vermouth package

Subpackages

• vermouth.data package
  • Submodules
    • vermouth.data.data module
  • Module contents
• vermouth.dssp package
  • Submodules
    • vermouth.dssp.dssp module
      • AnnotateDSSP
      • AnnotateMartiniSecondaryStructures
      • AnnotateResidues
      • DSSPError
      • annotate_dssp()
      • annotate_residues_from_sequence()
      • convert_dssp_annotation_to_martini()
      • convert_dssp_to_martini()
      • gmx_system_header()
      • read_dssp2()
      • run_dssp()
      • run_mdtraj()
      • sequence_from_residues()
  • Module contents
• vermouth.gmx package
  • Submodules
    • vermouth.gmx.gro module
      • read_gro()
      • write_gro()
    • vermouth.gmx.itp module
      • write_molecule_itp()
    • vermouth.gmx.itp_read module
      • ITPDirector
      • read_itp()
    • vermouth.gmx.rtp module
      • read_rtp()
    • vermouth.gmx.topology module
      • Atomtype
      • NonbondParam
      • sigma_epsilon_to_C6_C12()
      • write_atomtypes()
      • write_gmx_topology()
      • write_nonbond_params()
  • Module contents
• vermouth.pdb package
  • Submodules
    • vermouth.pdb.cif module
      • CIFReader
      • casting()
      • cif_entry_reader()
      • read_cif_file()
    • vermouth.pdb.pdb module
      • PDBParser
      • get_not_none()
      • read_pdb()
      • write_pdb()
      • write_pdb_string()
  • Module contents
• vermouth.processors package
  • Submodules
    • vermouth.processors.add_molecule_edges module
      • AddMoleculeEdgesAtDistance
      • MergeNucleicStrands
    • vermouth.processors.annotate_idrs module
      • AnnotateIDRs
      • annotate_disorder()
      • parse_residues()
    • vermouth.processors.annotate_mut_mod module
      • AnnotateMutMod
      • annotate_modifications()
      • parse_residue_spec()
      • residue_matches()
    • vermouth.processors.apply_posres module
      • ApplyPosres
      • apply_posres()
    • vermouth.processors.apply_rubber_band module
      • ApplyRubberBand
      • always_true()
      • apply_rubber_band()
      • are_connected()
      • build_connectivity_matrix()
      • build_pair_matrix()
      • compute_decay()
      • compute_force_constants()
      • make_same_region_criterion()
      • same_chain()
      • self_distance_matrix()
    • vermouth.processors.attach_mass module
      • AttachMass
      • attach_mass()
    • vermouth.processors.average_beads module
      • DoAverageBead
      • do_average_bead()
    • vermouth.processors.canonicalize_modifications module
      • CanonicalizeModifications
      • allowed_ptms()
      • find_ptm_atoms()
      • fix_ptm()
      • identify_ptms()
      • ptm_node_matcher()
    • vermouth.processors.cif_reader module
      • CIFInput
    • vermouth.processors.do_links module
      • DoLinks
      • match_link()
      • match_order()
    • vermouth.processors.do_mapping module
      • DoMapping
      • apply_block_mapping()
      • apply_mod_mapping()
      • attrs_from_node()
      • build_graph_mapping_collection()
      • cover()
      • do_mapping()
      • edge_matcher()
      • get_mod_mappings()
      • modification_matches()
      • node_matcher()
      • node_should_exist()
      • ptm_resname_match()
    • vermouth.processors.gro_reader module
      • GROInput
    • vermouth.processors.locate_charge_dummies module
      • LocateChargeDummies
      • colinear_pair()
      • fibonacci_sphere()
      • find_anchor()
      • locate_all_dummies()
      • locate_dummy()
    • vermouth.processors.make_bonds module
      • MakeBonds
      • make_bonds()
    • vermouth.processors.merge_all_molecules module
      • MergeAllMolecules
    • vermouth.processors.merge_chains module
      • MergeChains
      • merge_chains()
    • vermouth.processors.name_moltype module
      • NameMolType
    • vermouth.processors.pdb_reader module
      • PDBInput
    • vermouth.processors.processor module
      • Processor
    • vermouth.processors.quote module
      • Quoter
    • vermouth.processors.rename_modified_residues module
      • RenameModifiedResidues
      • rename_modified_residues()
    • vermouth.processors.repair_graph module
      • RepairGraph
      • get_default()
      • make_reference()
      • repair_graph()
      • repair_residue()
    • vermouth.processors.rtp_polisher module
      • RTPPolisher
      • add_angles()
      • add_dihedrals_and_pairs()
    • vermouth.processors.set_molecule_meta module
      • SetMoleculeMeta
    • vermouth.processors.sort_molecule_atoms module
      • SortMoleculeAtoms
    • vermouth.processors.stash_attributes module
      • StashAttributes
      • stash_attributes()
    • vermouth.processors.tune_cystein_bridges module
      • AddCysteinBridgesThreshold
      • RemoveCysteinBridgeEdges
      • remove_cystein_bridge_edges()
    • vermouth.processors.water_bias module
      • ComputeWaterBias
  • Module contents
• vermouth.rcsu package
  • Submodules
    • vermouth.rcsu.contact_map module
      • GenerateContactMap
      • atom2res()
      • do_contacts()
      • make_atom_map()
      • read_go_map()
    • vermouth.rcsu.go_pipeline module
      • GoProcessorPipeline
    • vermouth.rcsu.go_structure_bias module
      • ComputeStructuralGoBias
    • vermouth.rcsu.go_utils module
      • get_go_type_from_attributes()
    • vermouth.rcsu.go_vs_includes module
      • VirtualSiteCreator
  • Module contents

