LICENSE
MANIFEST.in
README.rst
setup.cfg
setup.py
versioneer.py
src/pmx/AbsRestraints.py
src/pmx/__init__.py
src/pmx/_version.py
src/pmx/alchemy.py
src/pmx/analysis.py
src/pmx/atom.py
src/pmx/atomselection.py
src/pmx/builder.py
src/pmx/chain.py
src/pmx/estimators.py
src/pmx/ffparser.py
src/pmx/forcefield.py
src/pmx/geometry.py
src/pmx/gmx.py
src/pmx/jobscript.py
src/pmx/library.py
src/pmx/ligand_alchemy.py
src/pmx/model.py
src/pmx/molecule.py
src/pmx/mutdb.py
src/pmx/ndx.py
src/pmx/options.py
src/pmx/parser.py
src/pmx/resselection.py
src/pmx/rosetta.py
src/pmx/rosetta_analyze.py
src/pmx/rotamer.py
src/pmx/summary.py
src/pmx/utils.py
src/pmx/xdrfile.py
src/pmx/xtc.py
src/pmx/data/aminoacids.pkl
src/pmx/data/bbdep.pkl
src/pmx/data/blosum62_new.mat
src/pmx/data/bp.pkl
src/pmx/data/bp_amber.pkl
src/pmx/data/bp_charmm.pkl
src/pmx/data/rna.pkl
src/pmx/data/mutff/atommass.dat
src/pmx/data/mutff/elements.dat
src/pmx/data/mutff/residuetypes.dat
src/pmx/data/mutff/spc216.gro
src/pmx/data/mutff/specbond.dat
src/pmx/data/mutff/vdwradii.dat
src/pmx/data/mutff/xlateat.dat
src/pmx/data/mutff/amber14sbmut.ff/Makefile.am
src/pmx/data/mutff/amber14sbmut.ff/Makefile.in
src/pmx/data/mutff/amber14sbmut.ff/aminoacids.arn
src/pmx/data/mutff/amber14sbmut.ff/aminoacids.c.tdb
src/pmx/data/mutff/amber14sbmut.ff/aminoacids.hdb
src/pmx/data/mutff/amber14sbmut.ff/aminoacids.n.tdb
src/pmx/data/mutff/amber14sbmut.ff/aminoacids.r2b
src/pmx/data/mutff/amber14sbmut.ff/aminoacids.rtp
src/pmx/data/mutff/amber14sbmut.ff/aminoacids.vsd
src/pmx/data/mutff/amber14sbmut.ff/atomtypes.atp
src/pmx/data/mutff/amber14sbmut.ff/dna.arn
src/pmx/data/mutff/amber14sbmut.ff/dna.hdb
src/pmx/data/mutff/amber14sbmut.ff/dna.r2b
src/pmx/data/mutff/amber14sbmut.ff/dna.rtp
src/pmx/data/mutff/amber14sbmut.ff/ffbonded.itp
src/pmx/data/mutff/amber14sbmut.ff/ffnonbonded.itp
src/pmx/data/mutff/amber14sbmut.ff/forcefield.doc
src/pmx/data/mutff/amber14sbmut.ff/forcefield.itp
src/pmx/data/mutff/amber14sbmut.ff/gbsa.itp
src/pmx/data/mutff/amber14sbmut.ff/ions.itp
src/pmx/data/mutff/amber14sbmut.ff/mutres.mtp
src/pmx/data/mutff/amber14sbmut.ff/mutres.rtp
src/pmx/data/mutff/amber14sbmut.ff/rna.arn
src/pmx/data/mutff/amber14sbmut.ff/rna.hdb
src/pmx/data/mutff/amber14sbmut.ff/rna.r2b
src/pmx/data/mutff/amber14sbmut.ff/rna.rtp
src/pmx/data/mutff/amber14sbmut.ff/spc.itp
src/pmx/data/mutff/amber14sbmut.ff/spce.itp
src/pmx/data/mutff/amber14sbmut.ff/tip3p.itp
src/pmx/data/mutff/amber14sbmut.ff/tip4p.itp
src/pmx/data/mutff/amber14sbmut.ff/tip4pew.itp
src/pmx/data/mutff/amber14sbmut.ff/tip5p.itp
src/pmx/data/mutff/amber14sbmut.ff/urea.itp
src/pmx/data/mutff/amber14sbmut.ff/watermodels.dat
src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/aminoacids.arn
src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/aminoacids.arn_backup
src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/aminoacids.c.tdb
src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/aminoacids.hdb
src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/aminoacids.n.tdb
src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/aminoacids.r2b
src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/aminoacids.rtp
src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/aminoacids.vsd
src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/atomtypes.atp
src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/backup_ffbonded_for_ildn_test.itp
src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/backup_mutres
src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/correct_ffbonded.itp
src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/dna.arn
src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/dna.hdb
src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/dna.r2b
src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/dna.rtp
src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/ffberger.itp
src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/ffbonded.itp
src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/ffnonbonded.itp
src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/forcefield.doc
src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/forcefield.itp
src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/gbsa.itp
src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/ions.itp
src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/mutres_dna.mtp
src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/mutres_dna.rtp
src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/popc_AmbBer.itp
src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/popc_AmbBer_posre.itp
src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/rna.arn
