Index

_

__call__() (vermouth.molecule.LinkParameterEffector method)

_apply() (vermouth.molecule.LinkParameterEffector method)

A

active_molecule (vermouth.pdb.pdb.PDBParser attribute) add_angles() (in module vermouth.processors.rtp_polisher) add_atom() (vermouth.molecule.Block method) add_block_from() (vermouth.map_parser.MappingBuilder method) add_block_to() (vermouth.map_parser.MappingBuilder method) add_dihedrals_and_pairs() (in module vermouth.processors.rtp_polisher) add_edge_from() (vermouth.map_parser.MappingBuilder method) add_edge_to() (vermouth.map_parser.MappingBuilder method) add_edges_at_distance() (in module vermouth.edge_tuning) add_edges_threshold() (in module vermouth.edge_tuning) add_element_attr() (in module vermouth.graph_utils) add_inter_molecule_edges() (in module vermouth.edge_tuning) add_interaction() (vermouth.molecule.Molecule method) add_mapping() (vermouth.map_parser.MappingBuilder method) add_molecule() (vermouth.system.System method) add_name() (vermouth.map_parser.MappingBuilder method) add_node() (vermouth.molecule.Molecule method) add_node_from() (vermouth.map_parser.MappingBuilder method) add_node_to() (vermouth.map_parser.MappingBuilder method) add_or_replace_interaction() (vermouth.molecule.Molecule method) add_reference() (vermouth.map_parser.MappingBuilder method) add_virtual_sites() (vermouth.rcsu.go_vs_includes.VirtualSiteCreator method) AddCysteinBridgesThreshold (class in vermouth.processors.tune_cystein_bridges) addHandler() (vermouth.log_helpers.PassingLoggerAdapter method) AddMoleculeEdgesAtDistance (class in vermouth.processors.add_molecule_edges) align (vermouth.truncating_formatter.FormatSpec attribute) allow_dist (vermouth.processors.make_bonds.MakeBonds attribute) allow_names (vermouth.processors.make_bonds.MakeBonds attribute) allowed_ptms() (in module vermouth.processors.canonicalize_modifications) alt (vermouth.truncating_formatter.FormatSpec attribute) always_true() (in module vermouth.processors.apply_rubber_band) analyze_symmetry() (vermouth.ismags.ISMAGS method) angle() (in module vermouth.geometry) anisou() (vermouth.pdb.pdb.PDBParser static method)

annotate_disorder() (in module vermouth.processors.annotate_idrs) annotate_dssp() (in module vermouth.dssp.dssp) annotate_modifications() (in module vermouth.processors.annotate_mut_mod) annotate_residues_from_sequence() (in module vermouth.dssp.dssp) AnnotateDSSP (class in vermouth.dssp.dssp) AnnotateIDRs (class in vermouth.processors.annotate_idrs) AnnotateMartiniSecondaryStructures (class in vermouth.dssp.dssp) AnnotateMutMod (class in vermouth.processors.annotate_mut_mod) AnnotateResidues (class in vermouth.dssp.dssp) apply_block_mapping() (in module vermouth.processors.do_mapping) apply_mod_mapping() (in module vermouth.processors.do_mapping) apply_posres() (in module vermouth.processors.apply_posres) apply_rubber_band() (in module vermouth.processors.apply_rubber_band) ApplyPosres (class in vermouth.processors.apply_posres) ApplyRubberBand (class in vermouth.processors.apply_rubber_band) are_all_equal() (in module vermouth.utils) are_connected() (in module vermouth.processors.apply_rubber_band) are_different() (in module vermouth.utils) assign_residue_water_bias() (vermouth.processors.water_bias.ComputeWaterBias method) atom() (vermouth.pdb.pdb.PDBParser method) atom_attrs (vermouth.molecule.DeleteInteraction attribute) atom_idxs (vermouth.gmx.itp_read.ITPDirector attribute) atoms (vermouth.gmx.topology.NonbondParam attribute) (vermouth.molecule.Block property) (vermouth.molecule.DeleteInteraction attribute) (vermouth.molecule.Interaction attribute) (vermouth.molecule.Molecule property) Atomtype (class in vermouth.gmx.topology) attach_mass() (in module vermouth.processors.attach_mass) AttachMass (class in vermouth.processors.attach_mass) attribute_keep (vermouth.processors.do_mapping.DoMapping attribute) attribute_must (vermouth.processors.do_mapping.DoMapping attribute) attributes_match() (in module vermouth.molecule) attrs_from_node() (in module vermouth.processors.do_mapping) author() (vermouth.pdb.pdb.PDBParser static method)