Submodules

• vermouth.citation_parser module
  • BibTexDirector
    • BibTexDirector.extract_fields()
    • BibTexDirector.find_entries()
    • BibTexDirector.parse()
    • BibTexDirector.parse_entry()
    • BibTexDirector.pop_entry_type()
    • BibTexDirector.pop_key()
    • BibTexDirector.prepare_file()
  • citation_formatter()
  • read_bib()
• vermouth.edge_tuning module
  • add_edges_at_distance()
  • add_edges_threshold()
  • add_inter_molecule_edges()
  • pairs_under_threshold()
  • prune_edges_between_selections()
  • prune_edges_with_selectors()
  • select_nodes_multi()
• vermouth.ffinput module
  • FFDirector
    • FFDirector.COMMENT_CHAR
    • FFDirector.METH_DICT
    • FFDirector.finalize_section()
    • FFDirector.get_context()
    • FFDirector.has_context()
    • FFDirector.interactions_natoms
    • FFDirector.parse_header()
  • read_ff()
• vermouth.file_writer module
  • DeferredFileWriter
    • DeferredFileWriter.close()
    • DeferredFileWriter.open()
    • DeferredFileWriter.write()
  • Singleton
  • deferred_open()
• vermouth.forcefield module
  • ForceField
    • ForceField.blocks
    • ForceField.links
    • ForceField.modifications
    • ForceField.citations
    • ForceField.renamed_residues
    • ForceField.name
    • ForceField.variables
    • ForceField.features
    • ForceField.has_feature()
    • ForceField.read_from()
    • ForceField.reference_graphs
  • find_force_fields()
  • get_native_force_field()
  • iter_force_field_files()
• vermouth.geometry module
  • angle()
  • dihedral()
  • dihedral_phase()
  • distance_matrix()
• vermouth.graph_utils module
  • MappingGraphMatcher
    • MappingGraphMatcher.semantic_feasibility()
  • add_element_attr()
  • categorical_cartesian_product()
  • categorical_maximum_common_subgraph()
  • categorical_modular_product()
  • collect_residues()
  • get_attrs()
  • make_residue_graph()
  • partition_graph()
  • rate_match()
• vermouth.ismags module
  • ISMAGS Algorithm
  • ISMAGS
    • ISMAGS.graph
    • ISMAGS.subgraph
    • ISMAGS.node_equality
    • ISMAGS.edge_equality
    • ISMAGS.analyze_symmetry()
    • ISMAGS.find_isomorphisms()
    • ISMAGS.is_isomorphic()
    • ISMAGS.isomorphisms_iter()
    • ISMAGS.largest_common_subgraph()
    • ISMAGS.subgraph_is_isomorphic()
    • ISMAGS.subgraph_isomorphisms_iter()
  • intersect()
  • make_partitions()
  • partition_to_color()
• vermouth.log_helpers module
  • BipolarFormatter
  • CountingHandler
    • CountingHandler.handle()
    • CountingHandler.number_of_counts_by()
  • Message
  • PassingLoggerAdapter
    • PassingLoggerAdapter.addHandler()
    • PassingLoggerAdapter.log()
    • PassingLoggerAdapter.manager
      • PassingLoggerAdapter.Logger.manager
    • PassingLoggerAdapter.process()
  • StyleAdapter
    • StyleAdapter.log()
  • TypeAdapter
    • TypeAdapter.process()
  • get_logger()
  • ignore_warnings_and_count()
• vermouth.map_input module
  • combine_mappings()
  • generate_all_self_mappings()
  • generate_self_mappings()
  • make_mapping_object()
  • read_backmapping_file()
  • read_mapping_directory()
  • read_mapping_file()
• vermouth.map_parser module
  • Mapping
    • Mapping.block_from
    • Mapping.block_to
    • Mapping.references
    • Mapping.ff_from
    • Mapping.ff_to
    • Mapping.names
    • Mapping.mapping
    • Mapping.map()
    • Mapping.reverse_mapping
  • MappingBuilder
    • MappingBuilder.mapping
    • MappingBuilder.blocks_from
    • MappingBuilder.blocks_to
    • MappingBuilder.ff_from
    • MappingBuilder.ff_to
    • MappingBuilder.names
    • MappingBuilder.references
    • MappingBuilder.add_block_from()
    • MappingBuilder.add_block_to()
    • MappingBuilder.add_edge_from()
    • MappingBuilder.add_edge_to()
    • MappingBuilder.add_mapping()
    • MappingBuilder.add_name()
    • MappingBuilder.add_node_from()
    • MappingBuilder.add_node_to()
    • MappingBuilder.add_reference()
    • MappingBuilder.from_ff()
    • MappingBuilder.get_mapping()
    • MappingBuilder.reset()
    • MappingBuilder.to_ff()
  • MappingDirector
    • MappingDirector.builder
    • MappingDirector.identifiers
