AUTHORS
CHANGELOG
INSTALL
LICENSE
MANIFEST.in
README
SUMMARY.txt
setup.cfg
setup.py
MDAnalysis/__init__.py
MDAnalysis/authors.py
MDAnalysis/due.py
MDAnalysis/exceptions.py
MDAnalysis/units.py
MDAnalysis/version.py
MDAnalysis.egg-info/PKG-INFO
MDAnalysis.egg-info/SOURCES.txt
MDAnalysis.egg-info/dependency_links.txt
MDAnalysis.egg-info/not-zip-safe
MDAnalysis.egg-info/requires.txt
MDAnalysis.egg-info/top_level.txt
MDAnalysis/analysis/__init__.py
MDAnalysis/analysis/align.py
MDAnalysis/analysis/base.py
MDAnalysis/analysis/contacts.py
MDAnalysis/analysis/density.py
MDAnalysis/analysis/diffusionmap.py
MDAnalysis/analysis/dihedrals.py
MDAnalysis/analysis/distances.py
MDAnalysis/analysis/gnm.py
MDAnalysis/analysis/helanal.py
MDAnalysis/analysis/hole.py
MDAnalysis/analysis/leaflet.py
MDAnalysis/analysis/lineardensity.py
MDAnalysis/analysis/nuclinfo.py
MDAnalysis/analysis/pca.py
MDAnalysis/analysis/polymer.py
MDAnalysis/analysis/psa.py
MDAnalysis/analysis/rdf.py
MDAnalysis/analysis/rms.py
MDAnalysis/analysis/waterdynamics.py
MDAnalysis/analysis/data/__init__.py
MDAnalysis/analysis/data/filenames.py
MDAnalysis/analysis/data/janin_ref_data.npy
MDAnalysis/analysis/data/rama_ref_data.npy
MDAnalysis/analysis/encore/__init__.py
MDAnalysis/analysis/encore/bootstrap.py
MDAnalysis/analysis/encore/confdistmatrix.py
MDAnalysis/analysis/encore/covariance.py
MDAnalysis/analysis/encore/cutils.c
MDAnalysis/analysis/encore/cutils.pyx
MDAnalysis/analysis/encore/similarity.py
MDAnalysis/analysis/encore/utils.py
MDAnalysis/analysis/encore/clustering/ClusterCollection.py
MDAnalysis/analysis/encore/clustering/ClusteringMethod.py
MDAnalysis/analysis/encore/clustering/__init__.py
MDAnalysis/analysis/encore/clustering/affinityprop.c
MDAnalysis/analysis/encore/clustering/affinityprop.pyx
MDAnalysis/analysis/encore/clustering/cluster.py
MDAnalysis/analysis/encore/clustering/include/ap.h
MDAnalysis/analysis/encore/clustering/src/ap.c
MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py
MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py
MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py
MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c
MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx
MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h
MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c
MDAnalysis/analysis/hbonds/__init__.py
MDAnalysis/analysis/hbonds/hbond_analysis.py
MDAnalysis/analysis/hbonds/hbond_autocorrel.py
MDAnalysis/analysis/hbonds/wbridge_analysis.py
MDAnalysis/analysis/hole2/__init__.py
MDAnalysis/analysis/hole2/hole.py
MDAnalysis/analysis/hole2/templates.py
MDAnalysis/analysis/hole2/utils.py
MDAnalysis/analysis/hydrogenbonds/__init__.py
MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py
MDAnalysis/analysis/legacy/__init__.py
MDAnalysis/analysis/legacy/x3dna.py
MDAnalysis/analysis/utils/__init__.py
MDAnalysis/auxiliary/XVG.py
MDAnalysis/auxiliary/__init__.py
MDAnalysis/auxiliary/base.py
MDAnalysis/auxiliary/core.py
MDAnalysis/coordinates/CRD.py
MDAnalysis/coordinates/DCD.py
MDAnalysis/coordinates/DLPoly.py
MDAnalysis/coordinates/DMS.py
MDAnalysis/coordinates/FHIAIMS.py
MDAnalysis/coordinates/GMS.py
MDAnalysis/coordinates/GRO.py
MDAnalysis/coordinates/GSD.py
MDAnalysis/coordinates/INPCRD.py
MDAnalysis/coordinates/LAMMPS.py
MDAnalysis/coordinates/MMTF.py
MDAnalysis/coordinates/MOL2.py
MDAnalysis/coordinates/NAMDBIN.py
MDAnalysis/coordinates/PDB.py
MDAnalysis/coordinates/PDBQT.py
MDAnalysis/coordinates/PQR.py
MDAnalysis/coordinates/ParmEd.py
MDAnalysis/coordinates/TRJ.py
MDAnalysis/coordinates/TRR.py
MDAnalysis/coordinates/TRZ.py
MDAnalysis/coordinates/TXYZ.py
MDAnalysis/coordinates/XDR.py
MDAnalysis/coordinates/XTC.py
MDAnalysis/coordinates/XYZ.py
MDAnalysis/coordinates/__init__.py
MDAnalysis/coordinates/base.py
MDAnalysis/coordinates/chain.py
MDAnalysis/coordinates/chemfiles.py
MDAnalysis/coordinates/core.py
MDAnalysis/coordinates/dcdtimeseries.c
MDAnalysis/coordinates/memory.py
MDAnalysis/coordinates/null.py
MDAnalysis/core/__init__.py
MDAnalysis/core/_get_readers.py
MDAnalysis/core/groups.py
MDAnalysis/core/selection.py
MDAnalysis/core/topology.py
MDAnalysis/core/topologyattrs.py
MDAnalysis/core/topologyobjects.py
MDAnalysis/core/universe.py
MDAnalysis/lib/NeighborSearch.py
MDAnalysis/lib/__init__.py
MDAnalysis/lib/_augment.cpp
MDAnalysis/lib/_augment.pyx
MDAnalysis/lib/_cutil.cpp
MDAnalysis/lib/_cutil.pxd
MDAnalysis/lib/_cutil.pyx
MDAnalysis/lib/c_distances.c
MDAnalysis/lib/c_distances.pyx
MDAnalysis/lib/c_distances_openmp.c
MDAnalysis/lib/c_distances_openmp.pyx
MDAnalysis/lib/correlations.py
MDAnalysis/lib/distances.py
MDAnalysis/lib/log.py
MDAnalysis/lib/mdamath.py
MDAnalysis/lib/nsgrid.cpp
MDAnalysis/lib/nsgrid.pyx
MDAnalysis/lib/pkdtree.py
MDAnalysis/lib/qcprot.c
MDAnalysis/lib/qcprot.pyx
MDAnalysis/lib/transformations.py
MDAnalysis/lib/util.py
MDAnalysis/lib/formats/__init__.py
MDAnalysis/lib/formats/cython_util.c
MDAnalysis/lib/formats/cython_util.pxd
MDAnalysis/lib/formats/cython_util.pyx
MDAnalysis/lib/formats/libdcd.c
MDAnalysis/lib/formats/libdcd.pyx
MDAnalysis/lib/formats/libmdaxdr.c
MDAnalysis/lib/formats/libmdaxdr.pyx
MDAnalysis/lib/formats/include/endianswap.h
MDAnalysis/lib/formats/include/fastio.h
MDAnalysis/lib/formats/include/readdcd.h
MDAnalysis/lib/formats/include/trr_seek.h
MDAnalysis/lib/formats/include/xdrfile.h
MDAnalysis/lib/formats/include/xdrfile_trr.h
MDAnalysis/lib/formats/include/xdrfile_xtc.h
MDAnalysis/lib/formats/include/xtc_seek.h
MDAnalysis/lib/formats/src/trr_seek.c
MDAnalysis/lib/formats/src/xdrfile.c
MDAnalysis/lib/formats/src/xdrfile_trr.c
MDAnalysis/lib/formats/src/xdrfile_xtc.c
MDAnalysis/lib/formats/src/xtc_seek.c
MDAnalysis/lib/include/calc_distances.h
MDAnalysis/lib/src/transformations/AUTHOR
MDAnalysis/lib/src/transformations/LICENCE
MDAnalysis/lib/src/transformations/transformations.c
MDAnalysis/selections/__init__.py
MDAnalysis/selections/base.py
MDAnalysis/selections/charmm.py
MDAnalysis/selections/gromacs.py
MDAnalysis/selections/jmol.py
MDAnalysis/selections/pymol.py
MDAnalysis/selections/vmd.py
MDAnalysis/tests/__init__.py
MDAnalysis/tests/datafiles.py
MDAnalysis/topology/CRDParser.py
MDAnalysis/topology/DLPolyParser.py
MDAnalysis/topology/DMSParser.py
MDAnalysis/topology/ExtendedPDBParser.py
MDAnalysis/topology/FHIAIMSParser.py
MDAnalysis/topology/GMSParser.py
MDAnalysis/topology/GROParser.py
MDAnalysis/topology/GSDParser.py
MDAnalysis/topology/HoomdXMLParser.py
MDAnalysis/topology/ITPParser.py
MDAnalysis/topology/LAMMPSParser.py
MDAnalysis/topology/MMTFParser.py
MDAnalysis/topology/MOL2Parser.py
MDAnalysis/topology/MinimalParser.py
MDAnalysis/topology/PDBParser.py
MDAnalysis/topology/PDBQTParser.py
MDAnalysis/topology/PQRParser.py
MDAnalysis/topology/PSFParser.py
MDAnalysis/topology/ParmEdParser.py
MDAnalysis/topology/TOPParser.py
MDAnalysis/topology/TPRParser.py
MDAnalysis/topology/TXYZParser.py
MDAnalysis/topology/XYZParser.py
MDAnalysis/topology/__init__.py
MDAnalysis/topology/base.py
MDAnalysis/topology/core.py
MDAnalysis/topology/guessers.py
MDAnalysis/topology/tables.py
MDAnalysis/topology/tpr/__init__.py
MDAnalysis/topology/tpr/obj.py
MDAnalysis/topology/tpr/setting.py
MDAnalysis/topology/tpr/utils.py
MDAnalysis/transformations/__init__.py
MDAnalysis/transformations/fit.py
MDAnalysis/transformations/positionaveraging.py
MDAnalysis/transformations/rotate.py
MDAnalysis/transformations/translate.py
MDAnalysis/transformations/wrap.py
MDAnalysis/visualization/__init__.py
MDAnalysis/visualization/streamlines.py
MDAnalysis/visualization/streamlines_3D.py
doc/README
doc/html/.buildinfo
doc/html/genindex.html
doc/html/index.html
doc/html/objects.inv
doc/html/py-modindex.html
doc/html/search.html
doc/html/searchindex.js
doc/html/sitemap.xml
doc/html/.doctrees/environment.pickle
doc/html/.doctrees/index.doctree
doc/html/.doctrees/documentation_pages/analysis_modules.doctree
doc/html/.doctrees/documentation_pages/auxiliary_modules.doctree
doc/html/.doctrees/documentation_pages/converters.doctree
doc/html/.doctrees/documentation_pages/coordinates_modules.doctree
