file altLocs, charges, icodes, names, occupancies, record_types, resnames, tempfactors masses + :ref:`PQR ` PQR file charges, icodes, names, radii, record_types, resnames masses, types + :ref:`PSF ` CHARMM, NAMD, or XPLOR PSF file angles, bonds, charges, dihedrals, impropers, names, resnames + :ref:`TOP, PRMTOP, PARM7 ` AMBER topology file angles, bonds, charges, dihedrals, impropers, names, resnames, type_indices + :ref:`TPR ` GROMACS run topology file angles, bonds, charges, dihedrals, impropers, molnums, moltypes, names, resnames + :ref:`TXYZ, ARC ` Tinker file bonds, names masses + :ref:`XML ` HOOMD XML file angles, bonds, charges, dihedrals, impropers, radii + :ref:`XPDB ` Extended PDB file altLocs, bonds, chainIDs, icodes, names, occupancies, record_types, resnames, tempfactors masses, types + :ref:`XYZ ` XYZ file elements, names masses, types + ====================================== =============================== =================================================================================================================================================================================================================== ==================== \ No newline at end of file diff --git a/requirements.txt b/requirements.txt index 5a01be414..36f4e483c 100644 --- a/requirements.txt +++ b/requirements.txt @@ -9,6 +9,7 @@ MDAnalysisTests nbsphinx==0.4.2 nglview==2.7.1 numpy==1.17.2 +parmed Sphinx==2.2.0 sphinxcontrib-bibtex sphinx-rtd-theme==0.4.3 From de6c48e9c8bbf92ab8ffc7402c05a73678f44c27 Mon Sep 17 00:00:00 2001 From: Lily Wang Date: Fri, 19 Jun 2020 12:33:33 +1000 Subject: [PATCH 11/18] unindented some tables; small fixes --- .../formats/reference/classes/CHEMFILES.txt | 8 ++-- .../formats/reference/classes/CONFIG.txt | 8 ++-- doc/source/formats/reference/classes/COOR.txt | 8 ++-- doc/source/formats/reference/classes/CRD.txt | 10 ++--- doc/source/formats/reference/classes/DATA.txt | 10 ++--- doc/source/formats/reference/classes/DCD.txt | 8 ++-- doc/source/formats/reference/classes/DMS.txt | 8 ++-- doc/source/formats/reference/classes/GMS.txt | 8 ++-- doc/source/formats/reference/classes/GRO.txt | 10 ++--- doc/source/formats/reference/classes/GSD.txt | 8 ++-- .../formats/reference/classes/HISTORY.txt | 8 ++-- doc/source/formats/reference/classes/IN.txt | 10 ++--- .../formats/reference/classes/INPCRD.txt | 6 +-- doc/source/formats/reference/classes/ITP.txt | 6 +-- .../formats/reference/classes/LAMMPS.txt | 8 ++-- .../formats/reference/classes/LAMMPSDUMP.txt | 8 ++-- doc/source/formats/reference/classes/MMTF.txt | 8 ++-- doc/source/formats/reference/classes/MOL2.txt | 10 ++--- doc/source/formats/reference/classes/NCDF.txt | 8 ++-- .../formats/reference/classes/PARMED.txt | 10 ++--- doc/source/formats/reference/classes/PDB.txt | 10 ++--- .../formats/reference/classes/PDBQT.txt | 10 ++--- doc/source/formats/reference/classes/PQR.txt | 10 ++--- doc/source/formats/reference/classes/PSF.txt | 6 +-- doc/source/formats/reference/classes/TOP.txt | 6 +-- doc/source/formats/reference/classes/TPR.txt | 6 +-- doc/source/formats/reference/classes/TRJ.txt | 6 +-- doc/source/formats/reference/classes/TRR.txt | 8 ++-- doc/source/formats/reference/classes/TRZ.txt | 8 ++-- doc/source/formats/reference/classes/TXYZ.txt | 8 ++-- doc/source/formats/reference/classes/XML.txt | 6 +-- doc/source/formats/reference/classes/XPDB.txt | 8 ++-- doc/source/formats/reference/classes/XTC.txt | 8 ++-- doc/source/formats/reference/classes/XYZ.txt | 10 ++--- doc/source/formats/reference/coor.rst | 10 +++-- doc/source/formats/reference/in.rst | 6 ++- doc/source/formats/reference/pdbqt.rst | 4 +- doc/source/formats/reference/trj.rst | 18 ++++---- doc/source/generated/.gitignore | 4 -- doc/source/generated/selections/.gitignore | 3 -- doc/source/generated/selections/base.txt | 7 +++ doc/source/generated/selections/nucleic.txt | 10 +++++ .../generated/selections/nucleic_backbone.txt | 6 +++ .../generated/selections/nucleic_sugar.txt | 6 +++ doc/source/generated/selections/protein.txt | 18 ++++++++ .../generated/selections/protein_backbone.txt | 6 +++ doc/source/generated/topology/.gitignore | 3 -- .../generated/topology/connectivityattrs.txt | 11 +++++ doc/source/generated/topology/defaults.txt | 45 +++++++++++++++++++ .../generated/topology/groupmethods.txt | 16 +++++++ .../generated/topology/topologyattrs.txt | 39 ++++++++++++++++ doc/source/scripts/base.py | 4 +- 52 files changed, 326 insertions(+), 168 deletions(-) create mode 100644 doc/source/generated/selections/base.txt create mode 100644 doc/source/generated/selections/nucleic.txt create mode 100644 doc/source/generated/selections/nucleic_backbone.txt create mode 100644 doc/source/generated/selections/nucleic_sugar.txt create mode 100644 doc/source/generated/selections/protein.txt create mode 100644 doc/source/generated/selections/protein_backbone.txt create mode 100644 doc/source/generated/topology/connectivityattrs.txt create mode 100644 doc/source/generated/topology/defaults.txt create mode 100644 doc/source/generated/topology/groupmethods.txt create mode 100644 doc/source/generated/topology/topologyattrs.txt diff --git a/doc/source/formats/reference/classes/CHEMFILES.txt b/doc/source/formats/reference/classes/CHEMFILES.txt index c0953963c..7af3618ec 100644 --- a/doc/source/formats/reference/classes/CHEMFILES.txt +++ b/doc/source/formats/reference/classes/CHEMFILES.txt @@ -1,7 +1,7 @@ .. Generated by gen_format_overview_classes.py - ===================== ========================================================= - **Coordinate reader** :class:`MDAnalysis.coordinates.chemfiles.ChemfilesReader` - **Coordinate writer** :class:`MDAnalysis.coordinates.chemfiles.ChemfilesWriter` - ===================== ========================================================= \ No newline at end of file +===================== ========================================================= +**Coordinate reader** :class:`MDAnalysis.coordinates.chemfiles.ChemfilesReader` +**Coordinate writer** :class:`MDAnalysis.coordinates.chemfiles.ChemfilesWriter` +===================== ========================================================= \ No newline at end of file diff --git a/doc/source/formats/reference/classes/CONFIG.txt b/doc/source/formats/reference/classes/CONFIG.txt index 2be82f5c1..f922feb00 100644 --- a/doc/source/formats/reference/classes/CONFIG.txt +++ b/doc/source/formats/reference/classes/CONFIG.txt @@ -1,7 +1,7 @@ .. Generated by gen_format_overview_classes.py - ===================== ====================================================== - **Coordinate reader** :class:`MDAnalysis.coordinates.DLPoly.ConfigReader` - **Topology parser** :class:`MDAnalysis.topology.DLPolyParser.ConfigParser` - ===================== ====================================================== \ No newline at end of file +===================== ====================================================== +**Coordinate reader** :class:`MDAnalysis.coordinates.DLPoly.ConfigReader` +**Topology parser** :class:`MDAnalysis.topology.DLPolyParser.ConfigParser` +===================== ====================================================== \ No newline at end of file diff --git a/doc/source/formats/reference/classes/COOR.txt b/doc/source/formats/reference/classes/COOR.txt index 69f96e117..fd6827ba9 100644 --- a/doc/source/formats/reference/classes/COOR.txt +++ b/doc/source/formats/reference/classes/COOR.txt @@ -1,7 +1,7 @@ .. Generated by gen_format_overview_classes.py - ===================== ===================================================== - **Coordinate reader** :class:`MDAnalysis.coordinates.NAMDBIN.NAMDBINReader` - **Coordinate writer** :class:`MDAnalysis.coordinates.NAMDBIN.NAMDBINWriter` - ===================== ===================================================== \ No newline at end of file +===================== ===================================================== +**Coordinate reader** :class:`MDAnalysis.coordinates.NAMDBIN.NAMDBINReader` +**Coordinate writer** :class:`MDAnalysis.coordinates.NAMDBIN.NAMDBINWriter` +===================== ===================================================== \ No newline at end of file diff --git a/doc/source/formats/reference/classes/CRD.txt b/doc/source/formats/reference/classes/CRD.txt index 60c623e98..c4c6f249b 100644 --- a/doc/source/formats/reference/classes/CRD.txt +++ b/doc/source/formats/reference/classes/CRD.txt @@ -1,8 +1,8 @@ .. Generated by gen_format_overview_classes.py - ===================== ================================================ - **Coordinate reader** :class:`MDAnalysis.coordinates.CRD.CRDReader` - **Coordinate writer** :class:`MDAnalysis.coordinates.CRD.CRDWriter` - **Topology parser** :class:`MDAnalysis.topology.CRDParser.CRDParser` - ===================== ================================================ \ No newline at end of file +===================== ================================================ +**Coordinate reader** :class:`MDAnalysis.coordinates.CRD.CRDReader` +**Coordinate writer** :class:`MDAnalysis.coordinates.CRD.CRDWriter` +**Topology parser** :class:`MDAnalysis.topology.CRDParser.CRDParser` +===================== ================================================ \ No newline at end of file diff --git a/doc/source/formats/reference/classes/DATA.txt b/doc/source/formats/reference/classes/DATA.txt index 66b2ec690..c44a0dec0 100644 --- a/doc/source/formats/reference/classes/DATA.txt +++ b/doc/source/formats/reference/classes/DATA.txt @@ -1,8 +1,8 @@ .. Generated by gen_format_overview_classes.py - ===================== ==================================================== - **Coordinate reader** :class:`MDAnalysis.coordinates.LAMMPS.DATAReader` - **Coordinate writer** :class:`MDAnalysis.coordinates.LAMMPS.DATAWriter` - **Topology parser** :class:`MDAnalysis.topology.LAMMPSParser.DATAParser` - ===================== ==================================================== \ No newline at end of file +===================== ==================================================== +**Coordinate