B

base_constant (vermouth.processors.apply_rubber_band.ApplyRubberBand attribute) BibTexDirector (class in vermouth.citation_parser) BipolarFormatter (class in vermouth.log_helpers) Block (class in vermouth.molecule) block_from (vermouth.map_parser.Mapping attribute) block_to (vermouth.map_parser.Mapping attribute) blocks (vermouth.forcefield.ForceField attribute)

blocks_from (vermouth.map_parser.MappingBuilder attribute) blocks_to (vermouth.map_parser.MappingBuilder attribute) bond_type (vermouth.processors.apply_rubber_band.ApplyRubberBand attribute) bond_type_variable (vermouth.processors.apply_rubber_band.ApplyRubberBand attribute) build_connectivity_matrix() (in module vermouth.processors.apply_rubber_band) build_graph_mapping_collection() (in module vermouth.processors.do_mapping) build_pair_matrix() (in module vermouth.processors.apply_rubber_band) builder (vermouth.map_parser.MappingDirector attribute)

C

calculate_go_contacts() (in module vermouth.rcsu.contact_map) CanonicalizeModifications (class in vermouth.processors.canonicalize_modifications) casting() (in module vermouth.pdb.cif) categorical_cartesian_product() (in module vermouth.graph_utils) categorical_maximum_common_subgraph() (in module vermouth.graph_utils) categorical_modular_product() (in module vermouth.graph_utils) caveat() (vermouth.pdb.pdb.PDBParser static method) Choice (class in vermouth.molecule) cif_entry_reader() (in module vermouth.pdb.cif) CIFInput (class in vermouth.processors.cif_reader) CIFReader (class in vermouth.pdb.cif) cispep() (vermouth.pdb.pdb.PDBParser static method) citation_formatter() (in module vermouth.citation_parser) citations (vermouth.forcefield.ForceField attribute) (vermouth.molecule.Molecule attribute) close() (vermouth.file_writer.DeferredFileWriter method) colinear_pair() (in module vermouth.processors.locate_charge_dummies) collect_residues() (in module vermouth.graph_utils) combine_mappings() (in module vermouth.map_input)

comma (vermouth.truncating_formatter.FormatSpec attribute) COMMENT_CHAR (vermouth.ffinput.FFDirector attribute) (vermouth.gmx.itp_read.ITPDirector attribute) (vermouth.map_parser.MappingDirector attribute) (vermouth.parser_utils.LineParser attribute) compnd() (vermouth.pdb.pdb.PDBParser static method) compute_decay() (in module vermouth.processors.apply_rubber_band) compute_force_constants() (in module vermouth.processors.apply_rubber_band) compute_go_interaction() (vermouth.rcsu.go_structure_bias.ComputeStructuralGoBias method) ComputeStructuralGoBias (class in vermouth.rcsu.go_structure_bias) ComputeWaterBias (class in vermouth.processors.water_bias) conect() (vermouth.pdb.pdb.PDBParser method) contact_selector() (vermouth.rcsu.go_structure_bias.ComputeStructuralGoBias method) convert_dssp_annotation_to_martini() (in module vermouth.dssp.dssp) convert_dssp_to_martini() (in module vermouth.dssp.dssp) copy() (vermouth.molecule.Molecule method) (vermouth.system.System method) CountingHandler (class in vermouth.log_helpers) cover() (in module vermouth.processors.do_mapping) cryst1() (vermouth.pdb.pdb.PDBParser method)

D

dbref() (vermouth.pdb.pdb.PDBParser static method) dbref1() (vermouth.pdb.pdb.PDBParser static method) dbref2() (vermouth.pdb.pdb.PDBParser static method) decay_factor (vermouth.processors.apply_rubber_band.ApplyRubberBand attribute) decay_power (vermouth.processors.apply_rubber_band.ApplyRubberBand attribute) decimal (vermouth.truncating_formatter.FormatSpec attribute) deferred_open() (in module vermouth.file_writer) DeferredFileWriter (class in vermouth.file_writer) delete_unknown (vermouth.processors.do_mapping.DoMapping attribute) (vermouth.processors.repair_graph.RepairGraph attribute) DeleteInteraction (class in vermouth.molecule) dihedral() (in module vermouth.geometry) dihedral_phase() (in module vermouth.geometry)

dispatch() (vermouth.gmx.itp_read.ITPDirector method) (vermouth.parser_utils.LineParser method) (vermouth.parser_utils.SectionLineParser method) (vermouth.pdb.pdb.PDBParser method) distance_matrix() (in module vermouth.geometry) do_average_bead() (in module vermouth.processors.average_beads) do_conect() (vermouth.pdb.pdb.PDBParser method) do_mapping() (in module vermouth.processors.do_mapping) DoAverageBead (class in vermouth.processors.average_beads) DoLinks (class in vermouth.processors.do_links) domain_criterion (vermouth.processors.apply_rubber_band.ApplyRubberBand attribute) DoMapping (class in vermouth.processors.do_mapping) DSSPError

E

edge_equality (vermouth.ismags.ISMAGS attribute) edge_matcher() (in module vermouth.processors.do_mapping) edges_between() (vermouth.molecule.Molecule method) end() (vermouth.pdb.pdb.PDBParser method) endmdl() (vermouth.pdb.pdb.PDBParser method) entry() (in module vermouth.bin.martinize2)

epsilon (vermouth.gmx.topology.Atomtype attribute) (vermouth.gmx.topology.NonbondParam attribute) exclude (vermouth.processors.cif_reader.CIFInput attribute) (vermouth.processors.pdb_reader.PDBInput attribute) expdta() (vermouth.pdb.pdb.PDBParser static method) extract_fields() (vermouth.citation_parser.BibTexDirector static method)

