vermouth.processors.tune_cystein_bridges module

Provides processors that can add and remove cystein bridges.

class vermouth.processors.tune_cystein_bridges.AddCysteinBridgesThreshold(threshold, template=[{'atomname': 'SG', 'resname': 'CYS'}], attribute='position')[source]

Bases: AddMoleculeEdgesAtDistance

Add edges corresponding to cystein bridges on a distance criterion.

The edge for a cystein bridge is an edge between two atoms that match at least one template from a list of templates if the two ends of the edge are closer than a given distance.

Parameters:

  • threshold (float) – Distance in nanometers under which to consider an edge.

  • template (list[dict]) – List of node templates.

class vermouth.processors.tune_cystein_bridges.RemoveCysteinBridgeEdges(template=[{'atomname': 'SG', 'resname': 'CYS'}])[source]

Bases: Processor

Processor removing edges corresponding to cystein bridges.

The edge for a cystein bridge is an edge between two atoms that match at least one template from a list of templates.

Parameters:

template (list[dict]) – List of node templates.

run_molecule(molecule)[source]
vermouth.processors.tune_cystein_bridges.remove_cystein_bridge_edges(molecule, templates=[{'atomname': 'SG', 'resname': 'CYS'}])[source]

Remove all the edges that correspond to cystein bridges from a molecule.

Cystein bridge edges link an atom from a cystein side chain to the same atom on an other cystein. Selecting the correct atom is done with a list of template node dictionaries. A template node dictionary functions in the same way as node matching in links. An atom that can be involved in a cystein bridge must match at least one of the templates of the list. The default template list selects the ‘SG’ bead of the residue ‘CYS’: [{'resname': 'CYS', 'atomname': 'SG'}, ].

A template is a dictionary that defines the key:value pairs that must be matched in the atoms. Values can be instances of LinkPredicate.

Parameters:

  • molecule (networkx.Graph) – Molecule to modify in-place.

  • templates (list[dict]) – A list of templates; selected atom must match at least one.