INSTALL.rst
LICENSE.rst
MANIFEST.in
README.md
pyproject.toml
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/requires.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_clustenm.py
prody/apps/prody_apps/prody_contacts.py
prody/apps/prody_apps/prody_eda.py
prody/apps/prody_apps/prody_energy.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_rtb.py
prody/apps/prody_apps/prody_select.py
prody/atomic/__init__.py
prody/atomic/acceptor.py
prody/atomic/angle.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/crossterm.py
prody/atomic/dihedral.py
prody/atomic/donor.py
prody/atomic/fields.py
prody/atomic/flags.py
prody/atomic/functions.py
prody/atomic/hierview.py
prody/atomic/improper.py
prody/atomic/nbexclusion.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/chromatin/straw.py
prody/compounds/__init__.py
prody/compounds/bird.py
prody/compounds/ccd.py
prody/compounds/functions.py
prody/compounds/pdbligands.py
prody/database/__init__.py
prody/database/bioexcel.py
prody/database/cath.py
prody/database/dali.py
prody/database/goa.py
prody/database/interpro.py
prody/database/pfam.py
prody/database/quartataweb.py
prody/database/uniprot.py
prody/domain_decomposition/__init__.py
prody/domain_decomposition/spectrus.py
prody/dynamics/__init__.py
prody/dynamics/adaptive.py
prody/dynamics/analysis.py
prody/dynamics/anm.py
prody/dynamics/anmd.py
prody/dynamics/bbenm.py
prody/dynamics/bbenmtools.c
prody/dynamics/bildfile.py
prody/dynamics/clustenm.py
prody/dynamics/compare.py
prody/dynamics/editing.py
prody/dynamics/entropy.py
prody/dynamics/essa.py
prody/dynamics/exanm.py
prody/dynamics/exgnm.py
prody/dynamics/functions.py
prody/dynamics/gamma.py
prody/dynamics/gnm.py
prody/dynamics/heatmapper.py
prody/dynamics/imanm.py
prody/dynamics/lda.py
prody/dynamics/logistic.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/ciffile.py
prody/proteins/cifheader.py
prody/proteins/compare.py
prody/proteins/dssp.py
prody/proteins/emdfile.py
prody/proteins/fixer.py
prody/proteins/functions.py
prody/proteins/header.py
prody/proteins/hpb.so
prody/proteins/interactions.py
prody/proteins/localpdb.py
prody/proteins/mmtffile.py
prody/proteins/opm.py
prody/proteins/pdbclusters.py
prody/proteins/pdbfile.py
prody/proteins/starfile.py
prody/proteins/stride.py
prody/proteins/tabulated_energies.txt
prody/proteins/waterbridges.py
prody/proteins/wwpdb.py
prody/proteins/ccealign/ccealignmodule.cpp
prody/proteins/ccealign/ccealignmodule.h
prody/proteins/hpbmodule/DT.h
prody/proteins/hpbmodule/f2c.h
prody/proteins/hpbmodule/find_vol_mod.h
prody/proteins/hpbmodule/hpbmodule.cpp
prody/proteins/hpbmodule/hpbmodule.h
prody/proteins/hpbmodule/reg_tet.c
prody/proteins/hpbmodule/type.h
prody/proteins/hpbmodule/hpb_Python2.7/hpb.so
prody/proteins/hpbmodule/hpb_Python3.10/hpb.so
prody/proteins/hpbmodule/hpb_Python3.11/hpb.so
prody/proteins/hpbmodule/hpb_Python3.12/hpb.so
prody/proteins/hpbmodule/hpb_Python3.8/hpb.so
prody/proteins/hpbmodule/hpb_Python3.9/hpb.so
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/database/__init__.py
prody/tests/database/test_bioexcel.py
prody/tests/database/test_cath.py
prody/tests/database/test_dali.py
prody/tests/database/test_goa.py
prody/tests/database/test_pfam.py
prody/tests/database/test_quartataweb.py
prody/tests/database/test_uniprot.py
prody/tests/datafiles/1pwc.mmtf
prody/tests/datafiles/1pwc.pdb
prody/tests/datafiles/1ubi.mmtf
prody/tests/datafiles/1ubi_anmd_mode1_ens.pdb
prody/tests/datafiles/2k39.mmtf
prody/tests/datafiles/2k39_PiCat.npy
prody/tests/datafiles/2k39_PiStack.npy
prody/tests/datafiles/2k39_all.npy
prody/tests/datafiles/2k39_all2.npy
prody/tests/datafiles/2k39_disu.npy
prody/tests/datafiles/2k39_hbs.npy
prody/tests/datafiles/2k39_hph.npy
prody/tests/datafiles/2k39_hph2.npy