F

features (vermouth.forcefield.ForceField property) ff_from (vermouth.map_parser.Mapping attribute) (vermouth.map_parser.MappingBuilder attribute) ff_to (vermouth.map_parser.Mapping attribute) (vermouth.map_parser.MappingBuilder attribute) FFDirector (class in vermouth.ffinput) fibonacci_sphere() (in module vermouth.processors.locate_charge_dummies) filename (vermouth.processors.cif_reader.CIFInput attribute) (vermouth.processors.pdb_reader.PDBInput attribute) fill (vermouth.truncating_formatter.FormatSpec attribute) filter_minimal() (in module vermouth.selectors) finalize() (vermouth.gmx.itp_read.ITPDirector method) (vermouth.parser_utils.LineParser method) (vermouth.parser_utils.SectionLineParser method) (vermouth.pdb.pdb.PDBParser method) finalize_section() (vermouth.ffinput.FFDirector method) (vermouth.gmx.itp_read.ITPDirector method) (vermouth.map_parser.MappingDirector method) (vermouth.parser_utils.SectionLineParser method)

find_anchor() (in module vermouth.processors.locate_charge_dummies) find_atoms() (vermouth.molecule.Molecule method) find_entries() (vermouth.citation_parser.BibTexDirector static method) find_force_fields() (in module vermouth.forcefield) find_isomorphisms() (vermouth.ismags.ISMAGS method) find_ptm_atoms() (in module vermouth.processors.canonicalize_modifications) first_alpha() (in module vermouth.utils) fix_ptm() (in module vermouth.processors.canonicalize_modifications) force_field (vermouth.molecule.Molecule property) (vermouth.system.System property) ForceField (class in vermouth.forcefield) format_atom_string() (in module vermouth.utils) format_field() (vermouth.truncating_formatter.TruncFormatter method) format_spec_re (vermouth.truncating_formatter.TruncFormatter attribute) FormatSpec (class in vermouth.truncating_formatter) formul() (vermouth.pdb.pdb.PDBParser static method) from_ff (vermouth.map_parser.MappingDirector attribute) from_ff() (vermouth.map_parser.MappingBuilder method) fudge (vermouth.processors.make_bonds.MakeBonds attribute)

G

generate_all_self_mappings() (in module vermouth.map_input) generate_self_mappings() (in module vermouth.map_input) GenerateContactMap (class in vermouth.rcsu.contact_map) get_attrs() (in module vermouth.graph_utils) get_context() (vermouth.ffinput.FFDirector method) get_default() (in module vermouth.processors.repair_graph) get_go_type_from_attributes() (in module vermouth.rcsu.go_utils) get_interaction() (vermouth.molecule.Molecule method) get_logger() (in module vermouth.log_helpers)

get_mapping() (vermouth.map_parser.MappingBuilder method) get_mod_mappings() (in module vermouth.processors.do_mapping) get_native_force_field() (in module vermouth.forcefield) get_not_none() (in module vermouth.pdb.pdb) gmx_system_header() (in module vermouth.dssp.dssp) GoProcessorPipeline (class in vermouth.rcsu.go_pipeline) graph (vermouth.ismags.ISMAGS attribute) GROInput (class in vermouth.processors.gro_reader) guess_angles() (vermouth.molecule.Block method) guess_dihedrals() (vermouth.molecule.Block method)

H

handle() (vermouth.log_helpers.CountingHandler method) has_category() (in module vermouth.selectors) has_context() (vermouth.ffinput.FFDirector method) has_dihedral_around() (vermouth.molecule.Block method) has_feature() (vermouth.forcefield.ForceField method) has_improper_around() (vermouth.molecule.Block method)

header() (vermouth.pdb.pdb.PDBParser static method) helix() (vermouth.pdb.pdb.PDBParser static method) het() (vermouth.pdb.pdb.PDBParser static method) hetatm() (vermouth.pdb.pdb.PDBParser method) hetnam() (vermouth.pdb.pdb.PDBParser static method) hetsyn() (vermouth.pdb.pdb.PDBParser static method)

I

identifiers (vermouth.map_parser.MappingDirector attribute) identify_ptms() (in module vermouth.processors.canonicalize_modifications) IDRCrossDomainInteractionRemoval (class in vermouth.processors.idr_cross_domain_interaction_removal) ignh (vermouth.processors.cif_reader.CIFInput attribute) (vermouth.processors.pdb_reader.PDBInput attribute) ignore_warnings_and_count() (in module vermouth.log_helpers) include_graph (vermouth.processors.repair_graph.RepairGraph attribute) Interaction (class in vermouth.molecule) interaction_match() (in module vermouth.molecule) interactions (vermouth.molecule.Molecule attribute)

interactions_natoms (vermouth.ffinput.FFDirector attribute) intersect() (in module vermouth.ismags) is_isomorphic() (vermouth.ismags.ISMAGS method) is_pragma() (vermouth.gmx.itp_read.ITPDirector static method) is_protein() (in module vermouth.selectors) is_section_header() (vermouth.parser_utils.SectionLineParser static method) ISMAGS (class in vermouth.ismags) isomorphisms_iter() (vermouth.ismags.ISMAGS method) iter_force_field_files() (in module vermouth.forcefield) iter_residues() (vermouth.molecule.Molecule method) ITPDirector (class in vermouth.gmx.itp_read)

