diff --git a/.gitignore b/.gitignore index eb6d47f52..7e5518a41 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/.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 diff --git a/doc/source/conf.py b/doc/source/conf.py index 62f2d0c6b..2fbe39087 100644 --- a/doc/source/conf.py +++ b/doc/source/conf.py @@ -54,11 +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. +# 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') @@ -174,6 +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 diff --git a/doc/source/contributing_code.rst b/doc/source/contributing_code.rst index 7c63450d4..1520b41c8 100644 --- a/doc/source/contributing_code.rst +++ b/doc/source/contributing_code.rst @@ -203,17 +203,17 @@ 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 \ - 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 +221,19 @@ 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 + +If you're using pip, it is a little simpler. However, some packages such as ``clustalw`` are not available via pip. + .. 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..30f302395 100644 --- a/doc/source/formats/coordinate_readers.txt +++ b/doc/source/formats/coordinate_readers.txt @@ -1,35 +1,46 @@ -===================================== ========================================= ============ ======== -File type Description Velocities Forces -===================================== ========================================= ============ ======== -:ref:`ARC ` Tinker file -:ref:`CONFIG ` DL_Poly CONFIG 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:`GMS ` GAMESS file -:ref:`GRO ` GROMACS structure file ✓ -:ref:`GSD ` HOOMD GSD file -:ref:`HISTORY ` DL_Poly HISTORY 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:`NC ` AMBER NETCDF format ✓ ✓ -:ref:`NCDF ` AMBER NETCDF format ✓ ✓ -: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 -===================================== ========================================= ============ ======== +.. + 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 ` 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:`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/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 eed1ef3b7..d3dde1cbd 100644 --- a/doc/source/formats/format_overview.txt +++ b/doc/source/formats/format_overview.txt @@ -1,41 +1,53 @@ -===================================== ========================================= ========== ============= ====== ======= -File type Description Topology Coordinates Read Write -===================================== ========================================= ========== ============= ====== ======= -:ref:`ARC ` Tinker file ✓ ✓ ✓ -:ref:`CONFIG ` DL_Poly CONFIG 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:`GMS ` GAMESS file ✓ ✓ ✓ -:ref:`GRO ` GROMACS structure file ✓ ✓ ✓ ✓ -:ref:`GSD ` HOOMD GSD file ✓ ✓ ✓ -:ref:`HISTORY ` DL_Poly HISTORY 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:`NC ` AMBER NETCDF format ✓ ✓ -:ref:`NCDF ` AMBER NETCDF format ✓ ✓ ✓ -:ref:`PARM7 ` AMBER topology file ✓ ✓ -: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 ✓ ✓ ✓ ✓ -===================================== ========================================= ========== ============= ====== ======= +.. + 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 ` 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/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/chemfiles.rst b/doc/source/formats/reference/chemfiles.rst new file mode 100644 index 000000000..c9d15c1ac --- /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/.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/formats/reference/classes/CHEMFILES.txt b/doc/source/formats/reference/classes/CHEMFILES.txt new file mode 100644 index 000000000..7af3618ec --- /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 index 1b872455e..f922feb00 100644 --- a/doc/source/formats/reference/classes/CONFIG.txt +++ b/doc/source/formats/reference/classes/CONFIG.txt @@ -1,4 +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..fd6827ba9 --- /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 index 950c764a2..c4c6f249b 100644 --- a/doc/source/formats/reference/classes/CRD.txt +++ b/doc/source/formats/reference/classes/CRD.txt @@ -1,5 +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 index d7aed82d3..c44a0dec0 100644 --- a/doc/source/formats/reference/classes/DATA.txt +++ b/doc/source/formats/reference/classes/DATA.txt @@ -1,5 +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 index c9877ca85..766b21b47 100644 --- a/doc/source/formats/reference/classes/DCD.txt +++ b/doc/source/formats/reference/classes/DCD.txt @@ -1,4 +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 index f913a4b33..2f2680167 100644 --- a/doc/source/formats/reference/classes/DMS.txt +++ b/doc/source/formats/reference/classes/DMS.txt @@ -1,4 +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 index 230ca2437..0e44b4cb2 100644 --- a/doc/source/formats/reference/classes/GMS.txt +++ b/doc/source/formats/reference/classes/GMS.txt @@ -1,4 +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 index e592d2e5c..b08fbacad 100644 --- a/doc/source/formats/reference/classes/GRO.txt +++ b/doc/source/formats/reference/classes/GRO.txt @@ -1,5 +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 index 1337593e0..4099a831f 100644 --- a/doc/source/formats/reference/classes/GSD.txt +++ b/doc/source/formats/reference/classes/GSD.txt @@ -1,4 +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 index 4c3ac24f5..694ab145b 100644 --- a/doc/source/formats/reference/classes/HISTORY.txt +++ b/doc/source/formats/reference/classes/HISTORY.txt @@ -1,4 +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..e0dad56f2 --- /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 index 874a4a7ca..7a3faecd5 100644 --- a/doc/source/formats/reference/classes/INPCRD.txt +++ b/doc/source/formats/reference/classes/INPCRD.txt @@ -1,3 +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 index f4073e3fb..c0fb53dd4 100644 --- a/doc/source/formats/reference/classes/ITP.txt +++ b/doc/source/formats/reference/classes/ITP.txt @@ -1,3 +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 index 4879b1251..d609dd556 100644 --- a/doc/source/formats/reference/classes/LAMMPS.txt +++ b/doc/source/formats/reference/classes/LAMMPS.txt @@ -1,4 +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 index dc5fdb9d8..0ecbed751 100644 --- a/doc/source/formats/reference/classes/LAMMPSDUMP.txt +++ b/doc/source/formats/reference/classes/LAMMPSDUMP.txt @@ -1,4 +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 index a3b725b24..30c368323 100644 --- a/doc/source/formats/reference/classes/MMTF.txt +++ b/doc/source/formats/reference/classes/MMTF.txt @@ -1,4 +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 index 36c9f5563..f497d63ac 100644 --- a/doc/source/formats/reference/classes/MOL2.txt +++ b/doc/source/formats/reference/classes/MOL2.txt @@ -1,5 +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 index e297dd7c7..3df3b4328 100644 --- a/doc/source/formats/reference/classes/NCDF.txt +++ b/doc/source/formats/reference/classes/NCDF.txt @@ -1,4 +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..47ef0d87e --- /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 index 67824dec7..0ccab700f 100644 --- a/doc/source/formats/reference/classes/PDB.txt +++ b/doc/source/formats/reference/classes/PDB.txt @@ -1,5 +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 index b5e2cc01e..c2fb27f54 100644 --- a/doc/source/formats/reference/classes/PDBQT.txt +++ b/doc/source/formats/reference/classes/PDBQT.txt @@ -1,5 +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 index 716ec423b..ad898aa60 100644 --- a/doc/source/formats/reference/classes/PQR.txt +++ b/doc/source/formats/reference/classes/PQR.txt @@ -1,5 +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 index 977aae370..302b167a7 100644 --- a/doc/source/formats/reference/classes/PSF.txt +++ b/doc/source/formats/reference/classes/PSF.txt @@ -1,3 +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 index d2066311c..f5a398233 100644 --- a/doc/source/formats/reference/classes/TOP.txt +++ b/doc/source/formats/reference/classes/TOP.txt @@ -1,3 +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 index a55166dc0..446fb130f 100644 --- a/doc/source/formats/reference/classes/TPR.txt +++ b/doc/source/formats/reference/classes/TPR.txt @@ -1,3 +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 index e9f645992..367d6bc2c 100644 --- a/doc/source/formats/reference/classes/TRJ.txt +++ b/doc/source/formats/reference/classes/TRJ.txt @@ -1,3 +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 index 7351c6d92..8eaa20f0d 100644 --- a/doc/source/formats/reference/classes/TRR.txt +++ b/doc/source/formats/reference/classes/TRR.txt @@ -1,4 +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 index 7de36e58a..90a5ba29f 100644 --- a/doc/source/formats/reference/classes/TRZ.txt +++ b/doc/source/formats/reference/classes/TRZ.txt @@ -1,4 +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 index 032b00031..7d1fa2c64 100644 --- a/doc/source/formats/reference/classes/TXYZ.txt +++ b/doc/source/formats/reference/classes/TXYZ.txt @@ -1,4 +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 index 5cb676f63..013d97f1f 100644 --- a/doc/source/formats/reference/classes/XML.txt +++ b/doc/source/formats/reference/classes/XML.txt @@ -1,3 +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 index 371c5dd99..397457b65 100644 --- a/doc/source/formats/reference/classes/XPDB.txt +++ b/doc/source/formats/reference/classes/XPDB.txt @@ -1,4 +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 index bdba2ee82..5844f5d2e 100644 --- a/doc/source/formats/reference/classes/XTC.txt +++ b/doc/source/formats/reference/classes/XTC.txt @@ -1,4 +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 index 5199cfd50..3b5ac8014 100644 --- a/doc/source/formats/reference/classes/XYZ.txt +++ b/doc/source/formats/reference/classes/XYZ.txt @@ -1,5 +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/reference/coor.rst b/doc/source/formats/reference/coor.rst new file mode 100644 index 000000000..2b6644b77 --- /dev/null +++ b/doc/source/formats/reference/coor.rst @@ -0,0 +1,10 @@ +.. -*- coding: utf-8 -*- +.. _COOR-format: + +========================================= +COOR, NAMBDIN (NAMD binary restart files) +========================================= + +.. 