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 75f42a1cbed0 value=['C2', 'N6']>, 'resname': <Choice at 75f42a0b6510 value=['DA', 'DA3', 'DA5']>}, {'atomname': <Choice at 75f42a0e5810 value=['N1', 'N2']>, 'resname': <Choice at 75f42a130050 value=['DG', 'DG3', 'DG5']>}, {'atomname': 'N4', 'resname': <Choice at 75f42a0e5940 value=['DC', 'DC3', 'DC5']>}, {'atomname': 'N3', 'resname': <Choice at 75f42a108b90 value=['DT', 'DT3', 'DT5']>}), templates_acceptors=({'atomname': 'N1', 'resname': <Choice at 75f42a0d28b0 value=['DA', 'DA3', 'DA5']>}, {'atomname': 'O6', 'resname': <Choice at 75f42a0d29c0 value=['DG', 'DG3', 'DG5']>}, {'atomname': <Choice at 75f42a124950 value=['N3', 'O2']>, 'resname': <Choice at 75f42a124850 value=['DC', 'DC3', 'DC5']>}, {'atomname': <Choice at 75f42a0b9e50 value=['O2', 'O4']>, 'resname': <Choice at 75f42a0b9d60 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.