├── .gitignore ├── AGENTS.md ├── CHANGELOG ├── INSTALL ├── LICENSE ├── NEWS ├── QUICKSTART.txt ├── README.md ├── TODO ├── UTILS.md ├── VERSION ├── clean.sh ├── mapman ├── ccp42ezd.sh ├── ezd2ccp4.sh └── lx_mapman ├── publications ├── 3V_cavity_channel_and_cleft_volume_calculator_and_extractor.pdf ├── Geometry_of_the_Ribosomal_Polypeptide_Exit_Tunnel.pdf └── NR_Voss-thesis-Geometric_Studies_of_RNA_and_Ribosomes.pdf ├── python ├── editBadMrc.py ├── mrcBisect.py ├── mrcFillCav.py ├── mrcTrim.py ├── mrcTwoBisect.py ├── pdbCrystal.py ├── pdblib.py ├── pyami │ ├── __init__.py │ ├── arraystats.py │ ├── mrc.py │ ├── resultcache.py │ └── weakattr.py ├── splitChainPDB.py └── splitPDB.py ├── src ├── Makefile ├── allchannel.cpp ├── allchannelexc.cpp ├── argument_helper.cpp ├── argument_helper.h ├── atmtypenumbers_data.h ├── cavities.cpp ├── channel.cpp ├── checkMalloc.sh ├── customvolume.cpp ├── fracDim.cpp ├── fsv_calc.cpp ├── pdb_io.cpp ├── pdb_io.h ├── pdb_to_xyzr.cpp ├── solvent.cpp ├── tunnel.cpp ├── twovolnocav.cpp ├── utils-main-legacy.cpp ├── utils-main.cpp ├── utils-mrc.cpp ├── utils-output.cpp ├── utils.h ├── vdw.cpp ├── volnocav.cpp ├── volume.cpp └── volume_original.cpp ├── test ├── test_pdb_to_xyzr.sh ├── test_suite.py ├── test_suite.yml ├── test_volume.sh ├── test_volume_classic.sh └── test_volumes.py └── xyzr ├── atmtypenumbers ├── pdb_to_xyzr.py └── pdb_to_xyzr.sh /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vosslab/vossvolvox/HEAD/.gitignore -------------------------------------------------------------------------------- /AGENTS.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vosslab/vossvolvox/HEAD/AGENTS.md -------------------------------------------------------------------------------- /CHANGELOG: -------------------------------------------------------------------------------- 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