def getRefChemAtom(self, nmrAtoms):
refChemAtom = nmrAtoms[0].chemAtom
if len(refChemAtom.chemBonds) == 1:
refChemAtom = getOtherAtom(refChemAtom, refChemAtom.chemBonds[0])
else:
refChemAtom = None
return refChemAtom
def createResidueProtonToHeavyAtom(residue):
ccpCode = residue.ccpCode
chemComp = residue.chemCompVar.chemComp
protonToHeavyAtom = {ccpCode: {}}
for heavyAtom in chemComp.sortedChemAtoms():
if heavyAtom.elementSymbol == 'H':
continue
atomName = heavyAtom.name
if atomName == 'OXT':
continue
bondedProtons = []
for bond in heavyAtom.chemBonds:
otherAtom = getOtherAtom(heavyAtom,bond)
if otherAtom.elementSymbol == 'H':
if atomName == 'N' and otherAtom.name != 'H':
continue
bondedProtons.append(otherAtom)
if bondedProtons:
chemAtomSet = bondedProtons[0].chemAtomSet
if chemAtomSet:
if chemAtomSet.isEquivalent or chemAtomSet.isProchiral == True:
protonKey = [bp.name for bp in bondedProtons]
protonKey.sort()
protonKey = tuple(protonKey)
protonToHeavyAtom[ccpCode][protonKey] = atomName
if chemAtomSet.isEquivalent:
continue
for bp in bondedProtons:
protonToHeavyAtom[ccpCode][bp.name] = atomName
return protonToHeavyAtom
def findRingCarbon(chemAtom, connectedAtoms):
returnConnectedAtoms = None
for chemBond in chemAtom.chemBonds:
otherChemAtom = getOtherAtom(chemAtom, chemBond)
if otherChemAtom == connectedAtoms[-1]:
returnConnectedAtoms = connectedAtoms[:]
break
elif otherChemAtom and otherChemAtom not in connectedAtoms and otherChemAtom.elementSymbol == 'C':
returnConnectedAtoms = findRingCarbon(
otherChemAtom,
connectedAtoms[:-1] + [otherChemAtom, connectedAtoms[-1]])
if returnConnectedAtoms:
break
return returnConnectedAtoms
def getStereoPriorities(stereoAtom, chemBondsHandled):
priorityList = []
priorityKeys = []
followPriorityKeys = []
for chemBond in stereoAtom.chemBonds:
if chemBond in chemBondsHandled:
otherAtom = None
priorityKey = (0, 0)
else:
otherAtom = getOtherAtom(stereoAtom, chemBond)
priorityKey = (otherAtom.chemElement.atomNumber,
bondDict[chemBond.bondType])
chemBondsHandled.append(chemBond)
if priorityKey not in priorityKeys:
priorityKeys.append(priorityKey)
elif priorityKey not in followPriorityKeys:
followPriorityKeys.append(priorityKey)
priorityList.append((priorityKey, otherAtom))
return (priorityList, followPriorityKeys)
def makeFullSugar(carboBaseName,
coordSystem,
baseGlycoCtCode,
testMode,
replace=False,
saveData=True):
carboMolType = 'carbohydrate'
namingSystemName = 'EuroCarbDb'
project = Implementation.MemopsRoot(name='chemComp')
project.currentUserId = 'ccpnRef'
#
# Set archive dir info
#
if testMode:
chemCompDataDir = testChemCompDataDir
chemCompCoordDataDir = testChemCompCoordDataDir
else:
chemCompDataDir = editChemCompDataDir
chemCompCoordDataDir = editChemCompCoordDataDir
#
# First import all mol2 files, pick one form as 'base' unit, adapt this one,
# then add coords from other chemComps
#
# TODO: This is currently very specific!
#
#
# TODO SET A STEREOCHEMISTRY CLASS FOR THE A/B CHEMATOMS!!
#
importDir = os.path.join(origMol2DataDir, 'carbo')
importFiles = os.listdir(os.path.join(importDir, carboBaseName))
for importFile in importFiles[:]:
if not importFile[-4:] == 'mol2':
importFiles.pop(importFiles.index(importFile))
importFiles.sort()
mol2Format = Mol2Format(project, guiParent=None, allowPopups=False)
molTypes = [carboMolType]
chemComps = []
rawChemComps = []
for importFile in importFiles:
# Should be 'a', 'b' or 'o'
anomericCenter = importFile[0]
if anomericCenter != 'a':
ccpCode = '%s-%s' % (anomericCenter, carboBaseName)
else:
ccpCode = carboBaseName
fileName = os.path.join(importDir, carboBaseName, importFile)
print "Reading mol2 file %s..." % fileName
ccs = mol2Format.readChemComps(fileName,
molTypes=molTypes,
ccpCodes=[ccpCode],
saveChemComp=False,
minimalPrompts=True,
makeNamingSystem=namingSystemName)
chemComps.append(ccs[0])
rawChemComps.append(mol2Format.rawChemComp)
#
# Check whether only open form available (e.g. aldi ones)
#
if len(chemComps) == 1 and chemComps[0].ccpCode[0] == 'o':
print " Warning: only open form available, not creating a/b isoforms."
hasOnlyOpenForm = True
else:
hasOnlyOpenForm = False
#print chemComps
#print rawChemComps
"""
for cch in project.chemCompHeads:
print cch.molType, cch.ccpCode
for ccv in cch.chemComp.chemCompVars:
print ccv.descriptor
print ccv.chemAtoms
print
"""
refChemComp = chemComps[0] # Should be the a form
#
# Reset save location, check if file already exists
#
chemCompXmlFile = findChemCompOrCoordFilePath(refChemComp,
testMode=testMode)
# In this case, getting nothing back with replace - False means that it does exist!
if chemCompXmlFile and not replace:
print " ChemComp %s, %s already exists - aborting creation." % (
carboMolType, carboBaseName)
try:
refChemComp = getChemComp(project,
carboMolType,
carboBaseName,
download=False,
chemCompArchiveDir=editChemCompDataDir,
copyFile=False)
except:
print "WARNING: chemcomp was already loaded!"
