schrodinger.application.mcpro.residuetools module

Classes for manipulating residues.

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.application.mcpro.residuetools.ResidueTools(outfh=<open file '<stdout>', mode 'w'>, debug=None)

Class with tools to help in manipulating proteins

deprotonateResidue(resid, delAtomName, newResname, protCt)

Method to deprotonate the residue in resid by deleting atom delAtomName, changing the formal charge on the attached atom by -1 and changing the residue name for all atoms to newResname

getAtomsInResidue(resid, protCt)

Method to return a list with atoms in the requested residue

getResName(resid, protCt)

Method to return the residue name of residue specified by the resid

getResid(atom)

Routine to return the residue ID, <chain>:<resnum>:<inscode> which should be a unique identifier for each residue

getResidueList(protCt, terz=0)

Method to return a list of reside IDs (<chain>:<resnum>:<inscode>) If terz=0 no TERZ are included in returned resids. If terz=1 they are included

getResiduesInRadius(protCt, ligCt, radii, keptResidues=None)

Method to return a dictionary of residues flagged with 1 if within a given radius of a ligand in a protein/ligand complex. keptResidues can be provided if its desired to have returned a dictionary with all residues rather than only those within the radii

isTERZ(residA, residB)

Routine to compare two resids and assess if a new chain is present

protonateResidue(resid, protAtomName, hydAtomName, newResname, protCt)

Method to protonate the residue in resid by adding a hydrogen to protAtomName, changing the formal charge on protAtomName by +1 and changing the residue name for all atoms to newResname

sortResiduesByDistance(protCt, ligCt)

Method to take a protein and ligand ct and return a list of resids sorted by min distance of CA to ligand. Also returns a hash of CA atom to ligand distances with resids as keys

splitResid(resid)

Routine to return a split residue ID as (chain, resnum, inscode)