INSTALL.rst
LICENSE.rst
MANIFEST.in
README.rst
setup.py
ProDy.egg-info/PKG-INFO
ProDy.egg-info/SOURCES.txt
ProDy.egg-info/dependency_links.txt
ProDy.egg-info/entry_points.txt
ProDy.egg-info/top_level.txt
prody/__init__.py
prody/apps/__init__.py
prody/apps/apptools.py
prody/apps/evol_apps/__init__.py
prody/apps/evol_apps/evol_coevol.py
prody/apps/evol_apps/evol_conserv.py
prody/apps/evol_apps/evol_fetch.py
prody/apps/evol_apps/evol_filter.py
prody/apps/evol_apps/evol_merge.py
prody/apps/evol_apps/evol_occupancy.py
prody/apps/evol_apps/evol_rankorder.py
prody/apps/evol_apps/evol_refine.py
prody/apps/evol_apps/evol_search.py
prody/apps/prody_apps/__init__.py
prody/apps/prody_apps/nmaoptions.py
prody/apps/prody_apps/prody_align.py
prody/apps/prody_apps/prody_anm.py
prody/apps/prody_apps/prody_biomol.py
prody/apps/prody_apps/prody_blast.py
prody/apps/prody_apps/prody_catdcd.py
prody/apps/prody_apps/prody_contacts.py
prody/apps/prody_apps/prody_eda.py
prody/apps/prody_apps/prody_fetch.py
prody/apps/prody_apps/prody_gnm.py
prody/apps/prody_apps/prody_pca.py
prody/apps/prody_apps/prody_select.py
prody/atomic/__init__.py
prody/atomic/atom.py
prody/atomic/atomgroup.py
prody/atomic/atomic.py
prody/atomic/atommap.py
prody/atomic/bond.py
prody/atomic/chain.py
prody/atomic/fields.py
prody/atomic/flags.py
prody/atomic/functions.py
prody/atomic/hierview.py
prody/atomic/pointer.py
prody/atomic/residue.py
prody/atomic/segment.py
prody/atomic/select.py
prody/atomic/selection.py
prody/atomic/subset.py
prody/chromatin/__init__.py
prody/chromatin/cluster.py
prody/chromatin/functions.py
prody/chromatin/hic.py
prody/chromatin/norm.py
prody/database/__init__.py
prody/database/cath.py
prody/database/dali.py
prody/database/pfam.py
prody/database/uniprot.py
prody/dynamics/__init__.py
prody/dynamics/analysis.py
prody/dynamics/anm.py
prody/dynamics/bbenm.py
prody/dynamics/bbenmtools.c
prody/dynamics/compare.py
prody/dynamics/editing.py
prody/dynamics/entropy.py
prody/dynamics/exanm.py
prody/dynamics/functions.py
prody/dynamics/gamma.py
prody/dynamics/gnm.py
prody/dynamics/heatmapper.py
prody/dynamics/mechstiff.py
prody/dynamics/mode.py
prody/dynamics/modeset.py
prody/dynamics/nma.py
prody/dynamics/nmdfile.py
prody/dynamics/pca.py
prody/dynamics/perturb.py
prody/dynamics/plotting.py
prody/dynamics/rtb.py
prody/dynamics/rtbtools.c
prody/dynamics/sampling.py
prody/dynamics/signature.py
prody/dynamics/smtools.c
prody/dynamics/vmdfile.py
prody/ensemble/__init__.py
prody/ensemble/conformation.py
prody/ensemble/ensemble.py
prody/ensemble/functions.py
prody/ensemble/pdbensemble.py
prody/kdtree/KDTree.c
prody/kdtree/KDTree.h
prody/kdtree/KDTreemodule.c
prody/kdtree/Neighbor.h
prody/kdtree/__init__.py
prody/kdtree/kdtree.py
prody/measure/__init__.py
prody/measure/contacts.py
prody/measure/measure.py
prody/measure/transform.py
prody/proteins/__init__.py
prody/proteins/blastpdb.py
prody/proteins/blastpdbUniProtKB.py
prody/proteins/ciffile.py
prody/proteins/compare.py
prody/proteins/dssp.py
prody/proteins/emdfile.py
prody/proteins/functions.py
prody/proteins/header.py
prody/proteins/localpdb.py
prody/proteins/pdbclusters.py
prody/proteins/pdbfile.py
prody/proteins/pdbligands.py
prody/proteins/psiblast.py
prody/proteins/starfile.py
prody/proteins/stride.py
prody/proteins/wwpdb.py
prody/proteins/ccealign/ccealignmodule.cpp
prody/proteins/ccealign/ccealignmodule.h
prody/sequence/__init__.py
prody/sequence/analysis.py
prody/sequence/msa.py
prody/sequence/msafile.py
prody/sequence/msaio.c
prody/sequence/msatools.c
prody/sequence/plotting.py
prody/sequence/seqtools.c
prody/sequence/sequence.py
prody/tests/__init__.py
prody/tests/apps/__init__.py
prody/tests/apps/test_prody_anm.py
prody/tests/apps/test_prody_catdcd.py
prody/tests/apps/test_prody_examples.py
prody/tests/apps/test_prody_gnm.py
prody/tests/apps/test_prody_pca.py
prody/tests/atomic/__init__.py
prody/tests/atomic/test_atomic.py
