From b6f2e4cf60950cdcfef9119f9f8cc8944d73ec7e Mon Sep 17 00:00:00 2001 From: Tyler Reddy Date: Fri, 23 Sep 2016 16:51:20 +0100 Subject: [PATCH 1/3] Updated citation information in README. --- package/README | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/package/README b/package/README index bff2bd164eb..06edfb3865f 100644 --- a/package/README +++ b/package/README @@ -63,7 +63,16 @@ file. Citation ========= -When using MDAnalysis in published work, please cite +When using MDAnalysis in published work, please cite the following +two papers: + + R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, + M. N. Melo, S. L. Seyler, D. L. Dotson, J. Domanski, + S. Buchoux, I. M. Kenney, and O. Beckstein. MDAnalysis: + A Python package for the rapid analysis of molecular + dynamics simulations. In S. Benthall and S. Rostrup, + editors, Proceedings of the 15th Python in Science + Conference, pages 102-109, Austin, TX, 2016. SciPy. N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. MDAnalysis: A Toolkit for the Analysis of Molecular From 9369b3e94f665e7110d77432f3875b499a8ef280 Mon Sep 17 00:00:00 2001 From: Tyler Reddy Date: Fri, 23 Sep 2016 17:09:11 +0100 Subject: [PATCH 2/3] Updated sphinx source files to reflect new citation requirements (index and references pages). --- .../sphinx/source/documentation_pages/references.rst | 10 ++++++++++ package/doc/sphinx/source/index.rst | 10 ++++++++++ 2 files changed, 20 insertions(+) diff --git a/package/doc/sphinx/source/documentation_pages/references.rst b/package/doc/sphinx/source/documentation_pages/references.rst index 019c12491cc..f70225a565f 100644 --- a/package/doc/sphinx/source/documentation_pages/references.rst +++ b/package/doc/sphinx/source/documentation_pages/references.rst @@ -10,6 +10,15 @@ Citation for the whole MDAnalysis library ========================================= When using MDAnalysis in published work, please cite +the following two papers: + +* R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, + M. N. Melo, S. L. Seyler, D. L. Dotson, J. Domanski, + S. Buchoux, I. M. Kenney, and O. Beckstein. `MDAnalysis: + A Python package for the rapid analysis of molecular + dynamics simulations`_. In S. Benthall and S. Rostrup, + editors, *Proceedings of the 15th Python in Science + Conference*, pages 102-109, Austin, TX, 2016. SciPy. * N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. MDAnalysis: A Toolkit for the Analysis of Molecular @@ -69,6 +78,7 @@ If you use the Path Similarity Analysis (PSA) code in Thanks! +.. _`MDAnalysis: A Python package for the rapid analysis of molecular dynamics simulations`: http://conference.scipy.org/proceedings/scipy2016/oliver_beckstein.html .. _`10.1002/jcc.21787`: http://dx.doi.org/10.1002/jcc.21787 .. _HELANAL: http://www.ccrnp.ncifcrf.gov/users/kumarsan/HELANAL/helanal.html .. _`10.1371/journal.pcbi.1004568`: http://dx.doi.org/10.1371/journal.pcbi.1004568 diff --git a/package/doc/sphinx/source/index.rst b/package/doc/sphinx/source/index.rst index d8785ccc8f0..53d7f1ef160 100644 --- a/package/doc/sphinx/source/index.rst +++ b/package/doc/sphinx/source/index.rst @@ -57,12 +57,22 @@ Citation ======== When using MDAnalysis in published work, please cite +the following two papers: + +* R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, + M. N. Melo, S. L. Seyler, D. L. Dotson, J. Domanski, + S. Buchoux, I. M. Kenney, and O. Beckstein. `MDAnalysis: + A Python package for the rapid analysis of molecular + dynamics simulations`_. In S. Benthall and S. Rostrup, + editors, *Proceedings of the 15th Python in Science + Conference*, pages 102-109, Austin, TX, 2016. SciPy. * N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. *J. Comput. Chem.* **32** (2011), 2319–2327. doi:`10.1002/jcc.21787`_ +.. _`MDAnalysis: A Python package for the rapid analysis of molecular dynamics simulations`: http://conference.scipy.org/proceedings/scipy2016/oliver_beckstein.html .. _`10.1002/jcc.21787`: http://dx.doi.org/10.1002/jcc.21787 MDAnalysis also contains specific algorithms and whole analysis From 7f43f21c1eeab73de126375d17a072ca58089f03 Mon Sep 17 00:00:00 2001 From: Tyler Reddy Date: Wed, 28 Sep 2016 12:52:16 +0100 Subject: [PATCH 3/3] Package file header metadata changes updated to reflect current proposal in Issue #1002. --- package/MDAnalysis/analysis/__init__.py | 12 +++++-- package/MDAnalysis/analysis/align.py | 12 +++++-- package/MDAnalysis/analysis/base.py | 12 +++++-- package/MDAnalysis/analysis/contacts.py | 12 +++++-- package/MDAnalysis/analysis/density.py | 12 +++++-- package/MDAnalysis/analysis/diffusionmap.py | 12 +++++-- package/MDAnalysis/analysis/distances.py | 22 ++++++++----- package/MDAnalysis/analysis/gnm.py | 12 +++++-- .../MDAnalysis/analysis/hbonds/__init__.py | 12 +++++-- .../analysis/hbonds/hbond_analysis.py | 12 +++++-- .../analysis/hbonds/hbond_autocorrel.py | 12 +++++-- package/MDAnalysis/analysis/helanal.py | 12 +++++-- package/MDAnalysis/analysis/hole.py | 12 +++++-- package/MDAnalysis/analysis/leaflet.py | 12 +++++-- .../MDAnalysis/analysis/legacy/__init__.py | 12 +++++-- package/MDAnalysis/analysis/legacy/x3dna.py | 12 +++++-- package/MDAnalysis/analysis/lineardensity.py | 12 +++++-- package/MDAnalysis/analysis/pca.py | 12 +++++-- package/MDAnalysis/analysis/polymer.py | 12 +++++-- package/MDAnalysis/analysis/psa.py | 12 +++++-- package/MDAnalysis/analysis/rdf.py | 12 +++++-- package/MDAnalysis/analysis/rms.py | 12 +++++-- package/MDAnalysis/analysis/waterdynamics.py | 12 +++++-- package/MDAnalysis/analysis/x3dna.py | 12 +++++-- package/MDAnalysis/auxiliary/XVG.py | 32 +++++++++++-------- package/MDAnalysis/auxiliary/__init__.py | 12 +++++-- package/MDAnalysis/auxiliary/base.py | 12 +++++-- package/MDAnalysis/auxiliary/core.py | 12 +++++-- package/MDAnalysis/coordinates/CRD.py | 12 +++++-- package/MDAnalysis/coordinates/DCD.py | 12 +++++-- package/MDAnalysis/coordinates/DLPoly.py | 12 +++++-- package/MDAnalysis/coordinates/DMS.py | 12 +++++-- package/MDAnalysis/coordinates/GMS.py | 22 ++++++++----- package/MDAnalysis/coordinates/GRO.py | 12 +++++-- package/MDAnalysis/coordinates/INPCRD.py | 12 +++++-- package/MDAnalysis/coordinates/LAMMPS.py | 12 +++++-- package/MDAnalysis/coordinates/MOL2.py | 12 +++++-- package/MDAnalysis/coordinates/PDB.py | 12 +++++-- package/MDAnalysis/coordinates/PDBQT.py | 12 +++++-- package/MDAnalysis/coordinates/PQR.py | 12 +++++-- package/MDAnalysis/coordinates/TRJ.py | 14 +++++--- package/MDAnalysis/coordinates/TRR.py | 12 +++++-- package/MDAnalysis/coordinates/TRZ.py | 14 +++++--- package/MDAnalysis/coordinates/XDR.py | 14 +++++--- package/MDAnalysis/coordinates/XTC.py | 12 +++++-- package/MDAnalysis/coordinates/XYZ.py | 12 +++++-- package/MDAnalysis/coordinates/__init__.py | 12 +++++-- package/MDAnalysis/coordinates/base.py | 12 +++++-- package/MDAnalysis/coordinates/core.py | 12 +++++-- .../MDAnalysis/coordinates/dcdtimeseries.pyx | 22 ++++++++----- package/MDAnalysis/coordinates/memory.py | 12 +++++-- package/MDAnalysis/core/AtomGroup.py | 12 +++++-- package/MDAnalysis/core/Selection.py | 12 +++++-- package/MDAnalysis/core/Timeseries.py | 12 +++++-- package/MDAnalysis/core/__init__.py | 12 +++++-- package/MDAnalysis/core/topologyobjects.py | 13 ++++++-- package/MDAnalysis/exceptions.py | 13 ++++++-- package/MDAnalysis/lib/NeighborSearch.py | 12 +++++-- package/MDAnalysis/lib/__init__.py | 12 +++++-- package/MDAnalysis/lib/c_distances.pyx | 22 ++++++++----- package/MDAnalysis/lib/c_distances_openmp.pyx | 22 ++++++++----- package/MDAnalysis/lib/distances.py | 22 ++++++++----- package/MDAnalysis/lib/formats/__init__.py | 12 +++++-- .../MDAnalysis/lib/formats/cython_util.pxd | 12 +++++-- .../MDAnalysis/lib/formats/cython_util.pyx | 12 +++++-- package/MDAnalysis/lib/formats/libmdaxdr.pyx | 12 +++++-- package/MDAnalysis/lib/log.py | 12 +++++-- package/MDAnalysis/lib/mdamath.py | 12 +++++-- package/MDAnalysis/lib/util.py | 12 +++++-- package/MDAnalysis/selections/__init__.py | 12 +++++-- package/MDAnalysis/selections/base.py | 12 +++++-- package/MDAnalysis/selections/charmm.py | 12 +++++-- package/MDAnalysis/selections/gromacs.py | 12 +++++-- package/MDAnalysis/selections/jmol.py | 12 +++++-- package/MDAnalysis/selections/pymol.py | 12 +++++-- package/MDAnalysis/selections/vmd.py | 12 +++++-- package/MDAnalysis/tests/__init__.py | 12 +++++-- package/MDAnalysis/tests/datafiles.py | 12 +++++-- package/MDAnalysis/topology/CRDParser.py | 13 ++++++-- package/MDAnalysis/topology/DLPolyParser.py | 12 +++++-- package/MDAnalysis/topology/DMSParser.py | 13 ++++++-- .../MDAnalysis/topology/ExtendedPDBParser.py | 13 ++++++-- package/MDAnalysis/topology/GMSParser.py | 13 ++++++-- package/MDAnalysis/topology/GROParser.py | 13 ++++++-- package/MDAnalysis/topology/HoomdXMLParser.py | 14 ++++++-- package/MDAnalysis/topology/LAMMPSParser.py | 13 ++++++-- package/MDAnalysis/topology/MOL2Parser.py | 13 ++++++-- package/MDAnalysis/topology/PDBParser.py | 13 ++++++-- package/MDAnalysis/topology/PDBQTParser.py | 13 ++++++-- package/MDAnalysis/topology/PQRParser.py | 13 ++++++-- package/MDAnalysis/topology/PSFParser.py | 13 ++++++-- .../MDAnalysis/topology/PrimitivePDBParser.py | 13 ++++++-- package/MDAnalysis/topology/TOPParser.py | 13 ++++++-- package/MDAnalysis/topology/TPRParser.py | 14 +++++--- package/MDAnalysis/topology/XYZParser.py | 13 ++++++-- package/MDAnalysis/topology/__init__.py | 13 ++++++-- package/MDAnalysis/topology/base.py | 13 ++++++-- package/MDAnalysis/topology/core.py | 13 ++++++-- package/MDAnalysis/topology/tables.py | 13 ++++++-- package/MDAnalysis/topology/tpr/__init__.py | 12 +++++-- package/MDAnalysis/topology/tpr/obj.py | 12 +++++-- package/MDAnalysis/topology/tpr/setting.py | 12 +++++-- package/MDAnalysis/topology/tpr/utils.py | 12 +++++-- package/MDAnalysis/units.py | 12 +++++-- package/MDAnalysis/version.py | 13 ++++++-- package/MDAnalysis/visualization/__init__.py | 12 +++++-- .../MDAnalysis/visualization/streamlines.py | 12 +++++-- .../visualization/streamlines_3D.py | 12 +++++-- package/setup.py | 13 +++++--- testsuite/MDAnalysisTests/__init__.py | 12 +++++-- .../MDAnalysisTests/analysis/test_align.py | 12 +++++-- .../MDAnalysisTests/analysis/test_base.py | 12 +++++-- .../MDAnalysisTests/analysis/test_contacts.py | 12 +++++-- .../MDAnalysisTests/analysis/test_density.py | 12 +++++-- .../analysis/test_diffusionmap.py | 12 +++++-- .../analysis/test_distances.py | 12 +++++-- .../MDAnalysisTests/analysis/test_gnm.py | 12 +++++-- .../MDAnalysisTests/analysis/test_hbonds.py | 12 +++++-- .../MDAnalysisTests/analysis/test_helanal.py | 12 +++++-- .../MDAnalysisTests/analysis/test_hole.py | 12 +++++-- .../analysis/test_hydrogenbondautocorrel.py | 12 +++++-- .../MDAnalysisTests/analysis/test_leaflet.py | 12 +++++-- .../analysis/test_lineardensity.py | 12 +++++-- .../MDAnalysisTests/analysis/test_nuclinfo.py | 12 +++++-- .../MDAnalysisTests/analysis/test_pca.py | 12 +++++-- .../analysis/test_persistencelength.py | 12 +++++-- .../MDAnalysisTests/analysis/test_psa.py | 12 +++++-- .../MDAnalysisTests/analysis/test_rdf.py | 12 +++++-- .../MDAnalysisTests/analysis/test_rms.py | 12 +++++-- .../analysis/test_waterdynamics.py | 12 +++++-- .../coordinates/test_coordinates.py | 12 +++++-- .../MDAnalysisTests/coordinates/test_mol2.py | 12 +++++-- .../MDAnalysisTests/coordinates/test_pdbqt.py | 12 +++++-- .../coordinates/test_reader_api.py | 12 +++++-- .../coordinates/test_timestep_api.py | 12 +++++-- testsuite/MDAnalysisTests/datafiles.py | 12 +++++-- .../MDAnalysisTests/formats/test_libmdaxdr.py | 12 +++++-- testsuite/MDAnalysisTests/plugins/__init__.py | 12 +++++-- .../MDAnalysisTests/plugins/capture_err.py | 12 +++++-- testsuite/MDAnalysisTests/plugins/cleanup.py | 12 +++++-- .../MDAnalysisTests/plugins/knownfailure.py | 12 +++++-- testsuite/MDAnalysisTests/plugins/memleak.py | 12 +++++-- .../MDAnalysisTests/plugins/open_files.py | 12 +++++-- testsuite/MDAnalysisTests/test_altloc.py | 12 +++++-- testsuite/MDAnalysisTests/test_atomgroup.py | 12 +++++-- .../MDAnalysisTests/test_atomselections.py | 12 +++++-- testsuite/MDAnalysisTests/test_authors.py | 12 +++++-- testsuite/MDAnalysisTests/test_datafiles.py | 12 +++++-- testsuite/MDAnalysisTests/test_deprecated.py | 12 +++++-- testsuite/MDAnalysisTests/test_distances.py | 12 +++++-- testsuite/MDAnalysisTests/test_failure.py | 12 +++++-- testsuite/MDAnalysisTests/test_imports.py | 12 +++++-- testsuite/MDAnalysisTests/test_lammpsdata.py | 13 ++++++-- testsuite/MDAnalysisTests/test_log.py | 12 +++++-- testsuite/MDAnalysisTests/test_meta.py | 12 +++++-- testsuite/MDAnalysisTests/test_modelling.py | 12 +++++-- testsuite/MDAnalysisTests/test_nuclinfo.py | 12 +++++-- testsuite/MDAnalysisTests/test_persistence.py | 12 +++++-- testsuite/MDAnalysisTests/test_qcprot.py | 12 +++++-- testsuite/MDAnalysisTests/test_selections.py | 12 +++++-- testsuite/MDAnalysisTests/test_streamio.py | 12 +++++-- testsuite/MDAnalysisTests/test_topology.py | 13 ++++++-- testsuite/MDAnalysisTests/test_tprparser.py | 12 +++++-- .../MDAnalysisTests/test_transformations.py | 12 +++++-- testsuite/MDAnalysisTests/test_units.py | 12 +++++-- testsuite/MDAnalysisTests/test_util.py | 12 +++++-- .../MDAnalysisTests/test_velocities_forces.py | 12 +++++-- .../MDAnalysisTests/topology/test_gro.py | 13 ++++++-- .../MDAnalysisTests/topology/test_pdb.py | 13 ++++++-- testsuite/setup.py | 13 +++++--- 170 files changed, 1599 insertions(+), 558 deletions(-) diff --git a/package/MDAnalysis/analysis/__init__.py b/package/MDAnalysis/analysis/__init__.py index 4e847906675..912d6d3d3ed 100644 --- a/package/MDAnalysis/analysis/__init__.py +++ b/package/MDAnalysis/analysis/__init__.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/analysis/align.py b/package/MDAnalysis/analysis/align.py index a0fc997f80e..a766c16c5b9 100644 --- a/package/MDAnalysis/analysis/align.py +++ b/package/MDAnalysis/analysis/align.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver -# Beckstein and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/analysis/base.py b/package/MDAnalysis/analysis/base.py index a0aa68624fc..35f14381889 100644 --- a/package/MDAnalysis/analysis/base.py +++ b/package/MDAnalysis/analysis/base.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver -# Beckstein and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/analysis/contacts.py b/package/MDAnalysis/analysis/contacts.py index 5a1f8cfb656..1fe8dd49d82 100644 --- a/package/MDAnalysis/analysis/contacts.py +++ b/package/MDAnalysis/analysis/contacts.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver -# Beckstein and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/analysis/density.py b/package/MDAnalysis/analysis/density.py index cdf07418d57..ac390bf994f 100644 --- a/package/MDAnalysis/analysis/density.py +++ b/package/MDAnalysis/analysis/density.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/analysis/diffusionmap.py b/package/MDAnalysis/analysis/diffusionmap.py index a6300212cc0..ae9835e4425 100644 --- a/package/MDAnalysis/analysis/diffusionmap.py +++ b/package/MDAnalysis/analysis/diffusionmap.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/analysis/distances.py b/package/MDAnalysis/analysis/distances.py index 707daf1e716..454984d61f5 100644 --- a/package/MDAnalysis/analysis/distances.py +++ b/package/MDAnalysis/analysis/distances.py @@ -1,18 +1,24 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2014 Naveen Michaud-Agrawal, -# Elizabeth J. Denning, Oliver Beckstein, -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) +# # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # -# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and -# O. Beckstein. MDAnalysis: A Toolkit for the Analysis of -# Molecular Dynamics Simulations. J. Comput. Chem. 32 (2011), 2319--2327, -# doi:10.1002/jcc.21787 +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# +# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. +# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. +# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 +# # """ diff --git a/package/MDAnalysis/analysis/gnm.py b/package/MDAnalysis/analysis/gnm.py index 100d516a218..af1b53ce46f 100644 --- a/package/MDAnalysis/analysis/gnm.py +++ b/package/MDAnalysis/analysis/gnm.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/analysis/hbonds/__init__.py b/package/MDAnalysis/analysis/hbonds/__init__.py index 9d487f37d5b..e1bd9d03ddc 100644 --- a/package/MDAnalysis/analysis/hbonds/__init__.py +++ b/package/MDAnalysis/analysis/hbonds/__init__.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/analysis/hbonds/hbond_analysis.py b/package/MDAnalysis/analysis/hbonds/hbond_analysis.py index 33c7a9caab1..85ecb3da02d 100644 --- a/package/MDAnalysis/analysis/hbonds/hbond_analysis.py +++ b/package/MDAnalysis/analysis/hbonds/hbond_analysis.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/analysis/hbonds/hbond_autocorrel.py b/package/MDAnalysis/analysis/hbonds/hbond_autocorrel.py index 31e4efabe1e..fdb5a0b7a9f 100644 --- a/package/MDAnalysis/analysis/hbonds/hbond_autocorrel.py +++ b/package/MDAnalysis/analysis/hbonds/hbond_autocorrel.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/analysis/helanal.py b/package/MDAnalysis/analysis/helanal.py index af987bcd81c..9346f55ed79 100644 --- a/package/MDAnalysis/analysis/helanal.py +++ b/package/MDAnalysis/analysis/helanal.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/analysis/hole.py b/package/MDAnalysis/analysis/hole.py index 1608c206885..3995162333e 100644 --- a/package/MDAnalysis/analysis/hole.py +++ b/package/MDAnalysis/analysis/hole.