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: vermouth.processors.processor.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=({'resname': <Choice at 7f67c7799750 value=['DA', 'DA3', 'DA5']>, 'atomname': <Choice at 7f67c7799790 value=['C2', 'N6']>}, {'resname': <Choice at 7f67c7799810 value=['DG', 'DG3', 'DG5']>, 'atomname': <Choice at 7f67c7799850 value=['N1', 'N2']>}, {'resname': <Choice at 7f67c7799890 value=['DC', 'DC3', 'DC5']>, 'atomname': 'N4'}, {'resname': <Choice at 7f67c77999d0 value=['DT', 'DT3', 'DT5']>, 'atomname': 'N3'}), templates_acceptors=({'resname': <Choice at 7f67c779e5d0 value=['DA', 'DA3', 'DA5']>, 'atomname': 'N1'}, {'resname': <Choice at 7f67c779e650 value=['DG', 'DG3', 'DG5']>, 'atomname': 'O6'}, {'resname': <Choice at 7f67c779e690 value=['DC', 'DC3', 'DC5']>, 'atomname': <Choice at 7f67c779e6d0 value=['N3', 'O2']>}, {'resname': <Choice at 7f67c779e710 value=['DT', 'DT3', 'DT5']>, 'atomname': <Choice at 7f67c779e750 value=['O2', 'O4']>}), attribute='position')[source]

Bases: vermouth.processors.add_molecule_edges.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.