def map2molecule(self, molecule):
"""
Map the tree to CING molecule instance.
"""
unmatchedAtomByResDict = {}
for chn in self.tree:
for res in chn:
# nTdebug("map2molecule res: %s" % res)
if res.skip or (not res.db):
continue
for atm in res:
atm.atom = None
if atm.skip or (not atm.db):
# nTerror("pdbParser#map2molecule was flagged before right?")
# nTdebug( '>> %s' % atm )
continue
#t = (IUPAC, chn.name, res.resNum, atm.db.name)
# GV the atm.db.name is BY DEFINITION in INTERNAL format!
# IUPAC and other mapping has already been done before and should not be
# repeated here. It also will cause a potential swap of atoms
t = (INTERNAL, chn.name, res.resNum, atm.db.name)
atm.atom = molecule.decodeNameTuple(t)
# if res.resNum==83:
# nTdebug( '>> %s %s %s', atm.name, t, atm.atom )
# if not atm.atom: # for the non-standard residues and atoms.
# t = (INTERNAL, chn.name, res.resNum, atm.db.name)
# atm.atom = molecule.decodeNameTuple(t)
if not atm.atom:
# JFD: Report all together now.
if not unmatchedAtomByResDict.has_key(res.resName):
unmatchedAtomByResDict[ res.resName ] = ([], [])
atmList = unmatchedAtomByResDict[res.resName][0]
resNumList = unmatchedAtomByResDict[res.resName][1]
if atm.name not in atmList:
atmList.append(atm.name)
if res.resNum not in resNumList:
resNumList.append(res.resNum)
#end if
#end if
#end for
#end for
#end for
self.molecule = molecule
if unmatchedAtomByResDict:
msg = "pdbParser.map2molecule: Strange! Warning mapping atom for:\n"
msg += unmatchedAtomByResDictToString(unmatchedAtomByResDict)
nTwarning(msg)
def map2molecule(self, molecule):
"""
Map the tree to CING molecule instance.
"""
unmatchedAtomByResDict = {}
for chn in self.tree:
for res in chn:
# nTdebug("map2molecule res: %s" % res)
if res.skip or (not res.db):
continue
for atm in res:
atm.atom = None
if atm.skip or (not atm.db):
# nTerror("pdbParser#map2molecule was flagged before right?")
# nTdebug( '>> %s' % atm )
continue
#t = (IUPAC, chn.name, res.resNum, atm.db.name)
# GV the atm.db.name is BY DEFINITION in INTERNAL format!
# IUPAC and other mapping has already been done before and should not be
# repeated here. It also will cause a potential swap of atoms
t = (INTERNAL, chn.name, res.resNum, atm.db.name)
atm.atom = molecule.decodeNameTuple(t)
# if res.resNum==83:
# nTdebug( '>> %s %s %s', atm.name, t, atm.atom )
# if not atm.atom: # for the non-standard residues and atoms.
# t = (INTERNAL, chn.name, res.resNum, atm.db.name)
# atm.atom = molecule.decodeNameTuple(t)
if not atm.atom:
# JFD: Report all together now.
if not unmatchedAtomByResDict.has_key(res.resName):
unmatchedAtomByResDict[res.resName] = ([], [])
atmList = unmatchedAtomByResDict[res.resName][0]
resNumList = unmatchedAtomByResDict[res.resName][1]
if atm.name not in atmList:
atmList.append(atm.name)
if res.resNum not in resNumList:
resNumList.append(res.resNum)
#end if
#end if
#end for
#end for
#end for
self.molecule = molecule
if unmatchedAtomByResDict:
msg = "pdbParser.map2molecule: Strange! Warning mapping atom for:\n"
msg += unmatchedAtomByResDictToString(unmatchedAtomByResDict)
nTwarning(msg)
def _matchResiduesAndAtoms(self):
"""
Match residues and Atoms in the tree to CING db using self.convention
"""
# nTdebug("Now in _matchResiduesAndAtoms")
unmatchedAtomByResDict = {}
# unmatchedResDict = {}
for res in self.tree.subNodes(depth = 2):
self.matchGame.matchResidue2Cing(res)
for atm in res:
if not self.matchGame.matchAtom2Cing(atm):
if not unmatchedAtomByResDict.has_key(res.resName):
unmatchedAtomByResDict[ res.resName ] = ([], [])
atmList = unmatchedAtomByResDict[res.resName][0]
resNumList = unmatchedAtomByResDict[res.resName][1]
if atm.name not in atmList:
atmList.append(atm.name)
if res.resNum not in resNumList:
resNumList.append(res.resNum)
if not self.allowNonStandardResidue:
atm.skip = True
continue
# aName = moveFirstDigitToEnd(atm.name) # worry about this?
atm.db = res.db.appendAtomDef(atm.name)
if not atm.db:
# nTwarning("Should have been possible to add a non-standard atom %s to the residue %s" % (atm.name, res.resName))
continue
msg = "==> Non-standard (residues and their) atoms"
if self.allowNonStandardResidue:
msg += " to add:\n"
else:
msg += " to skip:\n"
if unmatchedAtomByResDict:
msg += unmatchedAtomByResDictToString(unmatchedAtomByResDict)
if self.allowNonStandardResidue:
nTmessage(msg)
else:
nTerror(msg)
def _matchResiduesAndAtoms(self):
"""
Match residues and Atoms in the tree to CING db using self.convention
"""
# nTdebug("Now in _matchResiduesAndAtoms")
unmatchedAtomByResDict = {}
# unmatchedResDict = {}
for res in self.tree.subNodes(depth=2):
self.matchGame.matchResidue2Cing(res)
for atm in res:
if not self.matchGame.matchAtom2Cing(atm):
if not unmatchedAtomByResDict.has_key(res.resName):
unmatchedAtomByResDict[res.resName] = ([], [])
atmList = unmatchedAtomByResDict[res.resName][0]
resNumList = unmatchedAtomByResDict[res.resName][1]
if atm.name not in atmList:
atmList.append(atm.name)
if res.resNum not in resNumList:
resNumList.append(res.resNum)
if not self.allowNonStandardResidue:
atm.skip = True
continue
# aName = moveFirstDigitToEnd(atm.name) # worry about this?
atm.db = res.db.appendAtomDef(atm.name)
if not atm.db:
# nTwarning("Should have been possible to add a non-standard atom %s to the residue %s" % (atm.name, res.resName))
continue
msg = "==> Non-standard (residues and their) atoms"
if self.allowNonStandardResidue:
msg += " to add:\n"
else:
msg += " to skip:\n"
if unmatchedAtomByResDict:
msg += unmatchedAtomByResDictToString(unmatchedAtomByResDict)
if self.allowNonStandardResidue:
nTmessage(msg)
else:
nTerror(msg)