refChemComp = project.findFirstChemComp(molType=carboMolType,
ccpCode=carboBaseName)
return refChemComp
#
# Start creating/modifying...
#
print
print drawBox("Creating sugar information")
print
#
# Set the base Glyco CT code, this is always x-, except for -o only forms (aldehydes)
#
# TODO: might need to hack this for substituents so know which one is which... or just do it by order? Should be fine...
#
refGlycoCtCode = "RES\n1b:%s" % baseGlycoCtCode
print "Setting GlycoCT code to:\n\n%s\n" % refGlycoCtCode
print
project.override = True
try:
refChemComp.baseGlycoCtCode = refGlycoCtCode
refChemComp.findFirstChemCompVar().glycoCtCode = refGlycoCtCode
finally:
project.override = False
#
# Look for a C-O-C fragment. Should be O5 for 6 rings.
#
# Note: ONLY works on cyclic sugars!!!
#
centralOAtom = None
for chemAtom in refChemComp.sortedChemAtoms():
# TODO: should really do this from the Var level, but...
if chemAtom.elementSymbol == 'O' and len(chemAtom.chemBonds) == 2:
connectedToC = True
for chemBond in chemAtom.sortedChemBonds():
otherChemAtom = getOtherAtom(chemAtom, chemBond)
if otherChemAtom.elementSymbol != 'C':
connectedToC = False
break
if connectedToC:
centralOAtom = chemAtom
#
# Try to generically determine the carbon atoms in the ring... trying not to depend on names
# but if a C1 is connected to the O5, then start from there.
#
connectedAtoms = []
for chemBond in centralOAtom.sortedChemBonds():
otherChemAtom = getOtherAtom(centralOAtom, chemBond)
if otherChemAtom.name == 'C1':
connectedAtoms.insert(0, otherChemAtom)
else:
connectedAtoms.append(otherChemAtom)
#
# Start to loop... use recursive function to find right order
#
ringCarbons = findRingCarbon(connectedAtoms[0], connectedAtoms)
if not ringCarbons:
centralOAtom = None
continue
otherCarbons = []
for searchCarbon in refChemComp.findAllChemAtoms(
elementSymbol='C'):
if searchCarbon not in ringCarbons:
otherCarbons.append(searchCarbon)
break
if not centralOAtom and not hasOnlyOpenForm:
raise " Error: no central O atom found in ring!!"
#
# Now look for anomeric carbon and connection sites...
#
anomericCarbon = None
anomericOxygen = None
if not hasOnlyOpenForm:
for searchCarbon in [ringCarbons[0], ringCarbons[-1]]:
for chemBond in searchCarbon.chemBonds:
otherChemAtom = getOtherAtom(searchCarbon, chemBond)
if otherChemAtom and otherChemAtom.elementSymbol == 'O' and otherChemAtom != centralOAtom:
anomericCarbon = searchCarbon
anomericOxygen = otherChemAtom
break
if anomericCarbon:
break
else:
# Hardset these... not really anomeric but good enough
anomericCarbon = refChemComp.findFirstChemAtom(name='C1')
anomericOxygen = refChemComp.findFirstChemAtom(name='O1')
if not anomericCarbon:
raise " Error: no anomeric carbon found."
else:
for chemBond in anomericOxygen.chemBonds:
otherChemAtom = getOtherAtom(anomericOxygen, chemBond)
if otherChemAtom and otherChemAtom.elementSymbol == 'H':
anomericHydrogen = otherChemAtom
break
if not anomericHydrogen:
print " Warning: no anomeric hydrogen found."
#
# Set the stereo information for the anomeric carbon, then create subtypes for beta and open forms
#
#anomericCarbons = {'a': None, 'b': None, 'o': None}
stereoAtom = anomericCarbon
bondDict = {
'single': 1,
'double': 2,
'triple': 3,
'aromatic': 1.5,
'dative': 1.0,
'singleplanar': 1.5
} # TODO CHECK THIS!
"""
# OK to do this because is neutral 'real' chemComp, but otherwise need to start from chemCompVar!!!
#
# TODO TODO also need to track chemBonds, but ONLY at beginning
# then need to go back to coordinates to find out in which order the bonds appear based on the coords (when looking down
# the main bond)!
#
# Might be easiest to use Martin's code (or someone else's), use the atom names to link back to here...
#
totalChemBonds = chemComp.chemBonds
chemBondsHandled = []
priorityList = getStereoPriorities(stereoAtom,chemBondsHandled)
priorityList.sort()
priorityList.reverse()
priorityKeys = []
for (priorityKey,otherAtom) in priorityList:
priorityKeys.append(priorityKey)
for priorityKey in priorityKeys:
if priorityKeys.count(priorityKey) > 1:
print priorityKey
print priorityList
sys.exit()
"""
#
# Look for binding oxygens... has to be hydroxy group connected to carbon
#
bindingOxygens = []
bindingHydrogens = {}
#
# Set carbons to search for connected OH groups
#
if not hasOnlyOpenForm:
searchCarbons = ringCarbons + otherCarbons
else:
searchCarbons = list(refChemComp.findAllChemAtoms(elementSymbol='C'))
if 'aldi' in baseGlycoCtCode:
# Don't do anything on 1 position for these - alditols
searchCarbons.pop(searchCarbons.index(anomericCarbon))
for searchCarbon in searchCarbons:
validConnectedAtoms = {}
validOHgroups = []
for chemBond in searchCarbon.sortedChemBonds():
otherChemAtom = getOtherAtom(searchCarbon, chemBond)
if otherChemAtom:
for elementSymbol in ['O', 'N']:
if otherChemAtom.elementSymbol == elementSymbol and otherChemAtom != centralOAtom:
if not validConnectedAtoms.has_key(elementSymbol):
validConnectedAtoms[elementSymbol] = []
validConnectedAtoms[elementSymbol].append(
otherChemAtom)
otherChemBonds = list(otherChemAtom.chemBonds)
if elementSymbol == 'O' and len(otherChemBonds) == 2:
otherChemBond = otherChemBonds[not otherChemBonds.