J

jrnl() (vermouth.pdb.pdb.PDBParser static method)

K

keywds() (vermouth.pdb.pdb.PDBParser static method)

L

largest_common_subgraph() (vermouth.ismags.ISMAGS method) LineParser (class in vermouth.parser_utils) Link (class in vermouth.molecule) link() (vermouth.pdb.pdb.PDBParser static method) LinkParameterEffector (class in vermouth.molecule) LinkPredicate (class in vermouth.molecule)

links (vermouth.forcefield.ForceField attribute) locate_all_dummies() (in module vermouth.processors.locate_charge_dummies) locate_dummy() (in module vermouth.processors.locate_charge_dummies) LocateChargeDummies (class in vermouth.processors.locate_charge_dummies) log() (vermouth.log_helpers.PassingLoggerAdapter method) (vermouth.log_helpers.StyleAdapter method) lower_bound (vermouth.processors.apply_rubber_band.ApplyRubberBand attribute)

M

macros (vermouth.map_parser.MappingDirector attribute) (vermouth.parser_utils.SectionLineParser attribute) make_bonds() (in module vermouth.processors.make_bonds) make_edges_from_interaction_type() (vermouth.molecule.Molecule method) make_edges_from_interactions() (vermouth.molecule.Molecule method) make_mapping_object() (in module vermouth.map_input) make_partitions() (in module vermouth.ismags) make_reference() (in module vermouth.processors.repair_graph) make_residue_graph() (in module vermouth.graph_utils) make_same_region_criterion() (in module vermouth.processors.apply_rubber_band) MakeBonds (class in vermouth.processors.make_bonds) manager (logging.PassingLoggerAdapter.Logger attribute) (vermouth.log_helpers.PassingLoggerAdapter property) map() (vermouth.map_parser.Mapping method) Mapping (class in vermouth.map_parser) mapping (vermouth.map_parser.Mapping attribute) (vermouth.map_parser.MappingBuilder attribute) MappingBuilder (class in vermouth.map_parser) MappingDirector (class in vermouth.map_parser) MappingGraphMatcher (class in vermouth.graph_utils) mappings (vermouth.processors.do_mapping.DoMapping attribute) martinize() (in module vermouth.bin.martinize2) master() (vermouth.pdb.pdb.PDBParser static method) match() (vermouth.molecule.Choice method) (vermouth.molecule.LinkPredicate method) (vermouth.molecule.NotDefinedOrNot method) (vermouth.molecule.Regex method) match_link() (in module vermouth.processors.do_links) match_order() (in module vermouth.processors.do_links) maxes() (in module vermouth.utils) maxwarn() (in module vermouth.bin.martinize2) mdltyp() (vermouth.pdb.pdb.PDBParser static method) merge_chains() (in module vermouth.processors.merge_chains) merge_molecule() (vermouth.molecule.Molecule method) MergeAllMolecules (class in vermouth.processors.merge_all_molecules) MergeChains (class in vermouth.processors.merge_chains) MergeNucleicStrands (class in vermouth.processors.add_molecule_edges) Message (class in vermouth.log_helpers) meta (vermouth.gmx.topology.Atomtype attribute) (vermouth.gmx.topology.NonbondParam attribute) (vermouth.molecule.DeleteInteraction attribute) (vermouth.molecule.Interaction attribute) (vermouth.molecule.Molecule attribute) METH_DICT (vermouth.ffinput.FFDirector attribute) (vermouth.gmx.itp_read.ITPDirector attribute) (vermouth.map_parser.MappingDirector attribute) (vermouth.parser_utils.SectionLineParser attribute) minimum_force (vermouth.processors.apply_rubber_band.ApplyRubberBand attribute) model() (vermouth.pdb.pdb.PDBParser method) modelidx (vermouth.pdb.pdb.PDBParser attribute) (vermouth.processors.cif_reader.CIFInput attribute) (vermouth.processors.pdb_reader.PDBInput attribute) Modification (class in vermouth.molecule) modification_matches() (in module vermouth.processors.do_mapping) modifications (vermouth.forcefield.ForceField attribute) (vermouth.processors.annotate_mut_mod.AnnotateMutMod attribute) modres() (vermouth.pdb.pdb.PDBParser static method) module vermouth vermouth.bin vermouth.bin.martinize2 vermouth.citation_parser vermouth.data vermouth.data.data vermouth.dssp vermouth.dssp.dssp vermouth.edge_tuning vermouth.ffinput vermouth.file_writer vermouth.forcefield vermouth.geometry vermouth.gmx vermouth.gmx.gro vermouth.gmx.itp vermouth.gmx.itp_read vermouth.gmx.rtp vermouth.gmx.topology vermouth.graph_utils vermouth.ismags vermouth.log_helpers vermouth.map_input vermouth.map_parser vermouth.molecule vermouth.parser_utils vermouth.pdb vermouth.pdb.cif vermouth.pdb.pdb vermouth.processors vermouth.processors.add_molecule_edges vermouth.processors.annotate_idrs vermouth.processors.annotate_mut_mod vermouth.processors.apply_posres vermouth.processors.apply_rubber_band vermouth.processors.attach_mass vermouth.processors.average_beads vermouth.processors.canonicalize_modifications vermouth.processors.cif_reader vermouth.processors.do_links vermouth.processors.do_mapping vermouth.processors.gro_reader vermouth.processors.idr_cross_domain_interaction_removal vermouth.processors.locate_charge_dummies vermouth.processors.make_bonds vermouth.processors.merge_all_molecules vermouth.processors.merge_chains vermouth.processors.name_moltype vermouth.processors.pdb_reader vermouth.processors.processor vermouth.processors.quote vermouth.processors.rename_modified_residues vermouth.processors.repair_graph vermouth.processors.rtp_polisher vermouth.processors.set_molecule_meta vermouth.processors.sort_molecule_atoms vermouth.processors.stash_attributes vermouth.processors.tune_cystein_bridges vermouth.processors.water_bias vermouth.rcsu vermouth.rcsu.contact_map vermouth.rcsu.go_pipeline vermouth.rcsu.go_structure_bias vermouth.rcsu.go_utils vermouth.rcsu.go_vs_includes vermouth.selectors vermouth.system vermouth.truncating_formatter vermouth.utils