doc/html/.doctrees/documentation_pages/core_modules.doctree
doc/html/.doctrees/documentation_pages/exceptions.doctree
doc/html/.doctrees/documentation_pages/lib_modules.doctree
doc/html/.doctrees/documentation_pages/overview.doctree
doc/html/.doctrees/documentation_pages/references.doctree
doc/html/.doctrees/documentation_pages/selections.doctree
doc/html/.doctrees/documentation_pages/selections_modules.doctree
doc/html/.doctrees/documentation_pages/topology.doctree
doc/html/.doctrees/documentation_pages/topology_modules.doctree
doc/html/.doctrees/documentation_pages/trajectory_transformations.doctree
doc/html/.doctrees/documentation_pages/units.doctree
doc/html/.doctrees/documentation_pages/version.doctree
doc/html/.doctrees/documentation_pages/visualization_modules.doctree
doc/html/.doctrees/documentation_pages/analysis/align.doctree
doc/html/.doctrees/documentation_pages/analysis/base.doctree
doc/html/.doctrees/documentation_pages/analysis/contacts.doctree
doc/html/.doctrees/documentation_pages/analysis/data.doctree
doc/html/.doctrees/documentation_pages/analysis/density.doctree
doc/html/.doctrees/documentation_pages/analysis/diffusionmap.doctree
doc/html/.doctrees/documentation_pages/analysis/dihedrals.doctree
doc/html/.doctrees/documentation_pages/analysis/distances.doctree
doc/html/.doctrees/documentation_pages/analysis/encore.doctree
doc/html/.doctrees/documentation_pages/analysis/gnm.doctree
doc/html/.doctrees/documentation_pages/analysis/hbond_analysis.doctree
doc/html/.doctrees/documentation_pages/analysis/hbond_autocorrel.doctree
doc/html/.doctrees/documentation_pages/analysis/helanal.doctree
doc/html/.doctrees/documentation_pages/analysis/hole.doctree
doc/html/.doctrees/documentation_pages/analysis/hole2.doctree
doc/html/.doctrees/documentation_pages/analysis/hydrogenbonds.doctree
doc/html/.doctrees/documentation_pages/analysis/leaflet.doctree
doc/html/.doctrees/documentation_pages/analysis/legacy_modules.doctree
doc/html/.doctrees/documentation_pages/analysis/lineardensity.doctree
doc/html/.doctrees/documentation_pages/analysis/nuclinfo.doctree
doc/html/.doctrees/documentation_pages/analysis/pca.doctree
doc/html/.doctrees/documentation_pages/analysis/polymer.doctree
doc/html/.doctrees/documentation_pages/analysis/psa.doctree
doc/html/.doctrees/documentation_pages/analysis/rdf.doctree
doc/html/.doctrees/documentation_pages/analysis/rms.doctree
doc/html/.doctrees/documentation_pages/analysis/waterdynamics.doctree
doc/html/.doctrees/documentation_pages/analysis/wbridge_analysis.doctree
doc/html/.doctrees/documentation_pages/analysis/encore/bootstrap.doctree
doc/html/.doctrees/documentation_pages/analysis/encore/clustering.doctree
doc/html/.doctrees/documentation_pages/analysis/encore/confdistmatrix.doctree
doc/html/.doctrees/documentation_pages/analysis/encore/covariance.doctree
doc/html/.doctrees/documentation_pages/analysis/encore/dimensionality_reduction.doctree
doc/html/.doctrees/documentation_pages/analysis/encore/similarity.doctree
doc/html/.doctrees/documentation_pages/analysis/encore/utils.doctree
doc/html/.doctrees/documentation_pages/analysis/legacy/x3dna.doctree
doc/html/.doctrees/documentation_pages/auxiliary/XVG.doctree
doc/html/.doctrees/documentation_pages/auxiliary/base.doctree
doc/html/.doctrees/documentation_pages/auxiliary/core.doctree
doc/html/.doctrees/documentation_pages/auxiliary/init.doctree
doc/html/.doctrees/documentation_pages/converters/ParmEdParser.doctree
doc/html/.doctrees/documentation_pages/coordinates/CRD.doctree
doc/html/.doctrees/documentation_pages/coordinates/DCD.doctree
doc/html/.doctrees/documentation_pages/coordinates/DLPoly.doctree
doc/html/.doctrees/documentation_pages/coordinates/DMS.doctree
doc/html/.doctrees/documentation_pages/coordinates/FHIAIMS.doctree
doc/html/.doctrees/documentation_pages/coordinates/GMS.doctree
doc/html/.doctrees/documentation_pages/coordinates/GRO.doctree
doc/html/.doctrees/documentation_pages/coordinates/GSD.doctree
doc/html/.doctrees/documentation_pages/coordinates/INPCRD.doctree
doc/html/.doctrees/documentation_pages/coordinates/LAMMPS.doctree
doc/html/.doctrees/documentation_pages/coordinates/MMTF.doctree
doc/html/.doctrees/documentation_pages/coordinates/MOL2.doctree
doc/html/.doctrees/documentation_pages/coordinates/NAMDBIN.doctree
doc/html/.doctrees/documentation_pages/coordinates/PDB.doctree
doc/html/.doctrees/documentation_pages/coordinates/PDBQT.doctree
doc/html/.doctrees/documentation_pages/coordinates/PQR.doctree
doc/html/.doctrees/documentation_pages/coordinates/TRJ.doctree
doc/html/.doctrees/documentation_pages/coordinates/TRR.doctree
doc/html/.doctrees/documentation_pages/coordinates/TRZ.doctree
doc/html/.doctrees/documentation_pages/coordinates/TXYZ.doctree
doc/html/.doctrees/documentation_pages/coordinates/XDR.doctree
doc/html/.doctrees/documentation_pages/coordinates/XTC.doctree
doc/html/.doctrees/documentation_pages/coordinates/XYZ.doctree
doc/html/.doctrees/documentation_pages/coordinates/base.doctree
doc/html/.doctrees/documentation_pages/coordinates/chain.doctree
doc/html/.doctrees/documentation_pages/coordinates/chemfiles.doctree
doc/html/.doctrees/documentation_pages/coordinates/core.doctree
doc/html/.doctrees/documentation_pages/coordinates/init.doctree
doc/html/.doctrees/documentation_pages/coordinates/memory.doctree
doc/html/.doctrees/documentation_pages/coordinates/null.doctree
doc/html/.doctrees/documentation_pages/core/groups.doctree
doc/html/.doctrees/documentation_pages/core/init.doctree
doc/html/.doctrees/documentation_pages/core/selection.doctree
doc/html/.doctrees/documentation_pages/core/topology.doctree
doc/html/.doctrees/documentation_pages/core/topologyattrs.doctree
doc/html/.doctrees/documentation_pages/core/topologyobjects.doctree
doc/html/.doctrees/documentation_pages/core/universe.doctree
doc/html/.doctrees/documentation_pages/lib/NeighborSearch.doctree
doc/html/.doctrees/documentation_pages/lib/c_distances.doctree
doc/html/.doctrees/documentation_pages/lib/c_distances_openmp.doctree
doc/html/.doctrees/documentation_pages/lib/correlations.doctree
doc/html/.doctrees/documentation_pages/lib/distances.doctree
doc/html/.doctrees/documentation_pages/lib/log.doctree
doc/html/.doctrees/documentation_pages/lib/mdamath.doctree
doc/html/.doctrees/documentation_pages/lib/nsgrid.doctree
doc/html/.doctrees/documentation_pages/lib/pkdtree.doctree
doc/html/.doctrees/documentation_pages/lib/qcprot.doctree
doc/html/.doctrees/documentation_pages/lib/transformations.doctree
doc/html/.doctrees/documentation_pages/lib/util.doctree
doc/html/.doctrees/documentation_pages/lib/formats/libdcd.doctree
doc/html/.doctrees/documentation_pages/lib/formats/libmdaxdr.doctree
doc/html/.doctrees/documentation_pages/selections/base.doctree
doc/html/.doctrees/documentation_pages/selections/charmm.doctree
doc/html/.doctrees/documentation_pages/selections/gromacs.doctree
doc/html/.doctrees/documentation_pages/selections/jmol.doctree
doc/html/.doctrees/documentation_pages/selections/pymol.doctree
doc/html/.doctrees/documentation_pages/selections/vmd.doctree
doc/html/.doctrees/documentation_pages/topology/CRDParser.doctree
doc/html/.doctrees/documentation_pages/topology/DLPolyParser.doctree
doc/html/.doctrees/documentation_pages/topology/DMSParser.doctree
doc/html/.doctrees/documentation_pages/topology/ExtendedPDBParser.doctree
doc/html/.doctrees/documentation_pages/topology/FHIAIMSParser.doctree
doc/html/.doctrees/documentation_pages/topology/GMSParser.doctree
doc/html/.doctrees/documentation_pages/topology/GROParser.doctree
doc/html/.doctrees/documentation_pages/topology/GSDParser.doctree
doc/html/.doctrees/documentation_pages/topology/HoomdXMLParser.doctree
doc/html/.doctrees/documentation_pages/topology/ITPParser.doctree
doc/html/.doctrees/documentation_pages/topology/LAMMPSParser.doctree
doc/html/.doctrees/documentation_pages/topology/MMTFParser.doctree
doc/html/.doctrees/documentation_pages/topology/MOL2Parser.doctree
doc/html/.doctrees/documentation_pages/topology/MinimalParser.doctree
doc/html/.doctrees/documentation_pages/topology/PDBParser.doctree