index(chemBond)]
connectedChemAtom = getOtherAtom(
otherChemAtom, otherChemBond)
if connectedChemAtom.elementSymbol == 'H':
validOHgroups.append(otherChemAtom)
#
# Check if single OH (no double O, or amide, ...)
#
if len(validOHgroups) == 1:
if len(validConnectedAtoms) == 1:
# Carboxylic acid (except for ring O-C-OH!)
if len(validConnectedAtoms['O']
) == 2 and not searchCarbon == anomericCarbon:
print " Warning: ignoring oxygen %s - is carboxylic acid (or similar)" % validOHgroups[
0].name
validOHgroups = []
else:
# Amide or something similar
print " Warning: ignoring oxygen %s - is amide (or similar)" % validOHgroups[
0].name
validOHgroups = []
if validOHgroups:
bindingOxygens.append(validOHgroups[0])
bindingHydrogens[validOHgroups[0]] = connectedChemAtom
if not hasOnlyOpenForm and searchCarbon in otherCarbons:
print " Warning: setting oxygen %s as binding one (not directly connected to ring)." % (
validOHgroups[0].name)
#
# Now create variants...
#
# Need to have all combinations of:
#
# - anomeric a/b and free/bound
# - binding oxygens free/bound
#
bindingOxygenCombs = makePowerSet(bindingOxygens)
origAnomericCarbon = anomericCarbon
linkAtomsMapForCoordinates = {}
if hasOnlyOpenForm:
stereoTypes = ('open_1', )
else:
stereoTypes = ('stereo_1', 'stereo_2')
for stereoType in stereoTypes:
subType = int(stereoType.split('_')[1])
anomericCarbon = refChemComp.findFirstChemAtom(name='C1',
subType=subType)
if not anomericCarbon:
# Should only happen for stereo_2
creationDict = {'name': 'C1', 'subType': subType}
for attrName in ('elementSymbol', 'shortVegaType',
'waterExchangeable'):
creationDict[attrName] = getattr(origAnomericCarbon, attrName)
# TODO set chirality to OPPOSITE of whatever the first subtype is!
anomericCarbon = refChemComp.newChemAtom(**creationDict)
namingSystem = refChemComp.findFirstNamingSystem(
name=namingSystemName)
namingSystem.newAtomSysName(sysName=anomericCarbon.name,
atomName=anomericCarbon.name,
atomSubType=anomericCarbon.subType)
# Bonds and other atoms are exactly the same!
for chemBond in origAnomericCarbon.chemBonds:
otherChemAtom = getOtherAtom(origAnomericCarbon, chemBond)
refChemComp.newChemBond(chemAtoms=(anomericCarbon,
otherChemAtom),
bondType=chemBond.bondType,
stereochem=chemBond.stereochem)
for anomericBound in range(0, 2):
for i in range(0, len(bindingOxygenCombs)):
bindingOxygens = bindingOxygenCombs[i]
# Main list only contains real ChemAtoms!!
currentChemAtoms = list(
refChemComp.findAllChemAtoms(className='ChemAtom'))
anomericCarbons = refChemComp.findAllChemAtoms(name='C1')
for tempAnomericCarbon in anomericCarbons:
if tempAnomericCarbon != anomericCarbon and tempAnomericCarbon in currentChemAtoms:
currentChemAtoms.pop(
currentChemAtoms.index(tempAnomericCarbon))
# This is the neutral refChemComp - already exists!
if not anomericBound and not bindingOxygens:
continue
# Can't be both bound on the anomeric carbon and have an oxygen link there...
if anomericBound and len(
bindingOxygens
) == 1 and bindingOxygens[0] == anomericOxygen:
continue
# Can't have a link to 1 and something else...
if len(bindingOxygens
) > 1 and anomericOxygen in bindingOxygens:
continue
linkedAtomKeys = []
linkedAtoms = {}
linkAtoms = {}
if anomericBound and not hasOnlyOpenForm and 'aldi' not in baseGlycoCtCode:
