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outfh=sys.stdout,
debug=None) |
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getResid(self,
atom)
Routine to return the residue ID,
<chain>:<resnum>:<inscode> which should be a unique
identifier for each residue |
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splitResid(self,
resid)
Routine to return a split residue ID as (chain, resnum, inscode) |
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getResidueList(self,
protCt,
terz=0)
Method to return a list of reside IDs
(<chain>:<resnum>:<inscode>) If terz=0 no TERZ are
included in returned resids. |
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getResiduesInRadius(self,
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. |
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isTERZ(self,
residA,
residB)
Routine to compare two resids and assess if a new chain is present |
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getAtomsInResidue(self,
resid,
protCt)
Method to return a list with atoms in the requested residue |
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protonateResidue(self,
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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deprotonateResidue(self,
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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getResName(self,
resid,
protCt)
Method to return the residue name of residue specified by the resid |
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sortResiduesByDistance(self,
protCt,
ligCt)
Method to take a protein and ligand ct and return a list of resids
sorted by min distance of CA to ligand. |
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