doc/html/.doctrees/documentation_pages/topology/PDBQTParser.doctree
doc/html/.doctrees/documentation_pages/topology/PQRParser.doctree
doc/html/.doctrees/documentation_pages/topology/PSFParser.doctree
doc/html/.doctrees/documentation_pages/topology/TOPParser.doctree
doc/html/.doctrees/documentation_pages/topology/TPRParser.doctree
doc/html/.doctrees/documentation_pages/topology/TXYZParser.doctree
doc/html/.doctrees/documentation_pages/topology/XYZParser.doctree
doc/html/.doctrees/documentation_pages/topology/base.doctree
doc/html/.doctrees/documentation_pages/topology/core.doctree
doc/html/.doctrees/documentation_pages/topology/guessers.doctree
doc/html/.doctrees/documentation_pages/topology/init.doctree
doc/html/.doctrees/documentation_pages/topology/tables.doctree
doc/html/.doctrees/documentation_pages/topology/tpr_util.doctree
doc/html/.doctrees/documentation_pages/transformations/fit.doctree
doc/html/.doctrees/documentation_pages/transformations/positionaveraging.doctree
doc/html/.doctrees/documentation_pages/transformations/rotate.doctree
doc/html/.doctrees/documentation_pages/transformations/translate.doctree
doc/html/.doctrees/documentation_pages/transformations/wrap.doctree
doc/html/.doctrees/documentation_pages/visualization/streamlines.doctree
doc/html/.doctrees/documentation_pages/visualization/streamlines_3D.doctree
doc/html/_images/janin_demo_plot.png
doc/html/_images/rama_demo_plot.png
doc/html/_images/test_streamplot_3D.png
doc/html/_images/testing_streamline.png
doc/html/_modules/index.html
doc/html/_modules/numpy.html
doc/html/_modules/MDAnalysis/exceptions.html
doc/html/_modules/MDAnalysis/selections.html
doc/html/_modules/MDAnalysis/units.html
doc/html/_modules/MDAnalysis/analysis/align.html
doc/html/_modules/MDAnalysis/analysis/base.html
doc/html/_modules/MDAnalysis/analysis/contacts.html
doc/html/_modules/MDAnalysis/analysis/density.html
doc/html/_modules/MDAnalysis/analysis/diffusionmap.html
doc/html/_modules/MDAnalysis/analysis/dihedrals.html
doc/html/_modules/MDAnalysis/analysis/distances.html
doc/html/_modules/MDAnalysis/analysis/gnm.html
doc/html/_modules/MDAnalysis/analysis/helanal.html
doc/html/_modules/MDAnalysis/analysis/hole.html
doc/html/_modules/MDAnalysis/analysis/leaflet.html
doc/html/_modules/MDAnalysis/analysis/lineardensity.html
doc/html/_modules/MDAnalysis/analysis/nuclinfo.html
doc/html/_modules/MDAnalysis/analysis/pca.html
doc/html/_modules/MDAnalysis/analysis/polymer.html
doc/html/_modules/MDAnalysis/analysis/psa.html
doc/html/_modules/MDAnalysis/analysis/rdf.html
doc/html/_modules/MDAnalysis/analysis/rms.html
doc/html/_modules/MDAnalysis/analysis/waterdynamics.html
doc/html/_modules/MDAnalysis/analysis/encore/bootstrap.html
doc/html/_modules/MDAnalysis/analysis/encore/confdistmatrix.html
doc/html/_modules/MDAnalysis/analysis/encore/covariance.html
doc/html/_modules/MDAnalysis/analysis/encore/similarity.html
doc/html/_modules/MDAnalysis/analysis/encore/utils.html
doc/html/_modules/MDAnalysis/analysis/encore/clustering/ClusterCollection.html
doc/html/_modules/MDAnalysis/analysis/encore/clustering/ClusteringMethod.html
doc/html/_modules/MDAnalysis/analysis/encore/clustering/cluster.html
doc/html/_modules/MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.html
doc/html/_modules/MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.html
doc/html/_modules/MDAnalysis/analysis/hbonds/hbond_analysis.html
doc/html/_modules/MDAnalysis/analysis/hbonds/hbond_autocorrel.html
doc/html/_modules/MDAnalysis/analysis/hbonds/wbridge_analysis.html
doc/html/_modules/MDAnalysis/analysis/hole2/hole.html
doc/html/_modules/MDAnalysis/analysis/hole2/utils.html
doc/html/_modules/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.html
doc/html/_modules/MDAnalysis/analysis/legacy/x3dna.html
doc/html/_modules/MDAnalysis/auxiliary/XVG.html
doc/html/_modules/MDAnalysis/auxiliary/base.html
doc/html/_modules/MDAnalysis/auxiliary/core.html
doc/html/_modules/MDAnalysis/coordinates/CRD.html
doc/html/_modules/MDAnalysis/coordinates/DCD.html
doc/html/_modules/MDAnalysis/coordinates/DLPoly.html
doc/html/_modules/MDAnalysis/coordinates/DMS.html
doc/html/_modules/MDAnalysis/coordinates/FHIAIMS.html
doc/html/_modules/MDAnalysis/coordinates/GMS.html
doc/html/_modules/MDAnalysis/coordinates/GRO.html
doc/html/_modules/MDAnalysis/coordinates/GSD.html
doc/html/_modules/MDAnalysis/coordinates/INPCRD.html
doc/html/_modules/MDAnalysis/coordinates/LAMMPS.html
doc/html/_modules/MDAnalysis/coordinates/MMTF.html
doc/html/_modules/MDAnalysis/coordinates/MOL2.html
doc/html/_modules/MDAnalysis/coordinates/NAMDBIN.html
doc/html/_modules/MDAnalysis/coordinates/PDB.html
doc/html/_modules/MDAnalysis/coordinates/PDBQT.html
doc/html/_modules/MDAnalysis/coordinates/PQR.html
doc/html/_modules/MDAnalysis/coordinates/ParmEd.html
doc/html/_modules/MDAnalysis/coordinates/TRJ.html
doc/html/_modules/MDAnalysis/coordinates/TRR.html
doc/html/_modules/MDAnalysis/coordinates/TRZ.html
doc/html/_modules/MDAnalysis/coordinates/TXYZ.html
doc/html/_modules/MDAnalysis/coordinates/XDR.html
doc/html/_modules/MDAnalysis/coordinates/XTC.html
doc/html/_modules/MDAnalysis/coordinates/XYZ.html
doc/html/_modules/MDAnalysis/coordinates/base.html
doc/html/_modules/MDAnalysis/coordinates/chain.html
doc/html/_modules/MDAnalysis/coordinates/chemfiles.html
doc/html/_modules/MDAnalysis/coordinates/core.html
doc/html/_modules/MDAnalysis/coordinates/memory.html
doc/html/_modules/MDAnalysis/coordinates/null.html
doc/html/_modules/MDAnalysis/core/_get_readers.html
doc/html/_modules/MDAnalysis/core/groups.html
doc/html/_modules/MDAnalysis/core/selection.html
doc/html/_modules/MDAnalysis/core/topology.html
doc/html/_modules/MDAnalysis/core/topologyattrs.html
doc/html/_modules/MDAnalysis/core/topologyobjects.html
doc/html/_modules/MDAnalysis/core/universe.html
doc/html/_modules/MDAnalysis/lib/NeighborSearch.html
doc/html/_modules/MDAnalysis/lib/correlations.html
doc/html/_modules/MDAnalysis/lib/distances.html
doc/html/_modules/MDAnalysis/lib/log.html
doc/html/_modules/MDAnalysis/lib/mdamath.html
doc/html/_modules/MDAnalysis/lib/pkdtree.html
doc/html/_modules/MDAnalysis/lib/transformations.html
doc/html/_modules/MDAnalysis/lib/util.html
doc/html/_modules/MDAnalysis/selections/base.html
doc/html/_modules/MDAnalysis/selections/charmm.html
doc/html/_modules/MDAnalysis/selections/gromacs.html
doc/html/_modules/MDAnalysis/selections/jmol.html
doc/html/_modules/MDAnalysis/selections/pymol.html
doc/html/_modules/MDAnalysis/selections/vmd.html
doc/html/_modules/MDAnalysis/topology/CRDParser.html
doc/html/_modules/MDAnalysis/topology/DMSParser.html
doc/html/_modules/MDAnalysis/topology/ExtendedPDBParser.html
doc/html/_modules/MDAnalysis/topology/FHIAIMSParser.html
doc/html/_modules/MDAnalysis/topology/GMSParser.html
doc/html/_modules/MDAnalysis/topology/GROParser.html
doc/html/_modules/MDAnalysis/topology/GSDParser.html
doc/html/_modules/MDAnalysis/topology/HoomdXMLParser.html
doc/html/_modules/MDAnalysis/topology/ITPParser.html
doc/html/_modules/MDAnalysis/topology/LAMMPSParser.html
doc/html/_modules/MDAnalysis/topology/MMTFParser.html
doc/html/_modules/MDAnalysis/topology/MOL2Parser.html
doc/html/_modules/MDAnalysis/topology/MinimalParser.html
doc/html/_modules/MDAnalysis/topology/PDBParser.html
doc/html/_modules/MDAnalysis/topology/PDBQTParser.html
doc/html/_modules/MDAnalysis/topology/PQRParser.html
doc/html/_modules/MDAnalysis/topology/PSFParser.html
doc/html/_modules/MDAnalysis/topology/ParmEdParser.html
doc/html/_modules/MDAnalysis/topology/TOPParser.html
doc/html/_modules/MDAnalysis/topology/TPRParser.html
doc/html/_modules/MDAnalysis/topology/TXYZParser.html
doc/html/_modules/MDAnalysis/topology/XYZParser.html
doc/html/_modules/MDAnalysis/topology/base.html
doc/html/_modules/MDAnalysis/topology/guessers.html
doc/html/_modules/MDAnalysis/topology/tables.html
doc/html/_modules/MDAnalysis/topology/tpr/obj.html
doc/html/_modules/MDAnalysis/topology/tpr/utils.html
doc/html/_modules/MDAnalysis/transformations/fit.html
doc/html/_modules/MDAnalysis/transformations/positionaveraging.html