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/analysis/leaflet.py b/package/MDAnalysis/analysis/leaflet.py index e857e458bef..82b775161f5 100644 --- a/package/MDAnalysis/analysis/leaflet.py +++ b/package/MDAnalysis/analysis/leaflet.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/analysis/legacy/__init__.py b/package/MDAnalysis/analysis/legacy/__init__.py index aa7a25c5618..1b6b72fbac4 100644 --- a/package/MDAnalysis/analysis/legacy/__init__.py +++ b/package/MDAnalysis/analysis/legacy/__init__.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/analysis/legacy/x3dna.py b/package/MDAnalysis/analysis/legacy/x3dna.py index 5d3b734d5df..1a4922686f5 100644 --- a/package/MDAnalysis/analysis/legacy/x3dna.py +++ b/package/MDAnalysis/analysis/legacy/x3dna.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/analysis/lineardensity.py b/package/MDAnalysis/analysis/lineardensity.py index 498c6e3381b..e8422325cbd 100644 --- a/package/MDAnalysis/analysis/lineardensity.py +++ b/package/MDAnalysis/analysis/lineardensity.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver -# Beckstein and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/analysis/pca.py b/package/MDAnalysis/analysis/pca.py index 977154032e2..25ad99407a0 100644 --- a/package/MDAnalysis/analysis/pca.py +++ b/package/MDAnalysis/analysis/pca.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/analysis/polymer.py b/package/MDAnalysis/analysis/polymer.py index ce826f80b2d..6cb8a8711e8 100644 --- a/package/MDAnalysis/analysis/polymer.py +++ b/package/MDAnalysis/analysis/polymer.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver -# Beckstein and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/analysis/psa.py b/package/MDAnalysis/analysis/psa.py index 619ac5cb28d..d903a54369f 100644 --- a/package/MDAnalysis/analysis/psa.py +++ b/package/MDAnalysis/analysis/psa.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/analysis/rdf.py b/package/MDAnalysis/analysis/rdf.py index 33dfcbf94de..6c78571ec4e 100644 --- a/package/MDAnalysis/analysis/rdf.py +++ b/package/MDAnalysis/analysis/rdf.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver -# Beckstein and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/analysis/rms.py b/package/MDAnalysis/analysis/rms.py index ee61b3fba86..19242ad670a 100644 --- a/package/MDAnalysis/analysis/rms.py +++ b/package/MDAnalysis/analysis/rms.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver -# Beckstein and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/analysis/waterdynamics.py b/package/MDAnalysis/analysis/waterdynamics.py index 54b13462b23..2abecf625b7 100644 --- a/package/MDAnalysis/analysis/waterdynamics.py +++ b/package/MDAnalysis/analysis/waterdynamics.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/analysis/x3dna.py b/package/MDAnalysis/analysis/x3dna.py index 7e9a031ebb7..efadaa489d0 100644 --- a/package/MDAnalysis/analysis/x3dna.py +++ b/package/MDAnalysis/analysis/x3dna.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/auxiliary/XVG.py b/package/MDAnalysis/auxiliary/XVG.py index 38f7afd453f..55024994497 100644 --- a/package/MDAnalysis/auxiliary/XVG.py +++ b/package/MDAnalysis/auxiliary/XVG.py @@ -1,18 +1,24 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 -# -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver -# Beckstein and contributors (see AUTHORS for the full list) -# -# Released under the GNU Public Licence, v2 or any higher version -# -# Please cite your use of MDAnalysis in published work: -# -# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. -# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. -# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 -# +# +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) +# +# Released under the GNU Public Licence, v2 or any higher version +# +# Please cite your use of MDAnalysis in published work: +# +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# +# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. +# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. +# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 +# """ XVG auxiliary reader --- :mod:`MDAnalysis.auxiliary.XVG` diff --git a/package/MDAnalysis/auxiliary/__init__.py b/package/MDAnalysis/auxiliary/__init__.py index c63007bf034..c2d3fad3a5f 100644 --- a/package/MDAnalysis/auxiliary/__init__.py +++ b/package/MDAnalysis/auxiliary/__init__.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver -# Beckstein and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/auxiliary/base.py b/package/MDAnalysis/auxiliary/base.py index 26fa9736166..8eb645b5abe 100644 --- a/package/MDAnalysis/auxiliary/base.py +++ b/package/MDAnalysis/auxiliary/base.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver -# Beckstein and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/auxiliary/core.py b/package/MDAnalysis/auxiliary/core.py index 7dab9d738b2..7e26110a17c 100644 --- a/package/MDAnalysis/auxiliary/core.py +++ b/package/MDAnalysis/auxiliary/core.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver -# Beckstein and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/coordinates/CRD.py b/package/MDAnalysis/coordinates/CRD.py index e0a3228b375..c33a9697014 100644 --- a/package/MDAnalysis/coordinates/CRD.py +++ b/package/MDAnalysis/coordinates/CRD.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/coordinates/DCD.py b/package/MDAnalysis/coordinates/DCD.py index 50c834515d8..b6ae9476cff 100644 --- a/package/MDAnalysis/coordinates/DCD.py +++ b/package/MDAnalysis/coordinates/DCD.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/coordinates/DLPoly.py b/package/MDAnalysis/coordinates/DLPoly.py index 8c85049aac2..ce2a3e464e0 100644 --- a/package/MDAnalysis/coordinates/DLPoly.py +++ b/package/MDAnalysis/coordinates/DLPoly.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/coordinates/DMS.py b/package/MDAnalysis/coordinates/DMS.py index 6c80d31f0de..fa4a167852c 100644 --- a/package/MDAnalysis/coordinates/DMS.py +++ b/package/MDAnalysis/coordinates/DMS.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/coordinates/GMS.py b/package/MDAnalysis/coordinates/GMS.py index 449797f5011..09e883f5b50 100644 --- a/package/MDAnalysis/coordinates/GMS.py +++ b/package/MDAnalysis/coordinates/GMS.py @@ -1,18 +1,24 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2011 Naveen Michaud-Agrawal, -# Elizabeth J. Denning, Oliver Beckstein, -# and contributors (see website for details) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) +# # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # -# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and -# O. Beckstein. MDAnalysis: A Toolkit for the Analysis of -# Molecular Dynamics Simulations. J. Comput. Chem. 32 (2011), 2319--2327, -# doi:10.1002/jcc.21787 +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# +# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. +# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. +# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 +# # """GAMESS trajectory reader --- :mod:`MDAnalysis.coordinates.GMS` diff --git a/package/MDAnalysis/coordinates/GRO.py b/package/MDAnalysis/coordinates/GRO.py index 37a82be5f1c..394961ce370 100644 --- a/package/MDAnalysis/coordinates/GRO.py +++ b/package/MDAnalysis/coordinates/GRO.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/coordinates/INPCRD.py b/package/MDAnalysis/coordinates/INPCRD.py index 37f53e14927..79f24c4a956 100644 --- a/package/MDAnalysis/coordinates/INPCRD.py +++ b/package/MDAnalysis/coordinates/INPCRD.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/coordinates/LAMMPS.py b/package/MDAnalysis/coordinates/LAMMPS.py index 8581bd237be..200b21ca886 100644 --- a/package/MDAnalysis/coordinates/LAMMPS.py +++ b/package/MDAnalysis/coordinates/LAMMPS.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/coordinates/MOL2.py b/package/MDAnalysis/coordinates/MOL2.py index f02168a9c22..adf1583819b 100644 --- a/package/MDAnalysis/coordinates/MOL2.py +++ b/package/MDAnalysis/coordinates/MOL2.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/coordinates/PDB.py b/package/MDAnalysis/coordinates/PDB.py index d315112bf0d..32d2b6afa7b 100644 --- a/package/MDAnalysis/coordinates/PDB.py +++ b/package/MDAnalysis/coordinates/PDB.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver -# Beckstein and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/coordinates/PDBQT.py b/package/MDAnalysis/coordinates/PDBQT.py index 965c9fed2dc..bcbca37d500 100644 --- a/package/MDAnalysis/coordinates/PDBQT.py +++ b/package/MDAnalysis/coordinates/PDBQT.