prody/tests/atomic/test_atommap.py
prody/tests/atomic/test_fragment.py
prody/tests/atomic/test_hierview.py
prody/tests/atomic/test_select.py
prody/tests/atomic/test_subset.py
prody/tests/datafiles/__init__.py
prody/tests/datafiles/anm1ubi_evalues.dat
prody/tests/datafiles/anm1ubi_hessian.coo
prody/tests/datafiles/anm1ubi_vectors.dat
prody/tests/datafiles/dcd2k39_truncated.dcd
prody/tests/datafiles/gnm1ubi_evalues.dat
prody/tests/datafiles/gnm1ubi_kirchhoff.coo
prody/tests/datafiles/gnm1ubi_vectors.dat
prody/tests/datafiles/msa_Cys_knot.fasta
prody/tests/datafiles/msa_Cys_knot.slx
prody/tests/datafiles/msa_Cys_knot.sth
prody/tests/datafiles/msa_Cys_knot_di.dat
prody/tests/datafiles/msa_Cys_knot_sca.dat
prody/tests/datafiles/pdb1ejg.pdb
prody/tests/datafiles/pdb1ejg_oneatom.pdb
prody/tests/datafiles/pdb1r19_dssp.pdb
prody/tests/datafiles/pdb1ubi.pdb
prody/tests/datafiles/pdb1ubi_ca.pdb
prody/tests/datafiles/pdb2gb1_truncated.pdb
prody/tests/datafiles/pdb2k39_truncated.pdb
prody/tests/datafiles/pdb3mht.pdb
prody/tests/datafiles/pdbRTER.pdb
prody/tests/datafiles/rtb2gb1_hessian.coo
prody/tests/datafiles/rtb2gb1_project.coo
prody/tests/datafiles/xmlSTI.xml
prody/tests/dynamics/__init__.py
prody/tests/dynamics/test_editing.py
prody/tests/dynamics/test_enms.py
prody/tests/dynamics/test_signature.py
prody/tests/ensemble/__init__.py
prody/tests/ensemble/test_conformation.py
prody/tests/ensemble/test_ensemble.py
prody/tests/ensemble/test_functions.py
prody/tests/ensemble/test_pdbensemble.py
prody/tests/kdtree/__init__.py
prody/tests/kdtree/test_kdtree.py
prody/tests/measure/__init__.py
prody/tests/measure/test_contacts.py
prody/tests/measure/test_measure.py
prody/tests/measure/test_transform.py
prody/tests/proteins/__init__.py
prody/tests/proteins/test_dssp.py
prody/tests/proteins/test_header.py
prody/tests/proteins/test_localpdb.py
prody/tests/proteins/test_pdbfile.py
prody/tests/proteins/test_wwpdb.py
prody/tests/sequence/__init__.py
prody/tests/sequence/test_analysis.py
prody/tests/sequence/test_msa.py
prody/tests/sequence/test_msafile.py
prody/tests/sequence/test_sequence.py
prody/tests/trajectory/__init__.py
prody/tests/trajectory/test_dcdfile.py
prody/tests/trajectory/test_frame.py
prody/tests/utilities/__init__.py
prody/tests/utilities/test_checkers.py
prody/tests/utilities/test_misctools.py
prody/tests/utilities/test_pathtools.py
prody/trajectory/__init__.py
prody/trajectory/dcdfile.py
prody/trajectory/frame.py
prody/trajectory/psffile.py
prody/trajectory/trajbase.py
prody/trajectory/trajectory.py
prody/trajectory/trajfile.py
prody/utilities/__init__.py
prody/utilities/catchall.py
prody/utilities/checkers.py
prody/utilities/doctools.py
prody/utilities/legacy.py
prody/utilities/logger.py
prody/utilities/misctools.py
prody/utilities/pathtools.py
prody/utilities/settings.py
prody/utilities/datafiles/mod_res_map.dat
prody/utilities/datafiles/saxs_water.dat
prody/utilities/tnt/jama_cholesky.h
prody/utilities/tnt/jama_eig.h
prody/utilities/tnt/jama_lu.h
prody/utilities/tnt/jama_qr.h
prody/utilities/tnt/jama_svd.h
prody/utilities/tnt/tnt.h
prody/utilities/tnt/tnt_array1d.h
prody/utilities/tnt/tnt_array1d_utils.h
prody/utilities/tnt/tnt_array2d.h
prody/utilities/tnt/tnt_array2d_utils.h
prody/utilities/tnt/tnt_array3d.h
prody/utilities/tnt/tnt_array3d_utils.h
prody/utilities/tnt/tnt_cmat.h
prody/utilities/tnt/tnt_fortran_array1d.h
prody/utilities/tnt/tnt_fortran_array1d_utils.h
prody/utilities/tnt/tnt_fortran_array2d.h
prody/utilities/tnt/tnt_fortran_array2d_utils.h
prody/utilities/tnt/tnt_fortran_array3d.h
prody/utilities/tnt/tnt_fortran_array3d_utils.h
prody/utilities/tnt/tnt_i_refvec.h
prody/utilities/tnt/tnt_math_utils.h
prody/utilities/tnt/tnt_sparse_matrix_csr.h
prody/utilities/tnt/tnt_stopwatch.h
prody/utilities/tnt/tnt_subscript.h
prody/utilities/tnt/tnt_vec.h
prody/utilities/tnt/tnt_version.h
scripts/evol
scripts/evol.bat
scripts/prody
scripts/prody.bat