reader** :class:`MDAnalysis.coordinates.LAMMPS.DATAReader` +**Coordinate writer** :class:`MDAnalysis.coordinates.LAMMPS.DATAWriter` +**Topology parser** :class:`MDAnalysis.topology.LAMMPSParser.DATAParser` +===================== ==================================================== \ No newline at end of file diff --git a/doc/source/formats/reference/classes/DCD.txt b/doc/source/formats/reference/classes/DCD.txt index 22581106b..766b21b47 100644 --- a/doc/source/formats/reference/classes/DCD.txt +++ b/doc/source/formats/reference/classes/DCD.txt @@ -1,7 +1,7 @@ .. Generated by gen_format_overview_classes.py - ===================== ============================================= - **Coordinate reader** :class:`MDAnalysis.coordinates.DCD.DCDReader` - **Coordinate writer** :class:`MDAnalysis.coordinates.DCD.DCDWriter` - ===================== ============================================= \ No newline at end of file +===================== ============================================= +**Coordinate reader** :class:`MDAnalysis.coordinates.DCD.DCDReader` +**Coordinate writer** :class:`MDAnalysis.coordinates.DCD.DCDWriter` +===================== ============================================= \ No newline at end of file diff --git a/doc/source/formats/reference/classes/DMS.txt b/doc/source/formats/reference/classes/DMS.txt index 1b5162dd4..2f2680167 100644 --- a/doc/source/formats/reference/classes/DMS.txt +++ b/doc/source/formats/reference/classes/DMS.txt @@ -1,7 +1,7 @@ .. Generated by gen_format_overview_classes.py - ===================== ================================================ - **Coordinate reader** :class:`MDAnalysis.coordinates.DMS.DMSReader` - **Topology parser** :class:`MDAnalysis.topology.DMSParser.DMSParser` - ===================== ================================================ \ No newline at end of file +===================== ================================================ +**Coordinate reader** :class:`MDAnalysis.coordinates.DMS.DMSReader` +**Topology parser** :class:`MDAnalysis.topology.DMSParser.DMSParser` +===================== ================================================ \ No newline at end of file diff --git a/doc/source/formats/reference/classes/GMS.txt b/doc/source/formats/reference/classes/GMS.txt index 3416014d7..0e44b4cb2 100644 --- a/doc/source/formats/reference/classes/GMS.txt +++ b/doc/source/formats/reference/classes/GMS.txt @@ -1,7 +1,7 @@ .. Generated by gen_format_overview_classes.py - ===================== ================================================ - **Coordinate reader** :class:`MDAnalysis.coordinates.GMS.GMSReader` - **Topology parser** :class:`MDAnalysis.topology.GMSParser.GMSParser` - ===================== ================================================ \ No newline at end of file +===================== ================================================ +**Coordinate reader** :class:`MDAnalysis.coordinates.GMS.GMSReader` +**Topology parser** :class:`MDAnalysis.topology.GMSParser.GMSParser` +===================== ================================================ \ No newline at end of file diff --git a/doc/source/formats/reference/classes/GRO.txt b/doc/source/formats/reference/classes/GRO.txt index be5aeb55f..b08fbacad 100644 --- a/doc/source/formats/reference/classes/GRO.txt +++ b/doc/source/formats/reference/classes/GRO.txt @@ -1,8 +1,8 @@ .. Generated by gen_format_overview_classes.py - ===================== ================================================ - **Coordinate reader** :class:`MDAnalysis.coordinates.GRO.GROReader` - **Coordinate writer** :class:`MDAnalysis.coordinates.GRO.GROWriter` - **Topology parser** :class:`MDAnalysis.topology.GROParser.GROParser` - ===================== ================================================ \ No newline at end of file +===================== ================================================ +**Coordinate reader** :class:`MDAnalysis.coordinates.GRO.GROReader` +**Coordinate writer** :class:`MDAnalysis.coordinates.GRO.GROWriter` +**Topology parser** :class:`MDAnalysis.topology.GROParser.GROParser` +===================== ================================================ \ No newline at end of file diff --git a/doc/source/formats/reference/classes/GSD.txt b/doc/source/formats/reference/classes/GSD.txt index 5ef110d28..4099a831f 100644 --- a/doc/source/formats/reference/classes/GSD.txt +++ b/doc/source/formats/reference/classes/GSD.txt @@ -1,7 +1,7 @@ .. Generated by gen_format_overview_classes.py - ===================== ================================================ - **Coordinate reader** :class:`MDAnalysis.coordinates.GSD.GSDReader` - **Topology parser** :class:`MDAnalysis.topology.GSDParser.GSDParser` - ===================== ================================================ \ No newline at end of file +===================== ================================================ +**Coordinate reader** :class:`MDAnalysis.coordinates.GSD.GSDReader` +**Topology parser** :class:`MDAnalysis.topology.GSDParser.GSDParser` +===================== ================================================ \ No newline at end of file diff --git a/doc/source/formats/reference/classes/HISTORY.txt b/doc/source/formats/reference/classes/HISTORY.txt index 2bd2e6852..694ab145b 100644 --- a/doc/source/formats/reference/classes/HISTORY.txt +++ b/doc/source/formats/reference/classes/HISTORY.txt @@ -1,7 +1,7 @@ .. Generated by gen_format_overview_classes.py - ===================== ======================================================= - **Coordinate reader** :class:`MDAnalysis.coordinates.DLPoly.HistoryReader` - **Topology parser** :class:`MDAnalysis.topology.DLPolyParser.HistoryParser` - ===================== ======================================================= \ No newline at end of file +===================== ======================================================= +**Coordinate reader** :class:`MDAnalysis.coordinates.DLPoly.HistoryReader` +**Topology parser** :class:`MDAnalysis.topology.DLPolyParser.HistoryParser` +===================== ======================================================= \ No newline at end of file diff --git a/doc/source/formats/reference/classes/IN.txt b/doc/source/formats/reference/classes/IN.txt index cde49a08e..e0dad56f2 100644 --- a/doc/source/formats/reference/classes/IN.txt +++ b/doc/source/formats/reference/classes/IN.txt @@ -1,8 +1,8 @@ .. Generated by gen_format_overview_classes.py - ===================== ======================================================== - **Coordinate reader** :class:`MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader` - **Coordinate writer** :class:`MDAnalysis.coordinates.FHIAIMS.FHIAIMSWriter` - **Topology parser** :class:`MDAnalysis.topology.FHIAIMSParser.FHIAIMSParser` - ===================== ======================================================== \ No newline at end of file +===================== ======================================================== +**Coordinate reader** :class:`MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader` +**Coordinate writer** :class:`MDAnalysis.coordinates.FHIAIMS.FHIAIMSWriter` +**Topology parser** :class:`MDAnalysis.topology.FHIAIMSParser.FHIAIMSParser` +===================== ======================================================== \ No newline at end of file diff --git a/doc/source/formats/reference/classes/INPCRD.txt b/doc/source/formats/reference/classes/INPCRD.txt index 9f9d41f0a..7a3faecd5 100644 --- a/doc/source/formats/reference/classes/INPCRD.txt +++ b/doc/source/formats/reference/classes/INPCRD.txt @@ -1,6 +1,6 @@ .. Generated by gen_format_overview_classes.py - ===================== ================================================ - **Coordinate reader** :class:`MDAnalysis.coordinates.INPCRD.INPReader` - ===================== ================================================ \ No newline at end of file +===================== ================================================ +**Coordinate reader** :class:`MDAnalysis.coordinates.INPCRD.INPReader` +===================== ================================================ \ No newline at end of file diff --git a/doc/source/formats/reference/classes/ITP.txt b/doc/source/formats/reference/classes/ITP.txt index 678d355b7..c0fb53dd4 100644 --- a/doc/source/formats/reference/classes/ITP.txt +++ b/doc/source/formats/reference/classes/ITP.txt @@ -1,6 +1,6 @@ .. Generated by gen_format_overview_classes.py - =================== ================================================ - **Topology parser** :class:`MDAnalysis.topology.ITPParser.ITPParser` - =================== ================================================ \ No newline at end of file +=================== ================================================ +**Topology parser** :class:`MDAnalysis.topology.ITPParser.ITPParser` +=================== ================================================ \ No newline at end of file diff --git a/doc/source/formats/reference/classes/LAMMPS.txt b/doc/source/formats/reference/classes/LAMMPS.txt index df423bf4b..d609dd556 100644 --- a/doc/source/formats/reference/classes/LAMMPS.txt +++ b/doc/source/formats/reference/classes/LAMMPS.txt @@ -1,7 +1,7 @@ .. Generated by gen_format_overview_classes.py - ===================== ================================================ - **Coordinate reader** :class:`MDAnalysis.coordinates.LAMMPS.DCDReader` - **Coordinate writer** :class:`MDAnalysis.coordinates.LAMMPS.DCDWriter` - ===================== ================================================ \ No newline at end of file +===================== ================================================ +**Coordinate reader** :class:`MDAnalysis.coordinates.LAMMPS.DCDReader` +**Coordinate writer** :class:`MDAnalysis.coordinates.LAMMPS.DCDWriter` +===================== ================================================ \ No newline at end of file diff --git a/doc/source/formats/reference/classes/LAMMPSDUMP.txt b/doc/source/formats/reference/classes/LAMMPSDUMP.txt index 69a50f02f..0ecbed751 100644 --- a/doc/source/formats/reference/classes/LAMMPSDUMP.txt +++ b/doc/source/formats/reference/classes/LAMMPSDUMP.txt @@ -1,7 +1,7 @@ .. Generated by gen_format_overview_classes.py - ===================== ========================================================== - **Coordinate reader** :class:`MDAnalysis.coordinates.LAMMPS.DumpReader` - **Topology parser** :class:`MDAnalysis.topology.LAMMPSParser.LammpsDumpParser` - ===================== ========================================================== \ No newline at end of file +===================== ========================================================== +**Coordinate reader** :class:`MDAnalysis.coordinates.LAMMPS.DumpReader` +**Topology parser** :class:`MDAnalysis.topology.LAMMPSParser.LammpsDumpParser` +===================== ========================================================== \ No newline at end of file diff --git a/doc/source/formats/reference/classes/MMTF.txt b/doc/source/formats/reference/classes/MMTF.txt index 665ada298..30c368323 100644 --- a/doc/source/formats/reference/classes/MMTF.txt +++ b/doc/source/formats/reference/classes/MMTF.txt @@ -1,7 +1,7 @@ .. Generated by gen_format_overview_classes.py - ===================== ================================================== - **Coordinate reader** :class:`MDAnalysis.coordinates.MMTF.MMTFReader` - **Topology parser** :class:`MDAnalysis.topology.MMTFParser.MMTFParser` - ===================== ================================================== \ No newline at end of file +===================== ================================================== +**Coordinate reader** :class:`MDAnalysis.coordinates.MMTF.MMTFReader` +**Topology parser** :class:`MDAnalysis.topology.MMTFParser.MMTFParser` +===================== ================================================== \ No newline at end of file diff --git a/doc/source/formats/reference/classes/MOL2.txt b/doc/source/formats/reference/classes/MOL2.txt index 8b67c7c30..f497d63ac 100644 --- a/doc/source/formats/reference/classes/MOL2.txt +++ b/doc/source/formats/reference/classes/MOL2.txt @@ -1,8 +1,8 @@ .. Generated by gen_format_overview_classes.py - ===================== ================================================== - **Coordinate reader** :class:`MDAnalysis.coordinates.MOL2.MOL2Reader` - **Coordinate writer** :class:`MDAnalysis.coordinates.MOL2.MOL2Writer` - **Topology parser** :class:`MDAnalysis.topology.MOL2Parser.MOL2Parser` - ===================== ================================================== \ No newline at end of file +===================== ================================================== +**Coordinate reader** :class:`MDAnalysis.coordinates.MOL2.MOL2Reader` +**Coordinate writer** :class:`MDAnalysis.coordinates.MOL2.MOL2Writer` +**Topology parser** :class:`MDAnalysis.topology.MOL2Parser.MOL2Parser` +===================== ================================================== \ No newline at end of file diff --git a/doc/source/formats/reference/classes/NCDF.txt b/doc/source/formats/reference/classes/NCDF.txt index 3007edbe1..3df3b4328 100644 --- a/doc/source/formats/reference/classes/NCDF.txt +++ b/doc/source/formats/reference/classes/NCDF.txt @@ -1,7 +1,7 @@ .. Generated by gen_format_overview_classes.py - ===================== ============================================== - **Coordinate reader** :class:`MDAnalysis.coordinates.TRJ.NCDFReader` - **Coordinate writer** :class:`MDAnalysis.coordinates.TRJ.NCDFWriter` - ===================== ============================================== \ No newline at end of file +===================== ============================================== +**Coordinate reader** :class:`MDAnalysis.coordinates.TRJ.NCDFReader` +**Coordinate writer** :class:`MDAnalysis.coordinates.TRJ.NCDFWriter` +===================== ============================================== \ No newline at end of file diff --git a/doc/source/formats/reference/classes/PARMED.txt b/doc/source/formats/reference/classes/PARMED.txt index 720080d5f..47ef0d87e 100644 --- a/doc/source/formats/reference/classes/PARMED.txt +++ b/doc/source/formats/reference/classes/PARMED.txt @@ -1,8 +1,8 @@ .. Generated by gen_format_overview_classes.py - ===================== ====================================================== - **Converter** :class:`MDAnalysis.coordinates.ParmEd.ParmEdConverter` - **Coordinate reader** :class:`MDAnalysis.coordinates.ParmEd.ParmEdReader` - **Topology parser** :class:`MDAnalysis.topology.ParmEdParser.ParmEdParser` - ===================== ====================================================== \ No newline at end of file +===================== ====================================================== +**Converter** :class:`MDAnalysis.coordinates.ParmEd.ParmEdConverter` +**Coordinate reader** :class:`MDAnalysis.coordinates.ParmEd.ParmEdReader` +**Topology parser** :class:`MDAnalysis.topology.ParmEdParser.ParmEdParser` +===================== ====================================================== \ No newline at end of file diff --git a/doc/source/formats/reference/classes/PDB.txt b/doc/source/formats/reference/classes/PDB.txt index 83f9d4790..0ccab700f 100644 --- a/doc/source/formats/reference/classes/PDB.txt +++ b/doc/source/formats/reference/classes/PDB.txt @@ -1,8 +1,8 @@ .. Generated by gen_format_overview_classes.py - ===================== ================================================ - **Coordinate reader** :class:`MDAnalysis.coordinates.PDB.PDBReader` - **Coordinate writer** :class:`MDAnalysis.coordinates.PDB.PDBWriter` - **Topology parser** :class:`MDAnalysis.topology.PDBParser.PDBParser` - ===================== ================================================ \ No newline at end of file +===================== ================================================ +**Coordinate reader** :class:`MDAnalysis.coordinates.PDB.PDBReader` +**Coordinate writer** :class:`MDAnalysis.coordinates.PDB.PDBWriter` +**Topology parser** :class:`MDAnalysis.topology.PDBParser.PDBParser` +===================== ================================================ \ No newline at end of file diff --git a/doc/source/formats/reference/classes/PDBQT.txt b/doc/source/formats/reference/classes/PDBQT.txt index a44fac7e5..c2fb27f54 100644 --- a/doc/source/formats/reference/classes/PDBQT.txt +++ b/doc/source/formats/reference/classes/PDBQT.txt @@ -1,8 +1,8 @@ .. Generated by gen_format_overview_classes.py - ===================== ==================================================== - **Coordinate reader** :class:`MDAnalysis.coordinates.PDBQT.PDBQTReader` - **Coordinate writer** :class:`MDAnalysis.coordinates.PDBQT.PDBQTWriter` - **Topology parser** :class:`MDAnalysis.topology.PDBQTParser.PDBQTParser` - ===================== ==================================================== \ No newline at end of file +===================== ==================================================== +**Coordinate reader** :class:`MDAnalysis.coordinates.PDBQT.PDBQTReader` +**Coordinate writer** :class:`MDAnalysis.coordinates.PDBQT.PDBQTWriter` +**Topology parser** :class:`MDAnalysis.topology.PDBQTParser.PDBQTParser` +===================== ==================================================== \ No newline at end of file diff --git a/doc/source/formats/reference/classes/PQR.txt b/doc/source/formats/reference/classes/PQR.txt index 2bc1dc60e..ad898aa60 100644 --- a/doc/source/formats/reference/classes/PQR.txt +++ b/doc/source/formats/reference/classes/PQR.txt @@ -1,8 +1,8 @@ .. Generated by gen_format_overview_classes.py - ===================== ================================================ - **Coordinate reader** :class:`MDAnalysis.coordinates.PQR.PQRReader` - **Coordinate writer** :class:`MDAnalysis.coordinates.PQR.PQRWriter` - **Topology parser** :class:`MDAnalysis.topology.PQRParser.PQRParser` - ===================== ================================================ \ No newline at end of file +===================== ================================================ +**Coordinate reader** :class:`MDAnalysis.coordinates.PQR.PQRReader` +**Coordinate writer** :class:`MDAnalysis.coordinates.PQR.PQRWriter` +**Topology parser** :class:`MDAnalysis.topology.PQRParser.PQRParser` +===================== ================================================ \ No newline at end of file diff --git a/doc/source/formats/reference/classes/PSF.txt b/doc/source/formats/reference/classes/PSF.txt index b0f1f438c..302b167a7 100644 --- a/doc/source/formats/reference/classes/PSF.txt +++ b/doc/source/formats/reference/classes/PSF.txt @@ -1,6 +1,6 @@ .. Generated by gen_format_overview_classes.py - =================== ================================================ - **Topology parser** :class:`MDAnalysis.topology.PSFParser.PSFParser` - =================== ================================================ \ No newline at end of file +=================== ================================================ +**Topology parser** :class:`MDAnalysis.topology.PSFParser.PSFParser` +=================== ================================================ \ No newline at end of file diff --git a/doc/source/formats/reference/classes/TOP.txt b/doc/source/formats/reference/classes/TOP.txt index 1389beab1..f5a398233 100644 --- a/doc/source/formats/reference/classes/TOP.txt +++ b/doc/source/formats/reference/classes/TOP.txt @@ -1,6 +1,6 @@ .. Generated by gen_format_overview_classes.py - =================== ================================================ - **Topology parser** :class:`MDAnalysis.topology.TOPParser.TOPParser` - =================== ================================================ \ No newline at end of file +=================== ================================================ +**Topology parser** :class:`MDAnalysis.topology.TOPParser.TOPParser` +=================== ================================================ \ No newline at end of file diff --git a/doc/source/formats/reference/classes/TPR.txt b/doc/source/formats/reference/classes/TPR.txt index 30ae011af..446fb130f 100644 --- a/doc/source/formats/reference/classes/TPR.txt +++ b/doc/source/formats/reference/classes/TPR.txt @@ -1,6 +1,6 @@ .. Generated by gen_format_overview_classes.py - =================== ================================================ - **Topology parser** :class:`MDAnalysis.topology.TPRParser.TPRParser` - =================== ================================================ \ No newline at end of file +=================== ================================================ +**Topology parser** :class:`MDAnalysis.topology.TPRParser.TPRParser` +=================== ================================================ \ No newline at end of file diff --git a/doc/source/formats/reference/classes/TRJ.txt b/doc/source/formats/reference/classes/TRJ.txt index 28681453f..367d6bc2c 100644 --- a/doc/source/formats/reference/classes/TRJ.txt +++ b/doc/source/formats/reference/classes/TRJ.txt @@ -1,6 +1,6 @@ .. Generated by gen_format_overview_classes.py - ===================== ============================================= - **Coordinate reader** :class:`MDAnalysis.coordinates.TRJ.TRJReader` - ===================== ============================================= \ No newline at end of file +===================== ============================================= +**Coordinate reader** :class:`MDAnalysis.coordinates.TRJ.TRJReader` +===================== ============================================= \ No newline at end of file diff --git a/doc/source/formats/reference/classes/TRR.txt b/doc/source/formats/reference/classes/TRR.txt index 8cd1f3b42..8eaa20f0d 100644 --- a/doc/source/formats/reference/classes/TRR.txt +++ b/doc/source/formats/reference/classes/TRR.txt @@ -1,7 +1,7 @@ .. Generated by gen_format_overview_classes.py - ===================== ============================================= - **Coordinate reader** :class:`MDAnalysis.coordinates.TRR.TRRReader` - **Coordinate writer** :class:`MDAnalysis.coordinates.TRR.TRRWriter` - ===================== ============================================= \ No newline at end of file +===================== ============================================= +**Coordinate reader** :class:`MDAnalysis.coordinates.TRR.TRRReader` +**Coordinate writer** :class:`MDAnalysis.coordinates.TRR.TRRWriter` +===================== ============================================= \ No newline at end of file diff --git a/doc/source/formats/reference/classes/TRZ.txt b/doc/source/formats/reference/classes/TRZ.txt index 6d57845f5..90a5ba29f 100644 --- a/doc/source/formats/reference/classes/TRZ.txt +++ b/doc/source/formats/reference/classes/TRZ.txt @@ -1,7 +1,7 @@ .. Generated by gen_format_overview_classes.py - ===================== ============================================= - **Coordinate reader** :class:`MDAnalysis.coordinates.TRZ.TRZReader` - **Coordinate writer** :class:`MDAnalysis.coordinates.TRZ.TRZWriter` - ===================== ============================================= \ No newline at end of file +===================== ============================================= +**Coordinate reader** :class:`MDAnalysis.coordinates.TRZ.TRZReader` +**Coordinate writer** :class:`MDAnalysis.coordinates.TRZ.TRZWriter` +===================== ============================================= \ No newline at end of file diff --git a/doc/source/formats/reference/classes/TXYZ.txt b/doc/source/formats/reference/classes/TXYZ.txt index b4d458724..7d1fa2c64 100644 --- a/doc/source/formats/reference/classes/TXYZ.txt +++ b/doc/source/formats/reference/classes/TXYZ.txt @@ -1,7 +1,7 @@ .. Generated by gen_format_overview_classes.py - ===================== ================================================== - **Coordinate reader** :class:`MDAnalysis.coordinates.TXYZ.TXYZReader` - **Topology parser** :class:`MDAnalysis.topology.TXYZParser.TXYZParser` - ===================== ================================================== \ No newline at end of file +===================== ================================================== +**Coordinate reader** :class:`MDAnalysis.coordinates.TXYZ.TXYZReader` +**Topology parser** :class:`MDAnalysis.topology.TXYZParser.TXYZParser` +===================== ================================================== \ No newline at end of file diff --git a/doc/source/formats/reference/classes/XML.txt b/doc/source/formats/reference/classes/XML.txt index 03de05b2d..013d97f1f 100644 --- a/doc/source/formats/reference/classes/XML.txt +++ b/doc/source/formats/reference/classes/XML.txt @@ -1,6 +1,6 @@ .. Generated by gen_format_overview_classes.py - =================== ========================================================== - **Topology parser** :class:`MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser` - =================== ========================================================== \ No newline at end of file +=================== ========================================================== +**Topology parser** :class:`MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser` +=================== ========================================================== \ No newline at end of file diff --git a/doc/source/formats/reference/classes/XPDB.txt b/doc/source/formats/reference/classes/XPDB.txt index 003cd6d9d..397457b65 100644 --- a/doc/source/formats/reference/classes/XPDB.txt +++ b/doc/source/formats/reference/classes/XPDB.txt @@ -1,7 +1,7 @@ .. Generated by gen_format_overview_classes.py - ===================== ================================================================ - **Coordinate reader** :class:`MDAnalysis.coordinates.PDB.ExtendedPDBReader` - **Topology parser** :class:`MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser` - ===================== ================================================================ \ No newline at end of file +===================== ================================================================ +**Coordinate reader** :class:`MDAnalysis.coordinates.PDB.ExtendedPDBReader` +**Topology parser** :class:`MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser` +===================== ================================================================ \ No newline at end of file diff --git a/doc/source/formats/reference/classes/XTC.txt b/doc/source/formats/reference/classes/XTC.txt index ea898c8ba..5844f5d2e 100644 --- a/doc/source/formats/reference/classes/XTC.txt +++ b/doc/source/formats/reference/classes/XTC.txt @@ -1,7 +1,7 @@ .. Generated by gen_format_overview_classes.py - ===================== ============================================= - **Coordinate reader** :class:`MDAnalysis.coordinates.XTC.XTCReader` - **Coordinate writer** :class:`MDAnalysis.coordinates.XTC.XTCWriter` - ===================== ============================================= \ No newline at end of file +===================== ============================================= +**Coordinate reader** :class:`MDAnalysis.coordinates.XTC.XTCReader` +**Coordinate writer** :class:`MDAnalysis.coordinates.XTC.XTCWriter` +===================== ============================================= \ No newline at end of file diff --git a/doc/source/formats/reference/classes/XYZ.txt b/doc/source/formats/reference/classes/XYZ.txt index b8cd1e8af..3b5ac8014 100644 --- a/doc/source/formats/reference/classes/XYZ.txt +++ b/doc/source/formats/reference/classes/XYZ.txt @@ -1,8 +1,8 @@ .. Generated by gen_format_overview_classes.py - ===================== ================================================ - **Coordinate reader** :class:`MDAnalysis.coordinates.XYZ.XYZReader` - **Coordinate writer** :class:`MDAnalysis.coordinates.XYZ.XYZWriter` - **Topology parser** :class:`MDAnalysis.topology.XYZParser.XYZParser` - ===================== ================================================ \ No newline at end of file +===================== ================================================ +**Coordinate reader** :class:`MDAnalysis.coordinates.XYZ.XYZReader` +**Coordinate writer** :class:`MDAnalysis.coordinates.XYZ.XYZWriter` +**Topology parser** :class:`MDAnalysis.topology.XYZParser.XYZParser` +===================== ================================================ \ No newline at end of file diff --git a/doc/source/formats/reference/coor.rst b/doc/source/formats/reference/coor.rst index d64f696ab..2b6644b77 100644 --- a/doc/source/formats/reference/coor.rst +++ b/doc/source/formats/reference/coor.rst @@ -1,8 +1,10 @@ .. -*- coding: utf-8 -*- .. _COOR-format: -======================================= -COOR (NAMD binary restart files) -======================================= +========================================= +COOR, NAMBDIN (NAMD binary restart files) +========================================= -.. include:: classes/COOR.txt \ No newline at end of file +.. include:: classes/COOR.txt + +You can read or write coordinates from the `NAMD double-precision binary format `_ . \ No newline at end of file diff --git a/doc/source/formats/reference/in.rst b/doc/source/formats/reference/in.rst index 60513364d..91414b9ee 100644 --- a/doc/source/formats/reference/in.rst +++ b/doc/source/formats/reference/in.rst @@ -2,7 +2,9 @@ .. _IN-format: ======================================= -IN (FHI-aims input files) +IN, FHIAIMS (FHI-aims input files) ======================================= -.. include:: classes/IN.txt \ No newline at end of file +.. include:: classes/IN.txt + +FHI-aims_ input files are similar to :ref:`xyz <_XYZ-format>` in format. The specification is publically available at `online `_. \ No newline at end of file diff --git a/doc/source/formats/reference/pdbqt.rst b/doc/source/formats/reference/pdbqt.rst index 53a368177..6f73ee310 100644 --- a/doc/source/formats/reference/pdbqt.rst +++ b/doc/source/formats/reference/pdbqt.rst @@ -98,9 +98,7 @@ Records read: 79 - 80 LString(2) atomType AutoDOCK atom type *t*. ============= ============ =========== ============================================= -We ignore torsion notation and just pull the partial charge and atom type columns: - -.. code-block:: +We ignore torsion notation and just pull the partial charge and atom type columns:: COMPND NSC7810 REMARK 3 active torsions: diff --git a/doc/source/formats/reference/trj.rst