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/coordinates/PQR.py b/package/MDAnalysis/coordinates/PQR.py index e7b286b6f3e..54c39107b06 100644 --- a/package/MDAnalysis/coordinates/PQR.py +++ b/package/MDAnalysis/coordinates/PQR.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/coordinates/TRJ.py b/package/MDAnalysis/coordinates/TRJ.py index 27e735a0353..89d8e0ba91d 100644 --- a/package/MDAnalysis/coordinates/TRJ.py +++ b/package/MDAnalysis/coordinates/TRJ.py @@ -1,15 +1,19 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver -# Beckstein and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: - - +# +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. # # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. diff --git a/package/MDAnalysis/coordinates/TRR.py b/package/MDAnalysis/coordinates/TRR.py index 8c13541b38b..2757b846044 100644 --- a/package/MDAnalysis/coordinates/TRR.py +++ b/package/MDAnalysis/coordinates/TRR.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver -# Beckstein and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/coordinates/TRZ.py b/package/MDAnalysis/coordinates/TRZ.py index 1c97d9bd939..c4232caba70 100644 --- a/package/MDAnalysis/coordinates/TRZ.py +++ b/package/MDAnalysis/coordinates/TRZ.py @@ -1,18 +1,24 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 - +# # TRZ Reader written by Richard J. Gowers (2013) """TRZ trajectory I/O --- :mod:`MDAnalysis.coordinates.TRZ` diff --git a/package/MDAnalysis/coordinates/XDR.py b/package/MDAnalysis/coordinates/XDR.py index 65e7935a02a..f02ded1202d 100644 --- a/package/MDAnalysis/coordinates/XDR.py +++ b/package/MDAnalysis/coordinates/XDR.py @@ -1,17 +1,21 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver -# Beckstein and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. - - # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 # diff --git a/package/MDAnalysis/coordinates/XTC.py b/package/MDAnalysis/coordinates/XTC.py index 6d67650a05f..be2c99d0448 100644 --- a/package/MDAnalysis/coordinates/XTC.py +++ b/package/MDAnalysis/coordinates/XTC.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver -# Beckstein and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/coordinates/XYZ.py b/package/MDAnalysis/coordinates/XYZ.py index 951e1c08585..0f32af19eac 100644 --- a/package/MDAnalysis/coordinates/XYZ.py +++ b/package/MDAnalysis/coordinates/XYZ.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver -# Beckstein and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/coordinates/__init__.py b/package/MDAnalysis/coordinates/__init__.py index 300525775fa..87cfe517d7f 100644 --- a/package/MDAnalysis/coordinates/__init__.py +++ b/package/MDAnalysis/coordinates/__init__.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/coordinates/base.py b/package/MDAnalysis/coordinates/base.py index 0cafa01a81f..7fcf7564ed2 100644 --- a/package/MDAnalysis/coordinates/base.py +++ b/package/MDAnalysis/coordinates/base.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver -# Beckstein and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/coordinates/core.py b/package/MDAnalysis/coordinates/core.py index d30c851d070..4f5cfc79aac 100644 --- a/package/MDAnalysis/coordinates/core.py +++ b/package/MDAnalysis/coordinates/core.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/coordinates/dcdtimeseries.pyx b/package/MDAnalysis/coordinates/dcdtimeseries.pyx index 1f1d4f585e8..89bc6212f7e 100644 --- a/package/MDAnalysis/coordinates/dcdtimeseries.pyx +++ b/package/MDAnalysis/coordinates/dcdtimeseries.pyx @@ -1,18 +1,24 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://mdanalysis.googlecode.com -# Copyright (c) 2006-2014 Naveen Michaud-Agrawal, -# Elizabeth J. Denning, Oliver Beckstein, -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) +# # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # -# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and -# O. Beckstein. MDAnalysis: A Toolkit for the Analysis of -# Molecular Dynamics Simulations. J. Comput. Chem. 32 (2011), 2319--2327, -# doi:10.1002/jcc.21787 +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# +# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. +# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. +# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 +# # import numpy diff --git a/package/MDAnalysis/coordinates/memory.py b/package/MDAnalysis/coordinates/memory.py index e5282230492..f0202f52745 100644 --- a/package/MDAnalysis/coordinates/memory.py +++ b/package/MDAnalysis/coordinates/memory.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/core/AtomGroup.py b/package/MDAnalysis/core/AtomGroup.py index 6116aea7056..f289e8763fc 100644 --- a/package/MDAnalysis/core/AtomGroup.py +++ b/package/MDAnalysis/core/AtomGroup.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/core/Selection.py b/package/MDAnalysis/core/Selection.py index 66c32ac4515..dbee892784a 100644 --- a/package/MDAnalysis/core/Selection.py +++ b/package/MDAnalysis/core/Selection.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/core/Timeseries.py b/package/MDAnalysis/core/Timeseries.py index f73ab6a701b..e2b97cae67f 100644 --- a/package/MDAnalysis/core/Timeseries.py +++ b/package/MDAnalysis/core/Timeseries.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/core/__init__.py b/package/MDAnalysis/core/__init__.py index c053ccdb10c..b08aca2b75a 100644 --- a/package/MDAnalysis/core/__init__.py +++ b/package/MDAnalysis/core/__init__.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/core/topologyobjects.py b/package/MDAnalysis/core/topologyobjects.py index bedc73fcef7..15bb4bda2c9 100644 --- a/package/MDAnalysis/core/topologyobjects.py +++ b/package/MDAnalysis/core/topologyobjects.py @@ -1,13 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: +# +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/exceptions.py b/package/MDAnalysis/exceptions.py index 05f27a0523f..94b6a40c80a 100644 --- a/package/MDAnalysis/exceptions.py +++ b/package/MDAnalysis/exceptions.py @@ -1,13 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: +# +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/lib/NeighborSearch.py b/package/MDAnalysis/lib/NeighborSearch.py index 5e3fdf82fab..b077ef658fa 100644 --- a/package/MDAnalysis/lib/NeighborSearch.py +++ b/package/MDAnalysis/lib/NeighborSearch.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/lib/__init__.py b/package/MDAnalysis/lib/__init__.py index 7f5eb81893d..7dd76d5ecde 100644 --- a/package/MDAnalysis/lib/__init__.py +++ b/package/MDAnalysis/lib/__init__.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/lib/c_distances.pyx b/package/MDAnalysis/lib/c_distances.pyx index fef0c0913e3..b3c4c35d4f5 100644 --- a/package/MDAnalysis/lib/c_distances.pyx +++ b/package/MDAnalysis/lib/c_distances.pyx @@ -1,18 +1,24 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://mdanalysis.googlecode.com -# Copyright (c) 2006-2014 Naveen Michaud-Agrawal, -# Elizabeth J. Denning, Oliver Beckstein, -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) +# # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # -# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and -# O. Beckstein. MDAnalysis: A Toolkit for the Analysis of -# Molecular Dynamics Simulations. J. Comput. Chem. 32 (2011), 2319--2327, -# doi:10.1002/jcc.21787 +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# +# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. +# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. +# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 +# # """ diff --git a/package/MDAnalysis/lib/c_distances_openmp.pyx b/package/MDAnalysis/lib/c_distances_openmp.pyx index f653dc2bf12..6b3b9e74705 100644 --- a/package/MDAnalysis/lib/c_distances_openmp.pyx +++ b/package/MDAnalysis/lib/c_distances_openmp.pyx @@ -1,18 +1,24 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://mdanalysis.googlecode.com -# Copyright (c) 2006-2014 Naveen Michaud-Agrawal, -# Elizabeth J. Denning, Oliver Beckstein, -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) +# # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # -# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and -# O. Beckstein. MDAnalysis: A Toolkit for the Analysis of -# Molecular Dynamics Simulations. J. Comput. Chem. 32 (2011), 2319--2327, -# doi:10.1002/jcc.21787 +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# +# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. +# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. +# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 +# # """ diff --git a/package/MDAnalysis/lib/distances.py b/package/MDAnalysis/lib/distances.py index 7f649bebd70..eb9d6234be8 100644 --- a/package/MDAnalysis/lib/distances.py +++ b/package/MDAnalysis/lib/distances.py @@ -1,18 +1,24 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://mdanalysis.googlecode.com -# Copyright (c) 2006-2014 Naveen Michaud-Agrawal, -# Elizabeth J. Denning, Oliver Beckstein, -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) +# # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # -# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and -# O. Beckstein. MDAnalysis: A Toolkit for the Analysis of -# Molecular Dynamics Simulations. J. Comput. Chem. 32 (2011), 2319--2327, -# doi:10.1002/jcc.21787 +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# +# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. +# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. +# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 +# # """Fast distance array computation --- :mod:`MDAnalysis.lib.distances` diff --git a/package/MDAnalysis/lib/formats/__init__.py b/package/MDAnalysis/lib/formats/__init__.py index 719832d8cd5..99567c34e1f 100644 --- a/package/MDAnalysis/lib/formats/__init__.py +++ b/package/MDAnalysis/lib/formats/__init__.