def repairPointPdbRecord(tstD=None, tstFileName=False):
'''checks and repairs pointpdbrecord if it has no data in it'''
same = True
if tstD is None: # hasn't been read in already
tstD = tstdata.tstData(
tstFileName, necessaryKeys=tstdata.tstData.necessaryKeysForPocket)
lastPdbNum = tstD.dict['POINT_PDB_RECORD'][0][1]-1
for pointPdb in tstD.dict['POINT_PDB_RECORD']:
pdbNum = pointPdb[1]-1
if pdbNum != lastPdbNum:
same = False
if same: # needs repaired, otherwise this is over
pdbD = pdb.pdbData()
for line in tstD.dict['PDB_RECORD']:
pdbD.processLine(line)
ptCoords = {}
for pointXyz in tstD.dict['POINT_XYZ']:
ptCoords[pointXyz[0]] = tuple(pointXyz[1:])
coordToNearbyAtoms = pdbD.getNearbyAtoms(ptCoords.values())
newPointPdbRec = []
for pointPdb in tstD.dict['POINT_PDB_RECORD']:
atomFound = coordToNearbyAtoms[ptCoords[pointPdb[0]]][0]
newPointPdbRec.append([pointPdb[0], atomFound])
#replace old record with new record
tstD.dict['POINT_PDB_RECORD'] = newPointPdbRec
if tstFileName:
tstFile = open(tstFileName, 'a') # append into file
tstdata.writeEntryIntegers(
tstD.dict['POINT_PDB_RECORD'], "POINT_PDB_RECORD",
"END POINT_PDB_RECORD", tstFile)
tstFile.close()
def tstPocketMap(
tstFileName, phiFileName, tstD=None, ligandFileName=None,
nearbyDistance=0., appendTst=True, doPCA=True):
'''pocket mapping algorithm, finds all pockets on entire surface, puts in
tree and graph data structure, various outputs'''
print "read tst file"
if tstD is None: # hasn't been read in already
tstD = tstdata.tstData(
tstFileName, necessaryKeys=tstdata.tstData.necessaryKeysForPocket)
print "repairing nearby points if necessary"
repairPointPdbRecord(tstD, tstFileName)
print "calculating charges"
chargeXyz, hydroXyz = calculateCharges(tstD, charge.charge())
print "calculating curvatures"
edgeCurv, ptCurv, ptWeighCurv = tstCurvature.tstEdgeCurvature(
tstD.dict['TRIANGLE_POINT'], tstD.dict['POINT_XYZ'],
tstD.dict['POINT_TRIANGLE'], tstD.dict['POINT_NEIGHBOR'])
tstD.dict['POINT_CURVATURE_EDGE'] = ptWeighCurv
tstD.dict['CHARGE_XYZ'] = chargeXyz
tstD.dict['HYDROPHOBIC_XYZ'] = hydroXyz
print "read in phi file"
phiData = phi(phiFileName) # read in the phimap
print "making mesh data structure"
meshData, gridData = meshConstruct(
tstD, phiData, tstFileName, threshold="auto", cavities=True)
meshData.setPtHydro(tstD.dict['HYDROPHOBIC_XYZ'])
meshData.setPtCurvature(tstD.dict['POINT_CURVATURE_EDGE'])
gridSize = 1.0/phiData.scale
tstPdbRecord = tstD.dict['PDB_RECORD']
meshData.setSurfaceArea(tstD.dict['TRIANGLE_POINT'])
del tstD, phiData, gridData # not needed, reclaim memory
pdbD = pdb.pdbData()
pdbD.processLines(tstPdbRecord)
pointAtomList = meshData.calculateNearbyAtoms(pdbD, nearbyDistance)
meshData.setVolume(gridSize)
print "calculating travel depth"
meshData.calculateTravelDistance("traveldepth", [0], [2, 3, 5])
pointTravelDepth = meshData.getSurfaceTravelDistance("traveldepth")
if ligandFileName is not None: # if there is a ligand, read it
ligand = pdb.pdbData(ligandFileName)