Molecule (class in vermouth.molecule) molecule (vermouth.gmx.topology.Atomtype attribute) molecules (vermouth.pdb.pdb.PDBParser attribute) (vermouth.system.System attribute) mtrix1() (vermouth.pdb.pdb.PDBParser static method) mtrix2() (vermouth.pdb.pdb.PDBParser static method) mtrix3() (vermouth.pdb.pdb.PDBParser static method) mutations (vermouth.processors.annotate_mut_mod.AnnotateMutMod attribute)

N

n_keys_asked (vermouth.molecule.LinkParameterEffector attribute) (vermouth.molecule.ParamAngle attribute) (vermouth.molecule.ParamDihedral attribute) (vermouth.molecule.ParamDihedralPhase attribute) (vermouth.molecule.ParamDistance attribute) name (vermouth.dssp.dssp.AnnotateDSSP attribute) (vermouth.dssp.dssp.AnnotateMartiniSecondaryStructures attribute) (vermouth.dssp.dssp.AnnotateResidues attribute) (vermouth.forcefield.ForceField attribute) (vermouth.molecule.Block attribute) (vermouth.processors.merge_chains.MergeChains attribute) NameMolType (class in vermouth.processors.name_moltype) names (vermouth.map_parser.Mapping attribute) (vermouth.map_parser.MappingBuilder attribute)

NO_FETCH_BLOCK (vermouth.map_parser.MappingDirector attribute) node (vermouth.gmx.topology.Atomtype attribute) node_dict_factory (vermouth.molecule.Block attribute) (vermouth.molecule.Link attribute) (vermouth.molecule.Molecule attribute) node_equality (vermouth.ismags.ISMAGS attribute) node_matcher() (in module vermouth.processors.do_mapping) node_should_exist() (in module vermouth.processors.do_mapping) NonbondParam (class in vermouth.gmx.topology) NotDefinedOrNot (class in vermouth.molecule) nrexcl (vermouth.molecule.Molecule attribute) num_particles (vermouth.system.System property) number_of_counts_by() (vermouth.log_helpers.CountingHandler method) nummdl() (vermouth.pdb.pdb.PDBParser static method)

O

obslte() (vermouth.pdb.pdb.PDBParser static method) open() (vermouth.file_writer.DeferredFileWriter method)

origx1() (vermouth.pdb.pdb.PDBParser static method) origx2() (vermouth.pdb.pdb.PDBParser static method) origx3() (vermouth.pdb.pdb.PDBParser static method)

