schrodinger.application.mcpro.residuetools module¶
Classes for manipulating residues.
Copyright Schrodinger, LLC. All rights reserved.
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class
schrodinger.application.mcpro.residuetools.
ResidueTools
(outfh=<open file '<stdout>', mode 'w'>, debug=None)¶ Class with tools to help in manipulating proteins
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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
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getAtomsInResidue
(resid, protCt)¶ Method to return a list with atoms in the requested residue
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getResName
(resid, protCt)¶ Method to return the residue name of residue specified by the resid
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getResid
(atom)¶ Routine to return the residue ID, <chain>:<resnum>:<inscode> which should be a unique identifier for each residue
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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
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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
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isTERZ
(residA, residB)¶ Routine to compare two resids and assess if a new chain is present
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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
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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
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splitResid
(resid)¶ Routine to return a split residue ID as (chain, resnum, inscode)
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