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver -# Beckstein and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/lib/formats/cython_util.pxd b/package/MDAnalysis/lib/formats/cython_util.pxd index cb53a969b8f..2a31c3443e0 100644 --- a/package/MDAnalysis/lib/formats/cython_util.pxd +++ b/package/MDAnalysis/lib/formats/cython_util.pxd @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver -# Beckstein and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/lib/formats/cython_util.pyx b/package/MDAnalysis/lib/formats/cython_util.pyx index 5d96fbede9c..22c2ed0c2b5 100644 --- a/package/MDAnalysis/lib/formats/cython_util.pyx +++ b/package/MDAnalysis/lib/formats/cython_util.pyx @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver -# Beckstein and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/lib/formats/libmdaxdr.pyx b/package/MDAnalysis/lib/formats/libmdaxdr.pyx index 68d0ed65758..9cf8fa095b0 100644 --- a/package/MDAnalysis/lib/formats/libmdaxdr.pyx +++ b/package/MDAnalysis/lib/formats/libmdaxdr.pyx @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver -# Beckstein and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/lib/log.py b/package/MDAnalysis/lib/log.py index 20afc1338b4..d39e7268f4d 100644 --- a/package/MDAnalysis/lib/log.py +++ b/package/MDAnalysis/lib/log.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver -# Beckstein and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/lib/mdamath.py b/package/MDAnalysis/lib/mdamath.py index 28eb7c5ba2f..45ed5f4d58d 100644 --- a/package/MDAnalysis/lib/mdamath.py +++ b/package/MDAnalysis/lib/mdamath.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/lib/util.py b/package/MDAnalysis/lib/util.py index f793fde7ca1..c4ca722f9a0 100644 --- a/package/MDAnalysis/lib/util.py +++ b/package/MDAnalysis/lib/util.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/selections/__init__.py b/package/MDAnalysis/selections/__init__.py index b5fa501da43..71aea29a944 100644 --- a/package/MDAnalysis/selections/__init__.py +++ b/package/MDAnalysis/selections/__init__.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/selections/base.py b/package/MDAnalysis/selections/base.py index c6ac5146994..f00144b9149 100644 --- a/package/MDAnalysis/selections/base.py +++ b/package/MDAnalysis/selections/base.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/selections/charmm.py b/package/MDAnalysis/selections/charmm.py index b55caaa88c9..9f5504c8816 100644 --- a/package/MDAnalysis/selections/charmm.py +++ b/package/MDAnalysis/selections/charmm.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/selections/gromacs.py b/package/MDAnalysis/selections/gromacs.py index 89baa9acdd9..a9b53cb8ff5 100644 --- a/package/MDAnalysis/selections/gromacs.py +++ b/package/MDAnalysis/selections/gromacs.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/selections/jmol.py b/package/MDAnalysis/selections/jmol.py index fa566418e55..3b7b0b4e68d 100644 --- a/package/MDAnalysis/selections/jmol.py +++ b/package/MDAnalysis/selections/jmol.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/selections/pymol.py b/package/MDAnalysis/selections/pymol.py index 65e8beebdff..1ed1b5a9999 100644 --- a/package/MDAnalysis/selections/pymol.py +++ b/package/MDAnalysis/selections/pymol.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/selections/vmd.py b/package/MDAnalysis/selections/vmd.py index 459058af9fe..115257529c6 100644 --- a/package/MDAnalysis/selections/vmd.py +++ b/package/MDAnalysis/selections/vmd.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/tests/__init__.py b/package/MDAnalysis/tests/__init__.py index 14eb97e556f..ac71c07dda2 100644 --- a/package/MDAnalysis/tests/__init__.py +++ b/package/MDAnalysis/tests/__init__.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/tests/datafiles.py b/package/MDAnalysis/tests/datafiles.py index 26ad9465dd8..1c25882a1f2 100644 --- a/package/MDAnalysis/tests/datafiles.py +++ b/package/MDAnalysis/tests/datafiles.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/topology/CRDParser.py b/package/MDAnalysis/topology/CRDParser.py index fe4d26beefa..331aa337780 100644 --- a/package/MDAnalysis/topology/CRDParser.py +++ b/package/MDAnalysis/topology/CRDParser.py @@ -1,13 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding: utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: +# +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/topology/DLPolyParser.py b/package/MDAnalysis/topology/DLPolyParser.py index 2ade487e24f..573e13d7e8e 100644 --- a/package/MDAnalysis/topology/DLPolyParser.py +++ b/package/MDAnalysis/topology/DLPolyParser.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding: utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/topology/DMSParser.py b/package/MDAnalysis/topology/DMSParser.py index d6adff25188..1c1d97820ce 100644 --- a/package/MDAnalysis/topology/DMSParser.py +++ b/package/MDAnalysis/topology/DMSParser.py @@ -1,13 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding: utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: +# +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/topology/ExtendedPDBParser.py b/package/MDAnalysis/topology/ExtendedPDBParser.py index bbd8c40ae1b..fc9f5f97a49 100644 --- a/package/MDAnalysis/topology/ExtendedPDBParser.py +++ b/package/MDAnalysis/topology/ExtendedPDBParser.py @@ -1,13 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding: utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: +# +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/topology/GMSParser.py b/package/MDAnalysis/topology/GMSParser.py index 9ccde57d3c9..5441dd061bd 100644 --- a/package/MDAnalysis/topology/GMSParser.py +++ b/package/MDAnalysis/topology/GMSParser.py @@ -1,13 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding: utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: +# +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/topology/GROParser.py b/package/MDAnalysis/topology/GROParser.py index e2c3068b90a..0c179332581 100644 --- a/package/MDAnalysis/topology/GROParser.py +++ b/package/MDAnalysis/topology/GROParser.py @@ -1,13 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding: utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: +# +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/topology/HoomdXMLParser.py b/package/MDAnalysis/topology/HoomdXMLParser.py index 530f52c08ae..3cc1f525219 100644 --- a/package/MDAnalysis/topology/HoomdXMLParser.py +++ b/package/MDAnalysis/topology/HoomdXMLParser.py @@ -1,12 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding: utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: +# +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/topology/LAMMPSParser.py b/package/MDAnalysis/topology/LAMMPSParser.py index 27514afef42..70eb2f3ed57 100644 --- a/package/MDAnalysis/topology/LAMMPSParser.py +++ b/package/MDAnalysis/topology/LAMMPSParser.py @@ -1,13 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: +# +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/topology/MOL2Parser.py b/package/MDAnalysis/topology/MOL2Parser.py index 1a3183c5a9c..e745525d69a 100644 --- a/package/MDAnalysis/topology/MOL2Parser.py +++ b/package/MDAnalysis/topology/MOL2Parser.py @@ -1,13 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: +# +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/topology/PDBParser.py b/package/MDAnalysis/topology/PDBParser.py index 6fdfe558f75..e6faf3ca28e 100644 --- a/package/MDAnalysis/topology/PDBParser.py +++ b/package/MDAnalysis/topology/PDBParser.py @@ -2,13 +2,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver -# Beckstein and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: +# +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/topology/PDBQTParser.py