    • MappingDirector.section
    • MappingDirector.from_ff
    • MappingDirector.to_ff
    • MappingDirector.macros
    • MappingDirector.COMMENT_CHAR
    • MappingDirector.METH_DICT
    • MappingDirector.NO_FETCH_BLOCK
    • MappingDirector.RESIDUE_ATOM_SEP
    • MappingDirector.RESNAME_NUM_SEP
    • MappingDirector.SECTION_ENDS
    • MappingDirector.finalize_section()
  • parse_mapping_file()
• vermouth.molecule module
  • Block
    • Block.name
    • Block.add_atom()
    • Block.atoms
    • Block.guess_angles()
    • Block.guess_dihedrals()
    • Block.has_dihedral_around()
    • Block.has_improper_around()
    • Block.node_dict_factory
    • Block.to_molecule()
  • Choice
    • Choice.match()
  • DeleteInteraction
    • DeleteInteraction.atom_attrs
    • DeleteInteraction.atoms
    • DeleteInteraction.meta
    • DeleteInteraction.parameters
  • Interaction
    • Interaction.atoms
    • Interaction.meta
    • Interaction.parameters
  • Link
    • Link.node_dict_factory
    • Link.same_non_edges()
  • LinkParameterEffector
    • LinkParameterEffector.__call__()
    • LinkParameterEffector._apply()
    • LinkParameterEffector.n_keys_asked
  • LinkPredicate
    • LinkPredicate.match()
  • Modification
  • Molecule
    • Molecule.meta
    • Molecule.nrexcl
    • Molecule.interactions
    • Molecule.citations
    • Molecule.add_interaction()
    • Molecule.add_node()
    • Molecule.add_or_replace_interaction()
    • Molecule.atoms
    • Molecule.copy()
    • Molecule.edges_between()
    • Molecule.find_atoms()
    • Molecule.force_field
    • Molecule.get_interaction()
    • Molecule.iter_residues()
    • Molecule.make_edges_from_interaction_type()
    • Molecule.make_edges_from_interactions()
    • Molecule.merge_molecule()
    • Molecule.node_dict_factory
    • Molecule.remove_interaction()
    • Molecule.remove_matching_interaction()
    • Molecule.remove_node()
    • Molecule.remove_nodes_from()
    • Molecule.same_edges()
    • Molecule.same_interactions()
    • Molecule.same_nodes()
    • Molecule.share_moltype_with()
    • Molecule.sort_interactions()
    • Molecule.sorted_nodes
    • Molecule.subgraph()
  • NotDefinedOrNot
    • NotDefinedOrNot.match()
  • ParamAngle
    • ParamAngle.n_keys_asked
  • ParamDihedral
    • ParamDihedral.n_keys_asked
  • ParamDihedralPhase
    • ParamDihedralPhase.n_keys_asked
  • ParamDistance
    • ParamDistance.n_keys_asked
  • Regex
    • Regex.match()
  • attributes_match()
  • interaction_match()
• vermouth.parser_utils module
  • LineParser
    • LineParser.COMMENT_CHAR
    • LineParser.dispatch()
    • LineParser.finalize()
    • LineParser.parse()
    • LineParser.parse_line()
  • SectionLineParser
    • SectionLineParser.section
    • SectionLineParser.macros
    • SectionLineParser.METH_DICT
    • SectionLineParser.dispatch()
    • SectionLineParser.finalize()
    • SectionLineParser.finalize_section()
    • SectionLineParser.is_section_header()
    • SectionLineParser.parse_header()
    • SectionLineParser.parse_section()
  • SectionParser
    • SectionParser.section_parser()
  • split_comments()
• vermouth.selectors module
  • filter_minimal()
  • is_protein()
  • proto_multi_templates()
  • proto_select_attribute_in()
  • select_all()
  • select_backbone()
  • selector_has_position()
• vermouth.system module
  • System
    • System.molecules
    • System.add_molecule()
    • System.copy()
    • System.force_field
    • System.num_particles
• vermouth.truncating_formatter module
  • FormatSpec
    • FormatSpec.align
    • FormatSpec.alt
    • FormatSpec.comma
    • FormatSpec.decimal
    • FormatSpec.fill
    • FormatSpec.precision
    • FormatSpec.sign
    • FormatSpec.type
    • FormatSpec.width
    • FormatSpec.zero_padding
  • TruncFormatter
    • TruncFormatter.format_field()
    • TruncFormatter.format_spec_re
• vermouth.utils module
  • are_all_equal()
  • are_different()
  • first_alpha()
  • format_atom_string()
  • maxes()

Module contents

VerMoUTH: The Very Modular Universal Transformation Helper

Provides functionality for creating MD topologies from coordinate files. Powers the CLI tool martinize2.