├── .codecov.yml ├── .github └── workflows │ ├── deploy.yml │ └── run_tests.yml ├── .gitignore ├── .pylintrc ├── .readthedocs.yaml ├── .zenodo.json ├── LICENSE ├── README.md ├── bin └── martinize2 ├── doc ├── Makefile └── source │ ├── _static │ └── .empty_for_git │ ├── _templates │ └── layout.html │ ├── conf.py │ ├── data.rst │ ├── file_formats.rst │ ├── general_overview.rst │ ├── graph_algorithms.rst │ ├── gromacs_variables.rst │ ├── index.rst │ ├── martinize2_workflow.rst │ ├── processors.rst │ ├── technical_background.rst │ └── tutorials │ ├── 6_adding_residues_links │ ├── files │ │ ├── ala-sep-ala.pdb │ │ ├── force_fields │ │ │ ├── charmm │ │ │ │ ├── sep.ff │ │ │ │ └── sep.rtp │ │ │ └── martini3001 │ │ │ │ └── sep.ff │ │ └── mappings │ │ │ └── sep.charmm36.map │ └── index.rst │ ├── 7_adding_modifications │ ├── files │ │ ├── ala-sep-ala.pdb │ │ ├── force_fields │ │ │ ├── charmm │ │ │ │ └── mods.ff │ │ │ └── martini3001 │ │ │ │ └── modification.ff │ │ └── mappings │ │ │ └── SEP.mapping │ └── index.rst │ ├── basic_usage.rst │ ├── elastic_examples.png │ ├── elastic_networks.rst │ ├── go_models.rst │ ├── index.rst │ ├── mutations_and_modifications.rst │ └── water_biasing.rst ├── maintainers ├── head_template_data ├── head_template_py ├── releasing.md └── vim │ └── syntax │ ├── README.md │ └── ff.vim ├── pyproject.toml ├── requirements-docs.txt ├── requirements-tests.txt ├── setup.cfg ├── setup.py └── vermouth ├── __init__.py ├── citation_parser.py ├── data ├── __init__.py ├── citations.bib ├── data.py ├── force_fields │ ├── amber │ │ ├── 00-modifications.ff │ │ ├── 05-links.ff │ │ └── aminoacids.rtp │ ├── charmm │ │ ├── 00-modifications.ff │ │ ├── 05-links.ff │ │ ├── 10-small_molecule_charmm.ff │ │ ├── aminoacids.rtp │ │ └── lipidations.rtp │ ├── elnedyn21 │ │ ├── 00-general.ff │ │ ├── 05-aminoacids.ff │ │ ├── 10-modifications.ff │ │ └── citations.bib │ ├── elnedyn22 │ │ ├── 00-general.ff │ │ ├── 05-aminoacids.ff │ │ ├── 10-modifications.ff │ │ └── citations.bib │ ├── elnedyn22p │ │ ├── 00-general.ff │ │ ├── 05-aminoacids.ff │ │ ├── 10-modifications.ff │ │ └── citations.bib │ ├── gromos │ │ ├── 00-modifications.ff │ │ ├── 05-cofactors.ff │ │ └── aminoacids.rtp │ ├── martini22 │ │ ├── 00-general.ff │ │ ├── 05-aminoacids.ff │ │ ├── 10-modifications.ff │ │ ├── 15-nucleotides.ff │ │ └── citations.bib │ ├── martini22p │ │ ├── 00-general.ff │ │ ├── 05-aminoacids.ff │ │ ├── 10-modifications.ff │ │ └── citations.bib │ └── martini3001 │ │ ├── 00-general.ff │ │ ├── 05-aminoacids.ff │ │ ├── 10-modifications.ff │ │ ├── 15-links_M3.ff │ │ ├── 20-links_M3_IDR.ff │ │ ├── 25-small_molecule_martini3.ff │ │ └── citations.bib ├── mappings │ ├── ala.charmm36.map │ ├── ala.gromos.map │ ├── arg.charmm36.map │ ├── arg.charmm36.martini22p.map │ ├── arg.gromos.map │ ├── asn.charmm36.map │ ├── asn.charmm36.martini22p.map │ ├── asn.gromos.map │ ├── asp.charmm36.map │ ├── asp.charmm36.martini22p.map │ ├── asp.gromos.map │ ├── asp0.gromos.map │ ├── chol.charmm36.map │ ├── cys.charmm36.map │ ├── cys.gromos.map │ ├── dmpc.charmm36.map │ ├── dopc.charmm36.map │ ├── dppc.charmm36.map │ ├── dppg.charmm36.map │ ├── elnedyn │ │ ├── ala.charmm36.map │ │ ├── arg.charmm36.map │ │ ├── asn.charmm36.map │ │ ├── asp.charmm36.map │ │ ├── chol.charmm36.map │ │ ├── cys.charmm36.map │ │ ├── dmpc.charmm36.map │ │ ├── dopc.charmm36.map │ │ ├── dppc.charmm36.map │ │ ├── dppg.charmm36.map │ │ ├── elnedyn22p │ │ │ ├── arg.charmm36.elnedyn22p.map │ │ │ ├── asn.charmm36.elnedyn22p.map │ │ │ ├── asp.charmm36.elnedyn22p.map │ │ │ ├── gln.charmm36.elnedyn22p.map │ │ │ ├── glu.charmm36.elnedyn22p.map │ │ │ ├── lys.charmm36.elnedyn22p.map │ │ │ ├── ser.charmm36.elnedyn22p.map │ │ │ └── thr.charmm36.elnedyn22p.map │ │ ├── gln.charmm36.map │ │ ├── glu.charmm36.map │ │ ├── gly.charmm36.map │ │ ├── his.charmm36.map │ │ ├── ile.charmm36.map │ │ ├── leu.charmm36.map │ │ ├── lys.charmm36.map │ │ ├── met.charmm36.map │ │ ├── modifications.elnedyn21.mapping │ │ ├── modifications.elnedyn22.mapping │ │ ├── modifications.elnedyn22p.mapping │ │ ├── phe.charmm36.map │ │ ├── popc.charmm36.map │ │ ├── pope.charmm36.map │ │ ├── popg.charmm36.map │ │ ├── pops.charmm36.map │ │ ├── pro.charmm36.map │ │ ├── ser.charmm36.map │ │ ├── thr.charmm36.map │ │ ├── trp.charmm36.map │ │ ├── tyr.charmm36.map │ │ └── val.charmm36.map │ ├── elnedyn21 │ │ ├── ala.charmm36.map │ │ ├── arg.charmm36.elnedyn22p.map │ │ ├── arg.charmm36.map │ │ ├── asn.charmm36.elnedyn22p.map │ │ ├── asn.charmm36.map │ │ ├── asp.charmm36.elnedyn22p.map │ │ ├── asp.charmm36.map │ │ ├── cys.charmm36.map │ │ ├── gln.charmm36.elnedyn22p.map │ │ ├── gln.charmm36.map │ │ ├── glu.charmm36.elnedyn22p.map │ │ ├── glu.charmm36.map │ │ ├── gly.charmm36.map │ │ ├── his.charmm36.map │ │ ├── ile.charmm36.map │ │ ├── leu.charmm36.map │ │ ├── lys.charmm36.elnedyn22p.map │ │ ├── lys.charmm36.map │ │ ├── met.charmm36.map │ │ ├── modifications.mapping │ │ ├── phe.charmm36.map │ │ ├── pro.charmm36.map │ │ ├── ser.charmm36.elnedyn22p.map │ │ ├── ser.charmm36.map │ │ ├── thr.charmm36.elnedyn22p.map │ │ ├── thr.charmm36.map │ │ ├── trp.charmm36.map │ │ ├── tyr.charmm36.map │ │ └── val.charmm36.map │ ├── fmn.gromos.map │ ├── gln.charmm36.map │ ├── gln.charmm36.martini22p.map │ ├── gln.gromos.map │ ├── glu.charmm36.map │ ├── glu.charmm36.martini22p.map │ ├── glu.gromos.map │ ├── glu0.gromos.map │ ├── gly.charmm36.map │ ├── gly.gromos.map │ ├── his.charmm.mapping │ ├── his.charmm36.map │ ├── his.gromos.map │ ├── his.gromos.mapping │ ├── hsd.charmm36.map │ ├── hse.charmm36.map │ ├── hsp.charmm36.map │ ├── ile.charmm36.map │ ├── ile.gromos.map │ ├── leu.charmm36.map │ ├── leu.gromos.map │ ├── lys.charmm36.map │ ├── lys.charmm36.martini22p.map │ ├── lys.gromos.map │ ├── martini3001 │ │ ├── ala.amber.map │ │ ├── ala.charmm36.map │ │ ├── antr.charmm36.map │ │ ├── arg.amber.map │ │ ├── arg.charmm36.map │ │ ├── ash.amber.map │ │ ├── asn.amber.map │ │ ├── asn.charmm36.map │ │ ├── asp.amber.map │ │ ├── asp.charmm36.map │ │ ├── aspp.charmm36.map │ │ ├── bald.charmm36.map │ │ ├── benz.charmm36.map │ │ ├── c3.charmm36.map │ │ ├── chxe.charmm36.map │ │ ├── cpen.charmm36.map │ │ ├── cume.charmm36.map │ │ ├── cys.amber.map │ │ ├── cys.charmm36.map │ │ ├── cysf.map │ │ ├── cysg.map │ │ ├── cysp.map │ │ ├── diol.charmm36.map │ │ ├── diox.charmm36.map │ │ ├── dman.charmm36.map │ │ ├── eben.charmm36.map │ │ ├── fura.charmm36.map │ │ ├── glh.amber.map │ │ ├── gln.amber.map │ │ ├── gln.charmm36.map │ │ ├── glu.amber.map │ │ ├── glu.charmm36.map │ │ ├── glup.charmm36.map │ │ ├── gly.amber.map │ │ ├── gly.charmm36.map │ │ ├── glym.map │ │ ├── hid.amber.map │ │ ├── hie.amber.map │ │ ├── hip.amber.map │ │ ├── his.amber.map │ │ ├── his.charmm36.map │ │ ├── hsd.charmm36.map │ │ ├── hse.charmm36.map │ │ ├── hsp.charmm36.map │ │ ├── ile.amber.map │ │ ├── ile.charmm36.map │ │ ├── imia.charmm36.map │ │ ├── inda.charmm36.map │ │ ├── indo.charmm36.map │ │ ├── leu.amber.map │ │ ├── leu.charmm36.map │ │ ├── lsn.charmm36.map │ │ ├── lyn.amber.map │ │ ├── lys.amber.map │ │ ├── lys.charmm36.map │ │ ├── mboa.charmm36.map │ │ ├── mcpe.charmm36.map │ │ ├── meob.charmm36.map │ │ ├── met.amber.map │ │ ├── met.charmm36.map │ │ ├── mind.charmm36.map │ │ ├── modifications.amber.mapping │ │ ├── modifications.charmm36.mapping │ │ ├── mxyl.charmm36.map │ │ ├── naft.charmm36.map │ │ ├── nitb.charmm36.map │ │ ├── oxyl.charmm36.map │ │ ├── pcro.charmm36.map │ │ ├── phe.amber.map │ │ ├── phe.charmm36.map │ │ ├── phen.charmm36.map │ │ ├── phmk.charmm36.map │ │ ├── prld.charmm36.map │ │ ├── pro.amber.map │ │ ├── pro.charmm36.map │ │ ├── pxyl.charmm36.map │ │ ├── pyr1.charmm36.map │ │ ├── pyrd.charmm36.map │ │ ├── pyrl.charmm36.map │ │ ├── pyrm.charmm36.map │ │ ├── qinl.charmm36.map │ │ ├── ser.amber.map │ │ ├── ser.charmm36.map │ │ ├── sm139.charmm36.map │ │ ├── styr.charmm36.map │ │ ├── thaz.charmm36.map │ │ ├── thf.charmm36.map │ │ ├── thip.charmm36.map │ │ ├── thp.charmm36.map │ │ ├── thr.amber.map │ │ ├── thr.charmm36.map │ │ ├── tolu.charmm36.map │ │ ├── trp.amber.map │ │ ├── trp.charmm36.map │ │ ├── tyr.amber.map │ │ ├── tyr.charmm36.map │ │ ├── val.amber.map │ │ ├── val.charmm36.map │ │ ├── zimi.charmm36.map │ │ ├── zthp.charmm36.map │ │ └── zthz.charmm36.map │ ├── met.charmm36.map │ ├── met.gromos.map │ ├── modifications.gromos.mapping │ ├── modifications.mapping │ ├── nad.gromos.map │ ├── phe.charmm36.map │ ├── phe.gromos.map │ ├── popc.charmm36.map │ ├── pope.charmm36.map │ ├── popg.charmm36.map │ ├── pops.charmm36.map │ ├── pro.charmm36.map │ ├── pro.gromos.map │ ├── ser.charmm36.map │ ├── ser.charmm36.martini22p.map │ ├── ser.gromos.map │ ├── thr.charmm36.map │ ├── thr.charmm36.martini22p.map │ ├── thr.gromos.map │ ├── tpp.gromos.map │ ├── trp.charmm36.map │ ├── trp.gromos.map │ ├── tyr.charmm36.map │ ├── tyr.gromos.map │ ├── val.charmm36.map │ └── val.gromos.map └── quotes.txt ├── dssp ├── __init__.py └── dssp.py ├── edge_tuning.py ├── ffinput.py ├── file_writer.py ├── forcefield.py ├── geometry.py ├── gmx ├── __init__.py ├── gro.py ├── itp.py ├── itp_read.py ├── rtp.py └── topology.py ├── graph_utils.py ├── graphing └── grappa.py ├── ismags.py ├── log_helpers.py ├── map_input.py ├── map_parser.py ├── molecule.py ├── parser_utils.py ├── pdb ├── __init__.py ├── cif.py └── pdb.py ├── processors ├── __init__.py ├── add_molecule_edges.py ├── annotate_idrs.py ├── annotate_mut_mod.py ├── apply_posres.py ├── apply_rubber_band.py ├── attach_mass.py ├── average_beads.py ├── canonicalize_modifications.py ├── cif_reader.py ├── do_links.py ├── do_mapping.py ├── gro_reader.py ├── locate_charge_dummies.py ├── make_bonds.py ├── merge_all_molecules.py ├── merge_chains.py ├── name_moltype.py ├── pdb_reader.py ├── processor.py ├── quote.py ├── rename_modified_residues.py ├── repair_graph.py ├── rtp_polisher.py ├── set_molecule_meta.py ├── sort_molecule_atoms.py ├── stash_attributes.py ├── tune_cystein_bridges.py └── water_bias.py ├── rcsu ├── __init__.py ├── contact_map.py ├── go_pipeline.py ├── go_structure_bias.py ├── go_utils.py └── go_vs_includes.py ├── selectors.py ├── system.py ├── tests ├── __init__.py ├── data │ ├── 1UBQ.cif │ ├── 1UBQ.pdb │ ├── 1UBQ_nocell_occupancy.cif │ ├── 1bta.pdb │ ├── 1bta_mutated.pdb │ ├── 2QWO.pdb │ ├── 2dn2.pdb │ ├── 6E8W.pdb │ ├── ala5.pdb │ ├── ala5_cg.pdb │ ├── cif_missing_atomname.cif │ ├── cif_missing_resname.cif │ ├── dna-short.pdb │ ├── dssp_tests │ │ ├── dssp_1bta.ssd │ │ ├── mini-protein1_betasheet.pdb.v2.2.1-3b2-deb_cv1.ssd │ │ ├── mini-protein1_betasheet.pdb.v3.0.0-3b1-deb_cv1.ssd │ │ ├── mini-protein2_helix.pdb.v2.2.1-3b2-deb_cv1.ssd │ │ ├── mini-protein2_helix.pdb.v3.0.0-3b1-deb_cv1.ssd │ │ ├── mini-protein3_trp-cage.pdb.v2.2.1-3b2-deb_cv1.ssd │ │ └── mini-protein3_trp-cage.pdb.v3.0.0-3b1-deb_cv1.ssd │ ├── force_fields │ │ ├── martini-test │ │ │ └── aminoacids.ff │ │ ├── pepplane │ │ │ ├── ala.ff │ │ │ ├── general.ff │ │ │ └── modifications.ff │ │ └── universal-test │ │ │ ├── aminoacids.rtp │ │ │ └── modifications.ff │ ├── heme.pdb │ ├── integration_tests │ │ ├── tier-0 │ │ │ ├── dipro-termini │ │ │ │ ├── README │ │ │ │ ├── aa.pdb │ │ │ │ └── martinize2 │ │ │ │ │ ├── cg.pdb │ │ │ │ │ ├── citation │ │ │ │ │ ├── command │ │ │ │ │ ├── molecule_0.itp │ │ │ │ │ └── topol.top │ │ │ ├── mini-protein1_betasheet │ │ │ │ ├── README │ │ │ │ ├── aa.pdb │ │ │ │ └── martinize2 │ │ │ │ │ ├── cg.pdb │ │ │ │ │ ├── chain_A.ssd │ │ │ │ │ ├── citation │ │ │ │ │ ├── command │ │ │ │ │ ├── molecule_0.itp │ │ │ │ │ ├── screen.output │ │ │ │ │ └── topol.top │ │ │ ├── mini-protein2_helix │ │ │ │ ├── README │ │ │ │ ├── aa.pdb │ │ │ │ └── martinize2 │ │ │ │ │ ├── cg.pdb │ │ │ │ │ ├── chain_A.ssd │ │ │ │ │ ├── citation │ │ │ │ │ ├── command │ │ │ │ │ ├── molecule_0.itp │ │ │ │ │ ├── screen.output │ │ │ │ │ └── topol.top │ │ │ └── mini-protein3_trp-cage │ │ │ │ ├── README │ │ │ │ ├── aa.pdb │ │ │ │ └── martinize2 │ │ │ │ ├── cg.pdb │ │ │ │ ├── chain_A.ssd │ │ │ │ ├── citation │ │ │ │ ├── command │ │ │ │ ├── molecule_0.itp │ │ │ │ ├── screen.output │ │ │ │ └── topol.top │ │ └── tier-1 │ │ │ ├── 1UBQ │ │ │ ├── README │ │ │ ├── aa.pdb │ │ │ └── martinize2 │ │ │ │ ├── cg.pdb │ │ │ │ ├── citation │ │ │ │ ├── command │ │ │ │ ├── molecule_0.itp │ │ │ │ └── topol.top │ │ │ ├── 1mj5-charmm │ │ │ ├── README │ │ │ ├── aa.pdb │ │ │ └── martinize2 │ │ │ │ ├── cg.pdb │ │ │ │ ├── cg.top │ │ │ │ ├── chain_.ssd │ │ │ │ ├── citation │ │ │ │ ├── command │ │ │ │ ├── molecule_0.itp │ │ │ │ └── screen.output │ │ │ ├── 1mj5 │ │ │ ├── README │ │ │ ├── aa.pdb │ │ │ └── martinize2 │ │ │ │ ├── cg.pdb │ │ │ │ ├── cg.top │ │ │ │ ├── chain_.ssd │ │ │ │ ├── citation │ │ │ │ ├── command │ │ │ │ ├── molecule_0.itp │ │ │ │ └── screen.output │ │ │ ├── 3i40 │ │ │ ├── 3i40.pdb │ │ │ ├── README │ │ │ └── martinize2 │ │ │ │ ├── cg.pdb │ │ │ │ ├── cg.top │ │ │ │ ├── chain_A.ssd │ │ │ │ ├── chain_C.ssd │ │ │ │ ├── citation │ │ │ │ ├── command │ │ │ │ ├── insulin_dimer.itp │ │ │ │ ├── molecule_0.itp │ │ │ │ └── screen.output │ │ │ ├── 6LFO_gap │ │ │ ├── 6LFO_gap.pdb │ │ │ ├── README │ │ │ └── martinize2 │ │ │ │ ├── cg.pdb │ │ │ │ ├── cg.top │ │ │ │ ├── chain_R.ssd │ │ │ │ ├── citation │ │ │ │ ├── command │ │ │ │ ├── molecule_0.itp │ │ │ │ └── screen.output │ │ │ ├── EN_chain │ │ │ ├── README │ │ │ ├── aa.pdb │ │ │ └── martinize2 │ │ │ │ ├── cg.pdb │ │ │ │ ├── cg.top │ │ │ │ ├── chain_A.ssd │ │ │ │ ├── citation │ │ │ │ ├── command │ │ │ │ ├── molecule_0.itp │ │ │ │ └── screen.output │ │ │ ├── EN_region │ │ │ ├── README │ │ │ ├── aa.pdb │ │ │ └── martinize2 │ │ │ │ ├── cg.pdb │ │ │ │ ├── cg.top │ │ │ │ ├── chain_A.ssd │ │ │ │ ├── citation │ │ │ │ ├── command │ │ │ │ ├── molecule_0.itp │ │ │ │ └── screen.output │ │ │ ├── bpti │ │ │ ├── README │ │ │ ├── aa.pdb │ │ │ └── martinize2 │ │ │ │ ├── cg.pdb │ │ │ │ ├── chain_A.ssd │ │ │ │ ├── citation │ │ │ │ ├── command │ │ │ │ ├── molecule_0.itp │ │ │ │ ├── screen.output │ │ │ │ └── topol.top │ │ │ ├── hst5 │ │ │ ├── README │ │ │ ├── aa.pdb │ │ │ └── martinize2 │ │ │ │ ├── cg.pdb │ │ │ │ ├── citation │ │ │ │ ├── command │ │ │ │ ├── molecule_0.itp │ │ │ │ └── topol.top │ │ │ ├── lysozyme │ │ │ ├── README │ │ │ ├── aa.pdb │ │ │ └── martinize2 │ │ │ │ ├── cg.pdb │ │ │ │ ├── chain_A.ssd │ │ │ │ ├── citation │ │ │ │ ├── command │ │ │ │ ├── molecule_0.itp │ │ │ │ └── topol.top │ │ │ ├── lysozyme_ENbias │ │ │ ├── README │ │ │ ├── aa.pdb │ │ │ ├── map.map │ │ │ └── martinize2 │ │ │ │ ├── cg.pdb │ │ │ │ ├── citation │ │ │ │ ├── command │ │ │ │ ├── molecule_0.itp │ │ │ │ ├── topol.top │ │ │ │ ├── virtual_sites_atomtypes.itp │ │ │ │ └── virtual_sites_nonbond_params.itp │ │ │ ├── lysozyme_GO │ │ │ ├── README │ │ │ ├── aa.pdb │ │ │ ├── map.map │ │ │ └── martinize2 │ │ │ │ ├── cg.pdb │ │ │ │ ├── citation │ │ │ │ ├── command │ │ │ │ ├── go_atomtypes.itp │ │ │ │ ├── go_nbparams.itp │ │ │ │ ├── molecule_0.itp │ │ │ │ └── topol.top │ │ │ ├── lysozyme_GO_internal │ │ │ ├── README │ │ │ ├── aa.pdb │ │ │ └── martinize2 │ │ │ │ ├── cg.pdb │ │ │ │ ├── citation │ │ │ │ ├── command │ │ │ │ ├── go_atomtypes.itp │ │ │ │ ├── go_nbparams.itp │ │ │ │ ├── martinize_contact_map.out │ │ │ │ ├── molecule.itp │ │ │ │ └── topol.top │ │ │ ├── lysozyme_GObias │ │ │ ├── README │ │ │ ├── aa.pdb │ │ │ ├── map.map │ │ │ └── martinize2 │ │ │ │ ├── cg.pdb │ │ │ │ ├── citation │ │ │ │ ├── command │ │ │ │ ├── go_atomtypes.itp │ │ │ │ ├── go_nbparams.itp │ │ │ │ ├── molecule_0.itp │ │ │ │ └── topol.top │ │ │ ├── lysozyme_prot │ │ │ ├── README │ │ │ ├── aa.pdb │ │ │ ├── cg.pdb │ │ │ ├── chain_A.ssd │ │ │ ├── martinize2 │ │ │ │ ├── cg.pdb │ │ │ │ ├── chain_A.ssd │ │ │ │ ├── citation │ │ │ │ ├── command │ │ │ │ ├── molecule_0.itp │ │ │ │ ├── screen.output │ │ │ │ ├── test.itp │ │ │ │ └── topol.top │ │ │ ├── molecule_0.itp │ │ │ └── topol.top │ │ │ ├── prot_modf_charmm │ │ │ ├── README │ │ │ ├── input.pdb │ │ │ └── martinize2 │ │ │ │ ├── cg.pdb │ │ │ │ ├── cg.top │ │ │ │ ├── chain_.ssd │ │ │ │ ├── citation │ │ │ │ ├── command │ │ │ │ ├── molecule_0.itp │ │ │ │ ├── screen.output │ │ │ │ └── sys.top │ │ │ └── villin │ │ │ ├── README │ │ │ ├── aa.pdb │ │ │ └── martinize2 │ │ │ ├── cg.pdb │ │ │ ├── citation │ │ │ ├── command │ │ │ ├── molecule_0.itp │ │ │ ├── screen.output │ │ │ └── topol.top │ ├── mappings │ │ └── universal-test │ │ │ ├── martini-test │ │ │ └── ser.mapping │ │ │ └── pepplane │ │ │ ├── ala.mapping │ │ │ └── modifications.mapping │ ├── multiple.cif │ ├── test_molecule_contacts.out │ └── tri_alanine.pdb ├── datafiles.py ├── gmx │ ├── test_gro.py │ ├── test_itp.py │ └── test_topology.py ├── helper_functions.py ├── integration_tests │ ├── __init__.py │ └── test_integration.py ├── molecule_strategies.py ├── pdb │ ├── test_cif.py │ ├── test_read_pdb.py │ └── test_write_pdb.py ├── rcsu │ ├── test_contact_map.py │ ├── test_go_structure_bias.py │ ├── test_go_utils.py │ └── test_read_go_map.py ├── test_add_molecule_edges.py ├── test_annotate_idrs.py ├── test_annotate_mut_mod.py ├── test_apply_posres.py ├── test_apply_rubber_band.py ├── test_average_beads.py ├── test_cif_reader.py ├── test_do_mapping.py ├── test_dssp.py ├── test_edge_tuning.py ├── test_ff_files.py ├── test_ffinput.py ├── test_file_writer.py ├── test_forcefield.py ├── test_geometry.py ├── test_graph_utils.py ├── test_grappa.py ├── test_ismags.py ├── test_itp_files.py ├── test_links.py ├── test_logging.py ├── test_make_bonds.py ├── test_map_input.py ├── test_map_parser.py ├── test_mapping_integrative.py ├── test_merge_chains.py ├── test_molecule.py ├── test_name_moltype.py ├── test_native_forcefield.py ├── test_ptm_detection.py ├── test_repair_graph.py ├── test_section_parser.py ├── test_selectors.py ├── test_set_molecule_meta.py ├── test_sort_molecule_atoms.py ├── test_stash_attributes.py ├── test_system.py ├── test_tune_cystein_bridges.py ├── test_utils.py ├── test_version.py ├── test_vs_generation.py └── test_water_bias.py ├── truncating_formatter.py └── utils.py /.codecov.