def tstTravelSurfOutside(
tstFileName, phiFileName=False, tstDataIn=False, phiDataIn=False,
borderSize=10):
if tstDataIn:
#don't want to read in if calling function already did it for us
tstD = tstDataIn
else:
tstD = tstdata.tstData(tstFileName) # read the file into the data structure
if phiDataIn:
phiData = phiDataIn
else:
phiData = phi(phiFileName) # read in the phimap if possible
#depends on convex hull _only_ to decide how far out to put the border
if 'CONVEX_HULL_TRI_POINT_LIST' not in tstD.dict.keys():
print "Run tstConvexHull.py on this tst data file first."
sys.exit(1)
#these sets are useful to construct
convexHullPoints = set()
for record in tstD.dict['CONVEX_HULL_TRI_POINT_LIST']:
convexHullPoints.update(record[1:])
gridD, mins, maxs = grid.makeTrimmedGridFromPhi(
phiData, tstD.dict['POINT_XYZ'], convexHullPoints, 0.6, -2.0, 0,
borderSize)
gridSize = 1.0/phiData.scale
del phiData # no longer needed in this function, so delete this reference
#do the biggest disjoint set of tris/points stuff
allPoints, allTris, cavPoints, cavTris = cavity.assumeNoCavities(
tstD.dict['POINT_XYZ'], tstD.dict['TRIANGLE_POINT'],
tstD.dict['POINT_NEIGHBOR'])
#here's the (relatively simple) surface travel distance calculation finally
# assign following encoding -1 = outside ch, 0 = on border,
# pos ints = dist from border, -2 = far inside ms,
# other neg ints = -(dist)-3
extraEdges, surfaceEdgeBoxes = grid.findLongSurfEdges(
tstD.dict['POINT_XYZ'], tstD.dict['POINT_NEIGHBOR'], gridSize, mins, maxs)
for surfaceEdgeBox in surfaceEdgeBoxes.keys():
x, y, z = gridD[surfaceEdgeBox[0]][surfaceEdgeBox[1]][surfaceEdgeBox[2]][1:]
gridD[surfaceEdgeBox[0]][surfaceEdgeBox[1]][surfaceEdgeBox[2]] = (
-1., x, y, z)
pointTravelDist, traceback, volumePointDepths = \
travelDistNoMesh.calcTravelDist(
gridD, tstD.dict['POINT_XYZ'], gridSize, mins, maxs, allPoints,
extraEdges, surfaceEdgeBoxes, tstFileName)
#transform grid to actual travel distance
maxTD = grid.finalizeGridTravelDist(gridD, gridSize)
gridMaximaRanking = grid.getMaximaRanking(gridD)
#output the grids and the gridmaxima....
phiDataOut = phi()
phiDataOut.createFromGrid(
gridMaximaRanking, gridSize, toplabel="travel depth maxima rank")
phiDataOut.write(tstFileName+".travel.out.max.rank.phi")
phiDataOut = phi()
phiDataOut.createFromGrid(
gridD, gridSize, toplabel="travel depth surf-out", defaultValue=maxTD+1.0)
phiDataOut.write(tstFileName+".travel.out.phi")
return mins, maxs, gridSize, convexHullPoints, allPoints, allTris, \
extraEdges, surfaceEdgeBoxes, pointTravelDist, traceback, maxTD, gridD, \
gridMaximaRanking
def tstTravelSurfOutsideMesh(
tstFileName, phiFileName=None, tstDataIn=False, phiDataIn=None,
borderSize=10, threshold="auto"):
if tstDataIn:
#don't want to read in if calling function already did it for us
tstD = tstDataIn
else:
tstD = tstdata.tstData(
tstFileName, necessaryKeys=tstdata.tstData.necessaryKeysForMesh)
if phiDataIn is not None:
phiData = phiDataIn
else:
phiData = phi(phiFileName) # read in the phimap if possible
if 'CONVEX_HULL_TRI_POINT_LIST' not in tstD.dict.keys():
print "Run tstConvexHull.py on this tst data file first."
sys.exit(1)
#these sets are useful to construct
convexHullPoints = set()
for record in tstD.dict['CONVEX_HULL_TRI_POINT_LIST']:
convexHullPoints.update(record[1:])
maxPhi = phiData.getMaxValues()
if threshold == "auto" and maxPhi == 1.0:
threshold = 0.6
if threshold == "auto" and maxPhi == 10.0:
threshold = 6.0
gridD, mins, maxs = grid.makeTrimmedGridFromPhi(
phiData, tstD.dict['POINT_XYZ'],
convexHullPoints, threshold, -2, 0, borderSize)
gridSize = 1.0/phiData.scale
del phiData # no longer needed in this function, so delete this reference
#do the biggest disjoint set of tris/points stuff
allPoints, allTris, cavPoints, cavTris = cavity.assumeNoCavities(
tstD.dict['POINT_XYZ'], tstD.dict['TRIANGLE_POINT'],
tstD.dict['POINT_NEIGHBOR'])
#here is where code is mesh-specific
meshData = mesh.mesh(
gridD, tstD.dict['POINT_XYZ'], tstD.dict['POINT_NEIGHBOR'],
gridSize, 0, -2, "X") # no between
meshData.calculateTravelDistance("surfout", [3], [0, 2])
#transform grid to actual travel distance
maxTD = grid.finalizeGridTravelDist(gridD, gridSize)
gridMaximaRanking = grid.getMaximaRanking(gridD)
#output the grids and the gridmaxima....
