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.

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 7f51c4250d70 value=['C2', 'N6']>, 'resname': <Choice at 7f51c4250d10 value=['DA', 'DA3', 'DA5']>}, {'atomname': <Choice at 7f51c4251340 value=['N1', 'N2']>, 'resname': <Choice at 7f51c4250da0 value=['DG', 'DG3', 'DG5']>}, {'atomname': 'N4', 'resname': <Choice at 7f51c4251370 value=['DC', 'DC3', 'DC5']>}, {'atomname': 'N3', 'resname': <Choice at 7f51c42513a0 value=['DT', 'DT3', 'DT5']>}), templates_acceptors=({'atomname': 'N1', 'resname': <Choice at 7f51c42513d0 value=['DA', 'DA3', 'DA5']>}, {'atomname': 'O6', 'resname': <Choice at 7f51c4251400 value=['DG', 'DG3', 'DG5']>}, {'atomname': <Choice at 7f51c4251460 value=['N3', 'O2']>, 'resname': <Choice at 7f51c4251430 value=['DC', 'DC3', 'DC5']>}, {'atomname': <Choice at 7f51c42514c0 value=['O2', 'O4']>, 'resname': <Choice at 7f51c4251490 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.