# Only do C1 when relevant - for alditols it's not, always reducing end.
currentChemAtoms.pop(
currentChemAtoms.index(anomericOxygen))
if anomericHydrogen:
currentChemAtoms.pop(
currentChemAtoms.index(anomericHydrogen))
anomericCarbonKey = getChemAtomKey(anomericCarbon)
linkedAtomKeys.append(anomericCarbonKey)
linkedAtoms[anomericCarbonKey] = anomericCarbon
linkAtom = getLinkAtom(anomericCarbon, multi=True)
linkAtoms[anomericCarbonKey] = linkAtom
currentChemAtoms.append(linkAtom)
linkAtomsMapForCoordinates[(
linkAtom.name, linkAtom.subType)] = anomericOxygen.name
for bindingOxygen in bindingOxygens:
bindingHydrogen = bindingHydrogens[bindingOxygen]
if bindingHydrogen and bindingHydrogen in currentChemAtoms:
currentChemAtoms.pop(
currentChemAtoms.index(bindingHydrogen))
bindingOxygenKey = getChemAtomKey(bindingOxygen)
linkedAtomKeys.append(bindingOxygenKey)
linkedAtoms[bindingOxygenKey] = bindingOxygen
linkAtom = getLinkAtom(bindingOxygen)
linkAtoms[bindingOxygenKey] = linkAtom
currentChemAtoms.append(linkAtom)
linkAtomsMapForCoordinates[(
linkAtom.name,
linkAtom.subType)] = bindingHydrogen.name
linkedAtomKeys.sort()
# Possible for C1 linkages if not handled (only reducing end)
if not linkedAtomKeys:
continue
#
# Create linkEnds
#
linkInfo = []
for linkedAtomKey in linkedAtomKeys:
if linkedAtomKey[0] == 'C1':
linkCode = "%s_%s" % (linkedAtomKey[0],
linkedAtomKey[1])
else:
linkCode = linkedAtomKey[0]
linkInfo.append(linkCode)
if not refChemComp.findFirstLinkEnd(linkCode=linkCode):
boundChemAtom = linkedAtoms[linkedAtomKey]
boundLinkAtom = linkAtoms[linkedAtomKey]
linkEnd = refChemComp.newLinkEnd(
linkCode=linkCode,
boundChemAtom=boundChemAtom,
boundLinkAtom=boundLinkAtom)
# TODO THIS IS NOT GREAT - no way of telling what's what if atom names are messed up
#linking = 'none'
#descriptor = 'link:%s' % string.join(linkedAtomKeys,',')
linking = 'link:%s' % string.join(linkInfo, ',')
if stereoType.count('stereo'):
descriptor = '%s:C1' % stereoType
else:
descriptor = 'neutral'
if not refChemComp.findFirstChemCompVar(linking=linking,
descriptor=descriptor):
print " Trying %s,%s" % (linking, descriptor)
#for ca in currentChemAtoms:
# if ca.className == 'LinkAtom':
# print " LA:",ca.name, ca.subType
# else:
# print " CA:",ca.name, ca.subType
#print " ",linkedAtomKeys
# Create the stereospecific GlycoCt code
if stereoType == "stereo_1":
stereoCode = 'a'
elif stereoType == "stereo_2":
stereoCode = 'b'
elif stereoType == 'open_1':
stereoCode = 'o'
varGlycoCtCode = "RES\n1b:%s" % (stereoCode +
baseGlycoCtCode[1:])
ccv = refChemComp.newChemCompVar(
chemAtoms=currentChemAtoms,
linking=linking,
descriptor=descriptor,
glycoCtCode=varGlycoCtCode,
formalCharge=0,
isParamagnetic=False,
isAromatic=False)
#
# Make sure the chemElements are accessible
#
project.currentChemElementStore = project.findFirstChemElementStore()
#
# Reset the name and molType...
#
chMolType = 'carbohydrate'
project.override = True
try:
refChemComp.ccpCode = carboBaseName
refChemComp.molType = carboMolType
finally:
project.override = False
# TODO SET THESE CORRECTLY? Where do I get info from for this though? Can this come from MSD? Ask Dimitris!!
# Set the PDB/MSD name - NOTE that have to do this for the correct a/b forms! Var specific!!
#ChemComp.ChemCompSysName(refChemComp,namingSystem = 'PDB',sysName=ccpCode,specificChemCompVars = refChemComp.sortedChemCompVars())
#ChemComp.ChemCompSysName(refChemComp,namingSystem = 'MSD',sysName=ccpCode,specificChemCompVars = refChemComp.sortedChemCompVars())
#
# Check chemComp validatity and save
# TODO make this all options in running script!
#
refChemComp.checkAllValid()
if saveData:
#
# Get the original file GUID, if possible, when replacing existing file
#
if replace:
(existingGuid,
existingFile) = findExistingChemCompInfo(chemCompDataDir,
refChemComp.ccpCode,
refChemComp.molType)
if existingGuid:
project.override = True
try:
refChemComp.guid = existingGuid
finally:
project.override = False
(tmpFilePath,
existingFilePath) = saveTemporaryChemCompOrCoord(refChemComp,
testMode=testMode)
# Do a check here? Or don't bother?
consolidateTemporaryChemCompOrCoord(refChemComp,
tmpFilePath,
existingFilePath,
testMode=testMode,
replace=replace)
#
# Get the coordinates as well!
#
print " Creating coordinates!!"
chemCompCoord = project.newChemCompCoord(sourceName=coordSystem,
molType=refChemComp.molType,
ccpCode=refChemComp.ccpCode)
for i in range(len(rawChemComps)):
rawChemComp = rawChemComps[i]
# Identify which one we're dealing with!!
(dirName, baseName) = os.path.split(rawChemComp.parent.name)
if baseName[0] == 'a':
stereoDescriptor = "stereo_1:C1"
elif baseName[0] == 'b':
stereoDescriptor = "stereo_2:C1"
elif baseName[0] == 'o':
stereoDescriptor = "none"
else:
print " Not handling type '%s' for coordinates - ignored." % baseName[
0]