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/.codecov.yml -------------------------------------------------------------------------------- /.github/workflows/deploy.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/.github/workflows/deploy.yml -------------------------------------------------------------------------------- /.github/workflows/run_tests.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/.github/workflows/run_tests.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/.gitignore -------------------------------------------------------------------------------- /.pylintrc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/.pylintrc -------------------------------------------------------------------------------- /.readthedocs.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/.readthedocs.yaml -------------------------------------------------------------------------------- /.zenodo.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/.zenodo.json -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/README.md -------------------------------------------------------------------------------- /bin/martinize2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/bin/martinize2 -------------------------------------------------------------------------------- /doc/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/doc/Makefile -------------------------------------------------------------------------------- /doc/source/_static/.empty_for_git: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /doc/source/_templates/layout.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/doc/source/_templates/layout.html -------------------------------------------------------------------------------- /doc/source/conf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/doc/source/conf.py -------------------------------------------------------------------------------- /doc/source/data.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/doc/source/data.rst -------------------------------------------------------------------------------- /doc/source/file_formats.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/doc/source/file_formats.rst -------------------------------------------------------------------------------- /doc/source/general_overview.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/doc/source/general_overview.rst -------------------------------------------------------------------------------- /doc/source/graph_algorithms.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/doc/source/graph_algorithms.rst -------------------------------------------------------------------------------- /doc/source/gromacs_variables.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/doc/source/gromacs_variables.rst -------------------------------------------------------------------------------- /doc/source/index.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/doc/source/index.rst -------------------------------------------------------------------------------- /doc/source/martinize2_workflow.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/doc/source/martinize2_workflow.rst -------------------------------------------------------------------------------- /doc/source/processors.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/doc/source/processors.rst -------------------------------------------------------------------------------- /doc/source/technical_background.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/doc/source/technical_background.rst -------------------------------------------------------------------------------- /doc/source/tutorials/6_adding_residues_links/files/ala-sep-ala.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/doc/source/tutorials/6_adding_residues_links/files/ala-sep-ala.pdb -------------------------------------------------------------------------------- /doc/source/tutorials/6_adding_residues_links/files/force_fields/charmm/sep.ff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/doc/source/tutorials/6_adding_residues_links/files/force_fields/charmm/sep.ff -------------------------------------------------------------------------------- /doc/source/tutorials/6_adding_residues_links/files/force_fields/charmm/sep.rtp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/doc/source/tutorials/6_adding_residues_links/files/force_fields/charmm/sep.rtp -------------------------------------------------------------------------------- /doc/source/tutorials/6_adding_residues_links/files/force_fields/martini3001/sep.ff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/doc/source/tutorials/6_adding_residues_links/files/force_fields/martini3001/sep.ff -------------------------------------------------------------------------------- /doc/source/tutorials/6_adding_residues_links/files/mappings/sep.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/doc/source/tutorials/6_adding_residues_links/files/mappings/sep.charmm36.map -------------------------------------------------------------------------------- /doc/source/tutorials/6_adding_residues_links/index.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/doc/source/tutorials/6_adding_residues_links/index.rst -------------------------------------------------------------------------------- /doc/source/tutorials/7_adding_modifications/files/ala-sep-ala.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/doc/source/tutorials/7_adding_modifications/files/ala-sep-ala.pdb -------------------------------------------------------------------------------- /doc/source/tutorials/7_adding_modifications/files/force_fields/charmm/mods.ff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/doc/source/tutorials/7_adding_modifications/files/force_fields/charmm/mods.ff -------------------------------------------------------------------------------- /doc/source/tutorials/7_adding_modifications/files/force_fields/martini3001/modification.ff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/doc/source/tutorials/7_adding_modifications/files/force_fields/martini3001/modification.ff -------------------------------------------------------------------------------- /doc/source/tutorials/7_adding_modifications/files/mappings/SEP.mapping: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/doc/source/tutorials/7_adding_modifications/files/mappings/SEP.mapping -------------------------------------------------------------------------------- /doc/source/tutorials/7_adding_modifications/index.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/doc/source/tutorials/7_adding_modifications/index.rst -------------------------------------------------------------------------------- /doc/source/tutorials/basic_usage.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/doc/source/tutorials/basic_usage.rst -------------------------------------------------------------------------------- /doc/source/tutorials/elastic_examples.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/doc/source/tutorials/elastic_examples.png -------------------------------------------------------------------------------- /doc/source/tutorials/elastic_networks.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/doc/source/tutorials/elastic_networks.rst -------------------------------------------------------------------------------- /doc/source/tutorials/go_models.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/doc/source/tutorials/go_models.rst -------------------------------------------------------------------------------- /doc/source/tutorials/index.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/doc/source/tutorials/index.rst -------------------------------------------------------------------------------- /doc/source/tutorials/mutations_and_modifications.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/doc/source/tutorials/mutations_and_modifications.rst -------------------------------------------------------------------------------- /doc/source/tutorials/water_biasing.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/doc/source/tutorials/water_biasing.rst -------------------------------------------------------------------------------- /maintainers/head_template_data: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/maintainers/head_template_data -------------------------------------------------------------------------------- /maintainers/head_template_py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/maintainers/head_template_py -------------------------------------------------------------------------------- /maintainers/releasing.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/maintainers/releasing.md -------------------------------------------------------------------------------- /maintainers/vim/syntax/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/maintainers/vim/syntax/README.md -------------------------------------------------------------------------------- /maintainers/vim/syntax/ff.vim: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/maintainers/vim/syntax/ff.vim -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/pyproject.toml -------------------------------------------------------------------------------- /requirements-docs.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/requirements-docs.txt -------------------------------------------------------------------------------- /requirements-tests.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/requirements-tests.txt -------------------------------------------------------------------------------- /setup.cfg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/setup.cfg -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/setup.py -------------------------------------------------------------------------------- /vermouth/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/__init__.py -------------------------------------------------------------------------------- /vermouth/citation_parser.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/citation_parser.py -------------------------------------------------------------------------------- /vermouth/data/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/__init__.py -------------------------------------------------------------------------------- /vermouth/data/citations.bib: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/citations.bib -------------------------------------------------------------------------------- /vermouth/data/data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/data.py -------------------------------------------------------------------------------- /vermouth/data/force_fields/amber/00-modifications.ff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/force_fields/amber/00-modifications.ff -------------------------------------------------------------------------------- /vermouth/data/force_fields/amber/05-links.ff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/force_fields/amber/05-links.ff -------------------------------------------------------------------------------- /vermouth/data/force_fields/amber/aminoacids.rtp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/force_fields/amber/aminoacids.rtp -------------------------------------------------------------------------------- /vermouth/data/force_fields/charmm/00-modifications.ff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/force_fields/charmm/00-modifications.ff -------------------------------------------------------------------------------- /vermouth/data/force_fields/charmm/05-links.ff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/force_fields/charmm/05-links.ff -------------------------------------------------------------------------------- /vermouth/data/force_fields/charmm/10-small_molecule_charmm.ff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/force_fields/charmm/10-small_molecule_charmm.ff -------------------------------------------------------------------------------- /vermouth/data/force_fields/charmm/aminoacids.rtp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/force_fields/charmm/aminoacids.rtp -------------------------------------------------------------------------------- /vermouth/data/force_fields/charmm/lipidations.rtp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/force_fields/charmm/lipidations.rtp -------------------------------------------------------------------------------- /vermouth/data/force_fields/elnedyn21/00-general.ff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/force_fields/elnedyn21/00-general.ff -------------------------------------------------------------------------------- /vermouth/data/force_fields/elnedyn21/05-aminoacids.ff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/force_fields/elnedyn21/05-aminoacids.ff -------------------------------------------------------------------------------- /vermouth/data/force_fields/elnedyn21/10-modifications.ff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/force_fields/elnedyn21/10-modifications.ff -------------------------------------------------------------------------------- /vermouth/data/force_fields/elnedyn21/citations.bib: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/force_fields/elnedyn21/citations.bib -------------------------------------------------------------------------------- /vermouth/data/force_fields/elnedyn22/00-general.ff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/force_fields/elnedyn22/00-general.ff -------------------------------------------------------------------------------- /vermouth/data/force_fields/elnedyn22/05-aminoacids.ff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/force_fields/elnedyn22/05-aminoacids.ff -------------------------------------------------------------------------------- /vermouth/data/force_fields/elnedyn22/10-modifications.ff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/force_fields/elnedyn22/10-modifications.ff -------------------------------------------------------------------------------- /vermouth/data/force_fields/elnedyn22/citations.bib: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/force_fields/elnedyn22/citations.bib -------------------------------------------------------------------------------- /vermouth/data/force_fields/elnedyn22p/00-general.ff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/force_fields/elnedyn22p/00-general.ff -------------------------------------------------------------------------------- /vermouth/data/force_fields/elnedyn22p/05-aminoacids.ff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/force_fields/elnedyn22p/05-aminoacids.ff -------------------------------------------------------------------------------- /vermouth/data/force_fields/elnedyn22p/10-modifications.ff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/force_fields/elnedyn22p/10-modifications.ff -------------------------------------------------------------------------------- /vermouth/data/force_fields/elnedyn22p/citations.bib: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/force_fields/elnedyn22p/citations.bib -------------------------------------------------------------------------------- /vermouth/data/force_fields/gromos/00-modifications.ff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/force_fields/gromos/00-modifications.ff -------------------------------------------------------------------------------- /vermouth/data/force_fields/gromos/05-cofactors.ff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/force_fields/gromos/05-cofactors.ff -------------------------------------------------------------------------------- /vermouth/data/force_fields/gromos/aminoacids.rtp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/force_fields/gromos/aminoacids.rtp -------------------------------------------------------------------------------- /vermouth/data/force_fields/martini22/00-general.ff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/force_fields/martini22/00-general.ff -------------------------------------------------------------------------------- /vermouth/data/force_fields/martini22/05-aminoacids.ff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/force_fields/martini22/05-aminoacids.ff -------------------------------------------------------------------------------- /vermouth/data/force_fields/martini22/10-modifications.ff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/force_fields/martini22/10-modifications.ff -------------------------------------------------------------------------------- /vermouth/data/force_fields/martini22/15-nucleotides.ff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/force_fields/martini22/15-nucleotides.ff -------------------------------------------------------------------------------- /vermouth/data/force_fields/martini22/citations.bib: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/force_fields/martini22/citations.bib -------------------------------------------------------------------------------- /vermouth/data/force_fields/martini22p/00-general.ff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/force_fields/martini22p/00-general.ff -------------------------------------------------------------------------------- /vermouth/data/force_fields/martini22p/05-aminoacids.ff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/force_fields/martini22p/05-aminoacids.ff -------------------------------------------------------------------------------- /vermouth/data/force_fields/martini22p/10-modifications.ff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/force_fields/martini22p/10-modifications.ff -------------------------------------------------------------------------------- /vermouth/data/force_fields/martini22p/citations.bib: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/force_fields/martini22p/citations.bib -------------------------------------------------------------------------------- /vermouth/data/force_fields/martini3001/00-general.ff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/force_fields/martini3001/00-general.ff -------------------------------------------------------------------------------- /vermouth/data/force_fields/martini3001/05-aminoacids.ff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/force_fields/martini3001/05-aminoacids.ff -------------------------------------------------------------------------------- /vermouth/data/force_fields/martini3001/10-modifications.ff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/force_fields/martini3001/10-modifications.ff -------------------------------------------------------------------------------- /vermouth/data/force_fields/martini3001/15-links_M3.ff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/force_fields/martini3001/15-links_M3.ff -------------------------------------------------------------------------------- /vermouth/data/force_fields/martini3001/20-links_M3_IDR.ff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/force_fields/martini3001/20-links_M3_IDR.ff -------------------------------------------------------------------------------- /vermouth/data/force_fields/martini3001/25-small_molecule_martini3.ff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/force_fields/martini3001/25-small_molecule_martini3.ff -------------------------------------------------------------------------------- /vermouth/data/force_fields/martini3001/citations.bib: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/force_fields/martini3001/citations.bib -------------------------------------------------------------------------------- /vermouth/data/mappings/ala.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/ala.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/ala.gromos.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/ala.gromos.map -------------------------------------------------------------------------------- /vermouth/data/mappings/arg.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/arg.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/arg.charmm36.martini22p.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/arg.charmm36.martini22p.map -------------------------------------------------------------------------------- /vermouth/data/mappings/arg.gromos.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/arg.gromos.map -------------------------------------------------------------------------------- /vermouth/data/mappings/asn.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/asn.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/asn.charmm36.martini22p.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/asn.charmm36.martini22p.map -------------------------------------------------------------------------------- /vermouth/data/mappings/asn.gromos.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/asn.gromos.map -------------------------------------------------------------------------------- /vermouth/data/mappings/asp.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/asp.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/asp.charmm36.martini22p.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/asp.charmm36.martini22p.map -------------------------------------------------------------------------------- /vermouth/data/mappings/asp.gromos.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/asp.gromos.map -------------------------------------------------------------------------------- /vermouth/data/mappings/asp0.gromos.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/asp0.gromos.map -------------------------------------------------------------------------------- /vermouth/data/mappings/chol.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/chol.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/cys.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/cys.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/cys.gromos.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/cys.gromos.map -------------------------------------------------------------------------------- /vermouth/data/mappings/dmpc.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/dmpc.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/dopc.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/dopc.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/dppc.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/dppc.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/dppg.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/dppg.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn/ala.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn/ala.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn/arg.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn/arg.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn/asn.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn/asn.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn/asp.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn/asp.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn/chol.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn/chol.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn/cys.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn/cys.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn/dmpc.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn/dmpc.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn/dopc.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn/dopc.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn/dppc.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn/dppc.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn/dppg.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn/dppg.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn/elnedyn22p/arg.charmm36.elnedyn22p.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn/elnedyn22p/arg.charmm36.elnedyn22p.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn/elnedyn22p/asn.charmm36.elnedyn22p.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn/elnedyn22p/asn.charmm36.elnedyn22p.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn/elnedyn22p/asp.charmm36.elnedyn22p.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn/elnedyn22p/asp.charmm36.elnedyn22p.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn/elnedyn22p/gln.charmm36.elnedyn22p.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn/elnedyn22p/gln.charmm36.elnedyn22p.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn/elnedyn22p/glu.charmm36.elnedyn22p.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn/elnedyn22p/glu.charmm36.elnedyn22p.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn/elnedyn22p/lys.charmm36.elnedyn22p.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn/elnedyn22p/lys.charmm36.elnedyn22p.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn/elnedyn22p/ser.charmm36.elnedyn22p.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn/elnedyn22p/ser.charmm36.elnedyn22p.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn/elnedyn22p/thr.charmm36.elnedyn22p.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn/elnedyn22p/thr.charmm36.elnedyn22p.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn/gln.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn/gln.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn/glu.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn/glu.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn/gly.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn/gly.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn/his.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn/his.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn/ile.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn/ile.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn/leu.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn/leu.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn/lys.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn/lys.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn/met.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn/met.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn/modifications.elnedyn21.mapping: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn/modifications.elnedyn21.mapping -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn/modifications.elnedyn22.mapping: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn/modifications.elnedyn22.mapping -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn/modifications.elnedyn22p.mapping: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn/modifications.elnedyn22p.mapping -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn/phe.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn/phe.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn/popc.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn/popc.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn/pope.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn/pope.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn/popg.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn/popg.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn/pops.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn/pops.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn/pro.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn/pro.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn/ser.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn/ser.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn/thr.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn/thr.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn/trp.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn/trp.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn/tyr.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn/tyr.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn/val.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn/val.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn21/ala.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn21/ala.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn21/arg.charmm36.elnedyn22p.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn21/arg.charmm36.elnedyn22p.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn21/arg.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn21/arg.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn21/asn.charmm36.elnedyn22p.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn21/asn.charmm36.elnedyn22p.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn21/asn.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn21/asn.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn21/asp.charmm36.elnedyn22p.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn21/asp.charmm36.elnedyn22p.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn21/asp.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn21/asp.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn21/cys.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn21/cys.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn21/gln.charmm36.elnedyn22p.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn21/gln.charmm36.elnedyn22p.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn21/gln.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn21/gln.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn21/glu.charmm36.elnedyn22p.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn21/glu.charmm36.elnedyn22p.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn21/glu.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn21/glu.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn21/gly.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn21/gly.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn21/his.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn21/his.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn21/ile.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn21/ile.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn21/leu.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn21/leu.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn21/lys.charmm36.elnedyn22p.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn21/lys.charmm36.elnedyn22p.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn21/lys.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn21/lys.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn21/met.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn21/met.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn21/modifications.mapping: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn21/modifications.mapping -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn21/phe.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn21/phe.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn21/pro.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn21/pro.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn21/ser.charmm36.elnedyn22p.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn21/ser.charmm36.elnedyn22p.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn21/ser.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn21/ser.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn21/thr.charmm36.elnedyn22p.