def tstTravelDepthMesh(
tstFileName, phiFileName, ligandFileName=None, cavities=False,
threshold="auto"):
'''sets up a normal travel depth mesh run, calls tstTravelDepthMeshRun.
if cavities is set, it means we want the (new) travel depth of those too'''
distanceName = 'traveldepth'
tstD = tstdata.tstData(tstFileName) # read the file into the data structure
phiData = phi(phiFileName) # read in the phimap if possible
phiGridSpacing = 1. / phiData.scale
phiTravelDepthGrid, phiTravelDepth, meshData = tstTravelDepthMeshRun(
tstD, phiData, tstFileName, cavities=cavities,
threshold=threshold) # modifies tstD in place
if ligandFileName is not None:
ligand = pdb.pdbData(ligandFileName)
ligandXYZR = ligand.getHeavyAtomXYZRadius()
betweenList = meshData.getBetweenNodes()
surfaceList = meshData.getSurfaceNodes()
nodeWithinSet = meshData.getWithinNodesNoInside(ligandXYZR)
#print len(nodeWithinSet), len(ligandXYZR)
tracebackSet = meshData.getTracebackSet(nodeWithinSet, distanceName)
#print len(tracebackSet)
minW, maxW, meanW = meshData.getMinMaxMeanNodes(nodeWithinSet, distanceName)
minT, maxT, meanT = meshData.getMinMaxMeanNodes(tracebackSet, distanceName)
minB, maxB, meanB = meshData.getMinMaxMeanNodes(betweenList, distanceName)
minS, maxS, meanS = meshData.getMinMaxMeanNodes(surfaceList, distanceName)
#print all on one line, header printed earlier
print minW, maxW, meanW,
print minT, maxT, meanT,
print minB, maxB, meanB,
print minS, maxS, meanS,
volumeWithin = len(nodeWithinSet) * phiGridSpacing**3.
volumeTrace = len(tracebackSet) * phiGridSpacing**3.
print volumeWithin, volumeTrace # newline wanted here so no comma
#print phiGridSpacing
listWithin, listTrace = [], []
for node in nodeWithinSet:
listWithin.append(node.getXYZ())
for node in tracebackSet:
listTrace.append(node.getXYZ())
tstdebug.pointDebug(listWithin, filename=ligandFileName+".within.py")
tstdebug.pointDebug(listTrace, filename=ligandFileName+".trace.py")
#tstdebug.debugGridCountVals(phiTravelDepthGrid)
#transform grid to actual travel distance
phiTravelDepth.write(tstFileName+".travel.phi")
#write data to file
tstFile = open(tstFileName, 'a')
tstFile.write("DEPTH_TRAVEL_DIST\n")
for line in tstD.dict['DEPTH_TRAVEL_DIST']:
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()
def tstTravelFindHoles(
tstFileName, phiFileName, debugOut=False, borderSize=2, nearbyDistance=4.):
'''if debugout is set, additional files are created.
bordersize can change the amount of extra space around the protein.
nearbydistance changes the distance that nearby residues are gathered from.'''
