MANIFEST.in
basesetup.py
setup.py
examples/.gitignore
examples/1vii_3frames.pdb
examples/ala2.h5
examples/atom-selection.ipynb
examples/centroids.ipynb
examples/clustering.ipynb
examples/hbonds.ipynb
examples/iterload.ipynb
examples/native-contact.ipynb
examples/nmr.ipynb
examples/principal-components.ipynb
examples/ramachandran-plot.ipynb
examples/rmsd-benchmark.ipynb
examples/rmsd-drift.ipynb
examples/simulation-with-openmm.ipynb
examples/solvent-accessible-surface-area.ipynb
examples/test_examples.py
examples/two-pass-clustering.ipynb
examples/data/frame0.h5
examples/data/frame0.xtc
examples/data/native.pdb
mdtraj/.gitignore
mdtraj/__init__.py
mdtraj/io.py
mdtraj/version.py
mdtraj.egg-info/PKG-INFO
mdtraj.egg-info/SOURCES.txt
mdtraj.egg-info/dependency_links.txt
mdtraj.egg-info/entry_points.txt
mdtraj.egg-info/not-zip-safe
mdtraj.egg-info/top_level.txt
mdtraj/core/__init__.py
mdtraj/core/element.py
mdtraj/core/residue_names.py
mdtraj/core/selection.py
mdtraj/core/topology.py
mdtraj/core/trajectory.py
mdtraj/formats/__init__.py
mdtraj/formats/amberrst.py
mdtraj/formats/arc.py
mdtraj/formats/gro.py
mdtraj/formats/hdf5.py
mdtraj/formats/hoomdxml.py
mdtraj/formats/lammpstrj.py
mdtraj/formats/lh5.py
mdtraj/formats/mdcrd.py
mdtraj/formats/mol2.py
mdtraj/formats/netcdf.py
mdtraj/formats/openmmxml.py
mdtraj/formats/prmtop.py
mdtraj/formats/psf.py
mdtraj/formats/registry.py
mdtraj/formats/xyzfile.py
mdtraj/formats/binpos/.gitignore
mdtraj/formats/binpos/binpos.c
mdtraj/formats/binpos/binpos.pyx
mdtraj/formats/binpos/binposlib.pxd
mdtraj/formats/binpos/include/binposplugin.h
mdtraj/formats/binpos/include/largefiles.h
mdtraj/formats/binpos/include/molfile_plugin.h
mdtraj/formats/binpos/include/vmdplugin.h
mdtraj/formats/binpos/src/binposplugin.c
mdtraj/formats/dcd/.gitignore
mdtraj/formats/dcd/dcd.c
mdtraj/formats/dcd/dcd.pyx
mdtraj/formats/dcd/dcdlib.pxd
mdtraj/formats/dcd/include/dcdplugin.h
mdtraj/formats/dcd/include/endianswap.h
mdtraj/formats/dcd/include/fastio.h
mdtraj/formats/dcd/include/largefiles.h
mdtraj/formats/dcd/include/molfile_plugin.h
mdtraj/formats/dcd/include/vmdplugin.h
mdtraj/formats/dcd/src/dcdplugin.c
mdtraj/formats/dtr/.gitignore
mdtraj/formats/dtr/dtr.cpp
mdtraj/formats/dtr/dtr.pyx
mdtraj/formats/dtr/dtrlib.pxd
mdtraj/formats/dtr/include/dtrplugin.hxx
mdtraj/formats/dtr/include/endianswap.h
mdtraj/formats/dtr/include/molfile_plugin.h
mdtraj/formats/dtr/include/vmddir.h
mdtraj/formats/dtr/include/vmdplugin.h
mdtraj/formats/dtr/src/dtrplugin.cxx
mdtraj/formats/pdb/README.md
mdtraj/formats/pdb/__init__.py
mdtraj/formats/pdb/pdbfile.py
mdtraj/formats/pdb/pdbstructure.py
mdtraj/formats/pdb/data/pdbNames.xml
mdtraj/formats/pdb/data/residues.xml
mdtraj/formats/tng/.gitignore
mdtraj/formats/tng/tng.c
mdtraj/formats/tng/tng.pyx
mdtraj/formats/tng/include/compression/bwlzh.h
mdtraj/formats/tng/include/compression/bwt.h