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn21/thr.charmm36.elnedyn22p.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn21/thr.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn21/thr.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn21/trp.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn21/trp.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn21/tyr.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn21/tyr.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn21/val.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/elnedyn21/val.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/fmn.gromos.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/fmn.gromos.map -------------------------------------------------------------------------------- /vermouth/data/mappings/gln.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/gln.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/gln.charmm36.martini22p.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/gln.charmm36.martini22p.map -------------------------------------------------------------------------------- /vermouth/data/mappings/gln.gromos.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/gln.gromos.map -------------------------------------------------------------------------------- /vermouth/data/mappings/glu.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/glu.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/glu.charmm36.martini22p.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/glu.charmm36.martini22p.map -------------------------------------------------------------------------------- /vermouth/data/mappings/glu.gromos.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/glu.gromos.map -------------------------------------------------------------------------------- /vermouth/data/mappings/glu0.gromos.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/glu0.gromos.map -------------------------------------------------------------------------------- /vermouth/data/mappings/gly.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/gly.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/gly.gromos.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/gly.gromos.map -------------------------------------------------------------------------------- /vermouth/data/mappings/his.charmm.mapping: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/his.charmm.mapping -------------------------------------------------------------------------------- /vermouth/data/mappings/his.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/his.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/his.gromos.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/his.gromos.map -------------------------------------------------------------------------------- /vermouth/data/mappings/his.gromos.mapping: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/his.gromos.mapping -------------------------------------------------------------------------------- /vermouth/data/mappings/hsd.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/hsd.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/hse.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/hse.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/hsp.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/hsp.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/ile.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/ile.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/ile.gromos.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/ile.gromos.map -------------------------------------------------------------------------------- /vermouth/data/mappings/leu.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/leu.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/leu.gromos.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/leu.gromos.map -------------------------------------------------------------------------------- /vermouth/data/mappings/lys.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/lys.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/lys.charmm36.martini22p.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/lys.charmm36.martini22p.map -------------------------------------------------------------------------------- /vermouth/data/mappings/lys.gromos.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/lys.gromos.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/ala.amber.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/ala.amber.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/ala.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/ala.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/antr.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/antr.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/arg.amber.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/arg.amber.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/arg.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/arg.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/ash.amber.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/ash.amber.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/asn.amber.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/asn.amber.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/asn.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/asn.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/asp.amber.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/asp.amber.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/asp.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/asp.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/aspp.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/aspp.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/bald.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/bald.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/benz.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/benz.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/c3.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/c3.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/chxe.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/chxe.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/cpen.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/cpen.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/cume.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/cume.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/cys.amber.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/cys.amber.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/cys.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/cys.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/cysf.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/cysf.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/cysg.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/cysg.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/cysp.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/cysp.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/diol.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/diol.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/diox.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/diox.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/dman.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/dman.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/eben.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/eben.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/fura.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/fura.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/glh.amber.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/glh.amber.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/gln.amber.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/gln.amber.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/gln.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/gln.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/glu.amber.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/glu.amber.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/glu.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/glu.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/glup.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/glup.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/gly.amber.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/gly.amber.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/gly.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/gly.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/glym.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/glym.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/hid.amber.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/hid.amber.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/hie.amber.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/hie.amber.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/hip.amber.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/hip.amber.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/his.amber.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/his.amber.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/his.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/his.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/hsd.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/hsd.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/hse.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/hse.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/hsp.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/hsp.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/ile.amber.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/ile.amber.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/ile.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/ile.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/imia.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/imia.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/inda.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/inda.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/indo.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/indo.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/leu.amber.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/leu.amber.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/leu.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/leu.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/lsn.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/lsn.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/lyn.amber.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/lyn.amber.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/lys.amber.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/lys.amber.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/lys.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/lys.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/mboa.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/mboa.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/mcpe.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/mcpe.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/meob.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/meob.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/met.amber.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/met.amber.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/met.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/met.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/mind.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/mind.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/modifications.amber.mapping: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/modifications.amber.mapping -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/modifications.charmm36.mapping: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/modifications.charmm36.mapping -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/mxyl.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/mxyl.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/naft.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/naft.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/nitb.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/nitb.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/oxyl.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/oxyl.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/pcro.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/pcro.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/phe.amber.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/phe.amber.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/phe.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/phe.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/phen.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/phen.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/phmk.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/phmk.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/prld.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/prld.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/pro.amber.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/pro.amber.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/pro.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/pro.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/pxyl.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/pxyl.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/pyr1.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/pyr1.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/pyrd.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/pyrd.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/pyrl.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/pyrl.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/pyrm.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/pyrm.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/qinl.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/qinl.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/ser.amber.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/ser.amber.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/ser.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/ser.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/sm139.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/sm139.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/styr.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/styr.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/thaz.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/thaz.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/thf.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/thf.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/thip.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/thip.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/thp.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/thp.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/thr.amber.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/thr.amber.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/thr.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/thr.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/tolu.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/tolu.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/trp.amber.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/trp.amber.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/trp.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/trp.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/tyr.amber.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/tyr.amber.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/tyr.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/tyr.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/val.amber.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/val.amber.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/val.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/val.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/zimi.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/zimi.