src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/rna.hdb
src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/rna.r2b
src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/rna.rtp
src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/spc.itp
src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/spce.itp
src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/tip3p.itp
src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/tip4p.itp
src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/tip4pew.itp
src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/tip5p.itp
src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/urea.itp
src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/watermodels.dat
src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/aminoacids.arn
src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/aminoacids.c.tdb
src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/aminoacids.hdb
src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/aminoacids.n.tdb
src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/aminoacids.r2b
src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/aminoacids.rtp
src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/aminoacids.vsd
src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/atomtypes.atp
src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/backup_ffbonded_for_ildn_test.itp
src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/backup_mutres
src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/correct_ffbonded.itp
src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/dna.arn
src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/dna.hdb
src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/dna.r2b
src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/dna.rtp
src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/ffberger.itp
src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/ffbonded.itp
src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/ffnonbonded.itp
src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/forcefield.doc
src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/forcefield.itp
src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/gbsa.itp
src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/ions.itp
src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/mutres_dna.mtp
src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/mutres_dna.rtp
src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/popc_AmbBer.itp
src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/popc_AmbBer_posre.itp
src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/rna.arn
src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/rna.hdb
src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/rna.r2b
src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/rna.rtp
src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/spc.itp
src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/spce.itp
src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/tip3p.itp
src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/tip4p.itp
src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/tip4pew.itp
src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/tip5p.itp
src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/urea.itp
src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/watermodels.dat
src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/aminoacids.arn
src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/aminoacids.c.tdb
src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/aminoacids.hdb
src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/aminoacids.n.tdb
src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/aminoacids.r2b
src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/aminoacids.rtp
src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/aminoacids.vsd
src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/atomtypes.atp
src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/dna.arn
src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/dna.hdb
src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/dna.r2b
src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/dna.rtp
src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/ffbonded.itp
src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/ffnonbonded.itp
src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/forcefield.doc
src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/forcefield.itp
src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/gbsa.itp
src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/ions.itp
src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/mutres.mtp