mdtraj/formats/tng/include/compression/coder.h
mdtraj/formats/tng/include/compression/dict.h
mdtraj/formats/tng/include/compression/fixpoint.h
mdtraj/formats/tng/include/compression/huffman.h
mdtraj/formats/tng/include/compression/lz77.h
mdtraj/formats/tng/include/compression/merge_sort.h
mdtraj/formats/tng/include/compression/mtf.h
mdtraj/formats/tng/include/compression/my64bit.h
mdtraj/formats/tng/include/compression/rle.h
mdtraj/formats/tng/include/compression/tng_compress.h
mdtraj/formats/tng/include/compression/vals16.h
mdtraj/formats/tng/include/compression/warnmalloc.h
mdtraj/formats/tng/include/compression/widemuldiv.h
mdtraj/formats/tng/include/tng/md5.h
mdtraj/formats/tng/include/tng/tng_io.h
mdtraj/formats/tng/include/tng/tng_io.hpp
mdtraj/formats/tng/include/tng/tng_io_fwd.h
mdtraj/formats/tng/include/tng/version.h
mdtraj/formats/tng/src/compression/bwlzh.c
mdtraj/formats/tng/src/compression/bwt.c
mdtraj/formats/tng/src/compression/coder.c
mdtraj/formats/tng/src/compression/dict.c
mdtraj/formats/tng/src/compression/fixpoint.c
mdtraj/formats/tng/src/compression/huffman.c
mdtraj/formats/tng/src/compression/huffmem.c
mdtraj/formats/tng/src/compression/lz77.c
mdtraj/formats/tng/src/compression/merge_sort.c
mdtraj/formats/tng/src/compression/mtf.c
mdtraj/formats/tng/src/compression/rle.c
mdtraj/formats/tng/src/compression/tng_compress.c
mdtraj/formats/tng/src/compression/vals16.c
mdtraj/formats/tng/src/compression/warnmalloc.c
mdtraj/formats/tng/src/compression/widemuldiv.c
mdtraj/formats/tng/src/compression/xtc2.c
mdtraj/formats/tng/src/compression/xtc3.c
mdtraj/formats/tng/src/lib/md5.c
mdtraj/formats/tng/src/lib/tng_io.c
mdtraj/formats/xtc/.gitignore
mdtraj/formats/xtc/trr.c
mdtraj/formats/xtc/trr.pyx
mdtraj/formats/xtc/trrlib.pxd
mdtraj/formats/xtc/xdrlib.pxd
mdtraj/formats/xtc/xtc.c
mdtraj/formats/xtc/xtc.pyx
mdtraj/formats/xtc/include/ms_stdint.h
mdtraj/formats/xtc/include/trr_header.h
mdtraj/formats/xtc/include/xdr_seek.h
mdtraj/formats/xtc/include/xdrfile.h
mdtraj/formats/xtc/include/xdrfile_trr.h
mdtraj/formats/xtc/include/xdrfile_xtc.h
mdtraj/formats/xtc/src/README
mdtraj/formats/xtc/src/xdr_seek.c
mdtraj/formats/xtc/src/xdrfile.c
mdtraj/formats/xtc/src/xdrfile_trr.c
mdtraj/formats/xtc/src/xdrfile_xtc.c
mdtraj/geometry/.gitignore
mdtraj/geometry/__init__.py
mdtraj/geometry/alignment.py
mdtraj/geometry/angle.py
mdtraj/geometry/contact.py
mdtraj/geometry/dihedral.py
mdtraj/geometry/distance.py
mdtraj/geometry/drid.cpp
mdtraj/geometry/drid.pyx
mdtraj/geometry/dssp.py
mdtraj/geometry/hbond.py
mdtraj/geometry/internal.py
mdtraj/geometry/neighborlist.cpp
mdtraj/geometry/neighborlist.pyx
mdtraj/geometry/neighbors.cpp
mdtraj/geometry/neighbors.pyx
mdtraj/geometry/order.py
mdtraj/geometry/rdf.py
mdtraj/geometry/rg.py
mdtraj/geometry/sasa.py
mdtraj/geometry/thermodynamic_properties.py