phiDataOut = phi()
phiDataOut.createFromGrid(
gridMaximaRanking, gridSize, toplabel="travel depth maxima rank")
phiDataOut.write(tstFileName + ".mesh.travel.out.max.rank.phi")
phiDataOut = phi()
phiDataOut.createFromGrid(
gridD, gridSize, toplabel="travel depth surf-out",
defaultValue=maxTD + 1.0)
phiDataOut.write(tstFileName+".mesh.travel.out.phi")
def tstTravelSurfInside(tstFileName, phiFileName=False):
tstD = tstdata.tstData(tstFileName) # read the file into the data structure
phiData = phi(phiFileName) # read in the phimap if possible
if 'CONVEX_HULL_TRI_POINT_LIST' not in tstD.dict.keys():
print "Run tstConvexHull.py on this tst data file first."
sys.exit(1)
#these sets are useful to construct
convexHullPoints = set()
for record in tstD.dict['CONVEX_HULL_TRI_POINT_LIST']:
convexHullPoints.update(record[1:])
gridD, mins, maxs = grid.makeTrimmedGridFromPhi(
phiData, tstD.dict['POINT_XYZ'], convexHullPoints, 0.6, 0, -2.0, 2)
gridSize = 1.0/phiData.scale
del phiData # no longer needed in this function, so delete this reference
#do the biggest disjoint set of tris/points stuff
allPoints, allTris, cavPoints, cavTris = cavity.assumeNoCavities(
tstD.dict['POINT_XYZ'], tstD.dict['TRIANGLE_POINT'],
tstD.dict['POINT_NEIGHBOR'])
#here's the (relatively simple) surface travel distance calculation finally
# assign following encoding -1 = outside ch, 0 = on border,
# pos ints = dist from border, -2 = far inside ms,
# other neg ints = -(dist)-3
#whole algorithm wrapped into big function...
extraEdges, surfaceEdgeBoxes = grid.findLongSurfEdges(
tstD.dict['POINT_XYZ'], tstD.dict['POINT_NEIGHBOR'], gridSize, mins, maxs)
for surfaceEdgeBox in surfaceEdgeBoxes.keys():
x, y, z = gridD[surfaceEdgeBox[0]][surfaceEdgeBox[1]][surfaceEdgeBox[2]][1:]
gridD[surfaceEdgeBox[0]][surfaceEdgeBox[1]][surfaceEdgeBox[2]] = (
-1., x, y, z)
pointTravelDist, traceback, volumePointDepths = \
travelDistNoMesh.calcTravelDist(
gridD, tstD.dict['POINT_XYZ'], gridSize, mins, maxs, allPoints,
extraEdges, surfaceEdgeBoxes, tstFileName)
#transform grid to actual travel distance
maxTD = grid.finalizeGridTravelDist(gridD, gridSize)
phiDataOut = phi()
phiDataOut.createFromGrid(gridD, gridSize, toplabel="travel depth surf-in")
phiDataOut.write(tstFileName+".travel.in.phi")
pdbD = pdb.pdbData()
for line in tstD.dict['PDB_RECORD']:
pdbD.processLine(line)
atomTravelInDepths = grid.assignAtomDepths(gridD, gridSize, mins, maxs, pdbD)
#make a pdb file with the bfactor replaced
for index, atomTID in enumerate(atomTravelInDepths):
pdbD.updateFactors(index, (pdbD.factors[index][0], atomTID))
pdbD.write(tstFileName+".travelin.pdb")
#also add record to tstdata
atomTIDRecord = []
for index, atomTID in enumerate(atomTravelInDepths):
atomTIDRecord.append([index+1, atomTID])
tstD.dict['ATOM_TRAVEL_IN'] = atomTIDRecord
#write data into tst file
tstFile = open(tstFileName, 'a')
tstFile.write("ATOM_TRAVEL_IN\n")
for line in tstD.dict['ATOM_TRAVEL_IN']:
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 ATOM_TRAVEL_IN\n")
tstFile.close()
def tstTravelDepthNoPhi(tstFileName, gridSize=1.0):
'''does old style (v1.0) travel depth with no phi-map, finds own inside and
outside data, proceeds as normal'''
tstD = tstdata.tstData(tstFileName) # read the file into the data structure
if 'CONVEX_HULL_TRI_POINT_LIST' not in tstD.dict.keys():
print "Run tstConvexHull.py on this tst data file first."