P

pairs_under_threshold() (in module vermouth.edge_tuning) ParamAngle (class in vermouth.molecule) ParamDihedral (class in vermouth.molecule) ParamDihedralPhase (class in vermouth.molecule) ParamDistance (class in vermouth.molecule) parameters (vermouth.molecule.DeleteInteraction attribute) (vermouth.molecule.Interaction attribute) parse() (vermouth.citation_parser.BibTexDirector method) (vermouth.parser_utils.LineParser method) (vermouth.pdb.pdb.PDBParser method) parse_entry() (vermouth.citation_parser.BibTexDirector method) parse_header() (vermouth.ffinput.FFDirector method) (vermouth.gmx.itp_read.ITPDirector method) (vermouth.parser_utils.SectionLineParser method) parse_line() (vermouth.parser_utils.LineParser method) parse_mapping_file() (in module vermouth.map_parser) parse_pragma() (vermouth.gmx.itp_read.ITPDirector method) parse_residue_spec() (in module vermouth.processors.annotate_mut_mod) parse_residues() (in module vermouth.processors.annotate_idrs) parse_section() (vermouth.parser_utils.SectionLineParser method)

partition_graph() (in module vermouth.graph_utils) partition_to_color() (in module vermouth.ismags) PassingLoggerAdapter (class in vermouth.log_helpers) pdb_to_universal() (in module vermouth.bin.martinize2) PDBInput (class in vermouth.processors.pdb_reader) PDBParser (class in vermouth.pdb.pdb) pop_entry_type() (vermouth.citation_parser.BibTexDirector method) pop_key() (vermouth.citation_parser.BibTexDirector static method) precision (vermouth.truncating_formatter.FormatSpec attribute) prepare_file() (vermouth.citation_parser.BibTexDirector static method) prepare_run() (vermouth.rcsu.go_pipeline.GoProcessorPipeline method) process() (vermouth.log_helpers.PassingLoggerAdapter method) (vermouth.log_helpers.TypeAdapter method) Processor (class in vermouth.processors.processor) proto_multi_templates() (in module vermouth.selectors) proto_select_attribute_in() (in module vermouth.selectors) prune_edges_between_selections() (in module vermouth.edge_tuning) prune_edges_with_selectors() (in module vermouth.edge_tuning) ptm_node_matcher() (in module vermouth.processors.canonicalize_modifications) ptm_resname_match() (in module vermouth.processors.do_mapping)

Q

Quoter (class in vermouth.processors.quote)

R

rate_match() (in module vermouth.graph_utils) read_backmapping_file() (in module vermouth.map_input) read_bib() (in module vermouth.citation_parser) read_cif_file() (in module vermouth.pdb.cif) read_dssp2() (in module vermouth.dssp.dssp) read_ff() (in module vermouth.ffinput) read_from() (vermouth.forcefield.ForceField method) read_go_map() (in module vermouth.rcsu.contact_map) read_gro() (in module vermouth.gmx.gro) read_itp() (in module vermouth.gmx.itp_read) read_mapping_directory() (in module vermouth.map_input) read_mapping_file() (in module vermouth.map_input) read_pdb() (in module vermouth.pdb.pdb) read_rtp() (in module vermouth.gmx.rtp) read_system() (in module vermouth.bin.martinize2) reader() (vermouth.pdb.cif.CIFReader method) reference_graphs (vermouth.forcefield.ForceField property) references (vermouth.map_parser.Mapping attribute) (vermouth.map_parser.MappingBuilder attribute) Regex (class in vermouth.molecule) remark() (vermouth.pdb.pdb.PDBParser static method) remove_cross_elastic() (vermouth.processors.idr_cross_domain_interaction_removal.IDRCrossDomainInteractionRemoval method) remove_cross_nb_interactions() (vermouth.processors.idr_cross_domain_interaction_removal.IDRCrossDomainInteractionRemoval method) remove_cystein_bridge_edges() (in module vermouth.processors.tune_cystein_bridges) remove_interaction() (vermouth.molecule.Molecule method) remove_matching_interaction() (vermouth.molecule.Molecule method) remove_node() (vermouth.molecule.Molecule method) remove_nodes_from() (vermouth.molecule.Molecule method) RemoveCysteinBridgeEdges (class in vermouth.processors.tune_cystein_bridges) rename_modified_residues() (in module vermouth.processors.rename_modified_residues) renamed_residues (vermouth.forcefield.ForceField attribute) RenameModifiedResidues (class in vermouth.processors.rename_modified_residues) repair_graph() (in module vermouth.processors.repair_graph) repair_residue() (in module vermouth.processors.repair_graph) RepairGraph (class in vermouth.processors.repair_graph) res_min_dist (vermouth.processors.apply_rubber_band.ApplyRubberBand attribute) res_min_dist_variable (vermouth.processors.apply_rubber_band.ApplyRubberBand attribute) reset() (vermouth.map_parser.MappingBuilder method) RESIDUE_ATOM_SEP (vermouth.map_parser.MappingDirector attribute) residue_matches() (in module vermouth.processors.annotate_mut_mod) RESNAME_NUM_SEP (vermouth.map_parser.MappingDirector attribute) revdat() (vermouth.pdb.pdb.PDBParser static method) reverse_mapping (vermouth.map_parser.Mapping property) RTPPolisher (class in vermouth.processors.rtp_polisher) run_dssp() (in module vermouth.dssp.dssp) run_mdtraj() (in module vermouth.dssp.dssp) run_molecule() (vermouth.dssp.dssp.AnnotateDSSP method) (vermouth.dssp.dssp.AnnotateMartiniSecondaryStructures static method) (vermouth.dssp.dssp.AnnotateResidues method) (vermouth.processors.annotate_idrs.AnnotateIDRs method) (vermouth.processors.annotate_mut_mod.AnnotateMutMod method) (vermouth.processors.apply_posres.ApplyPosres method) (vermouth.processors.apply_rubber_band.ApplyRubberBand method) (vermouth.processors.attach_mass.AttachMass method) (vermouth.processors.average_beads.DoAverageBead method) (vermouth.processors.canonicalize_modifications.CanonicalizeModifications method) (vermouth.processors.do_links.DoLinks method) (vermouth.processors.do_mapping.DoMapping method) (vermouth.processors.locate_charge_dummies.LocateChargeDummies method) (vermouth.processors.merge_all_molecules.MergeAllMolecules static method) (vermouth.processors.processor.Processor method) (vermouth.processors.rename_modified_residues.RenameModifiedResidues method) (vermouth.processors.repair_graph.RepairGraph method) (vermouth.processors.rtp_polisher.RTPPolisher method) (vermouth.processors.set_molecule_meta.SetMoleculeMeta method) (vermouth.processors.sort_molecule_atoms.SortMoleculeAtoms method) (vermouth.processors.stash_attributes.StashAttributes method) (vermouth.processors.tune_cystein_bridges.RemoveCysteinBridgeEdges method) (vermouth.processors.water_bias.ComputeWaterBias method) (vermouth.rcsu.contact_map.GenerateContactMap method) (vermouth.rcsu.go_structure_bias.ComputeStructuralGoBias method) (vermouth.rcsu.go_vs_includes.VirtualSiteCreator method)