b/package/MDAnalysis/topology/PDBQTParser.py index 984007caa4b..ec7a5603476 100644 --- a/package/MDAnalysis/topology/PDBQTParser.py +++ b/package/MDAnalysis/topology/PDBQTParser.py @@ -1,13 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: +# +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/topology/PQRParser.py b/package/MDAnalysis/topology/PQRParser.py index adcf88b28df..3adfd161284 100644 --- a/package/MDAnalysis/topology/PQRParser.py +++ b/package/MDAnalysis/topology/PQRParser.py @@ -1,13 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: +# +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/topology/PSFParser.py b/package/MDAnalysis/topology/PSFParser.py index ae5a5d0afe2..990c2e255c4 100644 --- a/package/MDAnalysis/topology/PSFParser.py +++ b/package/MDAnalysis/topology/PSFParser.py @@ -1,13 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: +# +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/topology/PrimitivePDBParser.py b/package/MDAnalysis/topology/PrimitivePDBParser.py index ae2cac77b4a..32fc0e850b3 100644 --- a/package/MDAnalysis/topology/PrimitivePDBParser.py +++ b/package/MDAnalysis/topology/PrimitivePDBParser.py @@ -1,13 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver -# Beckstein and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: +# +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/topology/TOPParser.py b/package/MDAnalysis/topology/TOPParser.py index a1a78d2ae89..69f48e8ceed 100644 --- a/package/MDAnalysis/topology/TOPParser.py +++ b/package/MDAnalysis/topology/TOPParser.py @@ -1,13 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: +# +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/topology/TPRParser.py b/package/MDAnalysis/topology/TPRParser.py index b0ea22dd08b..e94019ec291 100644 --- a/package/MDAnalysis/topology/TPRParser.py +++ b/package/MDAnalysis/topology/TPRParser.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, -# Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: +# +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/topology/XYZParser.py b/package/MDAnalysis/topology/XYZParser.py index 233c9984f2a..c3e61ed4696 100644 --- a/package/MDAnalysis/topology/XYZParser.py +++ b/package/MDAnalysis/topology/XYZParser.py @@ -1,13 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: +# +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/topology/__init__.py b/package/MDAnalysis/topology/__init__.py index 22ed68401c1..57161008718 100644 --- a/package/MDAnalysis/topology/__init__.py +++ b/package/MDAnalysis/topology/__init__.py @@ -1,13 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: +# +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/topology/base.py b/package/MDAnalysis/topology/base.py index 6f4d9600b58..d177367541d 100644 --- a/package/MDAnalysis/topology/base.py +++ b/package/MDAnalysis/topology/base.py @@ -1,13 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: +# +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/topology/core.py b/package/MDAnalysis/topology/core.py index 2a8dd8356c9..fd071de21b4 100644 --- a/package/MDAnalysis/topology/core.py +++ b/package/MDAnalysis/topology/core.py @@ -1,13 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: +# +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/topology/tables.py b/package/MDAnalysis/topology/tables.py index 1191615ca16..eca7a0167aa 100644 --- a/package/MDAnalysis/topology/tables.py +++ b/package/MDAnalysis/topology/tables.py @@ -1,13 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: +# +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/topology/tpr/__init__.py b/package/MDAnalysis/topology/tpr/__init__.py index 4e2cda598d0..9fdd672ed24 100644 --- a/package/MDAnalysis/topology/tpr/__init__.py +++ b/package/MDAnalysis/topology/tpr/__init__.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/topology/tpr/obj.py b/package/MDAnalysis/topology/tpr/obj.py index 4b88e91b2f4..38135c6c95e 100644 --- a/package/MDAnalysis/topology/tpr/obj.py +++ b/package/MDAnalysis/topology/tpr/obj.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding: utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/topology/tpr/setting.py b/package/MDAnalysis/topology/tpr/setting.py index af77095ca70..0d1f5ab7428 100644 --- a/package/MDAnalysis/topology/tpr/setting.py +++ b/package/MDAnalysis/topology/tpr/setting.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding: utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/topology/tpr/utils.py b/package/MDAnalysis/topology/tpr/utils.py index e8855fa705e..fb722a4eb30 100644 --- a/package/MDAnalysis/topology/tpr/utils.py +++ b/package/MDAnalysis/topology/tpr/utils.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding: utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/units.py b/package/MDAnalysis/units.py index 64e9c24004a..ff7c4c85faf 100644 --- a/package/MDAnalysis/units.py +++ b/package/MDAnalysis/units.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding: utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/version.py b/package/MDAnalysis/version.py index 3d16bce997e..10a8852938b 100644 --- a/package/MDAnalysis/version.py +++ b/package/MDAnalysis/version.py @@ -1,13 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding: utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: +# +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/visualization/__init__.py b/package/MDAnalysis/visualization/__init__.py index e51512f5bd7..db983c722c1 100644 --- a/package/MDAnalysis/visualization/__init__.py +++ b/package/MDAnalysis/visualization/__init__.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/visualization/streamlines.py b/package/MDAnalysis/visualization/streamlines.py index 1a08803b0ed..555e9c4070d 100644 --- a/package/MDAnalysis/visualization/streamlines.py +++ b/package/MDAnalysis/visualization/streamlines.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/MDAnalysis/visualization/streamlines_3D.py b/package/MDAnalysis/visualization/streamlines_3D.py index 296349fd410..1b1006d5829 100644 --- a/package/MDAnalysis/visualization/streamlines_3D.py +++ b/package/MDAnalysis/visualization/streamlines_3D.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/package/setup.py b/package/setup.py index 834698e1966..2f8612c37ec 100755 --- a/package/setup.py +++ b/package/setup.py @@ -2,15 +2,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org - -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver -# Beckstein and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/MDAnalysisTests/__init__.py b/testsuite/MDAnalysisTests/__init__.py index 33afe6ad457..ea0c62324a5 100644 --- a/testsuite/MDAnalysisTests/__init__.py +++ b/testsuite/MDAnalysisTests/__init__.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/MDAnalysisTests/analysis/test_align.py b/testsuite/MDAnalysisTests/analysis/test_align.py index 119330f831e..efd6543b3bc 100644 --- a/testsuite/MDAnalysisTests/analysis/test_align.py +++ b/testsuite/MDAnalysisTests/analysis/test_align.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver -# Beckstein and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/MDAnalysisTests/analysis/test_base.py b/testsuite/MDAnalysisTests/analysis/test_base.py index 522433fd9fd..df73c3b2451 100644 --- a/testsuite/MDAnalysisTests/analysis/test_base.py +++ b/testsuite/MDAnalysisTests/analysis/test_base.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver -# Beckstein and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/MDAnalysisTests/analysis/test_contacts.py b/testsuite/MDAnalysisTests/analysis/test_contacts.py index dbcdad587b7..19db93be35f 100644 --- a/testsuite/MDAnalysisTests/analysis/test_contacts.py +++ b/testsuite/MDAnalysisTests/analysis/test_contacts.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver -# Beckstein and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/MDAnalysisTests/analysis/test_density.py b/testsuite/MDAnalysisTests/analysis/test_density.py index 9836bccadd6..a3bb2f279ce 100644 --- a/testsuite/MDAnalysisTests/analysis/test_density.py +++ b/testsuite/MDAnalysisTests/analysis/test_density.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/MDAnalysisTests/analysis/test_diffusionmap.py b/testsuite/MDAnalysisTests/analysis/test_diffusionmap.py index 0b5897bd27f..573801d5b2f 100644 --- a/testsuite/MDAnalysisTests/analysis/test_diffusionmap.py +++ b/testsuite/MDAnalysisTests/analysis/test_diffusionmap.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver -# Beckstein and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/MDAnalysisTests/analysis/test_distances.py b/testsuite/MDAnalysisTests/analysis/test_distances.py index 575cc7df720..52472d800e0 100644 --- a/testsuite/MDAnalysisTests/analysis/test_distances.py +++ b/testsuite/MDAnalysisTests/analysis/test_distances.