vermouth.processors.make_bonds module

Provides a processor that can add edges to a graph based on geometric criteria.

class vermouth.processors.make_bonds.MakeBonds(allow_name=True, allow_dist=True, fudge=1.2)

Bases: vermouth.processors.processor.Processor

run_system(system)

vermouth.processors.make_bonds.make_bonds(system, allow_name=True, allow_dist=True, fudge=1.2)

Creates bonds within molecules in the system.

First, edges will be created based on residue and atom names. Second, edges will be created based on a distance criterion. Nodes in system must have position and element attributes. The possible distance between nodes is determined by values in VDW_RADII. Edges within residues will only be guessed between atoms that are not known in the reference Block. The system will be split into connected components, keeping residues (identified by chain, residue name and residue id) within the same molecule. This does mean that the final molecules can be disconnected.

Notes

Edges for residues for which no block can be found will be added based on

the distance criterion. A warning will be issued if this is the case.

Elements that are not in VDW_RADII do not make bonds based on distances.

Parameters

• system (System) – The system in which to add edges.

• fudge (Number) – Scale the allowed distance by this factor.

Returns

Molecules in system, in which edges have been added based on atom names and possibly distance. The molecules have been split into connected components keeping residues intact. Molecules can be disconnected within residues.

Return type

List[Molecule]