def checkPathTst(tstFileName, pathFileName):
path = comparePaths.readCGOPath(pathFileName)
tstD = tstdata.tstData(tstFileName)
loopTris, loopPoints = tstTopology.getLoopsAndVerticesTst(tstD)
throughTris, throughPts = paths.checkPathPoints(
path, loopPoints, tstD.dict['POINT_XYZ'])
if throughTris: # it worked... make some more debugging output
tstdebug.debugTrianglesNotOrig(
throughTris, tstD.dict['POINT_XYZ'],
tstFileName + ".path.through.loop.py", ptList=throughPts)
print "path goes through a hole"
else:
print "path does NOT go through a hole"
def checkPathBarriers(prefix):
tstName = prefix + ".nocav.tst"
findHolesName = tstName + ".findholes.log"
findHolesFile = open(findHolesName, 'r')
findHolesLines = findHolesFile.readlines()
findHolesFile.close()
HolesName = tstName + ".sideshole.log" # holds all the output
goodHolesName = tstName + ".good.sideshole.log" # just the 1 1 0 1 1
sideHolesName = tstName + ".side.sideshole.log" # just the * * 1 * *
badHolesName = tstName + ".bad.sideshole.log" # all others
pdbWithBarriersFileName = "planes_" + prefix + ".pdb"
pdbBarriers = pdb.pdbData(pdbWithBarriersFileName)
#get the barriers read in and defined
barrierAtomList = [[], []]
for index, resName in enumerate(pdbBarriers.resNames):
if resName == "DUM":
if pdbBarriers.atoms[index][0] == "O":
barrierAtomList[0].append(pdbBarriers.coords[index])
elif pdbBarriers.atoms[index][0] == "N":
barrierAtomList[1].append(pdbBarriers.coords[index])
barrierZ = [barrierAtomList[0][0][2], barrierAtomList[1][0][2]]
barrierZ.sort()
barrierSep = geometry.distL2(barrierAtomList[0][0], barrierAtomList[1][0])
#barrier is just Z coordinate
#setup for main loop over paths
poreSuffix = ".pore.py"
logFile = open(HolesName, 'w')
goodLogFile = open(goodHolesName, 'w')
sideLogFile = open(sideHolesName, 'w')
badLogFile = open(badHolesName, 'w')
#the following 5 things are calculated and written for each path, headers
#the 6th, barrier separation, is really the same for each structure
logFile.write("endsBeyond1count barrier1count endsBetweenCount ")
logFile.write("barrier2count endsBeyond2count barrierSeparation\n")
goodLogFile.write("prefix ")
goodLogFile.write(string.strip(findHolesLines[0]) + " ")
goodLogFile.write("endsBeyond1count barrier1count endsBetweenCount ")
goodLogFile.write("barrier2count endsBeyond2count barrierSeparation\n")
sideLogFile.write("prefix ")
sideLogFile.write(string.strip(findHolesLines[0]) + " ")
sideLogFile.write("endsBeyond1count barrier1count endsBetweenCount ")
sideLogFile.write("barrier2count endsBeyond2count barrierSeparation\n")
badLogFile.write("prefix ")
badLogFile.write(string.strip(findHolesLines[0]) + " ")
badLogFile.write("endsBeyond1count barrier1count endsBetweenCount ")
badLogFile.write("barrier2count endsBeyond2count barrierSeparation\n")
holeNumber = 1
poreFile = tstName + "." + str(holeNumber) + poreSuffix
print poreFile
paths = []
sides, goods = [], []
endsToPaths = {}
pathsToEnds = {}
while os.path.exists(poreFile):
path = comparePaths.readCGOPath(poreFile)
pathRad = comparePaths.readCGOPathWithRadius(poreFile)
paths.append(pathRad)
pathNum = len(paths) - 1
for end in string.split(findHolesLines[holeNumber])[1:3]:
if pathNum not in pathsToEnds:
pathsToEnds[pathNum] = []
pathsToEnds[pathNum].append(end)
if end not in endsToPaths:
endsToPaths[end] = []
endsToPaths[end].append(pathNum)
intersections = [0, 0]