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/MDAnalysisTests/analysis/test_gnm.py b/testsuite/MDAnalysisTests/analysis/test_gnm.py index 3e605e51590..ebcae6e2809 100644 --- a/testsuite/MDAnalysisTests/analysis/test_gnm.py +++ b/testsuite/MDAnalysisTests/analysis/test_gnm.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver -# Beckstein and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/MDAnalysisTests/analysis/test_hbonds.py b/testsuite/MDAnalysisTests/analysis/test_hbonds.py index 0fe206c2280..1b7bc0de9e6 100644 --- a/testsuite/MDAnalysisTests/analysis/test_hbonds.py +++ b/testsuite/MDAnalysisTests/analysis/test_hbonds.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/MDAnalysisTests/analysis/test_helanal.py b/testsuite/MDAnalysisTests/analysis/test_helanal.py index edd68a2caf7..03c742cb3fa 100644 --- a/testsuite/MDAnalysisTests/analysis/test_helanal.py +++ b/testsuite/MDAnalysisTests/analysis/test_helanal.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/MDAnalysisTests/analysis/test_hole.py b/testsuite/MDAnalysisTests/analysis/test_hole.py index 33203776980..3ecf4393094 100644 --- a/testsuite/MDAnalysisTests/analysis/test_hole.py +++ b/testsuite/MDAnalysisTests/analysis/test_hole.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py b/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py index ca9aa3c9812..04f02ddbd1c 100644 --- a/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py +++ b/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver -# Beckstein and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/MDAnalysisTests/analysis/test_leaflet.py b/testsuite/MDAnalysisTests/analysis/test_leaflet.py index 4ee53a0b9ac..25dcb507811 100644 --- a/testsuite/MDAnalysisTests/analysis/test_leaflet.py +++ b/testsuite/MDAnalysisTests/analysis/test_leaflet.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/MDAnalysisTests/analysis/test_lineardensity.py b/testsuite/MDAnalysisTests/analysis/test_lineardensity.py index 42ed115038a..99d296f5ce8 100644 --- a/testsuite/MDAnalysisTests/analysis/test_lineardensity.py +++ b/testsuite/MDAnalysisTests/analysis/test_lineardensity.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver -# Beckstein and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/MDAnalysisTests/analysis/test_nuclinfo.py b/testsuite/MDAnalysisTests/analysis/test_nuclinfo.py index 81786e36580..e476efb97d0 100644 --- a/testsuite/MDAnalysisTests/analysis/test_nuclinfo.py +++ b/testsuite/MDAnalysisTests/analysis/test_nuclinfo.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver -# Beckstein and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/MDAnalysisTests/analysis/test_pca.py b/testsuite/MDAnalysisTests/analysis/test_pca.py index 29044fca5ac..257234404d5 100644 --- a/testsuite/MDAnalysisTests/analysis/test_pca.py +++ b/testsuite/MDAnalysisTests/analysis/test_pca.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver -# Beckstein and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/MDAnalysisTests/analysis/test_persistencelength.py b/testsuite/MDAnalysisTests/analysis/test_persistencelength.py index cf7af771e2a..48efee8950a 100644 --- a/testsuite/MDAnalysisTests/analysis/test_persistencelength.py +++ b/testsuite/MDAnalysisTests/analysis/test_persistencelength.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/MDAnalysisTests/analysis/test_psa.py b/testsuite/MDAnalysisTests/analysis/test_psa.py index 0a9b30d3a43..1d2ccb5e0fe 100644 --- a/testsuite/MDAnalysisTests/analysis/test_psa.py +++ b/testsuite/MDAnalysisTests/analysis/test_psa.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver -# Beckstein and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/MDAnalysisTests/analysis/test_rdf.py b/testsuite/MDAnalysisTests/analysis/test_rdf.py index 7c1505eed22..3400ad340aa 100644 --- a/testsuite/MDAnalysisTests/analysis/test_rdf.py +++ b/testsuite/MDAnalysisTests/analysis/test_rdf.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver -# Beckstein and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/MDAnalysisTests/analysis/test_rms.py b/testsuite/MDAnalysisTests/analysis/test_rms.py index 9076763ab64..a7d22e0e250 100644 --- a/testsuite/MDAnalysisTests/analysis/test_rms.py +++ b/testsuite/MDAnalysisTests/analysis/test_rms.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver -# Beckstein and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/MDAnalysisTests/analysis/test_waterdynamics.py b/testsuite/MDAnalysisTests/analysis/test_waterdynamics.py index 326d5ce54f7..918a309dc3b 100644 --- a/testsuite/MDAnalysisTests/analysis/test_waterdynamics.py +++ b/testsuite/MDAnalysisTests/analysis/test_waterdynamics.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/MDAnalysisTests/coordinates/test_coordinates.py b/testsuite/MDAnalysisTests/coordinates/test_coordinates.py index 9bbc5adfaee..9cd2176db8d 100644 --- a/testsuite/MDAnalysisTests/coordinates/test_coordinates.py +++ b/testsuite/MDAnalysisTests/coordinates/test_coordinates.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver -# Beckstein and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/MDAnalysisTests/coordinates/test_mol2.py b/testsuite/MDAnalysisTests/coordinates/test_mol2.py index 83472b99174..74f14d3b353 100644 --- a/testsuite/MDAnalysisTests/coordinates/test_mol2.py +++ b/testsuite/MDAnalysisTests/coordinates/test_mol2.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver -# Beckstein and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/MDAnalysisTests/coordinates/test_pdbqt.py b/testsuite/MDAnalysisTests/coordinates/test_pdbqt.py index f44895dcd25..4ba51d04547 100644 --- a/testsuite/MDAnalysisTests/coordinates/test_pdbqt.py +++ b/testsuite/MDAnalysisTests/coordinates/test_pdbqt.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver -# Beckstein and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/MDAnalysisTests/coordinates/test_reader_api.py b/testsuite/MDAnalysisTests/coordinates/test_reader_api.py index 663835d02b2..d2f80a5ff2e 100644 --- a/testsuite/MDAnalysisTests/coordinates/test_reader_api.py +++ b/testsuite/MDAnalysisTests/coordinates/test_reader_api.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py b/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py index 0884fee23e0..871225a4e13 100644 --- a/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py +++ b/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver -# Beckstein and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/MDAnalysisTests/datafiles.py b/testsuite/MDAnalysisTests/datafiles.py index f9578385f20..ce55f651fb3 100644 --- a/testsuite/MDAnalysisTests/datafiles.py +++ b/testsuite/MDAnalysisTests/datafiles.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/MDAnalysisTests/formats/test_libmdaxdr.py b/testsuite/MDAnalysisTests/formats/test_libmdaxdr.py index bb7c33d98c4..77531fa48ed 100644 --- a/testsuite/MDAnalysisTests/formats/test_libmdaxdr.py +++ b/testsuite/MDAnalysisTests/formats/test_libmdaxdr.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver -# Beckstein and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/MDAnalysisTests/plugins/__init__.py b/testsuite/MDAnalysisTests/plugins/__init__.py index d8295189dcd..5879aeb6ad9 100644 --- a/testsuite/MDAnalysisTests/plugins/__init__.py +++ b/testsuite/MDAnalysisTests/plugins/__init__.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/MDAnalysisTests/plugins/capture_err.py b/testsuite/MDAnalysisTests/plugins/capture_err.py index 653eb737352..bac49363656 100644 --- a/testsuite/MDAnalysisTests/plugins/capture_err.py +++ b/testsuite/MDAnalysisTests/plugins/capture_err.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/MDAnalysisTests/plugins/cleanup.py b/testsuite/MDAnalysisTests/plugins/cleanup.py index 0a32c929e60..191617aa082 100644 --- a/testsuite/MDAnalysisTests/plugins/cleanup.py +++ b/testsuite/MDAnalysisTests/plugins/cleanup.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/MDAnalysisTests/plugins/knownfailure.py b/testsuite/MDAnalysisTests/plugins/knownfailure.py index 27a9dd0f7a2..2c5b4d43284 100644 --- a/testsuite/MDAnalysisTests/plugins/knownfailure.py +++ b/testsuite/MDAnalysisTests/plugins/knownfailure.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/MDAnalysisTests/plugins/memleak.py b/testsuite/MDAnalysisTests/plugins/memleak.py index 2c8f4d5975b..b0c6a7f6d1a 100644 --- a/testsuite/MDAnalysisTests/plugins/memleak.py +++ b/testsuite/MDAnalysisTests/plugins/memleak.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/MDAnalysisTests/plugins/open_files.py b/testsuite/MDAnalysisTests/plugins/open_files.py index b5325d04eba..291d31fd3fa 100644 --- a/testsuite/MDAnalysisTests/plugins/open_files.py +++ b/testsuite/MDAnalysisTests/plugins/open_files.