print "reading tst and phi files"
tstD = tstdata.tstData(
tstFileName, necessaryKeys=tstdata.tstData.necessaryKeysForHoles)
phiData = phi(phiFileName) # read in the phimap if possible
gridSize = 1.0 / phiData.scale # needed later
numberHandles = tstD.countHandles()
print "there are ", numberHandles, " holes in this structure"
print "running travel depth now"
phiTravelDepthGrid, phiTravelDepthData, meshData = tstTravelDepthMeshRun(
tstD, phiData, tstFileName, borderSize=borderSize, threshold="auto")
del phiData, phiTravelDepthGrid, phiTravelDepthData
#not needed, reclaim memory
print "calculating travel out distance"
meshData.calculateTravelDistance("surfout", [3], [0, 2])
print "finding holes"
loopTrisSave, loopPointsSave, regLoopTris, regLoopPts, pointNeighbors, \
pointNeighborsNodes, outsidePoints, outsidePointsNodes, possHoleStarts = \
tstTopology.fillInHolesAndGrow(
tstD.dict['TRIANGLE_POINT'], tstD.dict['POINT_TRIANGLE'],
tstD.dict['POINT_XYZ'], tstD.dict['NORM_XYZ'], numberHandles,
tstFileName, debugOut, meshData, "surfout")
if debugOut:
tstdebug.debugTriangleList(
regLoopTris, tstD.dict['TRIANGLE_POINT'], tstD.dict['POINT_XYZ'],
tstFileName + ".regular.loops.py")
tstDPointXYZ = tstD.dict['POINT_XYZ'] # save for later
tstDPdbRecord = tstD.dict['PDB_RECORD'] # save for later
del tstD # rest of tstD isn't needed, so free memory
#output the possible places where HOLE could start... centers of regular plugs
print "writing output files"
paths.outputNodesText(possHoleStarts, tstFileName + ".HOLE.start.txt")
pathsList = meshData.getPaths(
"surfout", pointNeighbors, outsidePoints, possHoleStarts)
del meshData # deletes everything that has no other refs (from paths)
#print len(pointNeighbors), len(outsidePoints), len(possHoleStarts),
#print len(pathsList)
allPoints, outsidePts = [], []
for point in pointNeighborsNodes.keys():
allPoints.append(point.pathXyz)
for point in outsidePointsNodes:
outsidePts.append(point.pathXyz)
tstdebug.pointDebug(allPoints, filename=tstFileName+".tree.py")
tstdebug.pointDebug(
outsidePts, filename=tstFileName+".outside.py", mainColor=(.9, .1, .1),
radius=0.55)
#tstdebug.debugSetGridSpheres(
# pointNeighbors.keys(),, gridSize, tstFileName+".tree.radius.py",
# radius=True, mainColor=(0.01, 0.9, 0.05))
#testing new output of tree with radius
foundPaths = 0
pathFile = string.replace(tstFileName, ".nocav.tst", ".py")
#very very specific... probably bad but nice...
#can always rerun standalone later.
knownPathExists = os.path.isfile(pathFile)
logName = tstFileName + ".findholes.log"
logFile = open(logName, 'w')
logFile.write(
"number endNumOne endNumTwo plugs stepLength pathLength pathMinRadius " +
"pathMaxInsideRadius endMinOne endMinTwo minimaCount travelDepthMax " +
"windingMetric avgTheta ")
if knownPathExists:
logFile.write("pRMSD coverage span wrmsd less1 lessrad radiicomp")
logFile.write("\n")
if knownPathExists:
bestStats = ["err", "err", "err", "err", "err", "err", "err"]
bestStatsPaths = [0, 0, 0, 0, 0, 0, 0]
sortedByMinRadiusPaths = []
for pathIndex, (outsideOne, outsideTwo, plugs, nodePath) in enumerate(
pathsList):
pointPath, spheres = [], []
for node in nodePath:
pointPath.append(list(node.pathXyz))
spheres.append(list(node.pathXyz))
pointRadius = node.distances["surfout"] # add 'radius' info
if not pointRadius or pointRadius == 0.:
pointRadius = .000000001 # very small number, on surface
pointPath[-1].insert(0, pointRadius)
spheres[-1].append(pointRadius)
minRad = paths.pathMinRadius(pointPath)
newTuple = (
minRad, outsideOne, outsideTwo, plugs, nodePath, pointPath, spheres)
#insertion sort into new list
position = 0
while position < len(sortedByMinRadiusPaths) and \
sortedByMinRadiusPaths[position][0] > minRad:
#only if list can handle it and already inserted are bigger
position += 1
sortedByMinRadiusPaths.insert(position, newTuple)
print "output files for individual paths"
for pathIndex, newTuple in enumerate(sortedByMinRadiusPaths):
(minRad, outsideOne, outsideTwo, plugs, nodePath, pointPath, spheres) = \
newTuple # unpack the tuple into the various data
throughTris, throughPts = paths.checkPath(
pointPath, loopPointsSave, tstDPointXYZ)
if throughTris: # it worked... make some more debugging output
foundPaths += 1
outName = tstFileName + "." + str(foundPaths)
if debugOut and throughTris:
tstdebug.debugTrianglesNotOrig(
throughTris, tstDPointXYZ, outName+".through.loop.py",
ptList=throughPts)
#always do these 2
tstdebug.debugSetGridSpheres(
pointPath, gridSize, outName + ".pore.py", radius=True,
mainColor=(0.01, 0.9, 0.05))
tstdebug.debugSetGridSpheres(
pointPath, gridSize, outName + ".path.py", mainColor=(.01, 0.95, 0.9))
#mesh.meshFromSpheres(spheres, 0.5, outName + ".points.py")
paths.outputRadiiTxt(pointPath, outName + ".radii.txt")
paths.outputNearbyResidues(
pointPath, outName, tstDPdbRecord, nearbyDistance)
pathLen = paths.pathLength(pointPath)
minimaCount = paths.pathMinimaCount(pointPath)
maxRad, endMinOne, endMinTwo = paths.insideTwoMinimaRadiusMax(pointPath)
travelDepthMax = paths.pathMaxDistance(nodePath, 'traveldepth')
windingMetric = paths.computeWindingMetric(pointPath)
thetas, avgTheta = paths.averageTheta(pointPath)
#print endMinOne, endMinTwo, minimaCount, travelDepthMax, windingMetric,
#print avgTheta
#attempt to do pRMSD if possible...