doc/html/_modules/MDAnalysis/transformations/rotate.html
doc/html/_modules/MDAnalysis/transformations/translate.html
doc/html/_modules/MDAnalysis/transformations/wrap.html
doc/html/_modules/MDAnalysis/visualization/streamlines.html
doc/html/_modules/MDAnalysis/visualization/streamlines_3D.html
doc/html/_modules/gridData/core.html
doc/html/_sources/index.rst.txt
doc/html/_sources/documentation_pages/analysis_modules.rst.txt
doc/html/_sources/documentation_pages/auxiliary_modules.rst.txt
doc/html/_sources/documentation_pages/converters.rst.txt
doc/html/_sources/documentation_pages/coordinates_modules.rst.txt
doc/html/_sources/documentation_pages/core_modules.rst.txt
doc/html/_sources/documentation_pages/exceptions.rst.txt
doc/html/_sources/documentation_pages/lib_modules.rst.txt
doc/html/_sources/documentation_pages/overview.rst.txt
doc/html/_sources/documentation_pages/references.rst.txt
doc/html/_sources/documentation_pages/selections.rst.txt
doc/html/_sources/documentation_pages/selections_modules.rst.txt
doc/html/_sources/documentation_pages/topology.rst.txt
doc/html/_sources/documentation_pages/topology_modules.rst.txt
doc/html/_sources/documentation_pages/trajectory_transformations.rst.txt
doc/html/_sources/documentation_pages/units.rst.txt
doc/html/_sources/documentation_pages/version.rst.txt
doc/html/_sources/documentation_pages/visualization_modules.rst.txt
doc/html/_sources/documentation_pages/analysis/align.rst.txt
doc/html/_sources/documentation_pages/analysis/base.rst.txt
doc/html/_sources/documentation_pages/analysis/contacts.rst.txt
doc/html/_sources/documentation_pages/analysis/data.rst.txt
doc/html/_sources/documentation_pages/analysis/density.rst.txt
doc/html/_sources/documentation_pages/analysis/diffusionmap.rst.txt
doc/html/_sources/documentation_pages/analysis/dihedrals.rst.txt
doc/html/_sources/documentation_pages/analysis/distances.rst.txt
doc/html/_sources/documentation_pages/analysis/encore.rst.txt
doc/html/_sources/documentation_pages/analysis/gnm.rst.txt
doc/html/_sources/documentation_pages/analysis/hbond_analysis.rst.txt
doc/html/_sources/documentation_pages/analysis/hbond_autocorrel.rst.txt
doc/html/_sources/documentation_pages/analysis/helanal.rst.txt
doc/html/_sources/documentation_pages/analysis/hole.rst.txt
doc/html/_sources/documentation_pages/analysis/hole2.rst.txt
doc/html/_sources/documentation_pages/analysis/hydrogenbonds.rst.txt
doc/html/_sources/documentation_pages/analysis/leaflet.rst.txt
doc/html/_sources/documentation_pages/analysis/legacy_modules.rst.txt
doc/html/_sources/documentation_pages/analysis/lineardensity.rst.txt
doc/html/_sources/documentation_pages/analysis/nuclinfo.rst.txt
doc/html/_sources/documentation_pages/analysis/pca.rst.txt
doc/html/_sources/documentation_pages/analysis/polymer.rst.txt
doc/html/_sources/documentation_pages/analysis/psa.rst.txt
doc/html/_sources/documentation_pages/analysis/rdf.rst.txt
doc/html/_sources/documentation_pages/analysis/rms.rst.txt
doc/html/_sources/documentation_pages/analysis/waterdynamics.rst.txt
doc/html/_sources/documentation_pages/analysis/wbridge_analysis.rst.txt
doc/html/_sources/documentation_pages/analysis/encore/bootstrap.rst.txt
doc/html/_sources/documentation_pages/analysis/encore/clustering.rst.txt
doc/html/_sources/documentation_pages/analysis/encore/confdistmatrix.rst.txt
doc/html/_sources/documentation_pages/analysis/encore/covariance.rst.txt
doc/html/_sources/documentation_pages/analysis/encore/dimensionality_reduction.rst.txt
doc/html/_sources/documentation_pages/analysis/encore/similarity.rst.txt
doc/html/_sources/documentation_pages/analysis/encore/utils.rst.txt
doc/html/_sources/documentation_pages/analysis/legacy/x3dna.rst.txt
doc/html/_sources/documentation_pages/auxiliary/XVG.rst.txt
doc/html/_sources/documentation_pages/auxiliary/base.rst.txt
doc/html/_sources/documentation_pages/auxiliary/core.rst.txt
doc/html/_sources/documentation_pages/auxiliary/init.rst.txt
doc/html/_sources/documentation_pages/converters/ParmEdParser.rst.txt
doc/html/_sources/documentation_pages/coordinates/CRD.rst.txt
doc/html/_sources/documentation_pages/coordinates/DCD.rst.txt
doc/html/_sources/documentation_pages/coordinates/DLPoly.rst.txt
doc/html/_sources/documentation_pages/coordinates/DMS.rst.txt
doc/html/_sources/documentation_pages/coordinates/FHIAIMS.rst.txt
doc/html/_sources/documentation_pages/coordinates/GMS.rst.txt
doc/html/_sources/documentation_pages/coordinates/GRO.rst.txt
doc/html/_sources/documentation_pages/coordinates/GSD.rst.txt
doc/html/_sources/documentation_pages/coordinates/INPCRD.rst.txt
doc/html/_sources/documentation_pages/coordinates/LAMMPS.rst.txt
doc/html/_sources/documentation_pages/coordinates/MMTF.rst.txt
doc/html/_sources/documentation_pages/coordinates/MOL2.rst.txt
doc/html/_sources/documentation_pages/coordinates/NAMDBIN.rst.txt
doc/html/_sources/documentation_pages/coordinates/PDB.rst.txt
doc/html/_sources/documentation_pages/coordinates/PDBQT.rst.txt
doc/html/_sources/documentation_pages/coordinates/PQR.rst.txt
doc/html/_sources/documentation_pages/coordinates/TRJ.rst.txt
doc/html/_sources/documentation_pages/coordinates/TRR.rst.txt
doc/html/_sources/documentation_pages/coordinates/TRZ.rst.txt
doc/html/_sources/documentation_pages/coordinates/TXYZ.rst.txt
doc/html/_sources/documentation_pages/coordinates/XDR.rst.txt
doc/html/_sources/documentation_pages/coordinates/XTC.rst.txt
doc/html/_sources/documentation_pages/coordinates/XYZ.rst.txt
doc/html/_sources/documentation_pages/coordinates/base.rst.txt
doc/html/_sources/documentation_pages/coordinates/chain.rst.txt
doc/html/_sources/documentation_pages/coordinates/chemfiles.rst.txt
doc/html/_sources/documentation_pages/coordinates/core.rst.txt
doc/html/_sources/documentation_pages/coordinates/init.rst.txt
doc/html/_sources/documentation_pages/coordinates/memory.rst.txt
doc/html/_sources/documentation_pages/coordinates/null.rst.txt
doc/html/_sources/documentation_pages/core/groups.rst.txt
doc/html/_sources/documentation_pages/core/init.rst.txt
doc/html/_sources/documentation_pages/core/selection.rst.txt
doc/html/_sources/documentation_pages/core/topology.rst.txt
doc/html/_sources/documentation_pages/core/topologyattrs.rst.txt
doc/html/_sources/documentation_pages/core/topologyobjects.rst.txt
doc/html/_sources/documentation_pages/core/universe.rst.txt
doc/html/_sources/documentation_pages/lib/NeighborSearch.rst.txt
doc/html/_sources/documentation_pages/lib/c_distances.rst.txt
doc/html/_sources/documentation_pages/lib/c_distances_openmp.rst.txt
doc/html/_sources/documentation_pages/lib/correlations.rst.txt
doc/html/_sources/documentation_pages/lib/distances.rst.txt
doc/html/_sources/documentation_pages/lib/log.rst.txt
doc/html/_sources/documentation_pages/lib/mdamath.rst.txt
doc/html/_sources/documentation_pages/lib/nsgrid.rst.txt
doc/html/_sources/documentation_pages/lib/pkdtree.rst.txt
doc/html/_sources/documentation_pages/lib/qcprot.rst.txt
doc/html/_sources/documentation_pages/lib/transformations.rst.txt
doc/html/_sources/documentation_pages/lib/util.rst.txt
doc/html/_sources/documentation_pages/lib/formats/libdcd.rst.txt
doc/html/_sources/documentation_pages/lib/formats/libmdaxdr.rst.txt
doc/html/_sources/documentation_pages/selections/base.rst.txt
doc/html/_sources/documentation_pages/selections/charmm.rst.txt
doc/html/_sources/documentation_pages/selections/gromacs.rst.txt
doc/html/_sources/documentation_pages/selections/jmol.rst.txt
doc/html/_sources/documentation_pages/selections/pymol.rst.txt
doc/html/_sources/documentation_pages/selections/vmd.rst.txt
doc/html/_sources/documentation_pages/topology/CRDParser.rst.txt
doc/html/_sources/documentation_pages/topology/DLPolyParser.rst.txt
doc/html/_sources/documentation_pages/topology/DMSParser.rst.txt
doc/html/_sources/documentation_pages/topology/ExtendedPDBParser.rst.txt
doc/html/_sources/documentation_pages/topology/FHIAIMSParser.rst.txt
doc/html/_sources/documentation_pages/topology/GMSParser.rst.txt
doc/html/_sources/documentation_pages/topology/GROParser.rst.txt
doc/html/_sources/documentation_pages/topology/GSDParser.rst.txt
