vermouth.processors.annotate_idrs module

Provides processors that can add and remove IDR specific bonds

class vermouth.processors.annotate_idrs.AnnotateIDRs(id_regions=None)

Bases: Processor

Processor to annotate intrinsically disordered regions of a molecule.

This processor is designed primarily for the work described in the reference M3_GO, but is generally applicable for such circumstances where extra addition/removals are necessary.

Parameters:

id_regions – regions defining the IDRs

run_molecule(molecule)

Assign disordered regions for a single molecule

run_system(system)

Assign the water bias of the Go model to file. Biasing is always molecule specific i.e. no two different vermouth molecules can have the same bias.

Parameters:

system (vermouth.system.System)

vermouth.processors.annotate_idrs.annotate_disorder(molecule, id_regions, annotation='cgidr')

Annotate the disordered regions of the molecule

molecule: vermouth.molecule.Molecule

the molecule

idr_regions: list

dictionaries defining the disordered regions to annotate

annotation: str

name of the annotation in the node

vermouth.processors.annotate_idrs.parse_residues(resspec)

Parse a residue specification: [<chain>-][<resid_start>]:[<resid_end>] where resid is /[0-9]+/. Returns a dictionary with keys ‘chain’, ‘resid_start’, and ‘resid_end’ for the fields that are specified. Resids will be ints.

Parameters:

resspec (str)

Return type:

dict