vermouth.processors.repair_graph module

Provides a processor that repairs a graph based on a reference.

class vermouth.processors.repair_graph.RepairGraph(delete_unknown=False, include_graph=True)

Bases: vermouth.processors.processor.Processor

run_molecule(molecule)

run_system(system)

vermouth.processors.repair_graph.get_default(dictionary, attr, default)

Functions like dict.get(), except that when attr is in dictionary and dictionary[attr] is None, it will return default.

Parameters

• dictionary (dict) –

• attr (collections.abc.Hashable) –

• default –

Returns

The value of dictionary[attr] if attr is in dictionary and dictionary[attr] is not None. default otherwise.

Return type

object

vermouth.processors.repair_graph.make_reference(mol)

Takes an molecule graph (e.g. as read from a PDB file), and finds and returns the graph how it should look like, including all matching nodes between the input graph and the references. Requires residuenames to be correct.

Notes

The match between hydrogren atoms need not be perfect. See the documentation of isomorphism.

Parameters

mol (networkx.Graph) –

The graph read from e.g. a PDB file. Required node attributes:

resname

The residue name.

resid

The residue id.

chain

The chain identifier.

element

The element.

atomname

The atomname.

Returns

The constructed reference graph with the following node attributes:

resid

The residue id.

resname

The residue name.

chain

The chain identifier.

found

The residue subgraph from the PDB file.

reference

The residue subgraph used as reference.

match

A dictionary describing how the reference corresponds with the provided graph. Keys are node indices of the reference, values are node indices of the provided graph.

Return type

networkx.Graph

vermouth.processors.repair_graph.repair_graph(molecule, reference_graph, include_graph=True)

Repairs a molecule graph produced based on the information in reference_graph. Missing atoms will be added and atom- and residue- names will be canonicalized. Atoms not present in reference_graph will have the attribute PTM_atom set to True.

molecule is modified in place. Missing atoms (as per reference_graph) are added, atom and residue names are canonicalized, and PTM atoms are marked.

If include_graph is True, then the subgraph corresponding to each node is included in the node under the “graph” attribute.

Parameters

• molecule (molecule.Molecule) –

  The graph read from e.g. a PDB file. Required node attributes:

  resname

  The residue name.

  resid

  The residue id.

  element

  The element.

  atomname

  The atomname.

• reference_graph (networkx.Graph) –

  The reference graph as produced by make_reference. Required node attributes:

  resid

  The residue id.

  resname

  The residue name.

  found

  The residue subgraph from the PDB file.

  reference

  The residue subgraph used as reference.

  match

  A dictionary describing how the reference corresponds with the provided graph. Keys are node indices of the reference, values are node indices of the provided graph.

• include_graph (bool) – Include the subgraph in the nodes.

vermouth.processors.repair_graph.repair_residue(molecule, ref_residue, include_graph)

Rebuild missing atoms and canonicalize atomnames