continue
#
# Mark that generated by this script...
#
applData = Implementation.AppDataString(application='ccpNmr',
keyword='origin',
value='makeFullSugar.py')
chemCompCoord.addApplicationData(applData)
# Don't do any link atoms (yet)... could in principle use atoms that are 'missing'
# TODO: should decompose descriptor here, then check...
chemCompVars = refChemComp.findAllChemCompVars(
descriptor=stereoDescriptor)
chemAtomKeys = []
for ccv in chemCompVars:
for ca in ccv.sortedChemAtoms():
caKey = (ca.name, ca.subType)
if caKey not in chemAtomKeys:
chemAtomKeys.append(caKey)
#
# Create a dictionary for the coordinates, based on the 'raw' chemComp from the mol2 file
#
chemAtomCoordDict = {}
for chemAtomKey in chemAtomKeys:
coords = None
if linkAtomsMapForCoordinates.has_key(chemAtomKey):
useChemAtomName = linkAtomsMapForCoordinates[chemAtomKey]
else:
useChemAtomName = chemAtomKey[0]
for rawAtom in rawChemComp.atoms:
if rawAtom.name == useChemAtomName:
coords = (rawAtom.x, rawAtom.y, rawAtom.z)
break
if not coords:
print " Warning: no coordinate for %s, atom key %s." % (
coordSystem, chemAtomKey)
elif not chemAtomCoordDict.has_key(chemAtomKey):
chemAtomCoordDict[chemAtomKey] = coords
else:
print " Error: double atom key %s!" % chemAtomKey
#
# Set the coordinates
#
chemAtomCoords = {}
#print [ra.name for ra in rawChemComp.atoms]
for chemCompVar in chemCompVars:
#print chemCompVar
chemCompVarCoord = chemCompCoord.findFirstChemCompVarCoord(
linking=chemCompVar.linking, descriptor=chemCompVar.descriptor)
if not chemCompVarCoord:
chemCompVarCoord = chemCompCoord.newChemCompVarCoord(
linking=chemCompVar.linking,
descriptor=chemCompVar.descriptor)
#print chemCompVarCoord
for ca in chemCompVar.sortedChemAtoms():
caKey = (ca.name, ca.subType)
#print "%-20s" % str(caKey),
if chemAtomCoordDict.has_key(caKey):
coords = chemAtomCoordDict[caKey]
if coords:
if chemAtomCoords.has_key(caKey):
chemAtomCoord = chemAtomCoords[caKey]
else:
chemAtomCoord = chemCompCoord.newChemAtomCoord(
name=caKey[0],
subType=caKey[1],
x=coords[0],
y=coords[1],
z=coords[2])
chemAtomCoords[caKey] = chemAtomCoord
if chemAtomCoord not in chemCompVarCoord.chemAtomCoords:
chemCompVarCoord.addChemAtomCoord(chemAtomCoord)
#print chemAtomCoord.name, chemAtomCoord.subType,
#print
chemCompCoord.checkAllValid()
if saveData:
if replace:
(existingGuid, existingFile) = findExistingChemCompCoordInfo(
chemCompCoordDataDir, coordSystem, chemCompCoord.ccpCode,
chemCompCoord.molType)
if existingGuid:
project.override = True
try:
chemCompCoord.guid = existingGuid
finally:
project.override = False
(tmpFilePath,
existingFilePath) = saveTemporaryChemCompOrCoord(chemCompCoord,
testMode=testMode)
# Do a check here? Or don't bother? This is blank regeneration from reference data, so should be OK!
consolidateTemporaryChemCompOrCoord(chemCompCoord,
tmpFilePath,
existingFilePath,
testMode=testMode,
replace=replace)
return refChemComp
def addSubstituentToBaseUnit(baseUnitCcpCode,
baseUnitMolType,
testMode,
mergeInfoList,
coordSystem,
substRemoveAtomName='SUB',
saveData=True,
replace=False,
namingSystemName=None,
resetGlycoCtCode=False):
#
# Set directories to read/write data from/to
#
if testMode:
chemCompCoordDataDir = testChemCompCoordDataDir
chemCompDataDir = testChemCompDataDir
else:
chemCompCoordDataDir = editChemCompCoordDataDir
chemCompDataDir = editChemCompDataDir
#
# Now start setting up project
#
substIndexPatt = re.compile("(\d+)")
substituentDir = os.path.join(origMol2DataDir, 'subst')
ccpCode = baseUnitCcpCode
substituentList = []
for mergeInfoDict in mergeInfoList:
substituent = mergeInfoDict['substituent']
if not substituent in substituentList:
substituentList.append(substituent)
ccpCode += ":%s_%s" % (mergeInfoDict['baseBindingAtomName'],
substituentInfo[substituent]['shortCode'])
project = Implementation.MemopsRoot(name='chemComp')
project.currentUserId = 'ccpnRef'
project.currentChemElementStore = project.findFirstChemElementStore()