prody/tests/datafiles/2k39_insty.dcd
prody/tests/datafiles/2k39_insty.pdb
prody/tests/datafiles/2k39_insty_first.pdb
prody/tests/datafiles/2k39_rib.npy
prody/tests/datafiles/2k39_sbs.npy
prody/tests/datafiles/3o21_disu.npy
prody/tests/datafiles/4akeA_alg_fixed.pdb
prody/tests/datafiles/6zu5_sel_SE0_SF0_10-20.pdb
prody/tests/datafiles/MCV1900193.json
prody/tests/datafiles/MCV1900370.dcd
prody/tests/datafiles/__init__.py
prody/tests/datafiles/addH_pdb3enl.pdb
prody/tests/datafiles/anm1ubi_evalues.dat
prody/tests/datafiles/anm1ubi_hessian.coo
prody/tests/datafiles/anm1ubi_vectors.dat
prody/tests/datafiles/cath.xml
prody/tests/datafiles/commute1ubi.dat
prody/tests/datafiles/dcd2k39_truncated.dcd
prody/tests/datafiles/exanm2nwl_evalues.dat
prody/tests/datafiles/exanm2nwl_hessian.coo
prody/tests/datafiles/exanm2nwl_vectors.dat
prody/tests/datafiles/gnm1ubi_evalues.dat
prody/tests/datafiles/gnm1ubi_kirchhoff.coo
prody/tests/datafiles/gnm1ubi_vectors.dat
prody/tests/datafiles/hit1ubi.dat
prody/tests/datafiles/lda2k39_evalues.dat
prody/tests/datafiles/lda2k39_vectors.dat
prody/tests/datafiles/mmcif_1ake_chimerax.cif
prody/tests/datafiles/mmcif_3o21.cif
prody/tests/datafiles/mmcif_6yfy.cif
prody/tests/datafiles/mmcif_6zu5.cif
prody/tests/datafiles/mmcif_7cth.cif
prody/tests/datafiles/mmtf3enl.mmtf
prody/tests/datafiles/msa_3hsyA_3o21A.fasta
prody/tests/datafiles/msa_3hsyA_3o21A_clustalw.fasta
prody/tests/datafiles/msa_3hsyA_3o21A_new.fasta
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/pca2k39_cov.coo
prody/tests/datafiles/pca2k39_evalues.dat
prody/tests/datafiles/pca2k39_vectors.dat
prody/tests/datafiles/pdb1ake.pdb
prody/tests/datafiles/pdb1ejg.pdb
prody/tests/datafiles/pdb1ejg_oneatom.pdb
prody/tests/datafiles/pdb1r19_dssp.pdb
prody/tests/datafiles/pdb1tw7_step3_charmm2namd.pdb
prody/tests/datafiles/pdb1tw7_step3_charmm2namd_doubled_h36.pdb
prody/tests/datafiles/pdb1tw7_step3_charmm2namd_doubled_hex.pdb
prody/tests/datafiles/pdb1ubi.pdb
prody/tests/datafiles/pdb1ubi_ca.pdb
prody/tests/datafiles/pdb2gb1_truncated.pdb
prody/tests/datafiles/pdb2k39_ca.pdb
prody/tests/datafiles/pdb2k39_truncated.pdb
prody/tests/datafiles/pdb2nwl-opm.pdb
prody/tests/datafiles/pdb3enl.pdb
prody/tests/datafiles/pdb3hsy.pdb
prody/tests/datafiles/pdb3mht.pdb
prody/tests/datafiles/pdb3o21.pdb
prody/tests/datafiles/pdb3p3w.pdb
prody/tests/datafiles/pdb4v8r_h36.pdb
prody/tests/datafiles/pdb4v8r_hex.pdb
prody/tests/datafiles/pdb6flr.pdb
prody/tests/datafiles/pdb6flr_B234.pdb
prody/tests/datafiles/pdb6fpj_Bb_fixed_solv_ions.pdb
prody/tests/datafiles/pdb7pbl.pdb
prody/tests/datafiles/pdbRTER.pdb
prody/tests/datafiles/pdb_addH_1ubi.pdb
prody/tests/datafiles/probes_in.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_anmd.py
prody/tests/dynamics/test_editing.py
prody/tests/dynamics/test_enms.py
prody/tests/dynamics/test_lda.py
prody/tests/dynamics/test_pca.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_ciffile.py
prody/tests/proteins/test_dssp.py
prody/tests/proteins/test_fixer.py
prody/tests/proteins/test_header.py
prody/tests/proteins/test_insty.py
prody/tests/proteins/test_localpdb.py
prody/tests/proteins/test_mmtffile.py
prody/tests/proteins/test_pdbfile.py
prody/tests/proteins/test_pqrfile.py
prody/tests/proteins/test_waterbridges.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/TreeConstruction.py
prody/utilities/__init__.py
prody/utilities/catchall.py
prody/utilities/checkers.py
prody/utilities/doctools.py
prody/utilities/drawtools.py
prody/utilities/eigtools.py
prody/utilities/laptools.py
prody/utilities/legacy.py
prody/utilities/logger.py
prody/utilities/misctools.py
prody/utilities/pathtools.py
prody/utilities/seqtools.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