for index, barrier in enumerate(barrierZ):
intersections[index] = countCrossingsZ(path, barrier)
ends = [0, 0, 0]
for endPoint in [path[0], path[-1]]:
endPointZ = endPoint[2]
if endPointZ < barrierZ[0] and endPointZ < barrierZ[1]:
ends[0] += 1
elif endPointZ >= barrierZ[0] and endPointZ <= barrierZ[1]:
ends[1] += 1
elif endPointZ > barrierZ[0] and endPointZ > barrierZ[1]:
ends[2] += 1
outputThisTime = str(ends[0]) + " " + str(intersections[0]) + " " + \
str(ends[1]) + " " + str(intersections[1]) + " " + \
str(ends[2]) + " " + str(barrierSep) + " "
logFile.write(outputThisTime)
logFile.write("\n")
if ends[0] + ends[1] + ends[2] != 2:
print "problems sorting out the ends"
if ends[0] == 1 and ends[2] == 1 and intersections == [1, 1]:
#it is 'good'
goods.append(pathNum)
goodLogFile.write(prefix + " ")
goodLogFile.write(string.strip(findHolesLines[holeNumber]) + " ")
goodLogFile.write(outputThisTime + "\n")
elif ends[1] == 1:
sides.append(pathNum)
sideLogFile.write(prefix + " ")
sideLogFile.write(string.strip(findHolesLines[holeNumber]) + " ")
sideLogFile.write(outputThisTime + "\n")
else:
badLogFile.write(prefix + " ")
badLogFile.write(string.strip(findHolesLines[holeNumber]) + " ")
badLogFile.write(outputThisTime + "\n")
#and that is it for this path
holeNumber += 1 # get set up for next pass
poreFile = tstName + "." + str(holeNumber) + poreSuffix
logFile.close()
goodLogFile.close()
sideLogFile.close()
badLogFile.close()
#next lines are for debugging the new data structures
'''
print sides
print goods
print endsToPaths
print pathsToEnds
'''
#now want to find side branches of good paths
branches = 0
branchSuffix = ".branch.py"
branchFile = tstName + "." + str(branches) + branchSuffix
branchLog = open(tstName + ".branchholes.log", 'w')
branchLog.write(string.strip(findHolesLines[0]) + "\n")
for side in sides:
foundGoods = []
for sideEnd in pathsToEnds[side]:
for good in goods:
for goodEnd in pathsToEnds[good]:
if goodEnd == sideEnd:
foundGoods.append(good)
if len(foundGoods) > 0:
branchedPath = paths[side] # start with whole path
for good in foundGoods: # remove physiological intersecting paths
branchedPath = pathsModule.subtractPaths(branchedPath, paths[good])
if len(branchedPath) > 0: # has to have some length remaining
branches += 1
branchFile = tstName + "." + str(branches) + branchSuffix
print branches, side, foundGoods
tstdebug.debugSetGridSpheres(
branchedPath, 0.5, branchFile, radius=True,
mainColor=(0.01, 0.9, 0.35))
branchLog.write(str(branches) + " ")
branchLog.write(str(pathsToEnds[side][0]) + " ")
branchLog.write(str(pathsToEnds[side][1]) + " ")
branchLog.write("- ") # dummy, not real
branchLog.write("0. 0. 0. 0. 0. 0. 0. 0. 0. 0. \n")
branchLog.close()
addFoundHoleStats.redoFindholes(
prefix, nearbyDistance=4., logExt=".branchholes.log",
poreSuffix=".branch.py", nearbyName=".branch")
def checkPathBarriers(prefix):
tstName = prefix + ".nocav.tst"
findHolesName = tstName + ".findholes.log"
findHolesFile = open(findHolesName, 'r')
findHolesLines = findHolesFile.readlines()
findHolesFile.close()
HolesName = tstName + ".membranehole.log" # holds all the output
goodHolesName = tstName + ".good.membranehole.log" # just the 1 1 0 1 1
sideHolesName = tstName + ".side.membranehole.log" # just the * * 1 * *
badHolesName = tstName + ".bad.membranehole.log" # all others
pdbWithBarriersFileName = "planes_" + prefix + ".pdb"