src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/mutres.rtp
src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/rna.arn
src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/rna.hdb
src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/rna.r2b
src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/rna.rtp
src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/spc.itp
src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/spce.itp
src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/tip3p.itp
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src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/tip4pew.itp
src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/tip5p.itp
src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/urea.itp
src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/watermodels.dat
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src/pmx/data/mutff/charmm22star-mut.ff/aminoacids.hdb
src/pmx/data/mutff/charmm22star-mut.ff/aminoacids.n.tdb
src/pmx/data/mutff/charmm22star-mut.ff/aminoacids.r2b
src/pmx/data/mutff/charmm22star-mut.ff/aminoacids.rtp
src/pmx/data/mutff/charmm22star-mut.ff/aminoacids.vsd
src/pmx/data/mutff/charmm22star-mut.ff/atomtypes.atp
src/pmx/data/mutff/charmm22star-mut.ff/cmap.itp
src/pmx/data/mutff/charmm22star-mut.ff/dna.arn
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src/pmx/data/mutff/charmm22star-mut.ff/ffnabonded.itp
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src/pmx/data/mutff/charmm22star-mut.ff/ffnonbonded.itp
src/pmx/data/mutff/charmm22star-mut.ff/forcefield.doc
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src/pmx/data/mutff/charmm22star-mut.ff/ions.itp
src/pmx/data/mutff/charmm22star-mut.ff/lipids.hdb
src/pmx/data/mutff/charmm22star-mut.ff/lipids.rtp
src/pmx/data/mutff/charmm22star-mut.ff/mutres.arn
src/pmx/data/mutff/charmm22star-mut.ff/mutres.mtp
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src/pmx/data/mutff/charmm22star-mut.ff/spc.itp
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src/pmx/data/mutff/charmm22star-mut.ff/watermodels.dat
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src/pmx/data/mutff/charmm36m-mut.ff/cmap.itp
src/pmx/data/mutff/charmm36m-mut.ff/ffbonded.itp
src/pmx/data/mutff/charmm36m-mut.ff/ffnonbonded.itp
src/pmx/data/mutff/charmm36m-mut.ff/forcefield.doc
src/pmx/data/mutff/charmm36m-mut.ff/forcefield.itp
src/pmx/data/mutff/charmm36m-mut.ff/gb.itp
src/pmx/data/mutff/charmm36m-mut.ff/ions.itp
src/pmx/data/mutff/charmm36m-mut.ff/merged.arn
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src/pmx/data/mutff/charmm36m-mut.ff/watermodels.dat
src/pmx/extensions/pmx/Energy.c
src/pmx/extensions/pmx/Geometry.c
src/pmx/extensions/pmx/Geometry.h
src/pmx/extensions/pmx/cpp_test.cpp
src/pmx/extensions/pmx/init.c
src/pmx/extensions/pmx/pmx.h
src/pmx/extensions/pmx/wrap_Geometry.c
src/pmx/extensions/xdr/trr2xtc.c
src/pmx/extensions/xdr/xdrfile.c
src/pmx/extensions/xdr/xdrfile.h
src/pmx/extensions/xdr/xdrfile_c_test.c
src/pmx/extensions/xdr/xdrfile_trr.c
src/pmx/extensions/xdr/xdrfile_trr.h
src/pmx/extensions/xdr/xdrfile_xtc.c
src/pmx/extensions/xdr/xdrfile_xtc.h
src/pmx/rosetta_example/README
src/pmx/rosetta_example/analyze.py
src/pmx/rosetta_example/mut.dat
src/pmx/rosetta_example/plot_results.ipynb
src/pmx/rosetta_example/prot_zn.pdb
src/pmx/rosetta_example/rosetta_prepare.ipynb
src/pmx/rosetta_example/submit_jobscripts.py
src/pmx/scripts/__init__.py
src/pmx/scripts/analyze_dhdl.py
src/pmx/scripts/atomMapping.py
src/pmx/scripts/build_cyclic_top.py
src/pmx/scripts/cli.py
src/pmx/scripts/fill_cgenff_itp.py
src/pmx/scripts/fix_residue_names.py
src/pmx/scripts/gen_abs_restraints.py
src/pmx/scripts/generate_hybrid_residue.py
src/pmx/scripts/generate_hybrid_topology.py
src/pmx/scripts/hydrogen_atom_renaming.py
src/pmx/scripts/ligandHybrid.py
src/pmx/scripts/make_double_box.py
src/pmx/scripts/md_setup.py
src/pmx/scripts/mutate.py
src/pmx/scripts/parameterize_ligands.py
src/pmx/scripts/prepare_crooks_runs.py
src/pmx/scripts/repartition_mass.py
src/pmx/scripts/set_gmxlib.py
src/pmx/scripts/setup_abfe.py
src/pmx/scripts/icolos_entrypoints/__init__.py
src/pmx/scripts/icolos_entrypoints/assemble_systems.py
src/pmx_biobb.egg-info/PKG-INFO
src/pmx_biobb.egg-info/SOURCES.txt
src/pmx_biobb.egg-info/dependency_links.txt
src/pmx_biobb.egg-info/entry_points.txt
src/pmx_biobb.egg-info/not-zip-safe
src/pmx_biobb.egg-info/requires.txt
src/pmx_biobb.egg-info/top_level.txt
tests/test_alchemy.py
tests/test_chain.py
tests/test_dhdl.py
tests/test_estimators.py
tests/test_import.py
tests/test_model.py
tests/test_utils.py
tests/test_xdr.py