doc/html/_sources/documentation_pages/topology/HoomdXMLParser.rst.txt
doc/html/_sources/documentation_pages/topology/ITPParser.rst.txt
doc/html/_sources/documentation_pages/topology/LAMMPSParser.rst.txt
doc/html/_sources/documentation_pages/topology/MMTFParser.rst.txt
doc/html/_sources/documentation_pages/topology/MOL2Parser.rst.txt
doc/html/_sources/documentation_pages/topology/MinimalParser.rst.txt
doc/html/_sources/documentation_pages/topology/PDBParser.rst.txt
doc/html/_sources/documentation_pages/topology/PDBQTParser.rst.txt
doc/html/_sources/documentation_pages/topology/PQRParser.rst.txt
doc/html/_sources/documentation_pages/topology/PSFParser.rst.txt
doc/html/_sources/documentation_pages/topology/TOPParser.rst.txt
doc/html/_sources/documentation_pages/topology/TPRParser.rst.txt
doc/html/_sources/documentation_pages/topology/TXYZParser.rst.txt
doc/html/_sources/documentation_pages/topology/XYZParser.rst.txt
doc/html/_sources/documentation_pages/topology/base.rst.txt
doc/html/_sources/documentation_pages/topology/core.rst.txt
doc/html/_sources/documentation_pages/topology/guessers.rst.txt
doc/html/_sources/documentation_pages/topology/init.rst.txt
doc/html/_sources/documentation_pages/topology/tables.rst.txt
doc/html/_sources/documentation_pages/topology/tpr_util.rst.txt
doc/html/_sources/documentation_pages/transformations/fit.rst.txt
doc/html/_sources/documentation_pages/transformations/positionaveraging.rst.txt
doc/html/_sources/documentation_pages/transformations/rotate.rst.txt
doc/html/_sources/documentation_pages/transformations/translate.rst.txt
doc/html/_sources/documentation_pages/transformations/wrap.rst.txt
doc/html/_sources/documentation_pages/visualization/streamlines.rst.txt
doc/html/_sources/documentation_pages/visualization/streamlines_3D.rst.txt
doc/html/_static/ajax-loader.gif
doc/html/_static/basic.css
doc/html/_static/comment-bright.png
doc/html/_static/comment-close.png
doc/html/_static/comment.png
doc/html/_static/custom.css
doc/html/_static/doctools.js
doc/html/_static/documentation_options.js
doc/html/_static/down-pressed.png
doc/html/_static/down.png
doc/html/_static/file.png
doc/html/_static/jquery-3.2.1.js
doc/html/_static/jquery-3.5.1.js
doc/html/_static/jquery.js
doc/html/_static/language_data.js
doc/html/_static/mdanalysis-logo-thin.png
doc/html/_static/mdanalysis-logo.ico
doc/html/_static/minus.png
doc/html/_static/opensearch.xml
doc/html/_static/plus.png
doc/html/_static/pygments.css
doc/html/_static/readable.css
doc/html/_static/searchtools.js
doc/html/_static/underscore-1.3.1.js
doc/html/_static/underscore.js
doc/html/_static/up-pressed.png
doc/html/_static/up.png
doc/html/_static/websupport.js
doc/html/_static/css/badge_only.css
doc/html/_static/css/theme.css
doc/html/_static/fonts/fontawesome-webfont.eot
doc/html/_static/fonts/fontawesome-webfont.svg
doc/html/_static/fonts/fontawesome-webfont.ttf
doc/html/_static/fonts/fontawesome-webfont.woff
doc/html/_static/fonts/fontawesome-webfont.woff2
doc/html/_static/fonts/Lato/lato-bold.eot
doc/html/_static/fonts/Lato/lato-bold.ttf
doc/html/_static/fonts/Lato/lato-bold.woff
doc/html/_static/fonts/Lato/lato-bold.woff2
doc/html/_static/fonts/Lato/lato-bolditalic.eot
doc/html/_static/fonts/Lato/lato-bolditalic.ttf
doc/html/_static/fonts/Lato/lato-bolditalic.woff
doc/html/_static/fonts/Lato/lato-bolditalic.woff2
doc/html/_static/fonts/Lato/lato-italic.eot
doc/html/_static/fonts/Lato/lato-italic.ttf
doc/html/_static/fonts/Lato/lato-italic.woff
doc/html/_static/fonts/Lato/lato-italic.woff2
doc/html/_static/fonts/Lato/lato-regular.eot
doc/html/_static/fonts/Lato/lato-regular.ttf
doc/html/_static/fonts/Lato/lato-regular.woff
doc/html/_static/fonts/Lato/lato-regular.woff2
doc/html/_static/fonts/RobotoSlab/roboto-slab-v7-bold.eot
doc/html/_static/fonts/RobotoSlab/roboto-slab-v7-bold.ttf
doc/html/_static/fonts/RobotoSlab/roboto-slab-v7-bold.woff
doc/html/_static/fonts/RobotoSlab/roboto-slab-v7-bold.woff2
doc/html/_static/fonts/RobotoSlab/roboto-slab-v7-regular.eot
doc/html/_static/fonts/RobotoSlab/roboto-slab-v7-regular.ttf
doc/html/_static/fonts/RobotoSlab/roboto-slab-v7-regular.woff
doc/html/_static/fonts/RobotoSlab/roboto-slab-v7-regular.woff2
doc/html/_static/js/modernizr.min.js
doc/html/_static/js/theme.js
doc/html/_static/logos/AUTHOR
doc/html/_static/logos/mdanalysis-logo-127x55.png
doc/html/_static/logos/mdanalysis-logo-200x150.png
doc/html/_static/logos/mdanalysis-logo-thin.png
doc/html/_static/logos/mdanalysis-logo.ico
doc/html/_static/logos/mdanalysis-logo.pdf
doc/html/_static/logos/mdanalysis-logo.png
doc/html/_static/logos/mdanalysis-logo_square.pdf
doc/html/_static/logos/mdanalysis-logo_square.png
doc/html/_static/logos/mdanalysis-logo_square.svg
doc/html/_static/logos/mdanalysis-logo_square_45mm.pdf
doc/html/_static/logos/mdanalysis-logo_square_45mm.png
doc/html/_static/logos/mdanalysis-logo_square_72dpi.png
doc/html/doctrees/index.doctree
doc/html/doctrees/documentation_pages/analysis_modules.doctree
doc/html/doctrees/documentation_pages/auxiliary_modules.doctree
doc/html/doctrees/documentation_pages/converters.doctree
doc/html/doctrees/documentation_pages/coordinates_modules.doctree
doc/html/doctrees/documentation_pages/core_modules.doctree
doc/html/doctrees/documentation_pages/exceptions.doctree
doc/html/doctrees/documentation_pages/lib_modules.doctree
doc/html/doctrees/documentation_pages/overview.doctree
doc/html/doctrees/documentation_pages/references.doctree
doc/html/doctrees/documentation_pages/selections.doctree
doc/html/doctrees/documentation_pages/selections_modules.doctree
doc/html/doctrees/documentation_pages/topology.doctree
doc/html/doctrees/documentation_pages/topology_modules.doctree
doc/html/doctrees/documentation_pages/trajectory_transformations.doctree
doc/html/doctrees/documentation_pages/units.doctree
doc/html/doctrees/documentation_pages/version.doctree
doc/html/doctrees/documentation_pages/visualization_modules.doctree
doc/html/doctrees/documentation_pages/analysis/align.doctree
doc/html/doctrees/documentation_pages/analysis/base.doctree
doc/html/doctrees/documentation_pages/analysis/contacts.doctree
doc/html/doctrees/documentation_pages/analysis/data.doctree
doc/html/doctrees/documentation_pages/analysis/density.doctree
doc/html/doctrees/documentation_pages/analysis/diffusionmap.doctree
doc/html/doctrees/documentation_pages/analysis/dihedrals.doctree
doc/html/doctrees/documentation_pages/analysis/distances.doctree
doc/html/doctrees/documentation_pages/analysis/encore.doctree
doc/html/doctrees/documentation_pages/analysis/gnm.doctree
doc/html/doctrees/documentation_pages/analysis/hbond_analysis.doctree
doc/html/doctrees/documentation_pages/analysis/hbond_autocorrel.doctree
doc/html/doctrees/documentation_pages/analysis/helanal.doctree
doc/html/doctrees/documentation_pages/analysis/hole.doctree
doc/html/doctrees/documentation_pages/analysis/hole2.doctree
doc/html/doctrees/documentation_pages/analysis/hydrogenbonds.doctree
doc/html/doctrees/documentation_pages/analysis/leaflet.doctree
doc/html/doctrees/documentation_pages/analysis/legacy_modules.doctree
doc/html/doctrees/documentation_pages/analysis/lineardensity.doctree
doc/html/doctrees/documentation_pages/analysis/nuclinfo.doctree
doc/html/doctrees/documentation_pages/analysis/pca.doctree
doc/html/doctrees/documentation_pages/analysis/polymer.doctree
doc/html/doctrees/documentation_pages/analysis/psa.doctree
doc/html/doctrees/documentation_pages/analysis/rdf.doctree
doc/html/doctrees/documentation_pages/analysis/rms.doctree
doc/html/doctrees/documentation_pages/analysis/waterdynamics.doctree
doc/html/doctrees/documentation_pages/analysis/wbridge_analysis.doctree
doc/html/doctrees/documentation_pages/analysis/encore/bootstrap.doctree
doc/html/doctrees/documentation_pages/analysis/encore/clustering.doctree
doc/html/doctrees/documentation_pages/analysis/encore/confdistmatrix.doctree
doc/html/doctrees/documentation_pages/analysis/encore/covariance.doctree
doc/html/doctrees/documentation_pages/analysis/encore/dimensionality_reduction.doctree