prmsd, coverage, span, wrmsd, less1, lessrad, radiicomp = \
"err", "err", "err", "err", "err", "err", "err"
if knownPathExists:
try:
sourcePath, sourceRadii = [], []
for pathPt in pointPath:
sourcePath.append(pathPt[1:4])
sourceRadii.append(pathPt[0])
prmsd, coverage, span, wrmsd, less1, lessrad, radiicomp = \
comparePathsManyMetrics(False, pathFile, sourcePath, sourceRadii)
if bestStats[0] == 'err' or bestStats[0] > prmsd:
bestStats[0] = prmsd
bestStatsPaths[0] = foundPaths
if bestStats[1] == 'err' or bestStats[1] < coverage:
bestStats[1] = coverage
bestStatsPaths[1] = foundPaths
if bestStats[2] == 'err' or bestStats[2] < span:
bestStats[2] = span
bestStatsPaths[2] = foundPaths
if bestStats[3] == 'err' or bestStats[3] > wrmsd:
bestStats[3] = wrmsd
bestStatsPaths[3] = foundPaths
if bestStats[4] == 'err' or bestStats[4] < less1:
bestStats[4] = less1
bestStatsPaths[4] = foundPaths
if bestStats[5] == 'err' or bestStats[5] < lessrad:
bestStats[5] = lessrad
bestStatsPaths[5] = foundPaths
if bestStats[6] == 'err' or bestStats[6] < radiicomp:
bestStats[6] = radiicomp
bestStatsPaths[6] = foundPaths
except (IOError, TypeError):
#if there is no known path file, this should be the error
pass
#now output data
logFile.write(str(foundPaths) + " ")
logFile.write(str(outsideOne) + " ")
logFile.write(str(outsideTwo) + " ")
logFile.write(str(plugs) + " ")
logFile.write(str(len(pointPath)) + " ")
logFile.write(str(pathLen) + " ")
logFile.write(str(minRad) + " ")
logFile.write(str(maxRad) + " ")
logFile.write(str(endMinOne) + " ")
logFile.write(str(endMinTwo) + " ")
logFile.write(str(minimaCount) + " ")
logFile.write(str(travelDepthMax) + " ")
logFile.write(str(windingMetric) + " ")
logFile.write(str(avgTheta) + " ")
if knownPathExists:
logFile.write(str(prmsd) + " ")
logFile.write(str(coverage) + " ")
logFile.write(str(span) + " ")
logFile.write(str(wrmsd) + " ")
logFile.write(str(less1) + " ")
logFile.write(str(lessrad) + " ")
logFile.write(str(radiicomp) + " ")
logFile.write("\n") # that's all
logFile.close()
if knownPathExists: # output bestStats and bestStatsPaths
bestName = tstFileName + ".known.best.txt"
bestFile = open(bestName, 'w')
bestFile.write("pRMSD coverage span wrmsd less1 lessrad radiicomp ")
bestFile.write("pRMSD# coverage# span# wrmsd# less1# lessrad# radiicomp#\n")
for stat in bestStats:
bestFile.write(str(stat) + " ")
for stat in bestStatsPaths:
bestFile.write(str(stat) + " ")
bestFile.write("\n")
bestFile.close()
print "done with chunnel"