#
# First import all relevant subsituent mol2 files
# TODO could in principle have these 'pre-imported' in CCPN, in special dir...
# note though that the SUBST atoms have to be removed in that case...
#
mol2Format = Mol2Format(project, guiParent=None, allowPopups=False)
chemComps = {}
rawChemComps = {}
for substituent in substituentList:
fileName = os.path.join(substituentDir, "%s.mol2" % substituent)
ccs = mol2Format.readChemComps(fileName,
ccpCodes=[substituent],
saveChemComp=False,
minimalPrompts=True)
chemComps[substituent] = ccs[0]
rawChemComps[substituent] = mol2Format.rawChemComp
#
# Get the original base unit information
#
origBaseUnit = getChemComp(project,
baseUnitMolType,
baseUnitCcpCode,
chemCompArchiveDir=chemCompDataDir,
copyFile=False)
#
# If replacing, keep GUID of original as default
#
creationKeywds = {}
if replace:
if testMode:
dataDir = testChemCompDataDir
else:
dataDir = editChemCompDataDir
(existingGuid,
existingFile) = findExistingChemCompInfo(dataDir, ccpCode,
baseUnitMolType)
if existingGuid:
creationKeywds['guid'] = existingGuid
#
# Now create the new base unit, copy the original base unit file, change the guid in the file, then load it
#
baseUnit = project.newNonStdChemComp(molType=baseUnitMolType,
ccpCode=ccpCode,
**creationKeywds)
repository = project.findFirstRepository(name='userData')
isNewFile = copyBaseToModifiedFile(project,
baseUnit,
origBaseUnit,
testMode,
repository,
replace=replace)
if not isNewFile:
return
#print baseUnit.chemAtoms
origBaseUnitCcc = getChemCompCoord(
project,
coordSystem,
baseUnitMolType,
baseUnitCcpCode,
chemCompCoordArchiveDir=chemCompCoordDataDir,
copyFile=False)
if not origBaseUnitCcc:
raise ("Error: no coordinates available for %s!" % baseUnitCcpCode)
else:
#
# If replacing, keep GUID of original as default
#
creationKeywds = {}
if replace:
if testMode:
dataDir = testChemCompCoordDataDir
else:
dataDir = editChemCompCoordDataDir
(existingGuid, existingFile) = findExistingChemCompCoordInfo(
dataDir, coordSystem, ccpCode, baseUnitMolType)
if existingGuid:
creationKeywds['guid'] = existingGuid
baseUnitCcc = project.newChemCompCoord(sourceName=coordSystem,
molType=baseUnitMolType,
ccpCode=ccpCode,
**creationKeywds)
copyBaseToModifiedFile(project,
baseUnitCcc,
origBaseUnitCcc,
testMode,
repository,
replace=replace)
#print baseUnitCcc.chemAtomCoords
#
# Reset the glycoCtCode for the new base unit (if relevant)
#
if resetGlycoCtCode:
substGlycoCtText = ""
substGlycoCtInfo = {'RES': [], 'LIN': []}
resIndex = 2
linIndex = 1
# Note: this assumes the mergeInfoList is ordered!
for mergeInfoDict in mergeInfoList:
baseBindingAtomName = mergeInfoDict['baseBindingAtomName']
removeBaseAtomNames = mergeInfoDict['removeBaseAtomNames']
substituent = mergeInfoDict['substituent']
substGlycoCtInfo['RES'].append("%ds:%s" % (resIndex, substituent))
parentAtomIndex = int(baseBindingAtomName[-1])
if baseBindingAtomName[0] == 'O':
parentSubstitutionType = 'o'
else:
parentSubstitutionType = 'd'
substGlycoCtInfo['LIN'].append(
"%d:%d%s(%d+%d)%d%s" % (linIndex, 1, parentSubstitutionType,
parentAtomIndex, 1, resIndex, 'n'))
resIndex += 1
linIndex += 1
for tmpStr in substGlycoCtInfo['RES']:
substGlycoCtText += "\n" + tmpStr
substGlycoCtText += "\nLIN"
for tmpStr in substGlycoCtInfo['LIN']:
substGlycoCtText += "\n" + tmpStr
newBaseGlycoCtCode = origBaseUnit.baseGlycoCtCode + substGlycoCtText
project.override = True
try:
baseUnit.baseGlycoCtCode = newBaseGlycoCtCode
for chemCompVar in baseUnit.chemCompVars:
chemCompVar.glycoCtCode = chemCompVar.glycoCtCode + substGlycoCtText
finally:
project.override = False
print "Setting base GlycoCT code to:\n\n%s\n" % newBaseGlycoCtCode
print
#
# Set naming system
#
namingSystem = None
if namingSystemName:
namingSystem = baseUnit.findFirstNamingSystem(name=namingSystemName)
if not namingSystem:
namingSystem = baseUnit.newNamingSystem(name=namingSystemName)
print "Created new naming system %s" % namingSystemName
#
# Add substituent info, remove atoms from base unit
#
addVariants = {}
for mergeInfoDict in mergeInfoList:
#
# 0. Get the info from the mergeInfoDict, print a comment
#
baseBindingAtomName = mergeInfoDict['baseBindingAtomName']
removeBaseAtomNames = mergeInfoDict['removeBaseAtomNames']
substituent = mergeInfoDict['substituent']
renameSubstituentAtomNames = mergeInfoDict[
'renameSubstituentAtomNames']
baseBindingAtoms = baseUnit.findAllChemAtoms(name=baseBindingAtomName)
newBondType = substituentInfo[substituent]['bondType']
newStereochem = substituentInfo[substituent]['stereochem']
print
print drawBox("Creating link between base atom %s to substituent %s" %
(baseBindingAtomName, substituent))
print
#
# 1. Set the substUnitIndex - this is the identifier that is added to the substituents
# when part of the base chemComp. It is taken from whichever number is part of the baseBindingAtomName
#
# TODO: should be molType specific - use A,B,G,... for amino acids!!
#
substUnitSearch = substIndexPatt.search(baseBindingAtomName)
substUnitIndex = substUnitSearch.group(1)
