LICENSE
README.md
pyproject.toml
setup.py
src/mstool/__init__.py
src/mstool/authors.py
src/mstool/version.py
src/mstool.egg-info/PKG-INFO
src/mstool.egg-info/SOURCES.txt
src/mstool.egg-info/dependency_links.txt
src/mstool.egg-info/requires.txt
src/mstool.egg-info/top_level.txt
src/mstool/FF/amber14/DNA.OL15.xml
src/mstool/FF/amber14/DNA.bsc1.xml
src/mstool/FF/amber14/RNA.OL3.xml
src/mstool/FF/amber14/amber14-all.xml
src/mstool/FF/amber14/lipid17.xml
src/mstool/FF/amber14/protein.ff14SB.xml
src/mstool/FF/amber14/protein.ff15ipq.xml
src/mstool/FF/amber14/spce.xml
src/mstool/FF/amber14/tip3p.xml
src/mstool/FF/amber14/tip3pfb.xml
src/mstool/FF/amber14/tip4pew.xml
src/mstool/FF/amber14/tip4pfb.xml
src/mstool/FF/amber99/amber99sbildn.xml
src/mstool/FF/amber99/tip3p.xml
src/mstool/FF/charmm36/charmm36.xml
src/mstool/FF/charmm36/chyo.xml
src/mstool/FF/charmm36/clol.xml
src/mstool/FF/charmm36/pip.xml
src/mstool/FF/charmm36/triv.xml
src/mstool/FF/charmm36/water.xml
src/mstool/FF/martini2.2/martini_lipids_add.itp
src/mstool/FF/martini2.2/martini_v2.0_ions.itp
src/mstool/FF/martini2.2/martini_v2.0_lipids_all_201506.itp
src/mstool/FF/martini2.2/martini_v2.2.itp
src/mstool/FF/martini2.2/martini_v2.2.modified.LJ.itp
src/mstool/FF/martini2.2/martini_v2.2.modified.itp
src/mstool/FF/martini2.2/ti.itp
src/mstool/FF/martini2.2/toy.itp
src/mstool/FF/martini2.2/tp.itp
src/mstool/FF/martini2.2/structures/CHL1.pdb
src/mstool/FF/martini2.2/structures/CHOL.pdb
src/mstool/FF/martini2.2/structures/P005.pdb
src/mstool/FF/martini2.2/structures/P006.pdb
src/mstool/FF/martini2.2/structures/P007.pdb
src/mstool/FF/martini2.2/structures/P008.pdb
src/mstool/FF/martini2.2/structures/P010.pdb
src/mstool/FF/martini3.0.0/lipids.itp
src/mstool/FF/martini3.0.0/martini.itp
src/mstool/FF/martini3.0.0/phospholipids.itp
src/mstool/FF/martini3.0.0/protein.itp
src/mstool/backup/amberselection_20240510.py
src/mstool/backup/backmap.py
src/mstool/backup/bilayer_240429.py
src/mstool/backup/bilayerbuilder_240429.py
src/mstool/backup/fill.bck.py
src/mstool/backup/fill_loops.py
src/mstool/backup/fill_side.py
src/mstool/backup/gmx2dms2.py
src/mstool/backup/loopmodeler_230719.py
src/mstool/backup/martinizedms.231213.py
src/mstool/backup/martinizedms.240309.py
src/mstool/backup/openmmutils_230719.py
src/mstool/backup/orient_240621.py
src/mstool/backup/pandas2dict.py
src/mstool/backup/rem.bck.py
src/mstool/backup/rem_230719.py
src/mstool/backup/rem_230801.py
src/mstool/backup/rock_240306.py
src/mstool/backup/sphere_240304.py
src/mstool/backup/ungroup.py
src/mstool/backup/ungroup_240430.py
src/mstool/backup/universe_20240510.py
src/mstool/backup/universe_20240511.py
src/mstool/backup/cg2aa/cg2aa.py
src/mstool/core/__init__.py
src/mstool/core/backmap.py
src/mstool/core/checkstructure.py
src/mstool/core/checktetrahedron.py
src/mstool/core/dms2openmm.py
src/mstool/core/dmsfile.py
src/mstool/core/fill.py
src/mstool/core/gmx2dms.py
src/mstool/core/loopmodeler.py
src/mstool/core/map.py
src/mstool/core/martinizedms.py
src/mstool/core/mutate.py
src/mstool/core/orient.py
src/mstool/core/readmappings.py
src/mstool/core/readmartini.py
src/mstool/core/readxml.py
src/mstool/core/rem.py
src/mstool/core/reorderatoms.py
src/mstool/core/seq.py
src/mstool/core/solvate_martini.py
src/mstool/core/truncateprotein.py
src/mstool/core/ungroup.py
src/mstool/core/universe.py
src/mstool/examples/Backmapping/run_all.py
src/mstool/examples/Backmapping/Example1_methane/cg.pdb
src/mstool/examples/Backmapping/Example1_methane/ff.xml