run_system() (vermouth.dssp.dssp.AnnotateMartiniSecondaryStructures method) (vermouth.dssp.dssp.AnnotateResidues method) (vermouth.processors.add_molecule_edges.AddMoleculeEdgesAtDistance method) (vermouth.processors.annotate_idrs.AnnotateIDRs method) (vermouth.processors.annotate_mut_mod.AnnotateMutMod method) (vermouth.processors.cif_reader.CIFInput method) (vermouth.processors.do_mapping.DoMapping method) (vermouth.processors.gro_reader.GROInput method) (vermouth.processors.idr_cross_domain_interaction_removal.IDRCrossDomainInteractionRemoval method) (vermouth.processors.make_bonds.MakeBonds method) (vermouth.processors.merge_all_molecules.MergeAllMolecules method) (vermouth.processors.merge_chains.MergeChains method) (vermouth.processors.name_moltype.NameMolType method) (vermouth.processors.pdb_reader.PDBInput method) (vermouth.processors.processor.Processor method) (vermouth.processors.quote.Quoter method) (vermouth.processors.repair_graph.RepairGraph method) (vermouth.processors.stash_attributes.StashAttributes method) (vermouth.processors.water_bias.ComputeWaterBias method) (vermouth.rcsu.contact_map.GenerateContactMap method) (vermouth.rcsu.go_pipeline.GoProcessorPipeline method) (vermouth.rcsu.go_structure_bias.ComputeStructuralGoBias method) (vermouth.rcsu.go_vs_includes.VirtualSiteCreator method)

S

same_chain() (in module vermouth.processors.apply_rubber_band) same_edges() (vermouth.molecule.Molecule method) same_interactions() (vermouth.molecule.Molecule method) same_nodes() (vermouth.molecule.Molecule method) same_non_edges() (vermouth.molecule.Link method) scale1() (vermouth.pdb.pdb.PDBParser static method) scale2() (vermouth.pdb.pdb.PDBParser static method) scale3() (vermouth.pdb.pdb.PDBParser static method) section (vermouth.map_parser.MappingDirector attribute) (vermouth.parser_utils.SectionLineParser attribute) SECTION_ENDS (vermouth.map_parser.MappingDirector attribute) section_parser() (vermouth.parser_utils.SectionParser static method) SectionLineParser (class in vermouth.parser_utils) SectionParser (class in vermouth.parser_utils) select_all() (in module vermouth.selectors) select_backbone() (in module vermouth.selectors) select_nodes_multi() (in module vermouth.edge_tuning) selector (vermouth.processors.apply_rubber_band.ApplyRubberBand attribute) selector_has_position() (in module vermouth.selectors) self_distance_matrix() (in module vermouth.processors.apply_rubber_band) semantic_feasibility() (vermouth.graph_utils.MappingGraphMatcher method) seqadv() (vermouth.pdb.pdb.PDBParser static method) seqres() (vermouth.pdb.pdb.PDBParser static method) sequence_from_residues() (in module vermouth.dssp.dssp) SetMoleculeMeta (class in vermouth.processors.set_molecule_meta)