b/doc/source/formats/reference/trj.rst index d07599abc..58e036f43 100644 --- a/doc/source/formats/reference/trj.rst +++ b/doc/source/formats/reference/trj.rst @@ -31,12 +31,12 @@ Units are assumed to be the following default AMBER units: .. rubric:: Limitations -* Periodic boxes are only stored as box lengths A, B, C in an AMBER -trajectory; the reader always assumes that these are orthorhombic -boxes. -* The trajectory does not contain time information so we simply set -the time step to 1 ps :ref:`(or the user could provide it with the dt argument) ` -* Trajectories with fewer than 4 atoms probably fail to be read (BUG). -* If the trajectory contains exactly *one* atom then it is always -assumed to be non-periodic (for technical reasons). -* Velocities are currently *not supported* as ASCII trajectories. + * Periodic boxes are only stored as box lengths A, B, C in an AMBER + trajectory; the reader always assumes that these are orthorhombic + boxes. + * The trajectory does not contain time information so we simply set + the time step to 1 ps :ref:`(or the user could provide it with the dt argument) ` + * Trajectories with fewer than 4 atoms probably fail to be read (BUG). + * If the trajectory contains exactly *one* atom then it is always + assumed to be non-periodic (for technical reasons). + * Velocities are currently *not supported* as ASCII trajectories. diff --git a/doc/source/generated/.gitignore b/doc/source/generated/.gitignore index a3e637382..e69de29bb 100644 --- a/doc/source/generated/.gitignore +++ b/doc/source/generated/.gitignore @@ -1,4 +0,0 @@ -# Ignore everything here -*.* -!.gitignore -!*.txt diff --git a/doc/source/generated/selections/.gitignore b/doc/source/generated/selections/.gitignore index eeb90c660..e69de29bb 100644 --- a/doc/source/generated/selections/.gitignore +++ b/doc/source/generated/selections/.gitignore @@ -1,3 +0,0 @@ -# Ignore everything here -* -!.gitignore diff --git a/doc/source/generated/selections/base.txt b/doc/source/generated/selections/base.txt new file mode 100644 index 000000000..c60c3bcb0 --- /dev/null +++ b/doc/source/generated/selections/base.txt @@ -0,0 +1,7 @@ +.. + Generated by gen_standard_selections.py + +== == == == == == == === +N9 N7 C8 C5 C4 N3 C2 N1 +C6 O6 N2 N6 O2 N4 O4 C5M +== == == == == == == === \ No newline at end of file diff --git a/doc/source/generated/selections/nucleic.txt b/doc/source/generated/selections/nucleic.txt new file mode 100644 index 000000000..71fc395d3 --- /dev/null +++ b/doc/source/generated/selections/nucleic.txt @@ -0,0 +1,10 @@ +.. + Generated by gen_standard_selections.py + +=== === === === === === === === +ADE URA CYT GUA THY DA DC DG +DT RA RU RG RC A T U +C G DA5 DC5 DG5 DT5 DA3 DC3 +DG3 DT3 RA5 RU5 RG5 RC5 RA3 RU3 +RG3 RC3 +=== === === === === === === === \ No newline at end of file diff --git a/doc/source/generated/selections/nucleic_backbone.txt b/doc/source/generated/selections/nucleic_backbone.txt new file mode 100644 index 000000000..46ff5b483 --- /dev/null +++ b/doc/source/generated/selections/nucleic_backbone.txt @@ -0,0 +1,6 @@ +.. + Generated by gen_standard_selections.py + += === === === === +P C5' C3' O3' O5' += === === === === \ No newline at end of file diff --git a/doc/source/generated/selections/nucleic_sugar.txt b/doc/source/generated/selections/nucleic_sugar.txt new file mode 100644 index 000000000..4f636b81d --- /dev/null +++ b/doc/source/generated/selections/nucleic_sugar.txt @@ -0,0 +1,6 @@ +.. + Generated by gen_standard_selections.py + +=== === === === === +C1' C2' C3' C4' O4' +=== === === === === \ No newline at end of file diff --git a/doc/source/generated/selections/protein.txt b/doc/source/generated/selections/protein.txt new file mode 100644 index 000000000..4306e28e8 --- /dev/null +++ b/doc/source/generated/selections/protein.txt @@ -0,0 +1,18 @@ +.. + Generated by gen_standard_selections.py + +==== ==== ==== ==== ==== ==== ==== ==== +ACE ALA ALAD ARG ARGN ASF ASH ASN +ASN1 ASP ASPH CALA CARG CASF CASN CASP +CCYS CCYX CGLN CGLU CGLY CHID CHIE CHIP +CILE CLEU CLYS CME CMET CPHE CPRO CSER +CTHR CTRP CTYR CVAL CYM CYS CYS1 CYS2 +CYSH CYX DAB GLH GLN GLU GLUH GLY +HID HIE HIP HIS HIS1 HIS2 HISA HISB +HISD HISE HISH HSD HSE HSP HYP ILE +LEU LYN LYS LYSH MET MSE NALA NARG +NASN NASP NCYS NCYX NGLN NGLU NGLY NHID +NHIE NHIP NILE NLEU NLYS NME NMET NPHE +NPRO NSER NTHR NTRP NTYR NVAL ORN PGLU +PHE PRO QLN SER THR TRP TYR VAL +==== ==== ==== ==== ==== ==== ==== ==== \ No newline at end of file diff --git a/doc/source/generated/selections/protein_backbone.txt b/doc/source/generated/selections/protein_backbone.txt new file mode 100644 index 000000000..b6dfe5524 --- /dev/null +++ b/doc/source/generated/selections/protein_backbone.txt @@ -0,0 +1,6 @@ +.. + Generated by gen_standard_selections.py + += == = = +N CA C O += == = = \ No newline at end of file diff --git a/doc/source/generated/topology/.gitignore b/doc/source/generated/topology/.gitignore index eeb90c660..e69de29bb 100644 --- a/doc/source/generated/topology/.gitignore +++ b/doc/source/generated/topology/.gitignore @@ -1,3 +0,0 @@ -# Ignore everything here -* -!.gitignore diff --git a/doc/source/generated/topology/connectivityattrs.txt b/doc/source/generated/topology/connectivityattrs.txt new file mode 100644 index 000000000..bd386b74e --- /dev/null +++ b/doc/source/generated/topology/connectivityattrs.txt @@ -0,0 +1,11 @@ +.. + Generated by gen_topologyparser_attrs.py + +========= =========== ============================================================================================================================================================================================================================================================================================================================================================================ +Atom AtomGroup Supported formats +========= =========== ============================================================================================================================================================================================================================================================================================================================================================================ +angles angles :ref:`DATA `, :ref:`GSD `, :ref:`PARMED `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`XML ` +bonds bonds :ref:`DATA `, :ref:`DMS `, :ref:`GSD `, :ref:`MMTF `, :ref:`MOL2 `, :ref:`PARMED `, :ref:`PDB, ENT `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`TXYZ, ARC `, :ref:`XML `, :ref:`XPDB ` +dihedrals dihedrals :ref:`DATA `, :ref:`GSD `, :ref:`PARMED `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`XML ` +impropers impropers :ref:`DATA `, :ref:`GSD `, :ref:`PARMED `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`XML ` +========= =========== ============================================================================================================================================================================================================================================================================================================================================================================ \ No newline at end of file diff --git a/doc/source/generated/topology/defaults.txt b/doc/source/generated/topology/defaults.txt new file mode 100644 index 000000000..2bce7d35c --- /dev/null +++ b/doc/source/generated/topology/defaults.txt @@ -0,0 +1,45 @@ +.. + Generated by gen_topologyattr_defaults.py + +============= ============= ======================================== ======= ======================= +Atom AtomGroup default level type +============= ============= ======================================== ======= ======================= +altLocs altLoc '' atom +angles angles No default values atom +atomiccharges atomiccharge No default values atom +atomnums atomnum No default values atom +bfactors bfactor 0.0 atom +bonds bonds No default values atom +chainIDs chainID '' atom +chargegroups chargegroup No default values atom +charges charge 0.0 atom +cmaps cmaps No default values atom +dihedrals dihedrals No default values atom +elements element '' atom +epsilon14s epsilon14 0.0 atom +epsilons epsilon 0.0 atom +gbscreens gbscreen 0.0 atom +icodes icode '' residue +ids id continuous sequence from 1 to n_atoms atom +impropers impropers No default values atom +masses mass 0.0 atom +models model No default values segment +molnums molnum No default values residue +moltypes moltype No default values residue +names name '' atom +nbindices nbindex 0 atom +occupancies occupancy 0.0 atom +radii radius 0.0 atom +record_types record_type 'ATOM' atom +resids resid continuous sequence from 1 to n_residues residue +resnames resname '' residue +resnums resnum continuous sequence from 1 to n_residues residue +rmin14s rmin14 0.0 atom +rmins rmin 0.0 atom +segids segid '' segment +solventradii solventradius 0.0 atom +tempfactors tempfactor 0.0 atom +type_indices type_index No default values atom +types type '' atom +ureybradleys ureybradleys No default values atom +============= ============= ======================================== ======= ======================= \ No newline at end of file diff --git a/doc/source/generated/topology/groupmethods.txt b/doc/source/generated/topology/groupmethods.txt new file mode 100644 index 000000000..605da4236 --- /dev/null +++ b/doc/source/generated/topology/groupmethods.txt @@ -0,0 +1,16 @@ +.. + Generated by gen_topology_groupmethods.py + +================================================================== ====================================================================== ========== +Method Description Requires +================================================================== ====================================================================== ========== +:meth:`~MDAnalysis.core.topologyattrs.Charges.total_charge` Total charge of (compounds of) the group charges +:meth:`~MDAnalysis.core.topologyattrs.Masses.align_principal_axis` Align