vermouth.processors.annotate_mut_mod module

Provides a processor that annotates a molecule with desired mutations and modifications.

class vermouth.processors.annotate_mut_mod.AnnotateMutMod(modifications=None, mutations=None)

Bases: Processor

Annotates residues to have the required ‘modification’ and ‘mutation’ attributes on all nodes.

modifications

Type:

list[tuple[dict, str]]

mutations

Type:

list[tuple[dict, str]]

See also

annotate_modifications()

run_molecule(molecule)

run_system(system)

vermouth.processors.annotate_mut_mod.annotate_modifications(molecule, modifications, mutations, resspec_counts)

Annotate nodes in molecule with the desired modifications and mutations

Parameters:

• molecule (networkx.Graph)

• modifications (list[tuple[dict, str]]) – The modifications to apply. The first element is a dictionary contain the attributes a residue has to fulfill. It can contain the elements ‘chain’, ‘resname’ and ‘resid’. The second element is the modification that should be applied.

• mutations (list[tuple[dict, str]]) – The mutations to apply. The first element is a dictionary contain the attributes a residue has to fulfill. It can contain the elements ‘chain’, ‘resname’ and ‘resid’. The second element is the mutation that should be applied.

• resspec_counts (list[dict]) – List modified in place containing information about whether a modification/mutation has been applied successfully. If the target is found, the dictionary has one entry, {‘success’: True}. If not, ‘success’ is False and there are additional items to indicate information about the failure.

Raises:

NameError – When a modification is not recognized.

vermouth.processors.annotate_mut_mod.parse_residue_spec(resspec)

Parse a residue specification: [<chain>-][<resname>][[#]<resid>] where resid is /[0-9]+/. If resname ends in a number and a resid is also specified, the # separator is required. Returns a dictionary with keys ‘chain’, ‘resname’, and ‘resid’ for the fields that are specified. Resid will be an int.

Parameters:

resspec (str)

Return type:

dict

vermouth.processors.annotate_mut_mod.residue_matches(resspec, residue_graph, res_idx)

Returns True iff resspec describes residue_graph.nodes[res_idx]. The ‘resname’s nter and cter match the residues with a degree of 1 and with the lowest and highest residue numbers respectively.

Parameters:

• resspec (dict) – Attributes that must be present in the residue node. ‘resname’ is treated specially as described above.

• residue_graph (networkx.Graph) – A graph with one node per residue.

• res_idx (collections.abc.Hashable) – A node index in residue_graph.

Returns:

Whether resspec describes the node res_idx in residue_graph.

Return type:

bool