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/zthp.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/zthp.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/zthz.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/martini3001/zthz.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/met.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/met.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/met.gromos.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/met.gromos.map -------------------------------------------------------------------------------- /vermouth/data/mappings/modifications.gromos.mapping: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/modifications.gromos.mapping -------------------------------------------------------------------------------- /vermouth/data/mappings/modifications.mapping: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/modifications.mapping -------------------------------------------------------------------------------- /vermouth/data/mappings/nad.gromos.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/nad.gromos.map -------------------------------------------------------------------------------- /vermouth/data/mappings/phe.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/phe.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/phe.gromos.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/phe.gromos.map -------------------------------------------------------------------------------- /vermouth/data/mappings/popc.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/popc.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/pope.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/pope.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/popg.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/popg.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/pops.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/pops.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/pro.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/pro.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/pro.gromos.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/pro.gromos.map -------------------------------------------------------------------------------- /vermouth/data/mappings/ser.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/ser.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/ser.charmm36.martini22p.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/ser.charmm36.martini22p.map -------------------------------------------------------------------------------- /vermouth/data/mappings/ser.gromos.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/ser.gromos.map -------------------------------------------------------------------------------- /vermouth/data/mappings/thr.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/thr.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/thr.charmm36.martini22p.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/thr.charmm36.martini22p.map -------------------------------------------------------------------------------- /vermouth/data/mappings/thr.gromos.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/thr.gromos.map -------------------------------------------------------------------------------- /vermouth/data/mappings/tpp.gromos.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/tpp.gromos.map -------------------------------------------------------------------------------- /vermouth/data/mappings/trp.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/trp.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/trp.gromos.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/trp.gromos.map -------------------------------------------------------------------------------- /vermouth/data/mappings/tyr.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/tyr.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/tyr.gromos.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/tyr.gromos.map -------------------------------------------------------------------------------- /vermouth/data/mappings/val.charmm36.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/val.charmm36.map -------------------------------------------------------------------------------- /vermouth/data/mappings/val.gromos.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/mappings/val.gromos.map -------------------------------------------------------------------------------- /vermouth/data/quotes.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/data/quotes.txt -------------------------------------------------------------------------------- /vermouth/dssp/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/dssp/__init__.py -------------------------------------------------------------------------------- /vermouth/dssp/dssp.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/dssp/dssp.py -------------------------------------------------------------------------------- /vermouth/edge_tuning.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/edge_tuning.py -------------------------------------------------------------------------------- /vermouth/ffinput.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/ffinput.py -------------------------------------------------------------------------------- /vermouth/file_writer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/file_writer.py -------------------------------------------------------------------------------- /vermouth/forcefield.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/forcefield.py -------------------------------------------------------------------------------- /vermouth/geometry.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/geometry.py -------------------------------------------------------------------------------- /vermouth/gmx/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/gmx/__init__.py -------------------------------------------------------------------------------- /vermouth/gmx/gro.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/gmx/gro.py -------------------------------------------------------------------------------- /vermouth/gmx/itp.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/gmx/itp.py -------------------------------------------------------------------------------- /vermouth/gmx/itp_read.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/gmx/itp_read.py -------------------------------------------------------------------------------- /vermouth/gmx/rtp.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/gmx/rtp.py -------------------------------------------------------------------------------- /vermouth/gmx/topology.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/gmx/topology.py -------------------------------------------------------------------------------- /vermouth/graph_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/graph_utils.py -------------------------------------------------------------------------------- /vermouth/graphing/grappa.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/graphing/grappa.py -------------------------------------------------------------------------------- /vermouth/ismags.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/ismags.py -------------------------------------------------------------------------------- /vermouth/log_helpers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/log_helpers.py -------------------------------------------------------------------------------- /vermouth/map_input.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/map_input.py -------------------------------------------------------------------------------- /vermouth/map_parser.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/map_parser.py -------------------------------------------------------------------------------- /vermouth/molecule.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/molecule.py -------------------------------------------------------------------------------- /vermouth/parser_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/parser_utils.py -------------------------------------------------------------------------------- /vermouth/pdb/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/pdb/__init__.py -------------------------------------------------------------------------------- /vermouth/pdb/cif.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/pdb/cif.py -------------------------------------------------------------------------------- /vermouth/pdb/pdb.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/pdb/pdb.py -------------------------------------------------------------------------------- /vermouth/processors/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/processors/__init__.py -------------------------------------------------------------------------------- /vermouth/processors/add_molecule_edges.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/processors/add_molecule_edges.py -------------------------------------------------------------------------------- /vermouth/processors/annotate_idrs.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/processors/annotate_idrs.py -------------------------------------------------------------------------------- /vermouth/processors/annotate_mut_mod.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/processors/annotate_mut_mod.py -------------------------------------------------------------------------------- /vermouth/processors/apply_posres.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/processors/apply_posres.py -------------------------------------------------------------------------------- /vermouth/processors/apply_rubber_band.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/processors/apply_rubber_band.py -------------------------------------------------------------------------------- /vermouth/processors/attach_mass.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/processors/attach_mass.py -------------------------------------------------------------------------------- /vermouth/processors/average_beads.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/processors/average_beads.py -------------------------------------------------------------------------------- /vermouth/processors/canonicalize_modifications.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/processors/canonicalize_modifications.py -------------------------------------------------------------------------------- /vermouth/processors/cif_reader.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/processors/cif_reader.py -------------------------------------------------------------------------------- /vermouth/processors/do_links.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/processors/do_links.py -------------------------------------------------------------------------------- /vermouth/processors/do_mapping.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/processors/do_mapping.py -------------------------------------------------------------------------------- /vermouth/processors/gro_reader.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/processors/gro_reader.py -------------------------------------------------------------------------------- /vermouth/processors/locate_charge_dummies.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/processors/locate_charge_dummies.py -------------------------------------------------------------------------------- /vermouth/processors/make_bonds.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/processors/make_bonds.py -------------------------------------------------------------------------------- /vermouth/processors/merge_all_molecules.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/processors/merge_all_molecules.py -------------------------------------------------------------------------------- /vermouth/processors/merge_chains.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/processors/merge_chains.py -------------------------------------------------------------------------------- /vermouth/processors/name_moltype.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/processors/name_moltype.py -------------------------------------------------------------------------------- /vermouth/processors/pdb_reader.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/processors/pdb_reader.py -------------------------------------------------------------------------------- /vermouth/processors/processor.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/processors/processor.py -------------------------------------------------------------------------------- /vermouth/processors/quote.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/processors/quote.py -------------------------------------------------------------------------------- /vermouth/processors/rename_modified_residues.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/processors/rename_modified_residues.py -------------------------------------------------------------------------------- /vermouth/processors/repair_graph.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/processors/repair_graph.py -------------------------------------------------------------------------------- /vermouth/processors/rtp_polisher.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/processors/rtp_polisher.py -------------------------------------------------------------------------------- /vermouth/processors/set_molecule_meta.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/processors/set_molecule_meta.py -------------------------------------------------------------------------------- /vermouth/processors/sort_molecule_atoms.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/processors/sort_molecule_atoms.py -------------------------------------------------------------------------------- /vermouth/processors/stash_attributes.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/processors/stash_attributes.py -------------------------------------------------------------------------------- /vermouth/processors/tune_cystein_bridges.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/processors/tune_cystein_bridges.py -------------------------------------------------------------------------------- /vermouth/processors/water_bias.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/processors/water_bias.py -------------------------------------------------------------------------------- /vermouth/rcsu/__init__.py: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /vermouth/rcsu/contact_map.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/rcsu/contact_map.py -------------------------------------------------------------------------------- /vermouth/rcsu/go_pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/rcsu/go_pipeline.py -------------------------------------------------------------------------------- /vermouth/rcsu/go_structure_bias.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/rcsu/go_structure_bias.py -------------------------------------------------------------------------------- /vermouth/rcsu/go_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/rcsu/go_utils.py -------------------------------------------------------------------------------- /vermouth/rcsu/go_vs_includes.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/rcsu/go_vs_includes.py -------------------------------------------------------------------------------- /vermouth/selectors.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/selectors.py -------------------------------------------------------------------------------- /vermouth/system.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/system.py -------------------------------------------------------------------------------- /vermouth/tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/__init__.py -------------------------------------------------------------------------------- /vermouth/tests/data/1UBQ.cif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/1UBQ.cif -------------------------------------------------------------------------------- /vermouth/tests/data/1UBQ.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/1UBQ.pdb -------------------------------------------------------------------------------- /vermouth/tests/data/1UBQ_nocell_occupancy.cif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/1UBQ_nocell_occupancy.cif -------------------------------------------------------------------------------- /vermouth/tests/data/1bta.