principal axis with index `axis` with `vector` masses +:meth:`~MDAnalysis.core.topologyattrs.Masses.asphericity` Asphericity masses +:meth:`~MDAnalysis.core.topologyattrs.Masses.center_of_mass` Center of mass of (compounds of) the group masses +:meth:`~MDAnalysis.core.topologyattrs.Masses.moment_of_inertia` Tensor moment of inertia relative to center of mass as 3x3 numpy array masses +:meth:`~MDAnalysis.core.topologyattrs.Masses.principal_axes` Calculate the principal axes from the moment of inertia masses +:meth:`~MDAnalysis.core.topologyattrs.Masses.radius_of_gyration` Radius of gyration masses +:meth:`~MDAnalysis.core.topologyattrs.Masses.shape_parameter` Shape parameter masses +:meth:`~MDAnalysis.core.topologyattrs.Masses.total_mass` Total mass of (compounds of) the group masses +================================================================== ====================================================================== ========== \ No newline at end of file diff --git a/doc/source/generated/topology/topologyattrs.txt b/doc/source/generated/topology/topologyattrs.txt new file mode 100644 index 000000000..a9cd12a20 --- /dev/null +++ b/doc/source/generated/topology/topologyattrs.txt @@ -0,0 +1,39 @@ +.. + Generated by gen_topologyparser_attrs.py + +============= ============= ================================== ================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== +Atom AtomGroup Description Supported formats +============= ============= ================================== ================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== +altLoc altLocs Alternate location :ref:`MMTF `, :ref:`PARMED `, :ref:`PDB, ENT `, :ref:`PDBQT `, :ref:`XPDB ` +angles angles :ref:`DATA `, :ref:`GSD `, :ref:`PARMED `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`XML ` +atomiccharge atomiccharges Atomic number :ref:`GMS ` +atomnum atomnums ? :ref:`DMS ` +bfactor bfactors alias of tempfactor :ref:`MMTF ` +bonds bonds :ref:`DATA `, :ref:`DMS `, :ref:`GSD `, :ref:`MMTF `, :ref:`MOL2 `, :ref:`PARMED `, :ref:`PDB, ENT `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`TXYZ, ARC `, :ref:`XML `, :ref:`XPDB ` +chainID chainIDs chain ID :ref:`DMS `, :ref:`PARMED `, :ref:`PDB, ENT `, :ref:`XPDB ` +charge charges partial atomic charge :ref:`DATA `, :ref:`DMS `, :ref:`GSD `, :ref:`MMTF `, :ref:`MOL2 `, :ref:`PARMED `, :ref:`PDBQT `, :ref:`PQR `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`XML ` +chargegroup chargegroups +cmaps cmaps :ref:`PARMED ` +dihedrals dihedrals :ref:`DATA `, :ref:`GSD `, :ref:`PARMED `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`XML ` +element elements atom element :ref:`IN, FHIAIMS `, :ref:`PARMED `, :ref:`PDB, ENT `, :ref:`XYZ ` +epsilon epsilons :ref:`PARMED ` +epsilon14 epsilon14s :ref:`PARMED ` +gbscreen gbscreens :ref:`PARMED ` +icode icodes atom insertion code :ref:`MMTF `, :ref:`PDB, ENT `, :ref:`PDBQT `, :ref:`PQR `, :ref:`XPDB ` +impropers impropers :ref:`DATA `, :ref:`GSD `, :ref:`PARMED `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`XML ` +model models model number (from 0) :ref:`MMTF ` +molnum molnums [molecules] number (from 0) :ref:`TPR ` +moltype moltypes [moleculetype] name :ref:`TPR ` +name names atom names :ref:`CONFIG `, :ref:`CRD `, :ref:`DMS `, :ref:`GMS `, :ref:`GRO `, :ref:`GSD `, :ref:`HISTORY `, :ref:`IN, FHIAIMS `, :ref:`MMTF `, :ref:`MOL2 `, :ref:`PARMED `, :ref:`PDB, ENT `, :ref:`PDBQT `, :ref:`PQR `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`TXYZ, ARC `, :ref:`XPDB `, :ref:`XYZ ` +nbindex nbindices :ref:`PARMED ` +occupancy occupancies atom occupancy :ref:`MMTF `, :ref:`PARMED `, :ref:`PDB, ENT `, :ref:`PDBQT `, :ref:`XPDB ` +radius radii atomic radius :ref:`GSD `, :ref:`PQR `, :ref:`XML ` +record_type record_types ATOM / HETATM :ref:`PDB, ENT `, :ref:`PDBQT `, :ref:`PQR `, :ref:`XPDB ` +resname resnames residue name (except GSD has ints) :ref:`CRD `, :ref:`DMS `, :ref:`GRO `, :ref:`GSD `, :ref:`MMTF `, :ref:`MOL2 `, :ref:`PARMED `, :ref:`PDB, ENT `, :ref:`PDBQT `, :ref:`PQR `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`XPDB ` +rmin rmins :ref:`PARMED ` +rmin14 rmin14s :ref:`PARMED ` +solventradius solventradii :ref:`PARMED ` +tempfactor tempfactors B-factor :ref:`CRD `, :ref:`PARMED `, :ref:`PDB, ENT `, :ref:`PDBQT `, :ref:`XPDB ` +type_index type_indices amber atom type number :ref:`TOP, PRMTOP, PARM7 ` +ureybradleys ureybradleys :ref:`PARMED ` +============= ============= ================================== ================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== \ No newline at end of file diff --git a/doc/source/scripts/base.py b/doc/source/scripts/base.py index 170a8f3bd..0375872c9 100644 --- a/doc/source/scripts/base.py +++ b/doc/source/scripts/base.py @@ -76,7 +76,9 @@ def write_table(self): tabled = tabulate.tabulate(self.lines, headers=self.headings, tablefmt='rst') - f.write(textwrap.indent(tabled, ' ')) + if self.include_table: + tabled = textwrap.indent(tabled, ' ') + f.write(tabled) print('Wrote ', self.filename) # ==== HELPER FUNCTIONS ==== # From 01564804807c6e84005846dbfd95135b71e010db Mon Sep 17 00:00:00 2001 From: Lily Wang Date: Fri, 19 Jun 2020 13:04:46 +1000 Subject: [PATCH 12/18] add fhiaims link --- doc/source/formats/reference/in.rst | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/doc/source/formats/reference/in.rst b/doc/source/formats/reference/in.rst index 91414b9ee..5b5d853fe 100644 --- a/doc/source/formats/reference/in.rst +++ b/doc/source/formats/reference/in.rst @@ -7,4 +7,6 @@ IN, FHIAIMS (FHI-aims input files) .. include:: classes/IN.txt -FHI-aims_ input files are similar to :ref:`xyz <_XYZ-format>` in format. The specification is publically available at `online `_. \ No newline at end of file +FHI-aims_ input files are similar to :ref:`xyz <_XYZ-format>` in format. The specification is publically available at `online `_. + +.._FHI-aims: https://aimsclub.fhi-berlin.mpg.de/ \ No newline at end of file From d78c4b1ede3661c6c3c3c0bfbdac6fe93af63cfd Mon Sep 17 00:00:00 2001 From: Lily Wang Date: Fri, 19 Jun 2020 13:14:45 +1000 Subject: [PATCH 13/18] less shouty --- doc/source/formats/reference/chemfiles.rst | 2 +- doc/source/formats/reference/in.rst | 4 ++-- doc/source/formats/reference/parmed.rst | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/doc/source/formats/reference/chemfiles.rst b/doc/source/formats/reference/chemfiles.rst index 9e1e07800..c9d15c1ac 100644 --- a/doc/source/formats/reference/chemfiles.rst +++ b/doc/source/formats/reference/chemfiles.rst @@ -2,7 +2,7 @@ .. _CHEMFILES-format: ======================================== -CHEMFILES (chemfiles Trajectory or file) +chemfiles (chemfiles Trajectory or file) ======================================== .. include:: classes/CHEMFILES.txt diff --git a/doc/source/formats/reference/in.rst b/doc/source/formats/reference/in.rst index 5b5d853fe..b93034971 100644 --- a/doc/source/formats/reference/in.rst +++ b/doc/source/formats/reference/in.rst @@ -7,6 +7,6 @@ IN, FHIAIMS (FHI-aims input files) .. include:: classes/IN.txt -FHI-aims_ input files are similar to :ref:`xyz <_XYZ-format>` in format. The specification is publically available at `online `_. +`FHI-aims`_ input files are similar to :ref:`xyz <_XYZ-format>` in format. The specification is publically available at `online `_. -.._FHI-aims: https://aimsclub.fhi-berlin.mpg.de/ \ No newline at end of file +.._`FHI-aims`: https://aimsclub.fhi-berlin.mpg.de/ \ No newline at end of file diff --git a/doc/source/formats/reference/parmed.rst b/doc/source/formats/reference/parmed.rst index c8955f9d6..d995da42e 100644 --- a/doc/source/formats/reference/parmed.rst +++ b/doc/source/formats/reference/parmed.rst @@ -2,7 +2,7 @@ .. _PARMED-format: ========================= -PARMED (ParmEd Structure) +ParmEd (ParmEd Structure) ========================= .. include:: classes/PARMED.txt From 6a6f73e3b0b4a200247ec80ca7411fdf839b8734 Mon Sep 17 00:00:00 2001 From: Lily Wang <31115101+lilyminium@users.noreply.github.com> Date: Sat, 20 Jun 2020 17:29:49 +1000 Subject: [PATCH 14/18] fix fhiaims grammar Co-authored-by: Marcello Sega --- doc/source/formats/reference/in.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/source/formats/reference/in.rst b/doc/source/formats/reference/in.rst index b93034971..71c008a72 100644 --- a/doc/source/formats/reference/in.rst +++ b/doc/source/formats/reference/in.rst @@ -7,6 +7,6 @@ IN, FHIAIMS (FHI-aims input files) .. include:: classes/IN.txt -`FHI-aims`_ input files are similar to :ref:`xyz <_XYZ-format>` in format. The specification is publically available at `online `_. +`FHI-aims`_ input files are similar to :ref:`xyz <_XYZ-format>` in format. The specification is `publicly available `_. -.._`FHI-aims`: https://aimsclub.fhi-berlin.mpg.de/ \ No newline at end of file +.._`FHI-aims`: https://aimsclub.fhi-berlin.mpg.de/ From b01d0819fdf9061c4bda1a15dc1955eaf7b5626f Mon Sep 17 00:00:00 2001 From: Lily Wang Date: Sat, 20 Jun 2020 18:05:50 +1000 Subject: [PATCH 15/18] small fixes --- doc/source/formats/coordinate_readers.txt | 34 ++++---- doc/source/formats/format_overview.txt | 96 +++++++++++------------ doc/source/formats/reference/in.rst | 2 +- doc/source/formats/topology_parsers.txt | 54 ++++++------- doc/source/scripts/core.py | 4 +- 5 files changed, 95 insertions(+), 95 deletions(-) diff --git a/doc/source/formats/coordinate_readers.txt b/doc/source/formats/coordinate_readers.txt index 030a5055e..30f302395 100644 --- a/doc/source/formats/coordinate_readers.txt +++ b/doc/source/formats/coordinate_readers.txt @@ -3,25 +3,25 @@ .. table:: Table of supported coordinate readers and the information read - ===================================== ========================================= ============ ======== - File type Description Velocities Forces - ===================================== ========================================= ============ ======== + ===================================== ==================================================================== ============ ======== + File type Description Velocities Forces + ===================================== ==================================================================== ============ ======== :ref:`ARC ` Tinker file - :ref:`CHEMFILES ` chemfiles object - :ref:`CONFIG ` DL_Poly CONFIG file ✓ + :ref:`CHEMFILES ` use readers from `chemfiles `_ library + :ref:`CONFIG ` DL_Poly CONFIG file ✓ :ref:`COOR ` NAMD binary restart file :ref:`CRD ` CHARMM CARD file :ref:`CRDBOX ` AMBER ASCII trajectories - :ref:`DATA ` LAMMPS data file ✓ + :ref:`DATA ` LAMMPS data file ✓ :ref:`DCD ` CHARMM, NAMD, or LAMMPS binary trajectory - :ref:`DMS ` DESRES Molecular Structure file ✓ + :ref:`DMS ` DESRES Molecular Structure file ✓ :ref:`ENT ` Standard PDB file - :ref:`FHIAIMS ` FHI-aims input file ✓ + :ref:`FHIAIMS ` FHI-aims input file ✓ :ref:`GMS ` GAMESS file - :ref:`GRO ` GROMACS structure file ✓ + :ref:`GRO ` GROMACS structure file ✓ :ref:`GSD ` HOOMD GSD file - :ref:`HISTORY ` DL_Poly HISTORY file ✓ - :ref:`IN ` FHI-aims input file ✓ + :ref:`HISTORY ` DL_Poly HISTORY file ✓ + :ref:`IN ` FHI-aims input file ✓ :ref:`INPCRD ` AMBER restart file :ref:`LAMMPS ` a LAMMPS DCD trajectory :ref:`LAMMPSDUMP ` LAMMPS ascii dump file @@ -29,18 +29,18 @@ :ref:`MMTF ` MMTF file :ref:`MOL2 ` Tripos MOL2 file :ref:`NAMDBIN ` NAMD binary restart file - :ref:`NC ` AMBER NETCDF format ✓ ✓ - :ref:`NCDF ` AMBER NETCDF format ✓ ✓ - :ref:`PARMED ` parmed Structure + :ref:`NC ` AMBER NETCDF format ✓ ✓ + :ref:`NCDF ` AMBER NETCDF format ✓ ✓ + :ref:`PARMED ` `ParmEd `_ Structure :ref:`PDB ` Standard PDB file :ref:`PDBQT ` PDBQT file :ref:`PQR ` PQR file :ref:`RESTRT ` AMBER restart file :ref:`TRJ ` AMBER ASCII trajectories - :ref:`TRR ` GROMACS TRR trajectory ✓ ✓ - :ref:`TRZ ` IBIsCO or YASP binary trajectory ✓ + :ref:`TRR ` GROMACS TRR trajectory ✓ ✓ + :ref:`TRZ ` IBIsCO or YASP binary trajectory ✓ :ref:`TXYZ ` Tinker file :ref:`XPDB ` Extended PDB file :ref:`XTC ` GROMACS compressed trajectory :ref:`XYZ ` XYZ file - ===================================== ========================================= ============ ======== \ No newline at end of file + ===================================== ==================================================================== ============ ======== \ No newline at end of file diff --git a/doc/source/formats/format_overview.txt b/doc/source/formats/format_overview.txt index 00cd534a7..d3dde1cbd 100644 --- a/doc/source/formats/format_overview.txt +++ b/doc/source/formats/format_overview.txt @@ -3,51 +3,51 @@ .. table:: Table of all supported formats in MDAnalysis - ===================================== ========================================= ========== ============= ====== ======= - File type Description Topology Coordinates Read Write - ===================================== ========================================= ========== ============= ====== ======= - :ref:`ARC ` Tinker file ✓ ✓ ✓ - :ref:`CHEMFILES ` chemfiles object ✓ ✓ ✓ - :ref:`CONFIG ` DL_Poly CONFIG file ✓ ✓ ✓ - :ref:`COOR ` NAMD binary restart file ✓ ✓ ✓ - :ref:`CRD ` CHARMM CARD file ✓ ✓ ✓ ✓ - :ref:`CRDBOX ` AMBER ASCII trajectories ✓ ✓ - :ref:`DATA ` LAMMPS data file ✓ ✓ ✓ ✓ - :ref:`DCD ` CHARMM, NAMD, or LAMMPS binary trajectory ✓ ✓ ✓ - :ref:`DMS ` DESRES Molecular Structure file ✓ ✓ ✓ - :ref:`ENT ` Standard PDB file ✓ ✓ ✓ ✓ - :ref:`FHIAIMS ` FHI-aims input file ✓ ✓ ✓ ✓ - :ref:`GMS ` GAMESS file ✓ ✓ ✓ - :ref:`GRO ` GROMACS structure file ✓ ✓ ✓ ✓ - :ref:`GSD ` HOOMD GSD file ✓ ✓ ✓ - :ref:`HISTORY ` DL_Poly HISTORY file ✓ ✓ ✓ - :ref:`IN ` FHI-aims input file ✓ ✓ ✓ ✓ - :ref:`INPCRD ` AMBER restart file ✓ ✓ - :ref:`ITP ` GROMACS portable topology file ✓ ✓ - :ref:`LAMMPS ` a LAMMPS DCD trajectory ✓ ✓ ✓ - :ref:`LAMMPSDUMP ` LAMMPS ascii dump file ✓ ✓ ✓ - :ref:`MDCRD ` AMBER ASCII trajectories ✓ ✓ - :ref:`MMTF ` MMTF file ✓ ✓ ✓ - :ref:`MOL2 ` Tripos MOL2 file ✓ ✓ ✓ ✓ - :ref:`NAMDBIN ` NAMD binary restart file ✓ ✓ ✓ - :ref:`NC ` AMBER NETCDF format ✓ ✓ - :ref:`NCDF ` AMBER NETCDF format ✓ ✓ ✓ - :ref:`PARM7 ` AMBER topology file ✓ ✓ - :ref:`PARMED ` parmed Structure ✓ ✓ ✓ ✓ - :ref:`PDB ` Standard PDB file ✓ ✓ ✓ ✓ - :ref:`PDBQT ` PDBQT file ✓ ✓ ✓ ✓ - :ref:`PQR ` PQR file ✓ ✓ ✓ ✓ - :ref:`PRMTOP ` AMBER topology file ✓ ✓ - :ref:`PSF ` CHARMM, NAMD, or XPLOR PSF file ✓ ✓ - :ref:`RESTRT ` AMBER restart file ✓ ✓ - :ref:`TOP ` AMBER topology file ✓ ✓ - :ref:`TPR ` GROMACS run topology file ✓ ✓ - :ref:`TRJ ` AMBER ASCII trajectories ✓ ✓ - :ref:`TRR ` GROMACS TRR trajectory ✓ ✓ ✓ - :ref:`TRZ ` IBIsCO or YASP binary trajectory ✓ ✓ ✓ - :ref:`TXYZ ` Tinker file ✓ ✓ ✓ - :ref:`XML ` HOOMD XML file ✓ ✓ - :ref:`XPDB ` Extended PDB file ✓ ✓ ✓ - :ref:`XTC ` GROMACS compressed trajectory ✓ ✓ ✓ - :ref:`XYZ ` XYZ file ✓ ✓ ✓ ✓ - ===================================== ========================================= ========== ============= ====== ======= \ No newline at end of file + ===================================== ==================================================================== ========== ============= ====== ======= + File type Description Topology Coordinates Read Write + ===================================== ==================================================================== ========== ============= ====== ======= + :ref:`ARC ` Tinker file ✓ ✓ ✓ + :ref:`CHEMFILES ` use readers from `chemfiles `_ library ✓ ✓ ✓ + :ref:`CONFIG ` DL_Poly CONFIG file ✓ ✓ ✓ + :ref:`COOR ` NAMD binary restart file ✓ ✓ ✓ + :ref:`CRD ` CHARMM CARD file ✓ ✓ ✓ ✓ + :ref:`CRDBOX ` AMBER ASCII trajectories ✓ ✓ + :ref:`DATA ` LAMMPS data file ✓ ✓ ✓ ✓ + :ref:`DCD ` CHARMM, NAMD, or LAMMPS binary trajectory ✓ ✓ ✓ + :ref:`DMS ` DESRES Molecular Structure file ✓ ✓ ✓ + :ref:`ENT ` Standard PDB file ✓ ✓ ✓ ✓ + :ref:`FHIAIMS ` FHI-aims input file ✓ ✓ ✓ ✓ + :ref:`GMS ` GAMESS file ✓ ✓ ✓ + :ref:`GRO ` GROMACS structure file ✓ ✓ ✓ ✓ + :ref:`GSD ` HOOMD GSD file ✓ ✓ ✓ + :ref:`HISTORY ` DL_Poly HISTORY file ✓ ✓ ✓ + :ref:`IN ` FHI-aims input file ✓ ✓ ✓ ✓ + :ref:`INPCRD ` AMBER restart file ✓ ✓ + :ref:`ITP ` GROMACS portable topology file ✓ ✓ + :ref:`LAMMPS ` a LAMMPS DCD trajectory ✓ ✓ ✓ + :ref:`LAMMPSDUMP ` LAMMPS ascii dump file ✓ ✓ ✓ + :ref:`MDCRD ` AMBER ASCII trajectories ✓ ✓ + :ref:`MMTF ` MMTF file ✓ ✓ ✓ + :ref:`MOL2 ` Tripos MOL2 file ✓ ✓ ✓ ✓ + :ref:`NAMDBIN ` NAMD binary restart file ✓ ✓ ✓ + :ref:`NC ` AMBER NETCDF format ✓ ✓ + :ref:`NCDF ` AMBER NETCDF format ✓ ✓ ✓ + :ref:`PARM7 ` AMBER topology file ✓ ✓ + :ref:`PARMED ` `ParmEd `_ Structure ✓ ✓ ✓ ✓ + :ref:`PDB ` Standard PDB file ✓ ✓ ✓ ✓ + :ref:`PDBQT ` PDBQT file ✓ ✓ ✓ ✓ + :ref:`PQR ` PQR file ✓ ✓ ✓ ✓ + :ref:`PRMTOP ` AMBER topology file ✓ ✓ + :ref:`PSF ` CHARMM, NAMD, or XPLOR PSF file ✓ ✓ + :ref:`RESTRT ` AMBER restart file ✓ ✓ + :ref:`TOP ` AMBER topology file ✓ ✓ + :ref:`TPR ` GROMACS run topology file ✓ ✓ + :ref:`TRJ ` AMBER ASCII trajectories ✓ ✓ + :ref:`TRR ` GROMACS TRR trajectory ✓ ✓ ✓ + :ref:`TRZ ` IBIsCO or YASP binary trajectory ✓ ✓ ✓ + :ref:`TXYZ ` Tinker file ✓ ✓ ✓ + :ref:`XML ` HOOMD XML file ✓ ✓ + :ref:`XPDB ` Extended PDB file ✓ ✓ ✓ + :ref:`XTC ` GROMACS compressed trajectory ✓ ✓ ✓ + :ref:`XYZ ` XYZ file ✓ ✓ ✓ ✓ + ===================================== ==================================================================== ========== ============= ====== ======= \ No newline at end of file diff --git a/doc/source/formats/reference/in.rst b/doc/source/formats/reference/in.rst index b93034971..03d863e65 100644 --- a/doc/source/formats/reference/in.rst +++ b/doc/source/formats/reference/in.rst @@ -9,4 +9,4 @@ IN, FHIAIMS (FHI-aims input files) `FHI-aims`_ input files are similar to :ref:`xyz <_XYZ-format>` in format. The specification is publically available at `online `_. -.._`FHI-aims`: https://aimsclub.fhi-berlin.mpg.de/ \ No newline at end of file +.. _`FHI-aims`: https://aimsclub.fhi-berlin.mpg.de/ \ No newline at end of file diff --git a/doc/source/formats/topology_parsers.txt b/doc/source/formats/topology_parsers.txt index deb18f3a7..207567d1f 100644 --- a/doc/source/formats/topology_parsers.txt +++ b/doc/source/formats/topology_parsers.txt @@ -3,30 +3,30 @@ .. table:: Table of supported topology parsers and the attributes read - ====================================== =============================== =================================================================================================================================================================================================================== ==================== - Format Description Attributes read Attributes guessed - ====================================== =============================== =================================================================================================================================================================================================================== ==================== - :ref:`CONFIG ` DL_Poly CONFIG file names masses, types - :ref:`CRD ` CHARMM CARD file names, resnames, tempfactors masses, types - :ref:`DATA ` LAMMPS data file angles, bonds, charges, dihedrals, impropers - :ref:`DMS ` DESRES Molecular Structure file atomnums, bonds, chainIDs, charges, names, resnames types - :ref:`GMS ` GAMESS file atomiccharges, names masses, types - :ref:`GRO ` GROMACS structure file names, resnames masses, types - :ref:`GSD ` HOOMD GSD file angles, bonds, charges, dihedrals, impropers, names, radii, resnames - :ref:`HISTORY ` DL_Poly HISTORY file names masses, types - :ref:`IN, FHIAIMS ` FHI-aims input file elements, names masses, types - :ref:`LAMMPSDUMP ` LAMMPS ascii dump file masses - :ref:`MMTF ` MMTF file altLocs, bfactors, bonds, charges, icodes, models, names, occupancies, resnames masses - :ref:`MOL2 ` Tripos MOL2 file bonds, charges, names, resnames masses - :ref:`PARMED ` parmed Structure altLocs, angles, bonds, chainIDs, charges, cmaps, dihedrals, elements, epsilon14s, epsilons, gbscreens, impropers, names, nbindices, occupancies, resnames, rmin14s, rmins, solventradii, tempfactors, ureybradleys - :ref:`PDB, ENT ` Standard