#
# 2. Remove relevant atoms from the base unit, all subtypes
# Keep track of atom directly linked to the baseBindingAtom for recalculating coordinates!
#
baseAtomCoords = {}
for removeBaseAtomName in removeBaseAtomNames:
removeBaseAtoms = baseUnit.findAllChemAtoms(
name=removeBaseAtomName)
for removeBaseAtom in removeBaseAtoms:
# Search if bound to the baseBindingAtom
isBoundToBaseBindingAtom = False
for chemBond in baseUnit.chemBonds:
bondChemAtoms = list(chemBond.chemAtoms)
if removeBaseAtom in bondChemAtoms:
otherBondChemAtom = bondChemAtoms[
not bondChemAtoms.index(removeBaseAtom)]
if otherBondChemAtom in baseBindingAtoms:
isBoundToBaseBindingAtom = True
break
# Track the coordinates if bound to the baseBindingAtom
if isBoundToBaseBindingAtom:
for baseBindingAtom in baseBindingAtoms:
baseAtomCoords[baseBindingAtom] = {}
baseBindingAtomCoords = baseUnitCcc.findAllChemAtomCoords(
chemAtom=baseBindingAtom)
for baseBindingAtomCoord in baseBindingAtomCoords:
baseCoord = (baseBindingAtomCoord.x,
baseBindingAtomCoord.y,
baseBindingAtomCoord.z)
for chemCompVarCoord in baseBindingAtomCoord.chemCompVarCoords:
# Get the coordinates, if any
removeBaseAtomCoord = chemCompVarCoord.findFirstChemAtomCoord(
chemAtom=removeBaseAtom)
if removeBaseAtomCoord:
baseBoundCoord = (removeBaseAtomCoord.x,
removeBaseAtomCoord.y,
removeBaseAtomCoord.z)
jointCoords = (baseCoord, baseBoundCoord)
if not baseAtomCoords[
baseBindingAtom].has_key(
jointCoords):
baseAtomCoords[baseBindingAtom][
jointCoords] = []
baseAtomCoords[baseBindingAtom][
jointCoords].append(chemCompVarCoord)
# Now start deleting on chemComp and chemCompCoord levels
removeBaseAtomCoords = baseUnitCcc.findAllChemAtomCoords(
chemAtom=removeBaseAtom)
for removeBaseAtomCoord in removeBaseAtomCoords:
removeBaseAtomCoord.delete()
removeBaseAtom.delete()
print " Removed atom %s, subType %d from base unit..." % (
removeBaseAtomName, removeBaseAtom.subType)
for namingSystem in baseUnit.namingSystems:
for asn in namingSystem.atomSysNames:
if asn.atomName == removeBaseAtomName:
asn.delete()
#
# 2.1 Also rename all linkEnds and chemCompVars that have this atom in the descriptor - are now irrelevant
#
for chemCompVar in baseUnit.chemCompVars:
deleteVoidChemCompVar(chemCompVar, 'descriptor',
removeBaseAtomName, baseUnit,
baseUnitCcc)
deleteVoidChemCompVar(chemCompVar, 'linking',
removeBaseAtomName, baseUnit,
baseUnitCcc)
deleteLinkEnd(baseUnit, removeBaseAtomName)
#
# 3. Add the substituent info to the base unit
#
# Currently this works off the mol2 file. Could add, e.g. SUB_C, SUB_O, SUB_N, depending on substituted atom...
# for better coordinates later on. TODO: try to implement this!!!
#
# TODO: look into avoiding mol2 step, just put into CCPN in temporary library, use linkAtoms as linking ones.
# These can then also be identified by elementSymbol (O,C,N,...)
#
substUnit = chemComps[substituent]
rawSubstChemComp = rawChemComps[substituent]
#
# 3.1 Initialise information
# - determine which atom to remove from substituent (will need this for coordinates further down though)
# - get single bond coming from this atom to identify the binding atom on the substituent side
# - create substToBaseDict dictionary that maps substituent objects to newly created chemComp unit objects
# - deal with the coordinates
substRemoveAtom = substUnit.findFirstChemAtom(name=substRemoveAtomName)
chemBond = substRemoveAtom.findFirstChemBond(
) # Should only have ONE single bond!
substBindingAtom = getOtherAtom(substRemoveAtom, chemBond)
substCoords = [
getAtomOrigCoords(rawSubstChemComp, substRemoveAtomName),
getAtomOrigCoords(rawSubstChemComp, substBindingAtom.name)
]
substCoordsBaseAtoms = [None, None]
substToBaseDict = {}
#
# 3.2 Create chemAtoms and chemAtomSets
#
redoChemAtomSets = []
substChemAtoms = []
for chemAtomOrSet in substUnit.sortedChemAtoms(
) + substUnit.sortedChemAtomSets():
# Ignore atoms to be substituted
if chemAtomOrSet.name[:len(substRemoveAtomName
)] == substRemoveAtomName:
continue
createChemAtomOrSet = CreateChemAtomOrSet(chemAtomOrSet)
if renameSubstituentAtomNames.has_key(chemAtomOrSet.name):
createChemAtomOrSet.setForcedName(
renameSubstituentAtomNames[chemAtomOrSet.name])
else:
createChemAtomOrSet.setName(substUnitIndex)
redoChemAtomSets.extend(
createChemAtomOrSet.setChemAtomLinks(
chemAtomOrSet, substToBaseDict,
substRemoveAtomName)) # Only relevant for chemAtomSets!
if createChemAtomOrSet.checkExistence(baseUnit):
continue
newChemAtomOrSet = createChemAtomOrSet.createNewObject(baseUnit)
createChemAtomOrSet.setAtomSysName(namingSystem)
substToBaseDict[chemAtomOrSet] = newChemAtomOrSet
# Keep track of new chemAtoms, also track coordinates
if newChemAtomOrSet.className in ('LinkAtom', 'ChemAtom'):
substChemAtoms.append(newChemAtomOrSet)
if chemAtomOrSet == substBindingAtom:
baseSubstBindingAtom = newChemAtomOrSet
substCoordsBaseAtoms[1] = newChemAtomOrSet
else:
substCoordsBaseAtoms.append(newChemAtomOrSet)
substCoords.append(
getAtomOrigCoords(rawSubstChemComp,
chemAtomOrSet.name))