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/1bta.pdb -------------------------------------------------------------------------------- /vermouth/tests/data/1bta_mutated.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/1bta_mutated.pdb -------------------------------------------------------------------------------- /vermouth/tests/data/2QWO.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/2QWO.pdb -------------------------------------------------------------------------------- /vermouth/tests/data/2dn2.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/2dn2.pdb -------------------------------------------------------------------------------- /vermouth/tests/data/6E8W.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/6E8W.pdb -------------------------------------------------------------------------------- /vermouth/tests/data/ala5.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/ala5.pdb -------------------------------------------------------------------------------- /vermouth/tests/data/ala5_cg.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/ala5_cg.pdb -------------------------------------------------------------------------------- /vermouth/tests/data/cif_missing_atomname.cif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/cif_missing_atomname.cif -------------------------------------------------------------------------------- /vermouth/tests/data/cif_missing_resname.cif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/cif_missing_resname.cif -------------------------------------------------------------------------------- /vermouth/tests/data/dna-short.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/dna-short.pdb -------------------------------------------------------------------------------- /vermouth/tests/data/dssp_tests/dssp_1bta.ssd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/dssp_tests/dssp_1bta.ssd -------------------------------------------------------------------------------- /vermouth/tests/data/dssp_tests/mini-protein1_betasheet.pdb.v2.2.1-3b2-deb_cv1.ssd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/dssp_tests/mini-protein1_betasheet.pdb.v2.2.1-3b2-deb_cv1.ssd -------------------------------------------------------------------------------- /vermouth/tests/data/dssp_tests/mini-protein1_betasheet.pdb.v3.0.0-3b1-deb_cv1.ssd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/dssp_tests/mini-protein1_betasheet.pdb.v3.0.0-3b1-deb_cv1.ssd -------------------------------------------------------------------------------- /vermouth/tests/data/dssp_tests/mini-protein2_helix.pdb.v2.2.1-3b2-deb_cv1.ssd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/dssp_tests/mini-protein2_helix.pdb.v2.2.1-3b2-deb_cv1.ssd -------------------------------------------------------------------------------- /vermouth/tests/data/dssp_tests/mini-protein2_helix.pdb.v3.0.0-3b1-deb_cv1.ssd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/dssp_tests/mini-protein2_helix.pdb.v3.0.0-3b1-deb_cv1.ssd -------------------------------------------------------------------------------- /vermouth/tests/data/dssp_tests/mini-protein3_trp-cage.pdb.v2.2.1-3b2-deb_cv1.ssd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/dssp_tests/mini-protein3_trp-cage.pdb.v2.2.1-3b2-deb_cv1.ssd -------------------------------------------------------------------------------- /vermouth/tests/data/dssp_tests/mini-protein3_trp-cage.pdb.v3.0.0-3b1-deb_cv1.ssd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/dssp_tests/mini-protein3_trp-cage.pdb.v3.0.0-3b1-deb_cv1.ssd -------------------------------------------------------------------------------- /vermouth/tests/data/force_fields/martini-test/aminoacids.ff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/force_fields/martini-test/aminoacids.ff -------------------------------------------------------------------------------- /vermouth/tests/data/force_fields/pepplane/ala.ff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/force_fields/pepplane/ala.ff -------------------------------------------------------------------------------- /vermouth/tests/data/force_fields/pepplane/general.ff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/force_fields/pepplane/general.ff -------------------------------------------------------------------------------- /vermouth/tests/data/force_fields/pepplane/modifications.ff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/force_fields/pepplane/modifications.ff -------------------------------------------------------------------------------- /vermouth/tests/data/force_fields/universal-test/aminoacids.rtp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/force_fields/universal-test/aminoacids.rtp -------------------------------------------------------------------------------- /vermouth/tests/data/force_fields/universal-test/modifications.ff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/force_fields/universal-test/modifications.ff -------------------------------------------------------------------------------- /vermouth/tests/data/heme.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/heme.pdb -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-0/dipro-termini/README: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-0/dipro-termini/README -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-0/dipro-termini/aa.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-0/dipro-termini/aa.pdb -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-0/dipro-termini/martinize2/cg.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-0/dipro-termini/martinize2/cg.pdb -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-0/dipro-termini/martinize2/citation: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-0/dipro-termini/martinize2/citation -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-0/dipro-termini/martinize2/command: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-0/dipro-termini/martinize2/command -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-0/dipro-termini/martinize2/molecule_0.itp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-0/dipro-termini/martinize2/molecule_0.itp -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-0/dipro-termini/martinize2/topol.top: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-0/dipro-termini/martinize2/topol.top -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-0/mini-protein1_betasheet/README: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-0/mini-protein1_betasheet/README -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-0/mini-protein1_betasheet/aa.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-0/mini-protein1_betasheet/aa.pdb -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-0/mini-protein1_betasheet/martinize2/cg.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-0/mini-protein1_betasheet/martinize2/cg.pdb -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-0/mini-protein1_betasheet/martinize2/chain_A.ssd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-0/mini-protein1_betasheet/martinize2/chain_A.ssd -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-0/mini-protein1_betasheet/martinize2/citation: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-0/mini-protein1_betasheet/martinize2/citation -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-0/mini-protein1_betasheet/martinize2/command: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-0/mini-protein1_betasheet/martinize2/command -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-0/mini-protein1_betasheet/martinize2/molecule_0.itp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-0/mini-protein1_betasheet/martinize2/molecule_0.itp -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-0/mini-protein1_betasheet/martinize2/screen.output: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-0/mini-protein1_betasheet/martinize2/screen.output -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-0/mini-protein1_betasheet/martinize2/topol.top: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-0/mini-protein1_betasheet/martinize2/topol.top -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-0/mini-protein2_helix/README: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-0/mini-protein2_helix/README -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-0/mini-protein2_helix/aa.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-0/mini-protein2_helix/aa.pdb -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-0/mini-protein2_helix/martinize2/cg.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-0/mini-protein2_helix/martinize2/cg.pdb -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-0/mini-protein2_helix/martinize2/chain_A.ssd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-0/mini-protein2_helix/martinize2/chain_A.ssd -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-0/mini-protein2_helix/martinize2/citation: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-0/mini-protein2_helix/martinize2/citation -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-0/mini-protein2_helix/martinize2/command: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-0/mini-protein2_helix/martinize2/command -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-0/mini-protein2_helix/martinize2/molecule_0.itp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-0/mini-protein2_helix/martinize2/molecule_0.itp -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-0/mini-protein2_helix/martinize2/screen.output: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-0/mini-protein2_helix/martinize2/screen.output -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-0/mini-protein2_helix/martinize2/topol.top: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-0/mini-protein2_helix/martinize2/topol.top -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-0/mini-protein3_trp-cage/README: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-0/mini-protein3_trp-cage/README -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-0/mini-protein3_trp-cage/aa.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-0/mini-protein3_trp-cage/aa.pdb -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-0/mini-protein3_trp-cage/martinize2/cg.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-0/mini-protein3_trp-cage/martinize2/cg.pdb -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-0/mini-protein3_trp-cage/martinize2/chain_A.ssd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-0/mini-protein3_trp-cage/martinize2/chain_A.ssd -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-0/mini-protein3_trp-cage/martinize2/citation: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-0/mini-protein3_trp-cage/martinize2/citation -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-0/mini-protein3_trp-cage/martinize2/command: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-0/mini-protein3_trp-cage/martinize2/command -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-0/mini-protein3_trp-cage/martinize2/molecule_0.itp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-0/mini-protein3_trp-cage/martinize2/molecule_0.itp -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-0/mini-protein3_trp-cage/martinize2/screen.output: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-0/mini-protein3_trp-cage/martinize2/screen.output -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-0/mini-protein3_trp-cage/martinize2/topol.top: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-0/mini-protein3_trp-cage/martinize2/topol.top -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/1UBQ/README: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/1UBQ/README -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/1UBQ/aa.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/1UBQ/aa.pdb -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/1UBQ/martinize2/cg.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/1UBQ/martinize2/cg.pdb -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/1UBQ/martinize2/citation: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/1UBQ/martinize2/citation -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/1UBQ/martinize2/command: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/1UBQ/martinize2/command -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/1UBQ/martinize2/molecule_0.itp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/1UBQ/martinize2/molecule_0.itp -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/1UBQ/martinize2/topol.top: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/1UBQ/martinize2/topol.top -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/1mj5-charmm/README: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/1mj5-charmm/README -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/1mj5-charmm/aa.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/1mj5-charmm/aa.pdb -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/1mj5-charmm/martinize2/cg.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/1mj5-charmm/martinize2/cg.pdb -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/1mj5-charmm/martinize2/cg.top: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/1mj5-charmm/martinize2/cg.top -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/1mj5-charmm/martinize2/chain_.ssd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/1mj5-charmm/martinize2/chain_.ssd -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/1mj5-charmm/martinize2/citation: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/1mj5-charmm/martinize2/citation -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/1mj5-charmm/martinize2/command: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/1mj5-charmm/martinize2/command -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/1mj5-charmm/martinize2/molecule_0.itp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/1mj5-charmm/martinize2/molecule_0.itp -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/1mj5-charmm/martinize2/screen.output: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/1mj5-charmm/martinize2/screen.output -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/1mj5/README: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/1mj5/README -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/1mj5/aa.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/1mj5/aa.pdb -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/1mj5/martinize2/cg.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/1mj5/martinize2/cg.pdb -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/1mj5/martinize2/cg.top: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/1mj5/martinize2/cg.top -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/1mj5/martinize2/chain_.ssd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/1mj5/martinize2/chain_.ssd -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/1mj5/martinize2/citation: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/1mj5/martinize2/citation -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/1mj5/martinize2/command: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/1mj5/martinize2/command -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/1mj5/martinize2/molecule_0.itp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/1mj5/martinize2/molecule_0.itp -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/1mj5/martinize2/screen.output: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/1mj5/martinize2/screen.output -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/3i40/3i40.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/3i40/3i40.pdb -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/3i40/README: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/3i40/README -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/3i40/martinize2/cg.