share_moltype_with() (vermouth.molecule.Molecule method) sheet() (vermouth.pdb.pdb.PDBParser static method) sigma (vermouth.gmx.topology.Atomtype attribute) (vermouth.gmx.topology.NonbondParam attribute) sigma_epsilon_to_C6_C12() (in module vermouth.gmx.topology) sign (vermouth.truncating_formatter.FormatSpec attribute) Singleton (class in vermouth.file_writer) site() (vermouth.pdb.pdb.PDBParser static method) sort_interactions() (vermouth.molecule.Molecule static method) sortby_attrs (vermouth.processors.sort_molecule_atoms.SortMoleculeAtoms attribute) sorted_nodes (vermouth.molecule.Molecule property) SortMoleculeAtoms (class in vermouth.processors.sort_molecule_atoms) source() (vermouth.pdb.pdb.PDBParser static method) split_comments() (in module vermouth.parser_utils) splt() (vermouth.pdb.pdb.PDBParser static method) sprsde() (vermouth.pdb.pdb.PDBParser static method) ssbond() (vermouth.pdb.pdb.PDBParser static method) stash_attributes() (in module vermouth.processors.stash_attributes) StashAttributes (class in vermouth.processors.stash_attributes) StyleAdapter (class in vermouth.log_helpers) subgraph (vermouth.ismags.ISMAGS attribute) subgraph() (vermouth.molecule.Molecule method) subgraph_is_isomorphic() (vermouth.ismags.ISMAGS method) subgraph_isomorphisms_iter() (vermouth.ismags.ISMAGS method) System (class in vermouth.system)

T

target_attr (vermouth.processors.sort_molecule_atoms.SortMoleculeAtoms attribute) ter() (vermouth.pdb.pdb.PDBParser method) title() (vermouth.pdb.pdb.PDBParser static method) to_ff (vermouth.map_parser.MappingDirector attribute) (vermouth.processors.do_mapping.DoMapping attribute)

to_ff() (vermouth.map_parser.MappingBuilder method) to_molecule() (vermouth.molecule.Block method) TruncFormatter (class in vermouth.truncating_formatter) type (vermouth.truncating_formatter.FormatSpec attribute) TypeAdapter (class in vermouth.log_helpers)

U

upper_bound (vermouth.processors.apply_rubber_band.ApplyRubberBand attribute)

V

variables (vermouth.forcefield.ForceField attribute) vermouth module vermouth.bin module vermouth.bin.martinize2 module vermouth.citation_parser module vermouth.data module vermouth.data.data module vermouth.dssp module vermouth.dssp.dssp module vermouth.edge_tuning module vermouth.ffinput module vermouth.file_writer module vermouth.forcefield module vermouth.geometry module vermouth.gmx module vermouth.gmx.gro module vermouth.gmx.itp module vermouth.gmx.itp_read module vermouth.gmx.rtp module vermouth.gmx.topology module vermouth.graph_utils module vermouth.ismags module vermouth.log_helpers module vermouth.map_input module vermouth.map_parser module vermouth.molecule module vermouth.parser_utils module vermouth.pdb module vermouth.pdb.cif module vermouth.pdb.pdb module vermouth.processors module vermouth.processors.add_molecule_edges module vermouth.processors.annotate_idrs module vermouth.processors.annotate_mut_mod module vermouth.processors.apply_posres module vermouth.processors.apply_rubber_band module

vermouth.processors.attach_mass module vermouth.processors.average_beads module vermouth.processors.canonicalize_modifications module vermouth.processors.cif_reader module vermouth.processors.do_links module vermouth.processors.do_mapping module vermouth.processors.gro_reader module vermouth.processors.idr_cross_domain_interaction_removal module vermouth.processors.locate_charge_dummies module vermouth.processors.make_bonds module vermouth.processors.merge_all_molecules module vermouth.processors.merge_chains module vermouth.processors.name_moltype module vermouth.processors.pdb_reader module vermouth.processors.processor module vermouth.processors.quote module vermouth.processors.rename_modified_residues module vermouth.processors.repair_graph module vermouth.processors.rtp_polisher module vermouth.processors.set_molecule_meta module vermouth.processors.sort_molecule_atoms module vermouth.processors.stash_attributes module vermouth.processors.tune_cystein_bridges module vermouth.processors.water_bias module vermouth.rcsu module vermouth.rcsu.contact_map module vermouth.rcsu.go_pipeline module vermouth.rcsu.go_structure_bias module vermouth.rcsu.go_utils module vermouth.rcsu.go_vs_includes module vermouth.selectors module vermouth.system module vermouth.truncating_formatter module vermouth.utils module VirtualSiteCreator (class in vermouth.rcsu.go_vs_includes)

W

width (vermouth.truncating_formatter.FormatSpec attribute) write() (vermouth.file_writer.DeferredFileWriter method) write_atomtypes() (in module vermouth.gmx.topology) write_gmx_topology() (in module vermouth.gmx.topology)

write_gro() (in module vermouth.gmx.gro) write_molecule_itp() (in module vermouth.gmx.itp) write_nonbond_params() (in module vermouth.gmx.topology) write_pdb() (in module vermouth.pdb.pdb) write_pdb_string() (in module vermouth.pdb.pdb)

Z

zero_padding (vermouth.truncating_formatter.FormatSpec attribute)