doc/html/doctrees/documentation_pages/analysis/encore/similarity.doctree
doc/html/doctrees/documentation_pages/analysis/encore/utils.doctree
doc/html/doctrees/documentation_pages/analysis/legacy/x3dna.doctree
doc/html/doctrees/documentation_pages/auxiliary/XVG.doctree
doc/html/doctrees/documentation_pages/auxiliary/base.doctree
doc/html/doctrees/documentation_pages/auxiliary/core.doctree
doc/html/doctrees/documentation_pages/auxiliary/init.doctree
doc/html/doctrees/documentation_pages/converters/ParmEdParser.doctree
doc/html/doctrees/documentation_pages/coordinates/CRD.doctree
doc/html/doctrees/documentation_pages/coordinates/DCD.doctree
doc/html/doctrees/documentation_pages/coordinates/DLPoly.doctree
doc/html/doctrees/documentation_pages/coordinates/DMS.doctree
doc/html/doctrees/documentation_pages/coordinates/FHIAIMS.doctree
doc/html/doctrees/documentation_pages/coordinates/GMS.doctree
doc/html/doctrees/documentation_pages/coordinates/GRO.doctree
doc/html/doctrees/documentation_pages/coordinates/GSD.doctree
doc/html/doctrees/documentation_pages/coordinates/INPCRD.doctree
doc/html/doctrees/documentation_pages/coordinates/LAMMPS.doctree
doc/html/doctrees/documentation_pages/coordinates/MMTF.doctree
doc/html/doctrees/documentation_pages/coordinates/MOL2.doctree
doc/html/doctrees/documentation_pages/coordinates/NAMDBIN.doctree
doc/html/doctrees/documentation_pages/coordinates/PDB.doctree
doc/html/doctrees/documentation_pages/coordinates/PDBQT.doctree
doc/html/doctrees/documentation_pages/coordinates/PQR.doctree
doc/html/doctrees/documentation_pages/coordinates/TRJ.doctree
doc/html/doctrees/documentation_pages/coordinates/TRR.doctree
doc/html/doctrees/documentation_pages/coordinates/TRZ.doctree
doc/html/doctrees/documentation_pages/coordinates/TXYZ.doctree
doc/html/doctrees/documentation_pages/coordinates/XDR.doctree
doc/html/doctrees/documentation_pages/coordinates/XTC.doctree
doc/html/doctrees/documentation_pages/coordinates/XYZ.doctree
doc/html/doctrees/documentation_pages/coordinates/base.doctree
doc/html/doctrees/documentation_pages/coordinates/chain.doctree
doc/html/doctrees/documentation_pages/coordinates/chemfiles.doctree
doc/html/doctrees/documentation_pages/coordinates/core.doctree
doc/html/doctrees/documentation_pages/coordinates/init.doctree
doc/html/doctrees/documentation_pages/coordinates/memory.doctree
doc/html/doctrees/documentation_pages/coordinates/null.doctree
doc/html/doctrees/documentation_pages/core/groups.doctree
doc/html/doctrees/documentation_pages/core/init.doctree
doc/html/doctrees/documentation_pages/core/selection.doctree
doc/html/doctrees/documentation_pages/core/topology.doctree
doc/html/doctrees/documentation_pages/core/topologyattrs.doctree
doc/html/doctrees/documentation_pages/core/topologyobjects.doctree
doc/html/doctrees/documentation_pages/core/universe.doctree
doc/html/doctrees/documentation_pages/lib/NeighborSearch.doctree
doc/html/doctrees/documentation_pages/lib/c_distances.doctree
doc/html/doctrees/documentation_pages/lib/c_distances_openmp.doctree
doc/html/doctrees/documentation_pages/lib/correlations.doctree
doc/html/doctrees/documentation_pages/lib/distances.doctree
doc/html/doctrees/documentation_pages/lib/log.doctree
doc/html/doctrees/documentation_pages/lib/mdamath.doctree
doc/html/doctrees/documentation_pages/lib/nsgrid.doctree
doc/html/doctrees/documentation_pages/lib/pkdtree.doctree
doc/html/doctrees/documentation_pages/lib/qcprot.doctree
doc/html/doctrees/documentation_pages/lib/transformations.doctree
doc/html/doctrees/documentation_pages/lib/util.doctree
doc/html/doctrees/documentation_pages/lib/formats/libdcd.doctree
doc/html/doctrees/documentation_pages/lib/formats/libmdaxdr.doctree
doc/html/doctrees/documentation_pages/selections/base.doctree
doc/html/doctrees/documentation_pages/selections/charmm.doctree
doc/html/doctrees/documentation_pages/selections/gromacs.doctree
doc/html/doctrees/documentation_pages/selections/jmol.doctree
doc/html/doctrees/documentation_pages/selections/pymol.doctree
doc/html/doctrees/documentation_pages/selections/vmd.doctree
doc/html/doctrees/documentation_pages/topology/CRDParser.doctree
doc/html/doctrees/documentation_pages/topology/DLPolyParser.doctree
doc/html/doctrees/documentation_pages/topology/DMSParser.doctree
doc/html/doctrees/documentation_pages/topology/ExtendedPDBParser.doctree
doc/html/doctrees/documentation_pages/topology/FHIAIMSParser.doctree
doc/html/doctrees/documentation_pages/topology/GMSParser.doctree
doc/html/doctrees/documentation_pages/topology/GROParser.doctree
doc/html/doctrees/documentation_pages/topology/GSDParser.doctree
doc/html/doctrees/documentation_pages/topology/HoomdXMLParser.doctree
doc/html/doctrees/documentation_pages/topology/ITPParser.doctree
doc/html/doctrees/documentation_pages/topology/LAMMPSParser.doctree
doc/html/doctrees/documentation_pages/topology/MMTFParser.doctree
doc/html/doctrees/documentation_pages/topology/MOL2Parser.doctree
doc/html/doctrees/documentation_pages/topology/MinimalParser.doctree
doc/html/doctrees/documentation_pages/topology/PDBParser.doctree
doc/html/doctrees/documentation_pages/topology/PDBQTParser.doctree
doc/html/doctrees/documentation_pages/topology/PQRParser.doctree
doc/html/doctrees/documentation_pages/topology/PSFParser.doctree
doc/html/doctrees/documentation_pages/topology/TOPParser.doctree
doc/html/doctrees/documentation_pages/topology/TPRParser.doctree
doc/html/doctrees/documentation_pages/topology/TXYZParser.doctree
doc/html/doctrees/documentation_pages/topology/XYZParser.doctree
doc/html/doctrees/documentation_pages/topology/base.doctree
doc/html/doctrees/documentation_pages/topology/core.doctree
doc/html/doctrees/documentation_pages/topology/guessers.doctree
doc/html/doctrees/documentation_pages/topology/init.doctree
doc/html/doctrees/documentation_pages/topology/tables.doctree
doc/html/doctrees/documentation_pages/topology/tpr_util.doctree
doc/html/doctrees/documentation_pages/transformations/fit.doctree
doc/html/doctrees/documentation_pages/transformations/positionaveraging.doctree
doc/html/doctrees/documentation_pages/transformations/rotate.doctree
doc/html/doctrees/documentation_pages/transformations/translate.doctree
doc/html/doctrees/documentation_pages/transformations/wrap.doctree
doc/html/doctrees/documentation_pages/visualization/streamlines.doctree
doc/html/doctrees/documentation_pages/visualization/streamlines_3D.doctree
doc/html/documentation_pages/analysis_modules.html
doc/html/documentation_pages/auxiliary_modules.html
doc/html/documentation_pages/converters.html
doc/html/documentation_pages/coordinates_modules.html
doc/html/documentation_pages/core_modules.html
doc/html/documentation_pages/exceptions.html
doc/html/documentation_pages/lib_modules.html
doc/html/documentation_pages/overview.html
doc/html/documentation_pages/references.html
doc/html/documentation_pages/selections.html
doc/html/documentation_pages/selections_modules.html
doc/html/documentation_pages/topology.html
doc/html/documentation_pages/topology_modules.html
doc/html/documentation_pages/trajectory_transformations.html
doc/html/documentation_pages/units.html
doc/html/documentation_pages/version.html
doc/html/documentation_pages/visualization_modules.html
doc/html/documentation_pages/analysis/align.html
doc/html/documentation_pages/analysis/base.html
doc/html/documentation_pages/analysis/contacts.html
doc/html/documentation_pages/analysis/data.html
doc/html/documentation_pages/analysis/density.html
doc/html/documentation_pages/analysis/diffusionmap.html
doc/html/documentation_pages/analysis/dihedrals.html
doc/html/documentation_pages/analysis/distances.html
doc/html/documentation_pages/analysis/encore.html
doc/html/documentation_pages/analysis/gnm.html
doc/html/documentation_pages/analysis/hbond_analysis.html
doc/html/documentation_pages/analysis/hbond_autocorrel.html
doc/html/documentation_pages/analysis/helanal.html
doc/html/documentation_pages/analysis/hole.html
doc/html/documentation_pages/analysis/hole2.html
doc/html/documentation_pages/analysis/hydrogenbonds.html