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/3i40/martinize2/cg.pdb -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/3i40/martinize2/cg.top: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/3i40/martinize2/cg.top -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/3i40/martinize2/chain_A.ssd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/3i40/martinize2/chain_A.ssd -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/3i40/martinize2/chain_C.ssd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/3i40/martinize2/chain_C.ssd -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/3i40/martinize2/citation: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/3i40/martinize2/citation -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/3i40/martinize2/command: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/3i40/martinize2/command -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/3i40/martinize2/insulin_dimer.itp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/3i40/martinize2/insulin_dimer.itp -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/3i40/martinize2/molecule_0.itp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/3i40/martinize2/molecule_0.itp -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/3i40/martinize2/screen.output: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/3i40/martinize2/screen.output -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/6LFO_gap/6LFO_gap.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/6LFO_gap/6LFO_gap.pdb -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/6LFO_gap/README: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/6LFO_gap/README -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/6LFO_gap/martinize2/cg.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/6LFO_gap/martinize2/cg.pdb -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/6LFO_gap/martinize2/cg.top: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/6LFO_gap/martinize2/cg.top -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/6LFO_gap/martinize2/chain_R.ssd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/6LFO_gap/martinize2/chain_R.ssd -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/6LFO_gap/martinize2/citation: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/6LFO_gap/martinize2/citation -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/6LFO_gap/martinize2/command: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/6LFO_gap/martinize2/command -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/6LFO_gap/martinize2/molecule_0.itp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/6LFO_gap/martinize2/molecule_0.itp -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/6LFO_gap/martinize2/screen.output: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/6LFO_gap/martinize2/screen.output -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/EN_chain/README: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/EN_chain/README -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/EN_chain/aa.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/EN_chain/aa.pdb -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/EN_chain/martinize2/cg.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/EN_chain/martinize2/cg.pdb -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/EN_chain/martinize2/cg.top: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/EN_chain/martinize2/cg.top -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/EN_chain/martinize2/chain_A.ssd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/EN_chain/martinize2/chain_A.ssd -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/EN_chain/martinize2/citation: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/EN_chain/martinize2/citation -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/EN_chain/martinize2/command: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/EN_chain/martinize2/command -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/EN_chain/martinize2/molecule_0.itp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/EN_chain/martinize2/molecule_0.itp -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/EN_chain/martinize2/screen.output: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/EN_chain/martinize2/screen.output -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/EN_region/README: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/EN_region/README -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/EN_region/aa.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/EN_region/aa.pdb -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/EN_region/martinize2/cg.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/EN_region/martinize2/cg.pdb -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/EN_region/martinize2/cg.top: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/EN_region/martinize2/cg.top -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/EN_region/martinize2/chain_A.ssd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/EN_region/martinize2/chain_A.ssd -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/EN_region/martinize2/citation: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/EN_region/martinize2/citation -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/EN_region/martinize2/command: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/EN_region/martinize2/command -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/EN_region/martinize2/molecule_0.itp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/EN_region/martinize2/molecule_0.itp -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/EN_region/martinize2/screen.output: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/EN_region/martinize2/screen.output -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/bpti/README: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/bpti/README -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/bpti/aa.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/bpti/aa.pdb -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/bpti/martinize2/cg.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/bpti/martinize2/cg.pdb -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/bpti/martinize2/chain_A.ssd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/bpti/martinize2/chain_A.ssd -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/bpti/martinize2/citation: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/bpti/martinize2/citation -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/bpti/martinize2/command: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/bpti/martinize2/command -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/bpti/martinize2/molecule_0.itp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/bpti/martinize2/molecule_0.itp -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/bpti/martinize2/screen.output: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/bpti/martinize2/screen.output -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/bpti/martinize2/topol.top: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/bpti/martinize2/topol.top -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/hst5/README: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/hst5/README -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/hst5/aa.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/hst5/aa.pdb -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/hst5/martinize2/cg.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/hst5/martinize2/cg.pdb -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/hst5/martinize2/citation: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/hst5/martinize2/citation -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/hst5/martinize2/command: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/hst5/martinize2/command -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/hst5/martinize2/molecule_0.itp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/hst5/martinize2/molecule_0.itp -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/hst5/martinize2/topol.top: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/hst5/martinize2/topol.top -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme/README: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme/README -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme/aa.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme/aa.pdb -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme/martinize2/cg.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme/martinize2/cg.pdb -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme/martinize2/chain_A.ssd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme/martinize2/chain_A.ssd -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme/martinize2/citation: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme/martinize2/citation -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme/martinize2/command: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme/martinize2/command -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme/martinize2/molecule_0.itp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme/martinize2/molecule_0.itp -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme/martinize2/topol.top: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme/martinize2/topol.top -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/README: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/README -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/aa.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/aa.pdb -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/map.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/map.map -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/martinize2/cg.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/martinize2/cg.pdb -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/martinize2/citation: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/martinize2/citation -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/martinize2/command: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/martinize2/command -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/martinize2/molecule_0.itp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/martinize2/molecule_0.itp -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/martinize2/topol.top: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/martinize2/topol.top -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/martinize2/virtual_sites_atomtypes.itp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/martinize2/virtual_sites_atomtypes.itp -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/martinize2/virtual_sites_nonbond_params.itp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/martinize2/virtual_sites_nonbond_params.itp -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/README: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/README -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/aa.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/aa.pdb -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/map.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/map.map -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/cg.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/cg.pdb -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/citation: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/citation -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/command: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/command -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/go_atomtypes.itp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/go_atomtypes.itp -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/go_nbparams.itp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/go_nbparams.itp -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/molecule_0.itp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/molecule_0.itp -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/topol.top: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/topol.top -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_GO_internal/README: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO_internal/README -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_GO_internal/aa.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO_internal/aa.pdb -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_GO_internal/martinize2/cg.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO_internal/martinize2/cg.pdb -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_GO_internal/martinize2/citation: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO_internal/martinize2/citation -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_GO_internal/martinize2/command: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO_internal/martinize2/command -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_GO_internal/martinize2/go_atomtypes.itp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO_internal/martinize2/go_atomtypes.itp -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_GO_internal/martinize2/go_nbparams.itp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO_internal/martinize2/go_nbparams.itp -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_GO_internal/martinize2/martinize_contact_map.out: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO_internal/martinize2/martinize_contact_map.out -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_GO_internal/martinize2/molecule.itp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO_internal/martinize2/molecule.itp -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_GO_internal/martinize2/topol.top: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO_internal/martinize2/topol.top -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/README: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/README -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/aa.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/aa.pdb -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/map.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/map.map -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/cg.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/cg.pdb -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/citation: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/citation -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/command: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/command -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/go_atomtypes.itp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/go_atomtypes.itp -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/go_nbparams.itp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/go_nbparams.itp -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/molecule_0.itp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/molecule_0.itp -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/topol.top: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/topol.top -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_prot/README: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme_prot/README -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_prot/aa.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme_prot/aa.pdb -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_prot/cg.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme_prot/cg.pdb -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_prot/chain_A.ssd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme_prot/chain_A.ssd -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_prot/martinize2/cg.