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 new file mode 100644 index 000000000..edeae4640 --- /dev/null +++ b/doc/source/formats/reference/in.rst @@ -0,0 +1,12 @@ +.. -*- coding: utf-8 -*- +.. _IN-format: + +======================================= +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 `publicly available `_. + +.. _`FHI-aims`: https://aimsclub.fhi-berlin.mpg.de/ diff --git a/doc/source/formats/reference/parmed.rst b/doc/source/formats/reference/parmed.rst new file mode 100644 index 000000000..d995da42e --- /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/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/formats/selection_exporter_formats.txt b/doc/source/formats/selection_exporter_formats.txt index 9d8f3f00f..6fe94d789 100644 --- a/doc/source/formats/selection_exporter_formats.txt +++ b/doc/source/formats/selection_exporter_formats.txt @@ -1,9 +1,14 @@ -========== =========== ======================================== ====================================================== -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` -========== =========== ======================================== ====================================================== +.. + 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/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 720cabff3..207567d1f 100644 --- a/doc/source/formats/topology_parsers.txt +++ b/doc/source/formats/topology_parsers.txt @@ -1,25 +1,32 @@ -====================================== =============================== ========================================================================================= ==================== -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:`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:`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:`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 names masses, types -====================================== =============================== ========================================================================================= ==================== +.. + 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/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 index 7778e9564..c60c3bcb0 100644 --- a/doc/source/generated/selections/base.txt +++ b/doc/source/generated/selections/base.txt @@ -1,4 +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 index 85f7a6299..71fc395d3 100644 --- a/doc/source/generated/selections/nucleic.txt +++ b/doc/source/generated/selections/nucleic.txt @@ -1,7 +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 index 66590ec1c..46ff5b483 100644 --- a/doc/source/generated/selections/nucleic_backbone.txt +++ b/doc/source/generated/selections/nucleic_backbone.txt @@ -1,3 +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 index f112bed13..4f636b81d 100644 --- a/doc/source/generated/selections/nucleic_sugar.txt +++ b/doc/source/generated/selections/nucleic_sugar.txt @@ -1,3 +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 index 80cbd0c56..4306e28e8 100644 --- a/doc/source/generated/selections/protein.txt +++ b/doc/source/generated/selections/protein.txt @@ -1,3 +1,6 @@ +.. + Generated by gen_standard_selections.py + ==== ==== ==== ==== ==== ==== ==== ==== ACE ALA ALAD ARG ARGN ASF ASH ASN ASN1 ASP ASPH CALA CARG CASF CASN CASP @@ -12,4 +15,4 @@ 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 index 88371d41c..b6dfe5524 100644 --- a/doc/source/generated/selections/protein_backbone.txt +++ b/doc/source/generated/selections/protein_backbone.txt @@ -1,3 +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 index 55cecbcba..bd386b74e 100644 --- a/doc/source/generated/topology/connectivityattrs.txt +++ b/doc/source/generated/topology/connectivityattrs.txt @@ -1,8 +1,11 @@ -========= =========== ============================================================================================================================================================================================================================================================================================================================================= +.. + Generated by gen_topologyparser_attrs.py + +========= =========== ============================================================================================================================================================================================================================================================================================================================================================================ 