def analyzePdbBCompareFiles(firstFilename, compareFilename):
residues = ({}, {}) # a dict of dicts where the sub-dicts keys are atom names
pdbs = ([], []) # each list is a pdb, which has a dictionary of residues
for lindex, listFilename in enumerate((firstFilename, compareFilename)):
filenameList = []
if listFilename:
listFile = open(listFilename, 'r')
try:
for line in listFile:
if len(line) == 6:
filenameList.append(
line[0:4] + "." + line[4] + ".nocav.tst.mesh.travelin.pdb")
if len(line) == 5: # analyze non-domains
filenameList.append(line[0:4] + ".nocav.tst.mesh.travelin.pdb")
except StopIteration:
pass
listFile.close()
if filenameList:
for filename in filenameList:
pdbD = pdb.pdbData(filename)
tempRes = {}
for index, resName in enumerate(pdbD.resNames):
if pdbD.radii[index] > 0.:
if resName not in tempRes:
tempRes[resName] = {}
if resName not in residues[lindex]:
residues[lindex][resName] = {} # init sub-dict
if string.strip(pdbD.atoms[index]) not in residues[lindex][resName]:
residues[lindex][resName][string.strip(pdbD.atoms[index])] = []
if string.strip(pdbD.atoms[index]) not in tempRes[resName]:
tempRes[resName][string.strip(pdbD.atoms[index])] = []
#if pdbD.factors[index][1] > 30:
# #print pdbD.factors[index][1], filename #debugging
#print pdbD.atoms[index],
residues[lindex][resName][string.strip(pdbD.atoms[index])].append(
pdbD.factors[index][1])
tempRes[resName][string.strip(pdbD.atoms[index])].append(
pdbD.factors[index][1])
pdbs[lindex].append(tempRes)
#residues now contains all the b-factor (travelin) data
#need to change after this line to call new methods
listFilename = firstFilename + "." + compareFilename
analyzePdbB.makeCompareResidueReport(
residues, listFilename + ".residue.bfactor")
#do alternate pvalue tests and by file comparisons with pdbs lists
corrAll, corrBeta = analyzePdbB.makeCompareResidueReportAlternate(
pdbs, listFilename + ".residue.alt.bfactor")
#now do a p-value comparison that is corrected for the overall depth diffs
analyzePdbB.makeCompareResidueReportAlternate(
pdbs, listFilename + ".residue.alt.corr.bfactor",
correctionAll=corrAll, correctionBeta=corrBeta)
analyzePdbB.makeMeanPerProteinReport(
pdbs, outName=listFilename + ".meansbypdb.txt")
def analyzePdbBCompareFiles(firstFilename):
pdbs = {} # each list is a pdb, which has a dictionary of residues
filenameList = []
if firstFilename:
listFile = open(firstFilename, 'r')
try:
for line in listFile:
if len(line) == 6:
filenameList.append(
line[0:4] + "." + line[4] + ".nocav.tst.mesh.travelin.pdb")
elif len(line) == 5: # analyze non-domains
filenameList.append(line[0:4] + ".nocav.tst.mesh.travelin.pdb")
elif len(line) > 8:
filenameList.append(line[:-1])
else: # yeah just allow anything
filenameList.append(line[:-1])
except StopIteration:
pass
listFile.close()
if filenameList:
for filename in filenameList:
pdbs[filename] = []
pdbD = pdb.pdbData(filename)
tempRes = {}
for index, resName in enumerate(pdbD.resNames):
if pdbD.radii[index] > 0.:
if resName not in tempRes:
tempRes[resName] = {}
if string.strip(pdbD.atoms[index]) not in tempRes[resName]:
tempRes[resName][string.strip(pdbD.atoms[index])] = []
tempRes[resName][string.strip(pdbD.atoms[index])].append(
pdbD.factors[index][1])
pdbs[filename] = tempRes
#residues now contains all the b-factor (travelin) data
#need to change after this line to call new methods
listFilename = firstFilename
analyzePdbB.makeMeanPerProteinReport(
pdbs, outName=listFilename + ".meansbypdb.txt")