doc/html/documentation_pages/analysis/leaflet.html
doc/html/documentation_pages/analysis/legacy_modules.html
doc/html/documentation_pages/analysis/lineardensity.html
doc/html/documentation_pages/analysis/nuclinfo.html
doc/html/documentation_pages/analysis/pca.html
doc/html/documentation_pages/analysis/polymer.html
doc/html/documentation_pages/analysis/psa.html
doc/html/documentation_pages/analysis/rdf.html
doc/html/documentation_pages/analysis/rms.html
doc/html/documentation_pages/analysis/waterdynamics.html
doc/html/documentation_pages/analysis/wbridge_analysis.html
doc/html/documentation_pages/analysis/encore/bootstrap.html
doc/html/documentation_pages/analysis/encore/clustering.html
doc/html/documentation_pages/analysis/encore/confdistmatrix.html
doc/html/documentation_pages/analysis/encore/covariance.html
doc/html/documentation_pages/analysis/encore/dimensionality_reduction.html
doc/html/documentation_pages/analysis/encore/similarity.html
doc/html/documentation_pages/analysis/encore/utils.html
doc/html/documentation_pages/analysis/legacy/x3dna.html
doc/html/documentation_pages/auxiliary/XVG.html
doc/html/documentation_pages/auxiliary/base.html
doc/html/documentation_pages/auxiliary/core.html
doc/html/documentation_pages/auxiliary/init.html
doc/html/documentation_pages/converters/ParmEdParser.html
doc/html/documentation_pages/coordinates/CRD.html
doc/html/documentation_pages/coordinates/DCD.html
doc/html/documentation_pages/coordinates/DLPoly.html
doc/html/documentation_pages/coordinates/DMS.html
doc/html/documentation_pages/coordinates/FHIAIMS.html
doc/html/documentation_pages/coordinates/GMS.html
doc/html/documentation_pages/coordinates/GRO.html
doc/html/documentation_pages/coordinates/GSD.html
doc/html/documentation_pages/coordinates/INPCRD.html
doc/html/documentation_pages/coordinates/LAMMPS.html
doc/html/documentation_pages/coordinates/MMTF.html
doc/html/documentation_pages/coordinates/MOL2.html
doc/html/documentation_pages/coordinates/NAMDBIN.html
doc/html/documentation_pages/coordinates/PDB.html
doc/html/documentation_pages/coordinates/PDBQT.html
doc/html/documentation_pages/coordinates/PQR.html
doc/html/documentation_pages/coordinates/TRJ.html
doc/html/documentation_pages/coordinates/TRR.html
doc/html/documentation_pages/coordinates/TRZ.html
doc/html/documentation_pages/coordinates/TXYZ.html
doc/html/documentation_pages/coordinates/XDR.html
doc/html/documentation_pages/coordinates/XTC.html
doc/html/documentation_pages/coordinates/XYZ.html
doc/html/documentation_pages/coordinates/base.html
doc/html/documentation_pages/coordinates/chain.html
doc/html/documentation_pages/coordinates/chemfiles.html
doc/html/documentation_pages/coordinates/core.html
doc/html/documentation_pages/coordinates/init.html
doc/html/documentation_pages/coordinates/memory.html
doc/html/documentation_pages/coordinates/null.html
doc/html/documentation_pages/core/groups.html
doc/html/documentation_pages/core/init.html
doc/html/documentation_pages/core/selection.html
doc/html/documentation_pages/core/topology.html
doc/html/documentation_pages/core/topologyattrs.html
doc/html/documentation_pages/core/topologyobjects.html
doc/html/documentation_pages/core/universe.html
doc/html/documentation_pages/lib/NeighborSearch.html
doc/html/documentation_pages/lib/c_distances.html
doc/html/documentation_pages/lib/c_distances_openmp.html
doc/html/documentation_pages/lib/correlations.html
doc/html/documentation_pages/lib/distances.html
doc/html/documentation_pages/lib/log.html
doc/html/documentation_pages/lib/mdamath.html
doc/html/documentation_pages/lib/nsgrid.html
doc/html/documentation_pages/lib/pkdtree.html
doc/html/documentation_pages/lib/qcprot.html
doc/html/documentation_pages/lib/transformations.html
doc/html/documentation_pages/lib/util.html
doc/html/documentation_pages/lib/formats/libdcd.html
doc/html/documentation_pages/lib/formats/libmdaxdr.html
doc/html/documentation_pages/selections/base.html
doc/html/documentation_pages/selections/charmm.html
doc/html/documentation_pages/selections/gromacs.html
doc/html/documentation_pages/selections/jmol.html
doc/html/documentation_pages/selections/pymol.html
doc/html/documentation_pages/selections/vmd.html
doc/html/documentation_pages/topology/CRDParser.html
doc/html/documentation_pages/topology/DLPolyParser.html
doc/html/documentation_pages/topology/DMSParser.html
doc/html/documentation_pages/topology/ExtendedPDBParser.html
doc/html/documentation_pages/topology/FHIAIMSParser.html
doc/html/documentation_pages/topology/GMSParser.html
doc/html/documentation_pages/topology/GROParser.html
doc/html/documentation_pages/topology/GSDParser.html
doc/html/documentation_pages/topology/HoomdXMLParser.html
doc/html/documentation_pages/topology/ITPParser.html
doc/html/documentation_pages/topology/LAMMPSParser.html
doc/html/documentation_pages/topology/MMTFParser.html
doc/html/documentation_pages/topology/MOL2Parser.html
doc/html/documentation_pages/topology/MinimalParser.html
doc/html/documentation_pages/topology/PDBParser.html
doc/html/documentation_pages/topology/PDBQTParser.html
doc/html/documentation_pages/topology/PQRParser.html
doc/html/documentation_pages/topology/PSFParser.html
doc/html/documentation_pages/topology/TOPParser.html
doc/html/documentation_pages/topology/TPRParser.html
doc/html/documentation_pages/topology/TXYZParser.html
doc/html/documentation_pages/topology/XYZParser.html
doc/html/documentation_pages/topology/base.html
doc/html/documentation_pages/topology/core.html
doc/html/documentation_pages/topology/guessers.html
doc/html/documentation_pages/topology/init.html
doc/html/documentation_pages/topology/tables.html
doc/html/documentation_pages/topology/tpr_util.html
doc/html/documentation_pages/transformations/fit.html
doc/html/documentation_pages/transformations/positionaveraging.html
doc/html/documentation_pages/transformations/rotate.html
doc/html/documentation_pages/transformations/translate.html
doc/html/documentation_pages/transformations/wrap.html
doc/html/documentation_pages/visualization/streamlines.html
doc/html/documentation_pages/visualization/streamlines_3D.html
doc/sphinx/Makefile
doc/sphinx/source/conf.py
doc/sphinx/source/index.rst
doc/sphinx/source/_static/custom.css
doc/sphinx/source/_static/readable.css
doc/sphinx/source/_static/logos/AUTHOR
doc/sphinx/source/_static/logos/mdanalysis-logo-127x55.png
doc/sphinx/source/_static/logos/mdanalysis-logo-200x150.png
doc/sphinx/source/_static/logos/mdanalysis-logo-thin.png
doc/sphinx/source/_static/logos/mdanalysis-logo.ico
doc/sphinx/source/_static/logos/mdanalysis-logo.pdf
doc/sphinx/source/_static/logos/mdanalysis-logo.png
doc/sphinx/source/_static/logos/mdanalysis-logo_square.pdf
doc/sphinx/source/_static/logos/mdanalysis-logo_square.png
doc/sphinx/source/_static/logos/mdanalysis-logo_square.svg
doc/sphinx/source/_static/logos/mdanalysis-logo_square_45mm.pdf
doc/sphinx/source/_static/logos/mdanalysis-logo_square_45mm.png
doc/sphinx/source/_static/logos/mdanalysis-logo_square_72dpi.png
doc/sphinx/source/documentation_pages/analysis_modules.rst
doc/sphinx/source/documentation_pages/auxiliary_modules.rst
doc/sphinx/source/documentation_pages/converters.rst
doc/sphinx/source/documentation_pages/coordinates_modules.rst
doc/sphinx/source/documentation_pages/core_modules.rst
doc/sphinx/source/documentation_pages/exceptions.rst
doc/sphinx/source/documentation_pages/lib_modules.rst
doc/sphinx/source/documentation_pages/overview.rst
doc/sphinx/source/documentation_pages/references.rst
doc/sphinx/source/documentation_pages/selections.rst
doc/sphinx/source/documentation_pages/selections_modules.rst
doc/sphinx/source/documentation_pages/topology.rst
doc/sphinx/source/documentation_pages/topology_modules.rst
doc/sphinx/source/documentation_pages/trajectory_transformations.rst
doc/sphinx/source/documentation_pages/units.rst
doc/sphinx/source/documentation_pages/version.rst
doc/sphinx/source/documentation_pages/visualization_modules.rst
doc/sphinx/source/documentation_pages/analysis/align.rst
doc/sphinx/source/documentation_pages/analysis/base.rst
doc/sphinx/source/documentation_pages/analysis/contacts.rst