ligandXYZR = ligand.getHeavyAtomXYZRadius()
nodeWithinSet = meshData.getWithinNodesNoInside(ligandXYZR)
bestIU = 0. # intersection / union, 1 is perfect
#print nodeWithinSet, len(nodeWithinSet)
print "pocket mapping starting"
if ligandFileName is not None and len(nodeWithinSet) > 0:
outFileName = ligandFileName
#tstdebug.nodeDebug(nodeWithinSet, \
# filename = tstFileName+".within.ligand.py")
localMaxima, borders, tm3tree, surfNodeToLeaf = meshData.pocketMapping(
'traveldepth', [2, 3, 5], pointAtomList, pdbD,
outName=outFileName + ".", groupName='group',
ligandNodes=nodeWithinSet, doPCA=doPCA)
else:
outFileName = tstFileName
localMaxima, borders, tm3tree, surfNodeToLeaf = meshData.pocketMapping(
'traveldepth', [2, 3, 5], pointAtomList, pdbD,
outName=outFileName + ".", groupName='group', doPCA=doPCA)
#print len(localMaxima), len(borders), tm3tree, len(surfNodeToLeaf)
#tstdebug.nodeDebug(localMaxima, \
# filename=tstFileName+".localmaxima.pocketmap.py")
#tstdebug.nodeDebug(borders, \
# filename=tstFileName+".borders.pocketmap.py")
#tstdebug.nodeDebug(meshData.getSurfaceNodes(), \
# filename=tstFileName+".groups.pocketmap.py", name='group')
tm3tree.write(outFileName + ".tree.tm3")
#tm3tree.writeTNV(tstFileName + ".tree.tnv")
#doesn't seem to import into treemap correctly
if appendTst: # turn off sometimes since appends to tst file
print "appending data to tst file"
surfNodes = meshData.getSurfaceNodes()
pointLeafList = []
for aNode in surfNodes:
if aNode not in surfNodeToLeaf:
print aNode, aNode.distances
leafNum = 0 # made up and wrong for testing
else:
leafNum = surfNodeToLeaf[aNode]
pointLeafList.append([aNode, int(leafNum)])
#print pointLeafList
leafToGroup = tm3tree.getLeafToGroup()
leafGroupList = []
leafKeyMax = max(leafToGroup.keys())
for leaf in xrange(leafKeyMax):
tempList = [leaf + 1]
try:
tempList.extend(leafToGroup[leaf + 1])
except KeyError:
pass # means leaf doesn't exist
leafGroupList.append(tempList)
#print leafGroupList
tstFile = open(tstFileName, 'a')
tstdata.writeEntryIntegers(
pointLeafList, "POINT_LEAF LIST", "END POINT_LEAF", tstFile)
tstdata.writeEntryIntegers(
leafGroupList, "LEAF_GROUP LIST", "END LEAF_GROUP", tstFile)
tstdata.writeEntryIntegers(
pointAtomList, "POINT_NEARBY_ATOM LIST", "END POINT_NEARBY_ATOM",
tstFile)
#also write curvature and charge data here
tstdata.writeEntrySingleFloat(
ptWeighCurv, "POINT_CURVATURE_EDGE LIST", "END POINT_CURVATURE_EDGE",
tstFile)
tstdata.writeEntrySingleFloat(
chargeXyz, "CHARGE_XYZ", "END CHARGE_XYZ", tstFile)
tstdata.writeEntrySingleFloat(
hydroXyz, "HYDROPHOBIC_XYZ", "END HYDROPHOBIC_XYZ", tstFile)
#write data to file
tstFile.write("DEPTH_TRAVEL_DIST\n")
for line in pointTravelDepth:
lineOut = "%8d" % line[0]
for count in xrange(1, len(line)):
lineOut += "%+9.4f " % line[count]
noPlusLine = string.replace(lineOut, "+", " ")
tstFile.write(noPlusLine)
tstFile.write("\n")
tstFile.write("END DEPTH_TRAVEL_DIST\n")
tstFile.close()
print "pocket mapping complete"
