vermouth.processors package

Submodules

• vermouth.processors.add_molecule_edges module
  • AddMoleculeEdgesAtDistance
    • AddMoleculeEdgesAtDistance.run_system()
  • MergeNucleicStrands
• vermouth.processors.annotate_mut_mod module
  • AnnotateMutMod
    • AnnotateMutMod.modifications
    • AnnotateMutMod.mutations
    • AnnotateMutMod.run_molecule()
    • AnnotateMutMod.run_system()
  • annotate_modifications()
  • parse_residue_spec()
  • residue_matches()
• vermouth.processors.apply_posres module
  • ApplyPosres
    • ApplyPosres.run_molecule()
  • apply_posres()
• vermouth.processors.apply_rubber_band module
  • ApplyRubberBand
    • ApplyRubberBand.selector
    • ApplyRubberBand.lower_bound
    • ApplyRubberBand.upper_bound
    • ApplyRubberBand.decay_factor
    • ApplyRubberBand.decay_power
    • ApplyRubberBand.base_constant
    • ApplyRubberBand.minimum_force
    • ApplyRubberBand.bond_type
    • ApplyRubberBand.bond_type_variable
    • ApplyRubberBand.domain_criterion
    • ApplyRubberBand.res_min_dist
    • ApplyRubberBand.res_min_dist_variable
    • ApplyRubberBand.run_molecule()
  • 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
    • AttachMass.run_molecule()
  • attach_mass()
• vermouth.processors.average_beads module
  • DoAverageBead
    • DoAverageBead.run_molecule()
  • do_average_bead()
• vermouth.processors.canonicalize_modifications module
  • CanonicalizeModifications
    • CanonicalizeModifications.run_molecule()
  • allowed_ptms()
  • find_ptm_atoms()
  • fix_ptm()
  • identify_ptms()
  • ptm_node_matcher()
• vermouth.processors.do_links module
  • DoLinks
    • DoLinks.run_molecule()
  • match_link()
  • match_order()
• vermouth.processors.do_mapping module
  • DoMapping
    • DoMapping.mappings
    • DoMapping.to_ff
    • DoMapping.delete_unknown
    • DoMapping.attribute_keep
    • DoMapping.attribute_must
    • DoMapping.attribute_stash
    • DoMapping.run_molecule()
    • DoMapping.run_system()
  • 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
    • GROInput.run_system()
• vermouth.processors.locate_charge_dummies module
  • LocateChargeDummies
    • LocateChargeDummies.run_molecule()
  • colinear_pair()
  • fibonacci_sphere()
  • find_anchor()
  • locate_all_dummies()
  • locate_dummy()
• vermouth.processors.make_bonds module
  • MakeBonds
    • MakeBonds.allow_names
    • MakeBonds.allow_dist
    • MakeBonds.fudge
    • MakeBonds.run_system()
  • make_bonds()
• vermouth.processors.merge_all_molecules module
  • MergeAllMolecules
    • MergeAllMolecules.run_molecule()
    • MergeAllMolecules.run_system()
• vermouth.processors.merge_chains module
  • MergeChains
    • MergeChains.name
    • MergeChains.run_system()
  • merge_chains()
• vermouth.processors.name_moltype module
  • NameMolType
    • NameMolType.run_system()
• vermouth.processors.pdb_reader module
  • PDBInput
    • PDBInput.filename
    • PDBInput.exclude
    • PDBInput.ignh
    • PDBInput.modelidx
    • PDBInput.run_system()
• vermouth.processors.processor module
  • Processor
    • Processor.run_molecule()
    • Processor.run_system()
• vermouth.processors.quote module
  • Quoter
    • Quoter.run_system()
  • read_quote_file()
• vermouth.processors.rename_modified_residues module
  • RenameModifiedResidues
    • RenameModifiedResidues.run_molecule()
  • rename_modified_residues()
• vermouth.processors.repair_graph module
  • RepairGraph
    • RepairGraph.delete_unknown
    • RepairGraph.include_graph
    • RepairGraph.run_molecule()
    • RepairGraph.run_system()
  • get_default()
  • make_reference()
  • repair_graph()
  • repair_residue()
• vermouth.processors.set_molecule_meta module
  • SetMoleculeMeta
    • SetMoleculeMeta.run_molecule()
• vermouth.processors.sort_molecule_atoms module
  • SortMoleculeAtoms
    • SortMoleculeAtoms.sortby_attrs
    • SortMoleculeAtoms.target_attr
    • SortMoleculeAtoms.run_molecule()
• vermouth.processors.tune_cystein_bridges module
  • AddCysteinBridgesThreshold
  • RemoveCysteinBridgeEdges
    • RemoveCysteinBridgeEdges.run_molecule()
  • remove_cystein_bridge_edges()
• vermouth.processors.water_bias module
  • ComputeWaterBias
    • ComputeWaterBias.assign_residue_water_bias()
    • ComputeWaterBias.run_molecule()
    • ComputeWaterBias.run_system()

Module contents

Provides Processors, VerMoUTH’s work horses.