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 7f114fae0410 value=['C2', 'N6']>, 'resname': <Choice at 7f114fc3b0e0 value=['DA', 'DA3', 'DA5']>}, {'atomname': <Choice at 7f114fbdfbb0 value=['N1', 'N2']>, 'resname': <Choice at 7f114fae0550 value=['DG', 'DG3', 'DG5']>}, {'atomname': 'N4', 'resname': <Choice at 7f114fbdfce0 value=['DC', 'DC3', 'DC5']>}, {'atomname': 'N3', 'resname': <Choice at 7f114fbffad0 value=['DT', 'DT3', 'DT5']>}), templates_acceptors=({'atomname': 'N1', 'resname': <Choice at 7f114fae8270 value=['DA', 'DA3', 'DA5']>}, {'atomname': 'O6', 'resname': <Choice at 7f114fae8380 value=['DG', 'DG3', 'DG5']>}, {'atomname': <Choice at 7f114fad5f50 value=['N3', 'O2']>, 'resname': <Choice at 7f114fad5e50 value=['DC', 'DC3', 'DC5']>}, {'atomname': <Choice at 7f114fc1f110 value=['O2', 'O4']>, 'resname': <Choice at 7f114fc1f020 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.