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 ` -========= =========== ============================================================================================================================================================================================================================================================================================================================================= +========= =========== ============================================================================================================================================================================================================================================================================================================================================================================ +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 index 48d7c58c8..2bce7d35c 100644 --- a/doc/source/generated/topology/defaults.txt +++ b/doc/source/generated/topology/defaults.txt @@ -1,32 +1,45 @@ -============= ============ ======================================== ======= ======================= -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 +============= ============= ======================================== ======= ======================= \ No newline at end of file diff --git a/doc/source/generated/topology/groupmethods.txt b/doc/source/generated/topology/groupmethods.txt index 1880560ad..605da4236 100644 --- a/doc/source/generated/topology/groupmethods.txt +++ b/doc/source/generated/topology/groupmethods.txt @@ -1,3 +1,6 @@ +.. + Generated by gen_topology_groupmethods.py + ================================================================== ====================================================================== ========== Method Description Requires ================================================================== ====================================================================== ========== @@ -10,4 +13,4 @@ Method Description :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 index 7f47cd4e1..a9cd12a20 100644 --- a/doc/source/generated/topology/topologyattrs.txt +++ b/doc/source/generated/topology/topologyattrs.txt @@ -1,26 +1,39 @@ -============ ============= ================================== =================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== -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:`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/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/base.py b/doc/source/scripts/base.py index e733dcc9a..0375872c9 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 @@ -16,6 +17,7 @@ class TableWriter(object): """ filename = '' + include_table = False headings = [] preprocess = [] postprocess = [] @@ -68,11 +70,15 @@ 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(f'..\n Generated by {sys.argv[0].split("/")[-1]}\n\n') + if self.include_table: + f.write(f'.. table:: {self.include_table}\n\n') + tabled = tabulate.tabulate(self.lines, + headers=self.headings, + tablefmt='rst') + if self.include_table: + tabled = textwrap.indent(tabled, ' ') + f.write(tabled) print('Wrote ', self.filename) # ==== HELPER FUNCTIONS ==== # diff --git a/doc/source/scripts/core.py b/doc/source/scripts/core.py index 0c5fe84be..df1aec4a0 100644 --- a/doc/source/scripts/core.py +++ b/doc/source/scripts/core.py @@ -6,8 +6,10 @@ # ====== TOPOLOGY ====== # DESCRIPTIONS = { + 'CHEMFILES': 'use readers from `chemfiles `_ library', 'CRD': 'CHARMM CARD file', 'CONFIG': 'DL_Poly CONFIG file', + 'COOR': 'NAMD binary restart file', 'DCD': 'CHARMM, NAMD, or LAMMPS binary trajectory', 'HISTORY': 'DL_Poly HISTORY file', 'DMS': 'DESRES Molecular Structure file', @@ -19,11 +21,13 @@ 'DATA': 'LAMMPS data file', 'INPCRD': 'AMBER restart file', 'ITP': 'GROMACS portable topology file', + 'IN': 'FHI-aims input file', 'LAMMPS': 'a LAMMPS DCD trajectory', 'LAMMPSDUMP': 'LAMMPS ascii dump file', 'MMTF' : 'MMTF file', 'NCDF': 'AMBER NETCDF format', 'MOL2': 'Tripos MOL2 file', + 'PARMED': '`ParmEd `_ Structure', 'PDB': 'Standard PDB file', 'PDBQT' : 'PDBQT file', 'PQR' : 'PQR file', diff --git a/doc/source/scripts/gen_format_overview_classes.py b/doc/source/scripts/gen_format_overview_classes.py index bdd1c9a63..ace247eab 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 @@ -29,6 +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'] @@ -68,10 +70,13 @@ 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): 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..6129300e8 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) @@ -48,12 +51,17 @@ 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'] preprocess = ['keys'] filename = 'formats/topology_parsers.txt' + include_table = 'Table of supported topology parsers and the attributes read' sort = True def __init__(self): 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 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 ----------------- 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