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme_prot/martinize2/cg.pdb -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_prot/martinize2/chain_A.ssd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme_prot/martinize2/chain_A.ssd -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_prot/martinize2/citation: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme_prot/martinize2/citation -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_prot/martinize2/command: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme_prot/martinize2/command -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_prot/martinize2/molecule_0.itp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme_prot/martinize2/molecule_0.itp -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_prot/martinize2/screen.output: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme_prot/martinize2/screen.output -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_prot/martinize2/test.itp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme_prot/martinize2/test.itp -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_prot/martinize2/topol.top: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme_prot/martinize2/topol.top -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_prot/molecule_0.itp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme_prot/molecule_0.itp -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_prot/topol.top: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/lysozyme_prot/topol.top -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/prot_modf_charmm/README: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/prot_modf_charmm/README -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/prot_modf_charmm/input.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/prot_modf_charmm/input.pdb -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/prot_modf_charmm/martinize2/cg.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/prot_modf_charmm/martinize2/cg.pdb -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/prot_modf_charmm/martinize2/cg.top: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/prot_modf_charmm/martinize2/cg.top -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/prot_modf_charmm/martinize2/chain_.ssd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/prot_modf_charmm/martinize2/chain_.ssd -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/prot_modf_charmm/martinize2/citation: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/prot_modf_charmm/martinize2/citation -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/prot_modf_charmm/martinize2/command: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/prot_modf_charmm/martinize2/command -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/prot_modf_charmm/martinize2/molecule_0.itp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/prot_modf_charmm/martinize2/molecule_0.itp -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/prot_modf_charmm/martinize2/screen.output: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/prot_modf_charmm/martinize2/screen.output -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/prot_modf_charmm/martinize2/sys.top: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/prot_modf_charmm/martinize2/sys.top -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/villin/README: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/villin/README -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/villin/aa.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/villin/aa.pdb -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/villin/martinize2/cg.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/villin/martinize2/cg.pdb -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/villin/martinize2/citation: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/villin/martinize2/citation -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/villin/martinize2/command: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/villin/martinize2/command -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/villin/martinize2/molecule_0.itp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/villin/martinize2/molecule_0.itp -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/villin/martinize2/screen.output: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/villin/martinize2/screen.output -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/villin/martinize2/topol.top: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/integration_tests/tier-1/villin/martinize2/topol.top -------------------------------------------------------------------------------- /vermouth/tests/data/mappings/universal-test/martini-test/ser.mapping: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/mappings/universal-test/martini-test/ser.mapping -------------------------------------------------------------------------------- /vermouth/tests/data/mappings/universal-test/pepplane/ala.mapping: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/mappings/universal-test/pepplane/ala.mapping -------------------------------------------------------------------------------- /vermouth/tests/data/mappings/universal-test/pepplane/modifications.mapping: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/mappings/universal-test/pepplane/modifications.mapping -------------------------------------------------------------------------------- /vermouth/tests/data/multiple.cif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/multiple.cif -------------------------------------------------------------------------------- /vermouth/tests/data/test_molecule_contacts.out: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/test_molecule_contacts.out -------------------------------------------------------------------------------- /vermouth/tests/data/tri_alanine.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/data/tri_alanine.pdb -------------------------------------------------------------------------------- /vermouth/tests/datafiles.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/datafiles.py -------------------------------------------------------------------------------- /vermouth/tests/gmx/test_gro.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/gmx/test_gro.py -------------------------------------------------------------------------------- /vermouth/tests/gmx/test_itp.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/gmx/test_itp.py -------------------------------------------------------------------------------- /vermouth/tests/gmx/test_topology.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/gmx/test_topology.py -------------------------------------------------------------------------------- /vermouth/tests/helper_functions.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/helper_functions.py -------------------------------------------------------------------------------- /vermouth/tests/integration_tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/integration_tests/__init__.py -------------------------------------------------------------------------------- /vermouth/tests/integration_tests/test_integration.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/integration_tests/test_integration.py -------------------------------------------------------------------------------- /vermouth/tests/molecule_strategies.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/molecule_strategies.py -------------------------------------------------------------------------------- /vermouth/tests/pdb/test_cif.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/pdb/test_cif.py -------------------------------------------------------------------------------- /vermouth/tests/pdb/test_read_pdb.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/pdb/test_read_pdb.py -------------------------------------------------------------------------------- /vermouth/tests/pdb/test_write_pdb.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/pdb/test_write_pdb.py -------------------------------------------------------------------------------- /vermouth/tests/rcsu/test_contact_map.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/rcsu/test_contact_map.py -------------------------------------------------------------------------------- /vermouth/tests/rcsu/test_go_structure_bias.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/rcsu/test_go_structure_bias.py -------------------------------------------------------------------------------- /vermouth/tests/rcsu/test_go_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/rcsu/test_go_utils.py -------------------------------------------------------------------------------- /vermouth/tests/rcsu/test_read_go_map.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/rcsu/test_read_go_map.py -------------------------------------------------------------------------------- /vermouth/tests/test_add_molecule_edges.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/test_add_molecule_edges.py -------------------------------------------------------------------------------- /vermouth/tests/test_annotate_idrs.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/test_annotate_idrs.py -------------------------------------------------------------------------------- /vermouth/tests/test_annotate_mut_mod.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/test_annotate_mut_mod.py -------------------------------------------------------------------------------- /vermouth/tests/test_apply_posres.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/test_apply_posres.py -------------------------------------------------------------------------------- /vermouth/tests/test_apply_rubber_band.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/test_apply_rubber_band.py -------------------------------------------------------------------------------- /vermouth/tests/test_average_beads.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/test_average_beads.py -------------------------------------------------------------------------------- /vermouth/tests/test_cif_reader.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/test_cif_reader.py -------------------------------------------------------------------------------- /vermouth/tests/test_do_mapping.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/test_do_mapping.py -------------------------------------------------------------------------------- /vermouth/tests/test_dssp.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/test_dssp.py -------------------------------------------------------------------------------- /vermouth/tests/test_edge_tuning.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/test_edge_tuning.py -------------------------------------------------------------------------------- /vermouth/tests/test_ff_files.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/test_ff_files.py -------------------------------------------------------------------------------- /vermouth/tests/test_ffinput.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/test_ffinput.py -------------------------------------------------------------------------------- /vermouth/tests/test_file_writer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/test_file_writer.py -------------------------------------------------------------------------------- /vermouth/tests/test_forcefield.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/test_forcefield.py -------------------------------------------------------------------------------- /vermouth/tests/test_geometry.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/test_geometry.py -------------------------------------------------------------------------------- /vermouth/tests/test_graph_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/test_graph_utils.py -------------------------------------------------------------------------------- /vermouth/tests/test_grappa.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/test_grappa.py -------------------------------------------------------------------------------- /vermouth/tests/test_ismags.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/test_ismags.py -------------------------------------------------------------------------------- /vermouth/tests/test_itp_files.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/test_itp_files.py -------------------------------------------------------------------------------- /vermouth/tests/test_links.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/test_links.py -------------------------------------------------------------------------------- /vermouth/tests/test_logging.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/test_logging.py -------------------------------------------------------------------------------- /vermouth/tests/test_make_bonds.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/test_make_bonds.py -------------------------------------------------------------------------------- /vermouth/tests/test_map_input.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/test_map_input.py -------------------------------------------------------------------------------- /vermouth/tests/test_map_parser.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/test_map_parser.py -------------------------------------------------------------------------------- /vermouth/tests/test_mapping_integrative.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/test_mapping_integrative.py -------------------------------------------------------------------------------- /vermouth/tests/test_merge_chains.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/test_merge_chains.py -------------------------------------------------------------------------------- /vermouth/tests/test_molecule.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/test_molecule.py -------------------------------------------------------------------------------- /vermouth/tests/test_name_moltype.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/test_name_moltype.py -------------------------------------------------------------------------------- /vermouth/tests/test_native_forcefield.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/test_native_forcefield.py -------------------------------------------------------------------------------- /vermouth/tests/test_ptm_detection.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/test_ptm_detection.py -------------------------------------------------------------------------------- /vermouth/tests/test_repair_graph.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/test_repair_graph.py -------------------------------------------------------------------------------- /vermouth/tests/test_section_parser.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/test_section_parser.py -------------------------------------------------------------------------------- /vermouth/tests/test_selectors.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/test_selectors.py -------------------------------------------------------------------------------- /vermouth/tests/test_set_molecule_meta.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/test_set_molecule_meta.py -------------------------------------------------------------------------------- /vermouth/tests/test_sort_molecule_atoms.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/test_sort_molecule_atoms.py -------------------------------------------------------------------------------- /vermouth/tests/test_stash_attributes.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/test_stash_attributes.py -------------------------------------------------------------------------------- /vermouth/tests/test_system.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/test_system.py -------------------------------------------------------------------------------- /vermouth/tests/test_tune_cystein_bridges.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/test_tune_cystein_bridges.py -------------------------------------------------------------------------------- /vermouth/tests/test_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/test_utils.py -------------------------------------------------------------------------------- /vermouth/tests/test_version.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/test_version.py -------------------------------------------------------------------------------- /vermouth/tests/test_vs_generation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/test_vs_generation.py -------------------------------------------------------------------------------- /vermouth/tests/test_water_bias.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/tests/test_water_bias.py -------------------------------------------------------------------------------- /vermouth/truncating_formatter.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/truncating_formatter.py -------------------------------------------------------------------------------- /vermouth/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/HEAD/vermouth/utils.py --------------------------------------------------------------------------------