├── .gitignore ├── .gitmodules ├── .pre-commit-config.yaml ├── LICENSE ├── README.md ├── install.sh ├── notebooks └── .gitkeep ├── poetry.lock ├── pydock3 ├── __init__.py ├── blastermaster │ ├── __init__.py │ ├── blastermaster.py │ ├── blastermaster_config_schema.yaml │ ├── config.py │ ├── default_blastermaster_config.yaml │ ├── defaults │ │ ├── __init__.py │ │ ├── amb.crg.oxt │ │ ├── delphi.def │ │ ├── filt.params │ │ ├── prot.table.ambcrg.ambH │ │ ├── qnifft.parm │ │ ├── radii │ │ ├── reduce_wwPDB_het_dict.txt │ │ ├── residue_code_polar_h.yaml │ │ ├── rna_amb.crg.oxt │ │ ├── rna_prot.table.ambcrg.ambH │ │ ├── vdw.parms.amb.mindock │ │ └── vdw.siz │ ├── pdb.py │ ├── phi.py │ ├── programs │ │ ├── __init__.py │ │ ├── chemgrid │ │ │ ├── bin │ │ │ │ └── chemgrid │ │ │ └── src │ │ │ │ ├── Makefile │ │ │ │ ├── aesthetics.f │ │ │ │ ├── chemgrid.f │ │ │ │ ├── chemgrid.h │ │ │ │ ├── dconst.f │ │ │ │ ├── ddist.f │ │ │ │ ├── dist.f │ │ │ │ ├── grdout.f │ │ │ │ └── parmrec.f │ │ ├── dms │ │ │ ├── bin │ │ │ │ ├── dms │ │ │ │ ├── dms.1 │ │ │ │ ├── dms_servers.proto │ │ │ │ ├── dmsd │ │ │ │ └── radii │ │ │ └── src │ │ │ │ └── dms │ │ │ │ ├── GNUmakefile │ │ │ │ ├── README │ │ │ │ ├── atoms.h │ │ │ │ ├── compute.c │ │ │ │ ├── dms.1 │ │ │ │ ├── dms.html │ │ │ │ ├── dms_param.h │ │ │ │ ├── dms_paths.c │ │ │ │ ├── dms_servers.proto │ │ │ │ ├── dmsd │ │ │ │ ├── GNUmakefile │ │ │ │ ├── emalloc.c │ │ │ │ ├── freadv.c │ │ │ │ ├── lookat.c │ │ │ │ ├── server.c │ │ │ │ └── viewat.c │ │ │ │ ├── emalloc.c │ │ │ │ ├── fwritev.c │ │ │ │ ├── input.c │ │ │ │ ├── libpdb │ │ │ │ ├── GNUmakefile │ │ │ │ ├── ms.3 │ │ │ │ ├── ms.c │ │ │ │ ├── ms.h │ │ │ │ ├── pdb.3 │ │ │ │ ├── pdb.h │ │ │ │ ├── pdb_int.h │ │ │ │ ├── pdb_read.c │ │ │ │ ├── pdb_sprntf.c │ │ │ │ ├── pdb_sscanf.c │ │ │ │ ├── pdb_write.c │ │ │ │ ├── pdbrun.c │ │ │ │ ├── pdbrun5_read.i │ │ │ │ ├── pdbrun5_write.i │ │ │ │ ├── pdbrun6_read.i │ │ │ │ ├── pdbrun6_write.i │ │ │ │ ├── read_format.i │ │ │ │ └── write_format.i │ │ │ │ ├── ms.c │ │ │ │ ├── output.c │ │ │ │ ├── protocol.h │ │ │ │ ├── radii.proto │ │ │ │ ├── tokenize.c │ │ │ │ └── wanted.h │ │ ├── filt │ │ │ ├── bin │ │ │ │ └── filt │ │ │ └── src │ │ │ │ ├── Makefile │ │ │ │ └── filter1.f │ │ ├── makebox │ │ │ └── makebox.smallokay.pl │ │ ├── makespheres1 │ │ │ └── makespheres1.cli.pl │ │ ├── makespheres3 │ │ │ └── makespheres3.cli.pl │ │ ├── pdbtosph │ │ │ ├── bin │ │ │ │ └── pdbtosph │ │ │ └── src │ │ │ │ ├── Makefile │ │ │ │ └── pdbtosph.f │ │ ├── qnifft │ │ │ ├── bin │ │ │ │ └── qnifft22_193_pgf_32 │ │ │ └── src │ │ │ │ ├── Install.com │ │ │ │ ├── README │ │ │ │ ├── Tar.com │ │ │ │ ├── Untar.com │ │ │ │ ├── bin │ │ │ │ ├── chkchg │ │ │ │ ├── qnifft22_193_pgf_32 │ │ │ │ └── sumfld │ │ │ │ ├── bin_not_used │ │ │ │ ├── qnifft22_193 │ │ │ │ ├── qnifft22_193_new │ │ │ │ ├── qnifft22_193_new_static │ │ │ │ ├── qnifft22_193_newswap │ │ │ │ └── qnifft22_193_pgf │ │ │ │ ├── data │ │ │ │ ├── Bqequil_old.dat │ │ │ │ ├── README.cvff │ │ │ │ ├── charmm.crg │ │ │ │ ├── cvff.crg │ │ │ │ ├── cvff.siz │ │ │ │ ├── default.crg │ │ │ │ ├── default.rad │ │ │ │ ├── default.siz │ │ │ │ ├── nucleic_acid_amber.crg │ │ │ │ ├── nucleic_acid_cvff.crg │ │ │ │ ├── nucleic_acid_cvff.siz │ │ │ │ ├── nucleic_acid_full.crg │ │ │ │ ├── nucleic_acid_harvey.crg │ │ │ │ ├── opls.crg │ │ │ │ ├── opls.siz │ │ │ │ ├── parse.crg │ │ │ │ ├── parse.siz │ │ │ │ ├── parse_dec98.crg │ │ │ │ ├── parse_old.crg │ │ │ │ ├── parse_old1.crg │ │ │ │ ├── polar.rad │ │ │ │ ├── prot_full.crg │ │ │ │ ├── protein_amber.crg │ │ │ │ ├── protein_backbone.crg │ │ │ │ ├── protein_charmm.crg │ │ │ │ ├── protein_opls.crg │ │ │ │ ├── protein_opls.siz │ │ │ │ ├── qequil.dat │ │ │ │ ├── rna.crg │ │ │ │ ├── rna_amber.crg │ │ │ │ ├── rna_cvff.crg │ │ │ │ ├── rna_cvff_mod.crg │ │ │ │ ├── rna_cvff_orig.crg │ │ │ │ ├── rna_full.crg │ │ │ │ ├── spin_label.crg │ │ │ │ ├── sugar.crg │ │ │ │ ├── temp.crg │ │ │ │ ├── xplor.crg │ │ │ │ └── xplor.siz │ │ │ │ ├── delphi.def │ │ │ │ ├── delphi_parm.lis │ │ │ │ ├── delphi_parm1.lis │ │ │ │ ├── delphi_parm2.lis │ │ │ │ ├── examples │ │ │ │ ├── cylinder │ │ │ │ │ ├── README │ │ │ │ │ ├── cyl.atm │ │ │ │ │ ├── cyl.com │ │ │ │ │ ├── cyl.crg │ │ │ │ │ ├── cyl.eps │ │ │ │ │ ├── cyl.siz │ │ │ │ │ ├── cyl1.phi │ │ │ │ │ ├── cyl_15_97.sum │ │ │ │ │ ├── cyl_16_97.sum │ │ │ │ │ ├── cyl_16_97a.sum │ │ │ │ │ ├── cyl_16_97b.sum │ │ │ │ │ ├── cyl_19.sum │ │ │ │ │ ├── cyl_22.sum │ │ │ │ │ ├── cyl_I500_15_97.fld │ │ │ │ │ ├── cyl_I500_15_97o.fld │ │ │ │ │ ├── cyl_I500_16_97.fld │ │ │ │ │ ├── cyl_I500_16_97a.fld │ │ │ │ │ ├── cyl_I500_16_97ao.fld │ │ │ │ │ ├── cyl_I500_16_97b.fld │ │ │ │ │ ├── cyl_I500_16_97bo.fld │ │ │ │ │ ├── cyl_I500_16_97o.fld │ │ │ │ │ ├── cyl_I500_19.fld │ │ │ │ │ ├── cyl_I500_19o.fld │ │ │ │ │ ├── cyl_I500_22.fld │ │ │ │ │ ├── cyl_I500_22o.fld │ │ │ │ │ ├── cyl_I500_lnx.fld │ │ │ │ │ ├── cyl_I500_lnxbig.fld │ │ │ │ │ ├── cyl_I500_lnxbigo.fld │ │ │ │ │ ├── cyl_I500_lnxo.fld │ │ │ │ │ ├── cyl_I500_v16.fld │ │ │ │ │ ├── cyl_I500_v16o.fld │ │ │ │ │ ├── cyl_lnx.sum │ │ │ │ │ ├── cyl_lnxbig.sum │ │ │ │ │ ├── cyl_v16.sum │ │ │ │ │ ├── ionint.com │ │ │ │ │ ├── ionintm.com │ │ │ │ │ ├── ionintm.out │ │ │ │ │ ├── ionintm1.out │ │ │ │ │ ├── parm │ │ │ │ │ ├── parm1 │ │ │ │ │ ├── qnifft.frc │ │ │ │ │ └── reaction.fld │ │ │ │ ├── dna_drug │ │ │ │ │ ├── README │ │ │ │ │ ├── chkchg.out │ │ │ │ │ ├── dapdna.crg │ │ │ │ │ ├── dapi.com │ │ │ │ │ ├── dapi.sum │ │ │ │ │ ├── dapi.sum1a │ │ │ │ │ ├── dapi.sum1b │ │ │ │ │ ├── dapi.sum2 │ │ │ │ │ ├── dapi.sum3 │ │ │ │ │ ├── dapi.sum4 │ │ │ │ │ ├── dapi.sum5 │ │ │ │ │ ├── dapi.sum6 │ │ │ │ │ ├── dapi_288.sum │ │ │ │ │ ├── dapi_298.sum │ │ │ │ │ ├── dapi_new.com │ │ │ │ │ ├── dapin.log1 │ │ │ │ │ ├── dapin.log3 │ │ │ │ │ ├── dapin.log4 │ │ │ │ │ ├── dapin.log6 │ │ │ │ │ ├── dapout.log1 │ │ │ │ │ ├── dapout.log3 │ │ │ │ │ ├── dapout.log4 │ │ │ │ │ ├── dapout.log5 │ │ │ │ │ ├── dapout.log6 │ │ │ │ │ ├── default.siz │ │ │ │ │ ├── grepit.com │ │ │ │ │ ├── ion.out │ │ │ │ │ ├── ionint.com │ │ │ │ │ ├── ionintm.com │ │ │ │ │ ├── parm │ │ │ │ │ ├── parm2 │ │ │ │ │ ├── qnifft12_test.sum │ │ │ │ │ └── temp.atm │ │ │ │ ├── non_linear │ │ │ │ │ ├── README │ │ │ │ │ ├── dump19.map │ │ │ │ │ ├── ionint.com │ │ │ │ │ ├── ionint.out │ │ │ │ │ ├── ionintm.com │ │ │ │ │ ├── ionintm.out │ │ │ │ │ ├── parm │ │ │ │ │ ├── parm1 │ │ │ │ │ ├── qnifft.frc │ │ │ │ │ ├── reaction.fld │ │ │ │ │ ├── sph.atm │ │ │ │ │ ├── sph.com │ │ │ │ │ ├── sph.crg │ │ │ │ │ ├── sph.eps │ │ │ │ │ ├── sph.siz │ │ │ │ │ ├── sph_14node12.sum │ │ │ │ │ ├── sph_15a.sum │ │ │ │ │ ├── sph_16b.sum │ │ │ │ │ ├── sph_16c.sum │ │ │ │ │ ├── sph_17lnx.sum │ │ │ │ │ ├── sph_19lnx.sum │ │ │ │ │ ├── sph_22lnx.sum │ │ │ │ │ ├── sph_I0_14node12.fld │ │ │ │ │ ├── sph_I0_14node12o.fld │ │ │ │ │ ├── sph_I0_15a.fld │ │ │ │ │ ├── sph_I0_15ao.fld │ │ │ │ │ ├── sph_I0_16b.fld │ │ │ │ │ ├── sph_I0_16bo.fld │ │ │ │ │ ├── sph_I0_16c.fld │ │ │ │ │ ├── sph_I0_16co.fld │ │ │ │ │ ├── sph_I0_17lnx.fld │ │ │ │ │ ├── sph_I0_17lnxo.fld │ │ │ │ │ ├── sph_I0_19lnx.fld │ │ │ │ │ ├── sph_I0_19lnxo.fld │ │ │ │ │ ├── sph_I0_22lnx.fld │ │ │ │ │ ├── sph_I0_22lnxo.fld │ │ │ │ │ ├── sph_I0_lnx.fld │ │ │ │ │ ├── sph_I0_lnxo.fld │ │ │ │ │ ├── sph_I1lin_14node12.fld │ │ │ │ │ ├── sph_I1lin_14node12o.fld │ │ │ │ │ ├── sph_I1lin_15a.fld │ │ │ │ │ ├── sph_I1lin_15ao.fld │ │ │ │ │ ├── sph_I1lin_16b.fld │ │ │ │ │ ├── sph_I1lin_16bo.fld │ │ │ │ │ ├── sph_I1lin_16c.fld │ │ │ │ │ ├── sph_I1lin_16co.fld │ │ │ │ │ ├── sph_I1lin_17lnx.fld │ │ │ │ │ ├── sph_I1lin_17lnxo.fld │ │ │ │ │ ├── sph_I1lin_19lnx.fld │ │ │ │ │ ├── sph_I1lin_19lnxo.fld │ │ │ │ │ ├── sph_I1lin_22lnx.fld │ │ │ │ │ ├── sph_I1lin_22lnxo.fld │ │ │ │ │ ├── sph_I1lin_lnx.fld │ │ │ │ │ ├── sph_I1lin_lnxo.fld │ │ │ │ │ ├── sph_I1non_14node12.fld │ │ │ │ │ ├── sph_I1non_14node12o.fld │ │ │ │ │ ├── sph_I1non_15a.fld │ │ │ │ │ ├── sph_I1non_15ao.fld │ │ │ │ │ ├── sph_I1non_16b.fld │ │ │ │ │ ├── sph_I1non_16bo.fld │ │ │ │ │ ├── sph_I1non_16c.fld │ │ │ │ │ ├── sph_I1non_16co.fld │ │ │ │ │ ├── sph_I1non_17lnx.fld │ │ │ │ │ ├── sph_I1non_17lnxo.fld │ │ │ │ │ ├── sph_I1non_19lnx.fld │ │ │ │ │ ├── sph_I1non_19lnxo.fld │ │ │ │ │ ├── sph_I1non_22lnx.fld │ │ │ │ │ ├── sph_I1non_22lnxo.fld │ │ │ │ │ ├── sph_I1non_lnx.fld │ │ │ │ │ ├── sph_I1non_lnxo.fld │ │ │ │ │ ├── sph_lnx.sum │ │ │ │ │ ├── sphin.eps │ │ │ │ │ ├── sphin.phi │ │ │ │ │ ├── sphout.eps │ │ │ │ │ └── sphout.phi │ │ │ │ ├── sphere │ │ │ │ │ ├── Runme.com │ │ │ │ │ ├── Runme2.com │ │ │ │ │ ├── Runme3.com │ │ │ │ │ ├── contour.kt │ │ │ │ │ ├── delphi.def │ │ │ │ │ ├── parm │ │ │ │ │ ├── sph.crg │ │ │ │ │ ├── sph.fld │ │ │ │ │ └── sph.siz │ │ │ │ └── trypsin_pka │ │ │ │ │ ├── Readme │ │ │ │ │ ├── chkchg.out │ │ │ │ │ ├── def.siz │ │ │ │ │ ├── fort.14 │ │ │ │ │ ├── his40.crg │ │ │ │ │ ├── his40_neut.crg │ │ │ │ │ ├── parm │ │ │ │ │ ├── parm1 │ │ │ │ │ ├── qnifft12_test.sum │ │ │ │ │ ├── rat_ptb_his40.atm │ │ │ │ │ ├── tryp.eps │ │ │ │ │ ├── tryp0_hisn.log1 │ │ │ │ │ ├── tryp0_hisp.log1 │ │ │ │ │ ├── tryp_all.crg │ │ │ │ │ ├── tryp_full.crg │ │ │ │ │ ├── tryp_hisn.int │ │ │ │ │ ├── tryp_hisn.int1 │ │ │ │ │ ├── tryp_hisn.log1 │ │ │ │ │ ├── tryp_hisp.int │ │ │ │ │ ├── tryp_hisp.int1 │ │ │ │ │ ├── tryp_hisp.log1 │ │ │ │ │ ├── trypsin.com │ │ │ │ │ ├── trypsin.sum │ │ │ │ │ └── trypsin.sum1 │ │ │ │ ├── qnifft.parm │ │ │ │ ├── qnifft2.parm │ │ │ │ └── source │ │ │ │ ├── Makefile_all │ │ │ │ ├── Makefile_blank │ │ │ │ ├── Makefile_compaq │ │ │ │ ├── Makefile_gnu │ │ │ │ ├── Makefile_lahey │ │ │ │ ├── Makefile_sgi │ │ │ │ ├── qnifft │ │ │ │ ├── v1.4 │ │ │ │ │ ├── Makefile │ │ │ │ │ ├── Makefile_sgi │ │ │ │ │ ├── cent.f │ │ │ │ │ ├── cfind.f │ │ │ │ │ ├── charge.f │ │ │ │ │ ├── chrgal.f │ │ │ │ │ ├── chrgit.f │ │ │ │ │ ├── cputime.f │ │ │ │ │ ├── diff.com │ │ │ │ │ ├── diff.out │ │ │ │ │ ├── dtstmp.f │ │ │ │ │ ├── elb.f │ │ │ │ │ ├── expand5.f │ │ │ │ │ ├── expand6.f │ │ │ │ │ ├── fodder.f │ │ │ │ │ ├── getmaps.f │ │ │ │ │ ├── getpar.f │ │ │ │ │ ├── getpar1.f │ │ │ │ │ ├── getpdb.f │ │ │ │ │ ├── ichash.f │ │ │ │ │ ├── inewt.f │ │ │ │ │ ├── inewt2.f │ │ │ │ │ ├── irhash.f │ │ │ │ │ ├── lstmod.h │ │ │ │ │ ├── make.out │ │ │ │ │ ├── makefile_temp │ │ │ │ │ ├── mkmaps.f │ │ │ │ │ ├── phierg.f │ │ │ │ │ ├── phierg2.f │ │ │ │ │ ├── phierg2_old.f │ │ │ │ │ ├── phierg_smth.f │ │ │ │ │ ├── phintp.f │ │ │ │ │ ├── pwd.dat │ │ │ │ │ ├── qdiffpar.h │ │ │ │ │ ├── qdiffpar161.h │ │ │ │ │ ├── qdiffpar65.h │ │ │ │ │ ├── qdiffpar97.h │ │ │ │ │ ├── qhelp.f │ │ │ │ │ ├── qnifft13.f │ │ │ │ │ ├── qnifft14.f │ │ │ │ │ ├── qnifft14a.f │ │ │ │ │ ├── qnifft14b.f │ │ │ │ │ ├── qnifft_maps.f │ │ │ │ │ ├── radius.f │ │ │ │ │ ├── rent.f │ │ │ │ │ ├── rfind.f │ │ │ │ │ ├── scaler.f │ │ │ │ │ ├── session_record │ │ │ │ │ ├── setbc.f │ │ │ │ │ ├── setbc1.f │ │ │ │ │ ├── setbc_maps.f │ │ │ │ │ ├── smtheps.f │ │ │ │ │ ├── temp │ │ │ │ │ ├── temp1.f │ │ │ │ │ ├── up.f │ │ │ │ │ └── wrteps.f │ │ │ │ └── v2.2 │ │ │ │ │ ├── .gitignore │ │ │ │ │ ├── Makefile │ │ │ │ │ ├── Makefile.orig │ │ │ │ │ ├── cent.f │ │ │ │ │ ├── cfind.f │ │ │ │ │ ├── charge.f │ │ │ │ │ ├── chrgal.f │ │ │ │ │ ├── chrgit.f │ │ │ │ │ ├── cputime.f │ │ │ │ │ ├── debmemb.f │ │ │ │ │ ├── dmpeps.f │ │ │ │ │ ├── dtstmp.f │ │ │ │ │ ├── elb.f │ │ │ │ │ ├── getpar.f │ │ │ │ │ ├── getpdb.f │ │ │ │ │ ├── girdgen.f │ │ │ │ │ ├── inewt.f │ │ │ │ │ ├── lstmod.h │ │ │ │ │ ├── mapgen.f │ │ │ │ │ ├── mapgen1.f │ │ │ │ │ ├── mapgen2.f │ │ │ │ │ ├── mapgen3.f │ │ │ │ │ ├── mapgen4.f │ │ │ │ │ ├── mapgen5.f │ │ │ │ │ ├── mapgen5a.f │ │ │ │ │ ├── mapgen6.f │ │ │ │ │ ├── mapgen7.f │ │ │ │ │ ├── mapgen_try.f │ │ │ │ │ ├── mapit.f │ │ │ │ │ ├── mkepsd.f │ │ │ │ │ ├── mkmaps.f │ │ │ │ │ ├── phierg.f │ │ │ │ │ ├── phierg1.f │ │ │ │ │ ├── phifrc.f │ │ │ │ │ ├── phifrc1.f │ │ │ │ │ ├── phintp.f │ │ │ │ │ ├── phirxn.f │ │ │ │ │ ├── phirxn1.f │ │ │ │ │ ├── pntchk.f │ │ │ │ │ ├── qcall.f │ │ │ │ │ ├── qcen.f │ │ │ │ │ ├── qdiffpar.h │ │ │ │ │ ├── qdiffpar1.h │ │ │ │ │ ├── qdiffpar129.h │ │ │ │ │ ├── qdiffpar161.h │ │ │ │ │ ├── qdiffpar193.h │ │ │ │ │ ├── qdiffpar65.h │ │ │ │ │ ├── qhelp.f │ │ │ │ │ ├── qnifft22.f │ │ │ │ │ ├── qnifft22_193_pgf_32 │ │ │ │ │ ├── qnifft22_sub.f │ │ │ │ │ ├── radius.f │ │ │ │ │ ├── rent.f │ │ │ │ │ ├── rfind.f │ │ │ │ │ ├── sasgen.f │ │ │ │ │ ├── sasgen1.f │ │ │ │ │ ├── scaler.f │ │ │ │ │ ├── setbc.f │ │ │ │ │ ├── up.f │ │ │ │ │ ├── utility.f │ │ │ │ │ └── wrteps.f │ │ │ │ └── utility │ │ │ │ ├── Makefile │ │ │ │ ├── addmap.f │ │ │ │ ├── chkchg.f │ │ │ │ ├── ionintm.f │ │ │ │ ├── ionintm_rad.f │ │ │ │ └── sumfld.f │ │ ├── reduce │ │ │ ├── README.md │ │ │ └── reduce │ │ ├── showsphere │ │ │ ├── bin │ │ │ │ └── showsphere │ │ │ ├── doshowsph.csh │ │ │ └── src │ │ │ │ ├── Makefile │ │ │ │ └── showsphere.f │ │ ├── solvmap │ │ │ ├── bin │ │ │ │ └── solvmap │ │ │ └── src │ │ │ │ ├── INSEV.MS │ │ │ │ ├── INSEV.SAS │ │ │ │ ├── INSEV.SEV │ │ │ │ ├── INSEV.VDW │ │ │ │ ├── Makefile │ │ │ │ ├── acc.h │ │ │ │ ├── cube.f │ │ │ │ ├── cubic.h │ │ │ │ ├── dist.h │ │ │ │ ├── memalloc.c │ │ │ │ ├── pointer.h │ │ │ │ ├── sas.f │ │ │ │ └── solvmap.f │ │ ├── sphgen │ │ │ ├── bin │ │ │ │ └── sphgen │ │ │ └── src │ │ │ │ ├── Makefile │ │ │ │ └── sphgen.f │ │ ├── thinspheres │ │ │ ├── __init__.py │ │ │ ├── pdb_lib.py │ │ │ └── sph_lib.py │ │ └── visualization │ │ │ ├── create_LigDeSolv_DX.py │ │ │ ├── create_VDW_DX.py │ │ │ └── phi_to_dx.py │ ├── steps │ │ ├── __init__.py │ │ ├── binding_site_residues.py │ │ ├── binding_site_spheres.py │ │ ├── box.py │ │ ├── charged_receptor_deprotonation.py │ │ ├── close_spheres.py │ │ ├── electrostatics.py │ │ ├── ligand_desolvation.py │ │ ├── ligand_hetatm_renaming.py │ │ ├── low_dielectric_spheres.py │ │ ├── matching_spheres.py │ │ ├── molecular_surface.py │ │ ├── pdb_to_sph.py │ │ ├── receptor_most_occupied_residues_renaming.py │ │ ├── receptor_protonation.py │ │ ├── receptor_transformation_for_electrostatics.py │ │ ├── receptor_transformation_for_ligand_desolvation.py │ │ ├── sph_to_pdb.py │ │ ├── thin_spheres.py │ │ ├── vdw.py │ │ └── visualization.py │ └── util.py ├── config.py ├── criterion │ ├── __init__.py │ ├── criterion.py │ ├── enrichment │ │ ├── __init__.py │ │ ├── bonferroni.py │ │ ├── logauc.py │ │ ├── random_classifier_probability │ │ │ ├── table_100_actives.df │ │ │ ├── table_10_actives.df │ │ │ ├── table_11_actives.df │ │ │ ├── table_12_actives.df │ │ │ ├── table_13_actives.df │ │ │ ├── table_14_actives.df │ │ │ ├── table_15_actives.df │ │ │ ├── table_16_actives.df │ │ │ ├── table_17_actives.df │ │ │ ├── table_18_actives.df │ │ │ ├── table_19_actives.df │ │ │ ├── table_1_actives.df │ │ │ ├── table_20_actives.df │ │ │ ├── table_21_actives.df │ │ │ ├── table_22_actives.df │ │ │ ├── table_23_actives.df │ │ │ ├── table_24_actives.df │ │ │ ├── table_25_actives.df │ │ │ ├── table_26_actives.df │ │ │ ├── table_27_actives.df │ │ │ ├── table_28_actives.df │ │ │ ├── table_29_actives.df │ │ │ ├── table_2_actives.df │ │ │ ├── table_30_actives.df │ │ │ ├── table_31_actives.df │ │ │ ├── table_32_actives.df │ │ │ ├── table_33_actives.df │ │ │ ├── table_34_actives.df │ │ │ ├── table_35_actives.df │ │ │ ├── table_36_actives.df │ │ │ ├── table_37_actives.df │ │ │ ├── table_38_actives.df │ │ │ ├── table_39_actives.df │ │ │ ├── table_3_actives.df │ │ │ ├── table_40_actives.df │ │ │ ├── table_41_actives.df │ │ │ ├── table_42_actives.df │ │ │ ├── table_43_actives.df │ │ │ ├── table_44_actives.df │ │ │ ├── table_45_actives.df │ │ │ ├── table_46_actives.df │ │ │ ├── table_47_actives.df │ │ │ ├── table_48_actives.df │ │ │ ├── table_49_actives.df │ │ │ ├── table_4_actives.df │ │ │ ├── table_50_actives.df │ │ │ ├── table_51_actives.df │ │ │ ├── table_52_actives.df │ │ │ ├── table_53_actives.df │ │ │ ├── table_54_actives.df │ │ │ ├── table_55_actives.df │ │ │ ├── table_56_actives.df │ │ │ ├── table_57_actives.df │ │ │ ├── table_58_actives.df │ │ │ ├── table_59_actives.df │ │ │ ├── table_5_actives.df │ │ │ ├── table_60_actives.df │ │ │ ├── table_61_actives.df │ │ │ ├── table_62_actives.df │ │ │ ├── table_63_actives.df │ │ │ ├── table_64_actives.df │ │ │ ├── table_65_actives.df │ │ │ ├── table_66_actives.df │ │ │ ├── table_67_actives.df │ │ │ ├── table_68_actives.df │ │ │ ├── table_69_actives.df │ │ │ ├── table_6_actives.df │ │ │ ├── table_70_actives.df │ │ │ ├── table_71_actives.df │ │ │ ├── table_72_actives.df │ │ │ ├── table_73_actives.df │ │ │ ├── table_74_actives.df │ │ │ ├── table_75_actives.df │ │ │ ├── table_76_actives.df │ │ │ ├── table_77_actives.df │ │ │ ├── table_78_actives.df │ │ │ ├── table_79_actives.df │ │ │ ├── table_7_actives.df │ │ │ ├── table_80_actives.df │ │ │ ├── table_81_actives.df │ │ │ ├── table_82_actives.df │ │ │ ├── table_83_actives.df │ │ │ ├── table_84_actives.df │ │ │ ├── table_85_actives.df │ │ │ ├── table_86_actives.df │ │ │ ├── table_87_actives.df │ │ │ ├── table_88_actives.df │ │ │ ├── table_89_actives.df │ │ │ ├── table_8_actives.df │ │ │ ├── table_90_actives.df │ │ │ ├── table_91_actives.df │ │ │ ├── table_92_actives.df │ │ │ ├── table_93_actives.df │ │ │ ├── table_94_actives.df │ │ │ ├── table_95_actives.df │ │ │ ├── table_96_actives.df │ │ │ ├── table_97_actives.df │ │ │ ├── table_98_actives.df │ │ │ ├── table_99_actives.df │ │ │ └── table_9_actives.df │ │ └── roc.py │ └── pose │ │ └── __init__.py ├── docking │ ├── __init__.py │ └── rundock.bash ├── dockopt │ ├── __init__.py │ ├── config.py │ ├── default_dockopt_config.yaml │ ├── dock_files_modification │ │ └── matching_spheres_perturbation.py │ ├── docking_configuration.py │ ├── dockopt.py │ ├── dockopt_config_schema.yaml │ ├── parameters.py │ ├── pipeline.py │ ├── reporter.py │ ├── results.py │ └── util.py ├── files.py ├── job_schedulers.py ├── jobs.py ├── lsd │ ├── __init__.py │ ├── config.py │ ├── default_lsd_config.yaml │ ├── lsd.py │ └── lsd_config_schema.yaml ├── retrodock │ ├── retrodock.py │ └── retrospective_dataset.py ├── scripts.py ├── top_poses.py └── util.py ├── pyproject.toml └── tests └── .gitkeep /.gitignore: -------------------------------------------------------------------------------- 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