├── .gitignore ├── COPYING ├── README ├── README.md ├── pdbtools ├── __init__.py ├── addH.py ├── atom_renumber.py ├── bfactor.py ├── centerasu.py ├── centermass.py ├── charmm │ ├── __init__.py │ ├── gen_input.py │ └── interface.py ├── clean.py ├── closecontacts.py ├── contact.py ├── contactplot.py ├── coulomb.py ├── data │ ├── __init__.py │ ├── common.py │ ├── peptides │ │ ├── ala-ala-ala.pdb │ │ ├── ala-arg-ala.pdb │ │ ├── ala-asn-ala.pdb │ │ ├── ala-asp-ala.pdb │ │ ├── ala-cys-ala.pdb │ │ ├── ala-gln-ala.pdb │ │ ├── ala-glu-ala.pdb │ │ ├── ala-gly-ala.pdb │ │ ├── ala-his-ala.pdb │ │ ├── ala-ile-ala.pdb │ │ ├── ala-leu-ala.pdb │ │ ├── ala-lys-ala.pdb │ │ ├── ala-met-ala.pdb │ │ ├── ala-phe-ala.pdb │ │ ├── ala-pro-ala.pdb │ │ ├── ala-ser-ala.pdb │ │ ├── ala-thr-ala.pdb │ │ ├── ala-trp-ala.pdb │ │ ├── ala-tyr-ala.pdb │ │ ├── ala-val-ala.pdb │ │ └── rib │ │ │ ├── ala-ala-ala.rib │ │ │ ├── ala-arg-ala.rib │ │ │ ├── ala-asn-ala.rib │ │ │ ├── ala-asp-ala.rib │ │ │ ├── ala-cys-ala.rib │ │ │ ├── ala-gln-ala.rib │ │ │ ├── ala-glu-ala.rib │ │ │ ├── ala-gly-ala.rib │ │ │ ├── ala-his-ala.rib │ │ │ ├── ala-ile-ala.rib │ │ │ ├── ala-leu-ala.rib │ │ │ ├── ala-lys-ala.rib │ │ │ ├── ala-met-ala.rib │ │ │ ├── ala-phe-ala.rib │ │ │ ├── ala-pro-ala.rib │ │ │ ├── ala-ser-ala.rib │ │ │ ├── ala-thr-ala.rib │ │ │ ├── ala-trp-ala.rib │ │ │ ├── ala-tyr-ala.rib │ │ │ └── ala-val-ala.rib │ ├── polar.py │ ├── polar_param.txt │ └── voidoo-cavity.lib ├── development │ ├── pdb_template.py │ ├── template.py │ └── to-do ├── dist_filter.py ├── disulfide.py ├── download.py ├── exper.py ├── helper │ ├── __init__.py │ ├── cmdline.py │ ├── container.py │ └── geometry.py ├── iondist.py ├── ligand.py ├── moment.py ├── mutator.py ├── neighbors.py ├── offset.py ├── oligomer.py ├── param.py ├── residue_renumber.py ├── sasa.py ├── satk.py ├── satk │ ├── Makefile │ ├── README │ ├── crdfrmt.f │ ├── mkwij.f │ ├── prescan.f │ ├── satkelni.f │ └── statacc.f ├── seq.py ├── splitnmr.py ├── subset.py ├── torsion.py └── watercontact.py ├── scripts ├── pdb_addH ├── pdb_atom_renumber ├── pdb_bfactor ├── pdb_centerasu ├── pdb_centermass ├── pdb_clean ├── pdb_closecontacts ├── pdb_contact ├── pdb_contactplot ├── pdb_coulomb ├── pdb_dist_filter ├── pdb_disulfide ├── pdb_download ├── pdb_exper ├── pdb_iondist ├── pdb_ligand ├── pdb_moment ├── pdb_mutator ├── pdb_neighbors ├── pdb_offset ├── pdb_oligomer ├── pdb_param ├── pdb_pdb2dir ├── pdb_residue_renumber ├── pdb_sasa ├── pdb_satk ├── pdb_seq ├── pdb_splitnmr ├── pdb_subset ├── pdb_torsion └── pdb_watercontact └── setup.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/harmslab/pdbtools/HEAD/.gitignore -------------------------------------------------------------------------------- /COPYING: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/harmslab/pdbtools/HEAD/COPYING 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