doc/sphinx/source/documentation_pages/analysis/data.rst
doc/sphinx/source/documentation_pages/analysis/density.rst
doc/sphinx/source/documentation_pages/analysis/diffusionmap.rst
doc/sphinx/source/documentation_pages/analysis/dihedrals.rst
doc/sphinx/source/documentation_pages/analysis/distances.rst
doc/sphinx/source/documentation_pages/analysis/encore.rst
doc/sphinx/source/documentation_pages/analysis/gnm.rst
doc/sphinx/source/documentation_pages/analysis/hbond_analysis.rst
doc/sphinx/source/documentation_pages/analysis/hbond_autocorrel.rst
doc/sphinx/source/documentation_pages/analysis/helanal.rst
doc/sphinx/source/documentation_pages/analysis/hole.rst
doc/sphinx/source/documentation_pages/analysis/hole2.rst
doc/sphinx/source/documentation_pages/analysis/hydrogenbonds.rst
doc/sphinx/source/documentation_pages/analysis/leaflet.rst
doc/sphinx/source/documentation_pages/analysis/legacy_modules.rst
doc/sphinx/source/documentation_pages/analysis/lineardensity.rst
doc/sphinx/source/documentation_pages/analysis/nuclinfo.rst
doc/sphinx/source/documentation_pages/analysis/pca.rst
doc/sphinx/source/documentation_pages/analysis/polymer.rst
doc/sphinx/source/documentation_pages/analysis/psa.rst
doc/sphinx/source/documentation_pages/analysis/rdf.rst
doc/sphinx/source/documentation_pages/analysis/rms.rst
doc/sphinx/source/documentation_pages/analysis/waterdynamics.rst
doc/sphinx/source/documentation_pages/analysis/wbridge_analysis.rst
doc/sphinx/source/documentation_pages/analysis/encore/bootstrap.rst
doc/sphinx/source/documentation_pages/analysis/encore/clustering.rst
doc/sphinx/source/documentation_pages/analysis/encore/confdistmatrix.rst
doc/sphinx/source/documentation_pages/analysis/encore/covariance.rst
doc/sphinx/source/documentation_pages/analysis/encore/dimensionality_reduction.rst
doc/sphinx/source/documentation_pages/analysis/encore/similarity.rst
doc/sphinx/source/documentation_pages/analysis/encore/utils.rst
doc/sphinx/source/documentation_pages/analysis/legacy/x3dna.rst
doc/sphinx/source/documentation_pages/auxiliary/XVG.rst
doc/sphinx/source/documentation_pages/auxiliary/base.rst
doc/sphinx/source/documentation_pages/auxiliary/core.rst
doc/sphinx/source/documentation_pages/auxiliary/init.rst
doc/sphinx/source/documentation_pages/converters/ParmEdParser.rst
doc/sphinx/source/documentation_pages/coordinates/CRD.rst
doc/sphinx/source/documentation_pages/coordinates/DCD.rst
doc/sphinx/source/documentation_pages/coordinates/DLPoly.rst
doc/sphinx/source/documentation_pages/coordinates/DMS.rst
doc/sphinx/source/documentation_pages/coordinates/FHIAIMS.rst
doc/sphinx/source/documentation_pages/coordinates/GMS.rst
doc/sphinx/source/documentation_pages/coordinates/GRO.rst
doc/sphinx/source/documentation_pages/coordinates/GSD.rst
doc/sphinx/source/documentation_pages/coordinates/INPCRD.rst
doc/sphinx/source/documentation_pages/coordinates/LAMMPS.rst
doc/sphinx/source/documentation_pages/coordinates/MMTF.rst
doc/sphinx/source/documentation_pages/coordinates/MOL2.rst
doc/sphinx/source/documentation_pages/coordinates/NAMDBIN.rst
doc/sphinx/source/documentation_pages/coordinates/PDB.rst
doc/sphinx/source/documentation_pages/coordinates/PDBQT.rst
doc/sphinx/source/documentation_pages/coordinates/PQR.rst
doc/sphinx/source/documentation_pages/coordinates/TRJ.rst
doc/sphinx/source/documentation_pages/coordinates/TRR.rst
doc/sphinx/source/documentation_pages/coordinates/TRZ.rst
doc/sphinx/source/documentation_pages/coordinates/TXYZ.rst
doc/sphinx/source/documentation_pages/coordinates/XDR.rst
doc/sphinx/source/documentation_pages/coordinates/XTC.rst
doc/sphinx/source/documentation_pages/coordinates/XYZ.rst
doc/sphinx/source/documentation_pages/coordinates/base.rst
doc/sphinx/source/documentation_pages/coordinates/chain.rst
doc/sphinx/source/documentation_pages/coordinates/chemfiles.rst
doc/sphinx/source/documentation_pages/coordinates/core.rst
doc/sphinx/source/documentation_pages/coordinates/init.rst
doc/sphinx/source/documentation_pages/coordinates/memory.rst
doc/sphinx/source/documentation_pages/coordinates/null.rst
doc/sphinx/source/documentation_pages/core/groups.rst
doc/sphinx/source/documentation_pages/core/init.rst
doc/sphinx/source/documentation_pages/core/selection.rst
doc/sphinx/source/documentation_pages/core/topology.rst
doc/sphinx/source/documentation_pages/core/topologyattrs.rst
doc/sphinx/source/documentation_pages/core/topologyobjects.rst
doc/sphinx/source/documentation_pages/core/universe.rst
doc/sphinx/source/documentation_pages/lib/NeighborSearch.rst
doc/sphinx/source/documentation_pages/lib/c_distances.rst
doc/sphinx/source/documentation_pages/lib/c_distances_openmp.rst
doc/sphinx/source/documentation_pages/lib/correlations.rst
doc/sphinx/source/documentation_pages/lib/distances.rst
doc/sphinx/source/documentation_pages/lib/log.rst
doc/sphinx/source/documentation_pages/lib/mdamath.rst
doc/sphinx/source/documentation_pages/lib/nsgrid.rst
doc/sphinx/source/documentation_pages/lib/pkdtree.rst
doc/sphinx/source/documentation_pages/lib/qcprot.rst
doc/sphinx/source/documentation_pages/lib/transformations.rst
doc/sphinx/source/documentation_pages/lib/util.rst
doc/sphinx/source/documentation_pages/lib/formats/libdcd.rst
doc/sphinx/source/documentation_pages/lib/formats/libmdaxdr.rst
doc/sphinx/source/documentation_pages/selections/base.rst
doc/sphinx/source/documentation_pages/selections/charmm.rst
doc/sphinx/source/documentation_pages/selections/gromacs.rst
doc/sphinx/source/documentation_pages/selections/jmol.rst
doc/sphinx/source/documentation_pages/selections/pymol.rst
doc/sphinx/source/documentation_pages/selections/vmd.rst
doc/sphinx/source/documentation_pages/topology/CRDParser.rst
doc/sphinx/source/documentation_pages/topology/DLPolyParser.rst
doc/sphinx/source/documentation_pages/topology/DMSParser.rst
doc/sphinx/source/documentation_pages/topology/ExtendedPDBParser.rst
doc/sphinx/source/documentation_pages/topology/FHIAIMSParser.rst
doc/sphinx/source/documentation_pages/topology/GMSParser.rst
doc/sphinx/source/documentation_pages/topology/GROParser.rst
doc/sphinx/source/documentation_pages/topology/GSDParser.rst
doc/sphinx/source/documentation_pages/topology/HoomdXMLParser.rst
doc/sphinx/source/documentation_pages/topology/ITPParser.rst
doc/sphinx/source/documentation_pages/topology/LAMMPSParser.rst
doc/sphinx/source/documentation_pages/topology/MMTFParser.rst
doc/sphinx/source/documentation_pages/topology/MOL2Parser.rst
doc/sphinx/source/documentation_pages/topology/MinimalParser.rst
doc/sphinx/source/documentation_pages/topology/PDBParser.rst
doc/sphinx/source/documentation_pages/topology/PDBQTParser.rst
doc/sphinx/source/documentation_pages/topology/PQRParser.rst
doc/sphinx/source/documentation_pages/topology/PSFParser.rst
doc/sphinx/source/documentation_pages/topology/TOPParser.rst
doc/sphinx/source/documentation_pages/topology/TPRParser.rst
doc/sphinx/source/documentation_pages/topology/TXYZParser.rst
doc/sphinx/source/documentation_pages/topology/XYZParser.rst
doc/sphinx/source/documentation_pages/topology/base.rst
doc/sphinx/source/documentation_pages/topology/core.rst
doc/sphinx/source/documentation_pages/topology/guessers.rst
doc/sphinx/source/documentation_pages/topology/init.rst
doc/sphinx/source/documentation_pages/topology/tables.rst
doc/sphinx/source/documentation_pages/topology/tpr_util.rst
doc/sphinx/source/documentation_pages/transformations/fit.rst
doc/sphinx/source/documentation_pages/transformations/positionaveraging.rst
doc/sphinx/source/documentation_pages/transformations/rotate.rst
doc/sphinx/source/documentation_pages/transformations/translate.rst
doc/sphinx/source/documentation_pages/transformations/wrap.rst
doc/sphinx/source/documentation_pages/visualization/streamlines.rst
doc/sphinx/source/documentation_pages/visualization/streamlines_3D.rst
doc/sphinx/source/documentation_pages/visualization/test_streamplot_3D.png
doc/sphinx/source/documentation_pages/visualization/testing_streamline.png
doc/sphinx/source/images/janin_demo_plot.png
doc/sphinx/source/images/rama_demo_plot.png