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 76ce5788bd90 value=['C2', 'N6']>, 'resname': <Choice at 76ce577767b0 value=['DA', 'DA3', 'DA5']>}, {'atomname': <Choice at 76ce575a1e00 value=['N1', 'N2']>, 'resname': <Choice at 76ce5788bed0 value=['DG', 'DG3', 'DG5']>}, {'atomname': 'N4', 'resname': <Choice at 76ce575a1f30 value=['DC', 'DC3', 'DC5']>}, {'atomname': 'N3', 'resname': <Choice at 76ce575d0950 value=['DT', 'DT3', 'DT5']>}), templates_acceptors=({'atomname': 'N1', 'resname': <Choice at 76ce5777aad0 value=['DA', 'DA3', 'DA5']>}, {'atomname': 'O6', 'resname': <Choice at 76ce5777abe0 value=['DG', 'DG3', 'DG5']>}, {'atomname': <Choice at 76ce575ec950 value=['N3', 'O2']>, 'resname': <Choice at 76ce575ec850 value=['DC', 'DC3', 'DC5']>}, {'atomname': <Choice at 76ce5775a3f0 value=['O2', 'O4']>, 'resname': <Choice at 76ce5775a300 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.