pdbBarriers = pdb.pdbData(pdbWithBarriersFileName)
#get the barriers read in and defined
barrierAtomList = [[], []]
for index, resName in enumerate(pdbBarriers.resNames):
if resName == "DUM":
if pdbBarriers.atoms[index][0] == "O":
barrierAtomList[0].append(pdbBarriers.coords[index])
elif pdbBarriers.atoms[index][0] == "N":
barrierAtomList[1].append(pdbBarriers.coords[index])
barrierZ = [barrierAtomList[0][0][2], barrierAtomList[1][0][2]]
barrierZ.sort()
barrierSep = geometry.distL2(barrierAtomList[0][0], barrierAtomList[1][0])
#barrier is just Z coordinate
#setup for main loop over paths
poreSuffix = ".pore.py"
logFile = open(HolesName, 'w')
goodLogFile = open(goodHolesName, 'w')
sideLogFile = open(sideHolesName, 'w')
badLogFile = open(badHolesName, 'w')
#the following 5 things are calculated and written for each path, headers
#the 6th, barrier separation, is really the same for each structure
logFile.write("endsBeyond1count barrier1count endsBetweenCount ")
logFile.write("barrier2count endsBeyond2count barrierSeparation\n")
goodLogFile.write("prefix ")
goodLogFile.write(string.strip(findHolesLines[0]) + " ")
goodLogFile.write("endsBeyond1count barrier1count endsBetweenCount ")
goodLogFile.write("barrier2count endsBeyond2count barrierSeparation\n")
sideLogFile.write("prefix ")
sideLogFile.write(string.strip(findHolesLines[0]) + " ")
sideLogFile.write("endsBeyond1count barrier1count endsBetweenCount ")
sideLogFile.write("barrier2count endsBeyond2count barrierSeparation\n")
badLogFile.write("prefix ")
badLogFile.write(string.strip(findHolesLines[0]) + " ")
badLogFile.write("endsBeyond1count barrier1count endsBetweenCount ")
badLogFile.write("barrier2count endsBeyond2count barrierSeparation\n")
holeNumber = 1
poreFile = tstName + "." + str(holeNumber) + poreSuffix
print poreFile
paths = []
sides = []
while os.path.exists(poreFile):
path = comparePaths.readCGOPath(poreFile)
paths.append(path)
intersections = [0, 0]
for index, barrier in enumerate(barrierZ):
intersections[index] = countCrossingsZ(path, barrier)
ends = [0, 0, 0]
for endPoint in [path[0], path[-1]]:
endPointZ = endPoint[2]
if endPointZ < barrierZ[0] and endPointZ < barrierZ[1]:
ends[0] += 1
elif endPointZ >= barrierZ[0] and endPointZ <= barrierZ[1]:
ends[1] += 1
elif endPointZ > barrierZ[0] and endPointZ > barrierZ[1]:
ends[2] += 1
outputThisTime = str(ends[0]) + " " + str(intersections[0]) + " " + \
str(ends[1]) + " " + str(intersections[1]) + " " + \
str(ends[2]) + " " + str(barrierSep) + " "
logFile.write(outputThisTime)
logFile.write("\n")
if ends[0] + ends[1] + ends[2] != 2:
print "problems sorting out the ends"
if ends[0] == 1 and ends[2] == 1 and intersections == [1, 1]:
# it is 'good'
goodLogFile.write(prefix + " ")
goodLogFile.write(string.strip(findHolesLines[holeNumber]) + " ")
goodLogFile.write(outputThisTime + "\n")
elif ends[1] == 2:
sides.append(len(paths) - 1)
sideLogFile.write(prefix + " ")
sideLogFile.write(string.strip(findHolesLines[holeNumber]) + " ")
sideLogFile.write(outputThisTime + "\n")
else:
badLogFile.write(prefix + " ")
badLogFile.write(string.strip(findHolesLines[holeNumber]) + " ")
badLogFile.write(outputThisTime + "\n")
#and that is it for this path
holeNumber += 1 # get set up for next pass
poreFile = tstName + "." + str(holeNumber) + poreSuffix
print sides
logFile.close()
goodLogFile.close()
sideLogFile.close()
badLogFile.close()