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 7f20cf639e50 value=['DA', 'DA3', 'DA5']>, 'atomname': <Choice at 7f20cf639e90 value=['C2', 'N6']>}, {'resname': <Choice at 7f20cf639f10 value=['DG', 'DG3', 'DG5']>, 'atomname': <Choice at 7f20cf639f50 value=['N1', 'N2']>}, {'resname': <Choice at 7f20cf639f90 value=['DC', 'DC3', 'DC5']>, 'atomname': 'N4'}, {'resname': <Choice at 7f20cf63ecd0 value=['DT', 'DT3', 'DT5']>, 'atomname': 'N3'}), templates_acceptors=({'resname': <Choice at 7f20cf63e110 value=['DA', 'DA3', 'DA5']>, 'atomname': 'N1'}, {'resname': <Choice at 7f20cf63ed50 value=['DG', 'DG3', 'DG5']>, 'atomname': 'O6'}, {'resname': <Choice at 7f20cf63ed90 value=['DC', 'DC3', 'DC5']>, 'atomname': <Choice at 7f20cf63edd0 value=['N3', 'O2']>}, {'resname': <Choice at 7f20cf63ee10 value=['DT', 'DT3', 'DT5']>, 'atomname': <Choice at 7f20cf63ee50 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.