mdtraj/geometry/include/dridkernels.h
mdtraj/geometry/include/geometry.h
mdtraj/geometry/include/math_patch.h
mdtraj/geometry/include/moments.h
mdtraj/geometry/include/msvccompat.h
mdtraj/geometry/include/neighborlist.h
mdtraj/geometry/include/neighbors.hpp
mdtraj/geometry/include/sasa.h
mdtraj/geometry/include/vectorize_sse.h
mdtraj/geometry/src/.gitignore
mdtraj/geometry/src/_geometry.cpp
mdtraj/geometry/src/_geometry.pyx
mdtraj/geometry/src/dridkernels.cpp
mdtraj/geometry/src/dssp.cpp
mdtraj/geometry/src/geometry.cpp
mdtraj/geometry/src/image_molecules.pxi
mdtraj/geometry/src/moments.cpp
mdtraj/geometry/src/neighborlist.cpp
mdtraj/geometry/src/neighbors.cpp
mdtraj/geometry/src/sasa.cpp
mdtraj/geometry/src/kernels/anglekernels.h
mdtraj/geometry/src/kernels/dihedralkernels.h
mdtraj/geometry/src/kernels/distancekernels.h
mdtraj/nmr/__init__.py
mdtraj/nmr/scalar_couplings.py
mdtraj/nmr/shift_wrappers.py
mdtraj/reporters/__init__.py
mdtraj/reporters/basereporter.py
mdtraj/reporters/dcdreporter.py
mdtraj/reporters/hdf5reporter.py
mdtraj/reporters/netcdfreporter.py
mdtraj/rmsd/.gitignore
mdtraj/rmsd/README.md
mdtraj/rmsd/_lprmsd.cpp
mdtraj/rmsd/_lprmsd.pyx
mdtraj/rmsd/_rmsd.c
mdtraj/rmsd/_rmsd.pyx
mdtraj/rmsd/include/Munkres.h
mdtraj/rmsd/include/center.h
mdtraj/rmsd/include/euclidean_permutation.hpp
mdtraj/rmsd/include/fancy_index.hpp
mdtraj/rmsd/include/msvccompat.h
mdtraj/rmsd/include/rotation.h
mdtraj/rmsd/include/sse_swizzle.h
mdtraj/rmsd/include/theobald_rmsd.h
mdtraj/rmsd/include/util.h
mdtraj/rmsd/src/Munkres.cpp
mdtraj/rmsd/src/center.c
mdtraj/rmsd/src/euclidean_permutation.cpp
mdtraj/rmsd/src/fancy_index.cpp
mdtraj/rmsd/src/rotation.c
mdtraj/rmsd/src/theobald_rmsd.c
mdtraj/scripts/__init__.py
mdtraj/scripts/mdconvert.py
mdtraj/scripts/mdinspect.py
mdtraj/testing/__init__.py
mdtraj/testing/docscrape.py
mdtraj/testing/docstrings.py
mdtraj/testing/testing.py
mdtraj/utils/__init__.py
mdtraj/utils/contextmanagers.py
mdtraj/utils/delay_import.py
mdtraj/utils/rotation.py
mdtraj/utils/six.py
mdtraj/utils/unitcell.py
mdtraj/utils/validation.py
mdtraj/utils/zipped.py
mdtraj/utils/external/FETCH_EXTERNAL_PACKAGES.sh
mdtraj/utils/external/README.md
mdtraj/utils/external/__init__.py
mdtraj/utils/external/pyparsing.py
mdtraj/utils/external/astor/LICENSE
mdtraj/utils/external/astor/__init__.py
mdtraj/utils/external/astor/codegen.py
mdtraj/utils/external/astor/misc.py
mdtraj/utils/external/astor/treewalk.py
mdtraj/utils/unit/__init__.py
mdtraj/utils/unit/basedimension.py
mdtraj/utils/unit/baseunit.py
mdtraj/utils/unit/constants.py
mdtraj/utils/unit/doctests.py
mdtraj/utils/unit/mymatrix.py
mdtraj/utils/unit/prefix.py
mdtraj/utils/unit/quantity.py
mdtraj/utils/unit/standard_dimensions.py
mdtraj/utils/unit/unit.py
mdtraj/utils/unit/unit_definitions.py
mdtraj/utils/unit/unit_math.py
mdtraj/utils/unit/unit_operators.py