def getMolTypes():
'Return True on error'
outputFile = 'moltypes.csv'
pdbList = PDBEntryLists.getBmrbNmrGridEntries()[0:2]
#pdbList = PDBEntryLists.getBmrbNmrGridEntries()
#pdbList=['1a03']
#pdbList=['1brv']
print "Read pdb entries from NMR Restraints Grid:", len( pdbList )
pdbList.sort()
molTypes = {}
seq_length = {}
for entry in pdbList:
try:
inputFN = os.path.join(starDir,entry,entry+'_wattos.str')
headFN = os.path.join(tmpDir, entry+'_head.str')
f = File()
saveFrameRegExList = [r"^save_.*constraints", r"^save_conformer"]
f.getHeader(saveFrameRegExList, inputFN, headFN)
f.filename = headFN
f.read()
os.unlink( f.filename ) # removing temp file.
molTypesPerEntry = {}
molTypes[entry] = molTypesPerEntry
seq_lengthPerEntry = {}
seq_length[entry] = seq_lengthPerEntry
sfList = f.getSaveFrames( category = 'entity')
for node in sfList:
tT = node.tagtables[0]
# print tT
typeIdx = tT.tagnames.index('_Entity.Type')
# print typeIdx
type = tT.tagvalues[typeIdx][0]
poltype = ''
if '_Entity.Polymer_type' in tT.tagnames:
poltypeIdx = tT.tagnames.index('_Entity.Polymer_type')
# print poltypeIdx
poltype = tT.tagvalues[poltypeIdx][0]
# print "type", type, ", and poltype", poltype
key = type +'/' + poltype
if molTypesPerEntry.has_key(key):
molTypesPerEntry[key] += 1
else:
molTypesPerEntry[key] = 1
lengthIdx = -1
if '_Entity.Number_of_monomers' in tT.tagnames:
lengthIdx = tT.tagnames.index('_Entity.Number_of_monomers')
if lengthIdx>=0:
length = string.atoi(tT.tagvalues[lengthIdx][0])
else:
length = 0
if seq_lengthPerEntry.has_key(key):
seq_lengthPerEntry[key] += length
else:
seq_lengthPerEntry[key] = length
for key in molTypes[entry].keys():
str = entry+","+key+','+`molTypes[entry][key]`+','+`seq_length[entry][key]`
print str
except KeyboardInterrupt:
print "ERROR: Caught KeyboardInterrupt will exit(1)"
return True
except Exception, info:
print "Skipping entry: ", entry, info
pdbList = PDBEntryLists.getBmrbNmrGridEntries()[0:200]
#pdbList = PDBEntryLists.getBmrbNmrGridEntries()
#pdbList=['1a03']
#pdbList=['1brv']
print "Read pdb entries from NMR Restraints Grid:", len(pdbList)
pdbList.sort()
molTypes = {}
seq_length = {}
for entry in pdbList:
try:
inputFN = os.path.join(starDir, entry, entry + '_wattos.str')
headFN = os.path.join(tmpDir, entry + '_head.str')
f = File()
saveFrameRegExList = [r"^save_.*constraints", r"^save_conformer"]
f.getHeader(saveFrameRegExList, inputFN, headFN)
f.filename = headFN
f.read()
os.unlink(f.filename) # removing temp file.
molTypesPerEntry = {}
molTypes[entry] = molTypesPerEntry
seq_lengthPerEntry = {}
seq_length[entry] = seq_lengthPerEntry
sfList = f.getSaveFrames(category='entity')
for node in sfList:
tT = node.tagtables[0]
# print tT
typeIdx = tT.tagnames.index('_Entity.Type')
# print typeIdx
type = tT.tagvalues[typeIdx][0]
poltype = ''