src/mstool/examples/Backmapping/Example1_methane/mapping.dat
src/mstool/examples/Backmapping/Example1_methane/run.py
src/mstool/examples/Backmapping/Example2_ethane/cg.pdb
src/mstool/examples/Backmapping/Example2_ethane/mapping.dat
src/mstool/examples/Backmapping/Example2_ethane/run.py
src/mstool/examples/Backmapping/Example3_butene/cg.pdb
src/mstool/examples/Backmapping/Example3_butene/ff.xml
src/mstool/examples/Backmapping/Example3_butene/mapping.dat
src/mstool/examples/Backmapping/Example3_butene/run.py
src/mstool/examples/Backmapping/Example4_POPC/cg.pdb
src/mstool/examples/Backmapping/Example4_POPC/run.py
src/mstool/examples/Backmapping/Example5_Sphere/cg.pdb
src/mstool/examples/Backmapping/Example6_TRIO/cg.pdb
src/mstool/examples/Backmapping/Example6_TRIO/ff.xml
src/mstool/examples/Backmapping/Example6_TRIO/mapping.5.dat
src/mstool/examples/Backmapping/Example6_TRIO/mapping.dat
src/mstool/examples/Backmapping/Example6_TRIO/run.py
src/mstool/examples/Backmapping/Example6_TRIO/setup.py
src/mstool/examples/Backmapping/Example7_MembraneProtein/cg.pdb
src/mstool/examples/Backmapping/Example7_MembraneProtein/cg_nonprotein.pdb
src/mstool/examples/Backmapping/Example7_MembraneProtein/protein_AA.pdb
src/mstool/examples/Backmapping/Example7_MembraneProtein/run.py
src/mstool/examples/BackmappingMartini3/README.md
src/mstool/examples/BackmappingMartini3/b2ar_mix8.gro
src/mstool/examples/BackmappingMartini3/curved.gro
src/mstool/examples/BackmappingMartini3/ff.xml
src/mstool/examples/BackmappingMartini3/mapping.dat
src/mstool/examples/BackmappingMartini3/mix8_3017lipids.gro
src/mstool/examples/BackmappingMartini3/mix8_419lipids.gro
src/mstool/examples/BackmappingMartini3/mix8_5111lipids.gro
src/mstool/examples/BackmappingMartini3/run.py
src/mstool/examples/BilayerBuilder/run_all.py
src/mstool/examples/BilayerBuilder/run_martini3.py
src/mstool/examples/BilayerBuilder/showhalf.py
src/mstool/examples/BilayerBuilder/gpcr/run.py
src/mstool/examples/BilayerBuilder/sars/run.py
src/mstool/examples/BilayerBuilder/sars_small/run.py
src/mstool/lib/align.py
src/mstool/lib/distance.memory.py
src/mstool/lib/distance.py
src/mstool/lib/distancelib.pyx
src/mstool/lib/qcprot.pyx
src/mstool/lib/setup.py
src/mstool/mapping/martini.amber14.dat
src/mstool/mapping/martini.lipid.c36.dat
src/mstool/mapping/martini.protein.c36m.dat
src/mstool/mapping/martini3.protein.c36m.dat
src/mstool/mapping/structures/CHL1.pdb
src/mstool/mapping/structures/CHL1_AA.pdb
src/mstool/mapping/structures/CHYO.bck.pdb
src/mstool/mapping/structures/CHYO.pdb
src/mstool/mapping/structures/CHYO_AA.bck.pdb
src/mstool/mapping/structures/CHYO_AA.pdb
src/mstool/membrane/bilayer.py
src/mstool/membrane/bilayerbuilder.py
src/mstool/membrane/lipid.py
src/mstool/membrane/sphere.py
src/mstool/membrane/spherebuilder.py
src/mstool/membrane/sphereprotein.py
src/mstool/utils/__init__.py
src/mstool/utils/add_termini_atoms.py
src/mstool/utils/amberselection.py
src/mstool/utils/atomic_data.py
src/mstool/utils/cap_termini_residues.py
src/mstool/utils/change_his.py
src/mstool/utils/dump.py
src/mstool/utils/gmx_energy.py
src/mstool/utils/mdautils.py
src/mstool/utils/openmmutils.py
src/mstool/utils/performance.py
src/mstool/utils/protein_sel.py
src/mstool/utils/rock.py
src/mstool/utils/rockchain.py
src/mstool/utils/rockresidue.py
src/mstool/utils/saveargs.py
src/mstool/utils/sdminimizer.py
src/mstool/utils/sqlcmd.py
src/mstool/utils/util.py
src/mstool/utils/vismol.py