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 74b46c4bcf50 value=['C2', 'N6']>, 'resname': <Choice at 74b46c310050 value=['DA', 'DA3', 'DA5']>}, {'atomname': <Choice at 74b46c4ce060 value=['N1', 'N2']>, 'resname': <Choice at 74b46c4bd090 value=['DG', 'DG3', 'DG5']>}, {'atomname': 'N4', 'resname': <Choice at 74b46c4ce190 value=['DC', 'DC3', 'DC5']>}, {'atomname': 'N3', 'resname': <Choice at 74b46c4e97f0 value=['DT', 'DT3', 'DT5']>}), templates_acceptors=({'atomname': 'N1', 'resname': <Choice at 74b46c483df0 value=['DA', 'DA3', 'DA5']>}, {'atomname': 'O6', 'resname': <Choice at 74b46c483f00 value=['DG', 'DG3', 'DG5']>}, {'atomname': <Choice at 74b46c304f50 value=['N3', 'O2']>, 'resname': <Choice at 74b46c304e50 value=['DC', 'DC3', 'DC5']>}, {'atomname': <Choice at 74b46c466b70 value=['O2', 'O4']>, 'resname': <Choice at 74b46c466a80 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.