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, -# Oliver Beckstein and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/MDAnalysisTests/test_altloc.py b/testsuite/MDAnalysisTests/test_altloc.py index 5bef06f99e5..34e020ec7f3 100644 --- a/testsuite/MDAnalysisTests/test_altloc.py +++ b/testsuite/MDAnalysisTests/test_altloc.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver -# Beckstein and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/MDAnalysisTests/test_atomgroup.py b/testsuite/MDAnalysisTests/test_atomgroup.py index a83c52e5048..a7de1a8da5a 100644 --- a/testsuite/MDAnalysisTests/test_atomgroup.py +++ b/testsuite/MDAnalysisTests/test_atomgroup.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver -# Beckstein and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/MDAnalysisTests/test_atomselections.py b/testsuite/MDAnalysisTests/test_atomselections.py index 73a21feb91b..715370efe47 100644 --- a/testsuite/MDAnalysisTests/test_atomselections.py +++ b/testsuite/MDAnalysisTests/test_atomselections.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/MDAnalysisTests/test_authors.py b/testsuite/MDAnalysisTests/test_authors.py index d799980c410..07c700e7eb3 100644 --- a/testsuite/MDAnalysisTests/test_authors.py +++ b/testsuite/MDAnalysisTests/test_authors.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver -# Beckstein and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/MDAnalysisTests/test_datafiles.py b/testsuite/MDAnalysisTests/test_datafiles.py index 0367678d0ea..59d2d86832c 100644 --- a/testsuite/MDAnalysisTests/test_datafiles.py +++ b/testsuite/MDAnalysisTests/test_datafiles.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/MDAnalysisTests/test_deprecated.py b/testsuite/MDAnalysisTests/test_deprecated.py index 688fc920289..eba01dffcdd 100644 --- a/testsuite/MDAnalysisTests/test_deprecated.py +++ b/testsuite/MDAnalysisTests/test_deprecated.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/MDAnalysisTests/test_distances.py b/testsuite/MDAnalysisTests/test_distances.py index 3f6108d96f9..490164c803e 100644 --- a/testsuite/MDAnalysisTests/test_distances.py +++ b/testsuite/MDAnalysisTests/test_distances.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/MDAnalysisTests/test_failure.py b/testsuite/MDAnalysisTests/test_failure.py index 1ab8ee3f926..661a25b7289 100644 --- a/testsuite/MDAnalysisTests/test_failure.py +++ b/testsuite/MDAnalysisTests/test_failure.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, -# Oliver Beckstein and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/MDAnalysisTests/test_imports.py b/testsuite/MDAnalysisTests/test_imports.py index cce0d34b327..73774d7ed0f 100644 --- a/testsuite/MDAnalysisTests/test_imports.py +++ b/testsuite/MDAnalysisTests/test_imports.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/MDAnalysisTests/test_lammpsdata.py b/testsuite/MDAnalysisTests/test_lammpsdata.py index 72d6ac3469f..86320141682 100644 --- a/testsuite/MDAnalysisTests/test_lammpsdata.py +++ b/testsuite/MDAnalysisTests/test_lammpsdata.py @@ -1,13 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: +# +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/MDAnalysisTests/test_log.py b/testsuite/MDAnalysisTests/test_log.py index 33895529e85..1f851e35cf7 100644 --- a/testsuite/MDAnalysisTests/test_log.py +++ b/testsuite/MDAnalysisTests/test_log.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver -# Beckstein and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/MDAnalysisTests/test_meta.py b/testsuite/MDAnalysisTests/test_meta.py index 5b4aea61b07..e0c5a91d494 100644 --- a/testsuite/MDAnalysisTests/test_meta.py +++ b/testsuite/MDAnalysisTests/test_meta.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/MDAnalysisTests/test_modelling.py b/testsuite/MDAnalysisTests/test_modelling.py index 1a54f38acc7..73f7e1feaee 100644 --- a/testsuite/MDAnalysisTests/test_modelling.py +++ b/testsuite/MDAnalysisTests/test_modelling.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver -# Beckstein and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/MDAnalysisTests/test_nuclinfo.py b/testsuite/MDAnalysisTests/test_nuclinfo.py index 59c202aa94b..971fb2a4ce5 100644 --- a/testsuite/MDAnalysisTests/test_nuclinfo.py +++ b/testsuite/MDAnalysisTests/test_nuclinfo.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/MDAnalysisTests/test_persistence.py b/testsuite/MDAnalysisTests/test_persistence.py index 46aad0e4729..2d914b3155b 100644 --- a/testsuite/MDAnalysisTests/test_persistence.py +++ b/testsuite/MDAnalysisTests/test_persistence.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver -# Beckstein and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/MDAnalysisTests/test_qcprot.py b/testsuite/MDAnalysisTests/test_qcprot.py index bb6e58d5ed3..271e4247a71 100644 --- a/testsuite/MDAnalysisTests/test_qcprot.py +++ b/testsuite/MDAnalysisTests/test_qcprot.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/MDAnalysisTests/test_selections.py b/testsuite/MDAnalysisTests/test_selections.py index 1f765a96246..f0a787d8d87 100644 --- a/testsuite/MDAnalysisTests/test_selections.py +++ b/testsuite/MDAnalysisTests/test_selections.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/MDAnalysisTests/test_streamio.py b/testsuite/MDAnalysisTests/test_streamio.py index 4bf917f4bba..7388f928b74 100644 --- a/testsuite/MDAnalysisTests/test_streamio.py +++ b/testsuite/MDAnalysisTests/test_streamio.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver -# Beckstein and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/MDAnalysisTests/test_topology.py b/testsuite/MDAnalysisTests/test_topology.py index 6442a58f881..768f9299cb0 100644 --- a/testsuite/MDAnalysisTests/test_topology.py +++ b/testsuite/MDAnalysisTests/test_topology.py @@ -1,13 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: +# +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/MDAnalysisTests/test_tprparser.py b/testsuite/MDAnalysisTests/test_tprparser.py index 39081f4ea92..725f73c3ca3 100644 --- a/testsuite/MDAnalysisTests/test_tprparser.py +++ b/testsuite/MDAnalysisTests/test_tprparser.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/MDAnalysisTests/test_transformations.py b/testsuite/MDAnalysisTests/test_transformations.py index 100a1659a77..fa540a9010d 100644 --- a/testsuite/MDAnalysisTests/test_transformations.py +++ b/testsuite/MDAnalysisTests/test_transformations.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/MDAnalysisTests/test_units.py b/testsuite/MDAnalysisTests/test_units.py index 27e63c69630..9718614c4d4 100644 --- a/testsuite/MDAnalysisTests/test_units.py +++ b/testsuite/MDAnalysisTests/test_units.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/MDAnalysisTests/test_util.py b/testsuite/MDAnalysisTests/test_util.py index c32f416830d..0ca176096f9 100644 --- a/testsuite/MDAnalysisTests/test_util.py +++ b/testsuite/MDAnalysisTests/test_util.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver -# Beckstein and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/MDAnalysisTests/test_velocities_forces.py b/testsuite/MDAnalysisTests/test_velocities_forces.py index d2e62e66b2d..4084b0ac019 100644 --- a/testsuite/MDAnalysisTests/test_velocities_forces.py +++ b/testsuite/MDAnalysisTests/test_velocities_forces.py @@ -1,14 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/MDAnalysisTests/topology/test_gro.py b/testsuite/MDAnalysisTests/topology/test_gro.py index 3ac15411938..3ccc3d1b92b 100644 --- a/testsuite/MDAnalysisTests/topology/test_gro.py +++ b/testsuite/MDAnalysisTests/topology/test_gro.py @@ -1,13 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: +# +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/MDAnalysisTests/topology/test_pdb.py b/testsuite/MDAnalysisTests/topology/test_pdb.py index bfe0faeb7ce..d68ffd4a542 100644 --- a/testsuite/MDAnalysisTests/topology/test_pdb.py +++ b/testsuite/MDAnalysisTests/topology/test_pdb.py @@ -1,13 +1,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein -# and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: +# +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 diff --git a/testsuite/setup.py b/testsuite/setup.py index bff0d5805aa..ed51f707bd0 100755 --- a/testsuite/setup.py +++ b/testsuite/setup.py @@ -2,15 +2,20 @@ # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # -# MDAnalysis --- http://www.MDAnalysis.org - -# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver -# Beckstein and contributors (see AUTHORS for the full list) +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version # # Please cite your use of MDAnalysis in published work: # +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787