#
# 3.2.1 Now set chemAtomSets that are linked to other chemAtomSets - have to do this later because
# otherwise could have not been created yet. Could in principle do this in above loop by
# organising list of chemAtomSets, but this is easier.
#
for chemAtomSet in redoChemAtomSets:
createChemAtomOrSet = CreateChemAtomOrSet(chemAtomSet)
if renameSubstituentAtomNames.has_key(chemAtomSet.name):
createChemAtomOrSet.setForcedName(
renameSubstituentAtomNames[chemAtomSet.name])
else:
createChemAtomOrSet.setName(substUnitIndex)
createChemAtomOrSet.setChemAtomSetLinks()
if createChemAtomOrSet.checkExistence(baseUnit):
continue
newChemAtomSet = createChemAtomOrSet.createNewObject(baseUnit)
createChemAtomOrSet.setAtomSysName(namingSystem)
substToBaseDict[chemAtomSet] = newChemAtomSet
#
# 3.3 Now add all other objects connected to the chemComp (see global chemCompLinkList)
#
# TODO: this is not fully functional - have to add specific settings for some links (but probably never required, so will wait)
#
for ccLinkName in chemCompLinkList:
for substObject in getattr(substUnit, ccLinkName):
createCcpnObject = CreateCcpnObject(substObject)
if not createCcpnObject.setLinks(substToBaseDict):
continue
newCcpnObject = createCcpnObject.createNewObject(baseUnit)
substToBaseDict[substObject] = newCcpnObject
"""
# TODO: LINKS THAT REQUIRE SPECIAL TREATMENT/MERGING WITH EXISTING INFO
# 'chemCompVars', 'applicationData',
# TODO: object that require special treatment (have to be renamed, ...): chemAtomSysNames, chemCompSysNames (?)
"""
#
# 4. Connect base binding atom(s) to the new subsituent atoms
#
for baseBindingAtom in baseBindingAtoms:
#
# 4.1 First remove all chemCompVars and linkEnds that have linking vars including this atom!
#
for chemCompVar in baseBindingAtom.chemCompVars:
deleteVoidChemCompVar(chemCompVar,
'linking',
baseBindingAtomName,
baseUnit,
baseUnitCcc,
actionType='binding')
deleteLinkEnd(baseUnit,
baseBindingAtomName,
actionType='binding')
#
# 4.2 Calculate the new coordinates for the substituent atoms
#
coordsForChemCompVar = {}
if baseAtomCoords.has_key(baseBindingAtom):
for jointCoords in baseAtomCoords[baseBindingAtom]:
newSubstCoords = tuple([
tuple(coord) for coord in superposeNewVectorsOnOld(
jointCoords, substCoords)
])
coordsForChemCompVar[newSubstCoords] = baseAtomCoords[
baseBindingAtom][jointCoords]
#
# 4.3 Now create the bond between the new substituent and the existing base unit
#
baseUnit.newChemBond(chemAtoms=(baseBindingAtom,
baseSubstBindingAtom),
bondType=newBondType,
stereochem=newStereochem)
#print " Creating chemBond between base atom %s and subsituent atom %s" % (baseBindingAtom.name,baseSubstBindingAtom.name)
for chemCompVar in baseBindingAtom.chemCompVars:
#print " ", baseSubstBindingAtom.name, baseSubstBindingAtom.subType,chemCompVar.linking,chemCompVar.descriptor
for substChemAtom in substChemAtoms:
chemCompVar.addChemAtom(substChemAtom)
# TODO: have to RENAME the chemCompVar in case there are variants for the substituent!!
#
# 4.4 Finally set the new coordinates... ignore first one (is the substituted atom from the substituent!)
#
for newSubstCoords in coordsForChemCompVar.keys():
for i in range(1, len(substCoordsBaseAtoms)):
newSubstCoord = newSubstCoords[i]
substChemAtom = substCoordsBaseAtoms[i]
substChemAtomCoord = baseUnitCcc.findFirstChemAtomCoord(
chemAtom=substChemAtom,
x=newSubstCoord[0],
y=newSubstCoord[1],
z=newSubstCoord[2])
if not substChemAtomCoord:
substChemAtomCoord = baseUnitCcc.newChemAtomCoord(
name=substChemAtom.name,
subType=substChemAtom.subType,
x=newSubstCoord[0],
y=newSubstCoord[1],
z=newSubstCoord[2])
for cccv in coordsForChemCompVar[newSubstCoords]:
if not cccv.isDeleted:
cccv.addChemAtomCoord(substChemAtomCoord)
print " Connected new substituent chemAtom %s,%s to base unit atom %s,%s, and included in relevant chemCompVars" % (
baseSubstBindingAtom.name, baseSubstBindingAtom.subType,
baseBindingAtom.name, baseBindingAtom.subType)
#
# NEXT ON LIST: make sure the chemCompVars make sense if there are any for the substituent!!!
#
# ALSO try this on amino acids when working for carbs - need split code and rename some variables though
#
#
# Check validity and save
#
baseUnit.checkAllValid(complete=True)
if baseUnitCcc:
baseUnitCcc.checkAllValid(complete=True)
if saveData:
(filePath,
existingFilePath) = saveTemporaryChemCompOrCoord(baseUnit,
testMode=testMode)
consolidateTemporaryChemCompOrCoord(baseUnit,
filePath,
existingFilePath,
testMode=testMode,
replace=replace)
if baseUnitCcc:
(filePath, existingFilePath) = saveTemporaryChemCompOrCoord(
baseUnitCcc, testMode=testMode)
consolidateTemporaryChemCompOrCoord(baseUnitCcc,
filePath,
existingFilePath,
testMode=testMode,
replace=replace)