PDB file altLocs, bonds, chainIDs, elements, icodes, names, occupancies, record_types, resnames, tempfactors masses, types - :ref:`PDBQT ` PDBQT file altLocs, charges, icodes, names, occupancies, record_types, resnames, tempfactors masses - :ref:`PQR ` PQR file charges, icodes, names, radii, record_types, resnames masses, types - :ref:`PSF ` CHARMM, NAMD, or XPLOR PSF file angles, bonds, charges, dihedrals, impropers, names, resnames - :ref:`TOP, PRMTOP, PARM7 ` AMBER topology file angles, bonds, charges, dihedrals, impropers, names, resnames, type_indices - :ref:`TPR ` GROMACS run topology file angles, bonds, charges, dihedrals, impropers, molnums, moltypes, names, resnames - :ref:`TXYZ, ARC ` Tinker file bonds, names masses - :ref:`XML ` HOOMD XML file angles, bonds, charges, dihedrals, impropers, radii - :ref:`XPDB ` Extended PDB file altLocs, bonds, chainIDs, icodes, names, occupancies, record_types, resnames, tempfactors masses, types - :ref:`XYZ ` XYZ file elements, names masses, types - ====================================== =============================== =================================================================================================================================================================================================================== ==================== \ No newline at end of file + ====================================== ==================================================================== =================================================================================================================================================================================================================== ==================== + Format Description Attributes read Attributes guessed + ====================================== ==================================================================== =================================================================================================================================================================================================================== ==================== + :ref:`CONFIG ` DL_Poly CONFIG file names masses, types + :ref:`CRD ` CHARMM CARD file names, resnames, tempfactors masses, types + :ref:`DATA ` LAMMPS data file angles, bonds, charges, dihedrals, impropers + :ref:`DMS ` DESRES Molecular Structure file atomnums, bonds, chainIDs, charges, names, resnames types + :ref:`GMS ` GAMESS file atomiccharges, names masses, types + :ref:`GRO ` GROMACS structure file names, resnames masses, types + :ref:`GSD ` HOOMD GSD file angles, bonds, charges, dihedrals, impropers, names, radii, resnames + :ref:`HISTORY ` DL_Poly HISTORY file names masses, types + :ref:`IN, FHIAIMS ` FHI-aims input file elements, names masses, types + :ref:`LAMMPSDUMP ` LAMMPS ascii dump file masses + :ref:`MMTF ` MMTF file altLocs, bfactors, bonds, charges, icodes, models, names, occupancies, resnames masses + :ref:`MOL2 ` Tripos MOL2 file bonds, charges, names, resnames masses + :ref:`PARMED ` `ParmEd `_ Structure altLocs, angles, bonds, chainIDs, charges, cmaps, dihedrals, elements, epsilon14s, epsilons, gbscreens, impropers, names, nbindices, occupancies, resnames, rmin14s, rmins, solventradii, tempfactors, ureybradleys + :ref:`PDB, ENT ` Standard PDB file altLocs, bonds, chainIDs, elements, icodes, names, occupancies, record_types, resnames, tempfactors masses, types + :ref:`PDBQT ` PDBQT file altLocs, charges, icodes, names, occupancies, record_types, resnames, tempfactors masses + :ref:`PQR ` PQR file charges, icodes, names, radii, record_types, resnames masses, types + :ref:`PSF ` CHARMM, NAMD, or XPLOR PSF file angles, bonds, charges, dihedrals, impropers, names, resnames + :ref:`TOP, PRMTOP, PARM7 ` AMBER topology file angles, bonds, charges, dihedrals, impropers, names, resnames, type_indices + :ref:`TPR ` GROMACS run topology file angles, bonds, charges, dihedrals, impropers, molnums, moltypes, names, resnames + :ref:`TXYZ, ARC ` Tinker file bonds, names masses + :ref:`XML ` HOOMD XML file angles, bonds, charges, dihedrals, impropers, radii + :ref:`XPDB ` Extended PDB file altLocs, bonds, chainIDs, icodes, names, occupancies, record_types, resnames, tempfactors masses, types + :ref:`XYZ ` XYZ file elements, names masses, types + ====================================== ==================================================================== =================================================================================================================================================================================================================== ==================== \ No newline at end of file diff --git a/doc/source/scripts/core.py b/doc/source/scripts/core.py index 639f2afc5..df1aec4a0 100644 --- a/doc/source/scripts/core.py +++ b/doc/source/scripts/core.py @@ -6,8 +6,7 @@ # ====== TOPOLOGY ====== # DESCRIPTIONS = { - 'CHEMFILES': 'chemfiles object', - 'PARMED': 'parmed Structure', + 'CHEMFILES': 'use readers from `chemfiles `_ library', 'CRD': 'CHARMM CARD file', 'CONFIG': 'DL_Poly CONFIG file', 'COOR': 'NAMD binary restart file', @@ -28,6 +27,7 @@ 'MMTF' : 'MMTF file', 'NCDF': 'AMBER NETCDF format', 'MOL2': 'Tripos MOL2 file', + 'PARMED': '`ParmEd `_ Structure', 'PDB': 'Standard PDB file', 'PDBQT' : 'PDBQT file', 'PQR' : 'PQR file', From 02c2fee4324ebe3e1e00cecaae32067d3021f0ac Mon Sep 17 00:00:00 2001 From: Lily Wang Date: Sun, 21 Jun 2020 00:16:46 +1000 Subject: [PATCH 16/18] add parmed and chemfiles intersphinx --- doc/source/conf.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/doc/source/conf.py b/doc/source/conf.py index b1113584b..2fbe39087 100644 --- a/doc/source/conf.py +++ b/doc/source/conf.py @@ -175,6 +175,8 @@ def sort_authors(filename): 'https://docs.scipy.org/doc/numpy/': None, 'https://www.mdanalysis.org/docs/': None, 'https://docs.pytest.org/en/latest/': None, + 'https://chemfiles.org/chemfiles.py/latest/': None, + 'http://parmed.github.io/ParmEd/html/': None, } # nbsphinx From 7d9f81d7f649a43dc3cb8150db91f7502920ab62 Mon Sep 17 00:00:00 2001 From: Lily Wang Date: Sun, 21 Jun 2020 11:15:04 +1000 Subject: [PATCH 17/18] add quotes to seaborn dep --- doc/source/contributing_code.rst | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/doc/source/contributing_code.rst b/doc/source/contributing_code.rst index 506341bb9..d53e07aed 100644 --- a/doc/source/contributing_code.rst +++ b/doc/source/contributing_code.rst @@ -203,17 +203,16 @@ Building MDAnalysis ------------------- Make sure that you have :ref:`cloned the repository ` -and activated your virtual environment. First we need to install dependencies: +and activated your virtual environment. First we need to install dependencies. If you're using conda, you'll need a mix of conda and pip installations: .. code-block:: bash - # if using conda conda install -c biobuilds -c conda-forge \ biopython chemfiles clustalw==2.1 codecov cython \ griddataformats gsd hypothesis joblib>=0.12 \ matplotlib mmtf-python mock netcdf4 networkx \ numpy>=1.17.3 psutil pytest scikit-learn scipy \ - seaborn>=0.7.0,<0.9 sphinx==1.8.5 tidynamics>=1.0.0 \ + "seaborn>=0.7.0,<0.9" sphinx==1.8.5 tidynamics>=1.0.0 \ tqdm>=4.43.0 # if using conda with python 3.7 or 3.8, also run @@ -225,13 +224,14 @@ and activated your virtual environment. First we need to install dependencies: # documentation dependencies pip install sphinx-sitemap sphinx_rtd_theme msmb_theme==1.2.0 +If you're using pip, it is a little simpler: + .. code-block:: bash - # if using pip and virtualenv pip install biopython chemfiles codecov cython \ griddataformats gsd hypothesis joblib>=0.12 matplotlib \ msmb_theme==1.2.0 netcdf4 networkx numpy>=1.17.3 \ - parmed psutil pytest scikit-learn scipy seaborn>=0.7.0,<0.9 \ + parmed psutil pytest scikit-learn scipy "seaborn>=0.7.0,<0.9" \ sphinx==1.8.5 sphinx_rtd_theme tidynamics>=1.0.0 \ tqdm>=4.43.0 From 11951639b799200f867053b3efbac23c9c91adf8 Mon Sep 17 00:00:00 2001 From: Lily Wang Date: Sun, 21 Jun 2020 11:23:40 +1000 Subject: [PATCH 18/18] quote all things and reminder about pip --- doc/source/contributing_code.rst | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/doc/source/contributing_code.rst b/doc/source/contributing_code.rst index d53e07aed..1520b41c8 100644 --- a/doc/source/contributing_code.rst +++ b/doc/source/contributing_code.rst @@ -209,11 +209,11 @@ and activated your virtual environment. First we need to install dependencies. I conda install -c biobuilds -c conda-forge \ biopython chemfiles clustalw==2.1 codecov cython \ - griddataformats gsd hypothesis joblib>=0.12 \ + griddataformats gsd hypothesis "joblib>=0.12" \ matplotlib mmtf-python mock netcdf4 networkx \ - numpy>=1.17.3 psutil pytest scikit-learn scipy \ - "seaborn>=0.7.0,<0.9" sphinx==1.8.5 tidynamics>=1.0.0 \ - tqdm>=4.43.0 + "numpy>=1.17.3" psutil pytest scikit-learn scipy \ + "seaborn>=0.7.0,<0.9" sphinx==1.8.5 "tidynamics>=1.0.0" \ + "tqdm>=4.43.0" # if using conda with python 3.7 or 3.8, also run conda install -c conda-forge parmed @@ -224,16 +224,16 @@ and activated your virtual environment. First we need to install dependencies. I # documentation dependencies pip install sphinx-sitemap sphinx_rtd_theme msmb_theme==1.2.0 -If you're using pip, it is a little simpler: +If you're using pip, it is a little simpler. However, some packages such as ``clustalw`` are not available via pip. .. code-block:: bash pip install biopython chemfiles codecov cython \ - griddataformats gsd hypothesis joblib>=0.12 matplotlib \ - msmb_theme==1.2.0 netcdf4 networkx numpy>=1.17.3 \ + griddataformats gsd hypothesis "joblib>=0.12" matplotlib \ + msmb_theme==1.2.0 netcdf4 networkx "numpy>=1.17.3" \ parmed psutil pytest scikit-learn scipy "seaborn>=0.7.0,<0.9" \ - sphinx==1.8.5 sphinx_rtd_theme tidynamics>=1.0.0 \ - tqdm>=4.43.0 + sphinx==1.8.5 sphinx_rtd_theme "tidynamics>=1.0.0" \ + "tqdm>=4.43.0" Ensure that you have a working C/C++ compiler (e.g. gcc or clang). You will also need Python ≥ 3.4. We will now install MDAnalysis.