vermouth.processors.add_molecule_edges module

Processor adding edges between molecules.

class vermouth.processors.add_molecule_edges.AddMoleculeEdgesAtDistance(threshold, templates_from, templates_to, attribute='position', min_edges=0)[source]

Bases: Processor

Processor that adds edges within and between molecules.

The processor adds edges between atoms, within or between molecules, when the atoms are part of the selections provided for each end of the edges, and the atoms are closer than a given threshold.

Parameters:

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

  • templates_from (list[dict]) – List of node templates to select the atoms at one end of the edges.

  • templates_to (list[dict]) – List of node template to select the atoms at the other end of the edges.

  • attribute (str) – Name of the attribute under which are stores the coordinates.

See also

vermouth.molecule.attributes_match

run_system(system)[source]

Run the processor on the system.

class vermouth.processors.add_molecule_edges.MergeNucleicStrands(threshold=0.3, templates_donnors=({'atomname': <Choice at 7f3fb96bd810 value=['C2', 'N6']>, 'resname': <Choice at 7f3fb972c050 value=['DA', 'DA3', 'DA5']>}, {'atomname': <Choice at 7f3fb96a6650 value=['N1', 'N2']>, 'resname': <Choice at 7f3fb96bd950 value=['DG', 'DG3', 'DG5']>}, {'atomname': 'N4', 'resname': <Choice at 7f3fb96a6780 value=['DC', 'DC3', 'DC5']>}, {'atomname': 'N3', 'resname': <Choice at 7f3fb970d130 value=['DT', 'DT3', 'DT5']>}), templates_acceptors=({'atomname': 'N1', 'resname': <Choice at 7f3fb971c380 value=['DA', 'DA3', 'DA5']>}, {'atomname': 'O6', 'resname': <Choice at 7f3fb971c490 value=['DG', 'DG3', 'DG5']>}, {'atomname': <Choice at 7f3fb9720750 value=['N3', 'O2']>, 'resname': <Choice at 7f3fb9720650 value=['DC', 'DC3', 'DC5']>}, {'atomname': <Choice at 7f3fb9730140 value=['O2', 'O4']>, 'resname': <Choice at 7f3fb9730050 value=['DT', 'DT3', 'DT5']>}), attribute='position')[source]

Bases: AddMoleculeEdgesAtDistance

Add edges between complementary nucleic acid strands.

By default, the edges are added in place of the hydrogen bonds between complementary bases.

Parameters:

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

  • templates_donnors (list[dict]) – List of templates describing hydrogen donnors.

  • templates_acceptors (list[dict]) – List of templates describing hydrogen acceptors.

  • attribute (str) – Name of the attribute under which are store the node coordinates.