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 7fcff0283e60 value=['C2', 'N6']>, 'resname': <Choice at 7fcff0283e00 value=['DA', 'DA3', 'DA5']>}, {'atomname': <Choice at 7fcff02ac4a0 value=['N1', 'N2']>, 'resname': <Choice at 7fcff0283e90 value=['DG', 'DG3', 'DG5']>}, {'atomname': 'N4', 'resname': <Choice at 7fcff02ac4d0 value=['DC', 'DC3', 'DC5']>}, {'atomname': 'N3', 'resname': <Choice at 7fcff02ac500 value=['DT', 'DT3', 'DT5']>}), templates_acceptors=({'atomname': 'N1', 'resname': <Choice at 7fcff02ac530 value=['DA', 'DA3', 'DA5']>}, {'atomname': 'O6', 'resname': <Choice at 7fcff02ac560 value=['DG', 'DG3', 'DG5']>}, {'atomname': <Choice at 7fcff02ac5c0 value=['N3', 'O2']>, 'resname': <Choice at 7fcff02ac590 value=['DC', 'DC3', 'DC5']>}, {'atomname': <Choice at 7fcff02ac620 value=['O2', 'O4']>, 'resname': <Choice at 7fcff02ac5f0 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.