sys.exit(1)
#these sets are useful to construct
convexHullPoints = set()
for record in tstD.dict['CONVEX_HULL_TRI_POINT_LIST']:
convexHullPoints.update(record[1:])
#do the biggest disjoint set of tris/points stuff
allPoints, allTris, cavPoints, cavTris = cavity.assumeNoCavities(
tstD.dict['POINT_XYZ'], tstD.dict['TRIANGLE_POINT'],
tstD.dict['POINT_NEIGHBOR'])
#find the minimum coordinates in each dimension
mins = tstD.dict['POINT_XYZ'][0][1:]
maxs = tstD.dict['POINT_XYZ'][0][1:]
for point in convexHullPoints:
xyz = tstD.dict['POINT_XYZ'][point-1][1:]
for coord in range(3):
mins[coord] = min(mins[coord], xyz[coord])
maxs[coord] = max(maxs[coord], xyz[coord])
#floor and ceiling everything to whole numbers
minsSave = mins[:]
maxsSave = maxs[:]
#cache a bunch of computations on each triangle
#triTuples does not contain the ones that are for cavities
triTuples = geometry.cacheTriangle(
tstD.dict['TRIANGLE_POINT'], tstD.dict['POINT_XYZ'], allTris)
convexTriTuples = geometry.cacheTriangle(
tstD.dict['CONVEX_HULL_TRI_POINT_LIST'], tstD.dict['POINT_XYZ'])
#grid encoding -1 = outside ch, 0 = between ch, ms, -2 = inside ms
mins, maxs = [], [] # so values computed are saved
mins = [math.floor(x)-gridSize for x in minsSave]
maxs = [math.ceil(x)+gridSize for x in maxsSave]
gridD = grid.makeNewEmptyGrid(mins, maxs, gridSize, -1) # set to outside ch
#tstdebug.debugGridCountVals(gridD)
#first step, check and set outside ch
orstHelper.decideInside(
gridD, convexTriTuples, convexHullPoints,
tstD.dict['CONVEX_HULL_POINT_TRI_LIST'], tstD.dict['POINT_XYZ'],
tstD.dict['CONVEX_HULL_TRI_POINT_LIST'], 0, False, 2)
#0 inside convex hull, False any value, 2=max tris
#tstdebug.debugGridCountVals(gridD)
#now find inside molecular surface
orstHelper.decideInside(
gridD, triTuples, allPoints, tstD.dict['POINT_TRIANGLE'],
tstD.dict['POINT_XYZ'], tstD.dict['TRIANGLE_POINT'], -2)
#-2 inside everything
#tstdebug.debugGridCountVals(gridD)
#following lines make files that allow visual debugging in pymol
#tstdebug.debugGrid(gridD, "debug.grid." + str(gridSize) + ".py")
#tstdebug.debugGridNoBlue(gridD, "debug.grid.nb." + str(gridSize) + ".py")
#tstdebug.debugGridJustGreen(gridD, "debug.grid.jg." + str(gridSize) + ".py")
#now...
#here's the (relatively simple) surface travel distance calculation finally
# assign following encoding -1 = outside ch, 0 = on border,
# pos ints = dist from border, -2 = far inside ms,
# other neg ints = -(dist)-3
#whole algorithm wrapped into big function...
extraEdges, surfaceEdgeBoxes = grid.findLongSurfEdges(
tstD.dict['POINT_XYZ'], tstD.dict['POINT_NEIGHBOR'], gridSize, mins, maxs)
volumePoints = False
if 'POINT_TRAVEL_DEPTH_CHECK' in tstD.dict.keys():
volumePoints = tstD.dict['POINT_TRAVEL_DEPTH_CHECK']
pointTravelDist, traceback, volumePointDepths = \
travelDistNoMesh.calcTravelDist(
gridD, tstD.dict['POINT_XYZ'], gridSize, mins, maxs, allPoints,
extraEdges, surfaceEdgeBoxes, tstFileName, volumePoints)
#tstdebug.debugGridCountVals(gridD)
#reassign -1 to max+1 (cavities)
maximumTD = max([xxx[1] for xxx in pointTravelDist])
for onePoint in pointTravelDist:
if onePoint[1] < 0.0:
onePoint[1] = maximumTD + 1.0
maxTD = grid.finalizeGridTravelDist(gridD, gridSize)
phiDataOut = phi()
phiDataOut.createFromGrid(gridD, gridSize, toplabel="travel depth")
phiDataOut.write(tstFileName+".travel.oldmethod.phi")
#more pymol debugging if desired
#tstdebug.debugTravelGrid(
# gridD,"debug.travel.grid." + str(gridSize) + ".py", maximumTD)
#tstdebug.debugTravelSurfGrid(
# gridD, "debug.travel.surf.grid." + str(gridSize) + ".py",
# extraEdges, mins, maxs, gridSize, maximumTD)
#save data into tstData
tstD.dict['DEPTH_TRAVEL_DIST'] = pointTravelDist
#write data to file
tstFile = open(tstFileName, 'a')
tstFile.write("DEPTH_TRAVEL_DIST\n")
for line in pointTravelDist:
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()
if volumePointDepths:
tstD.dict['POINT_TRAVEL_DEPTH_REPORT'] = volumePointDepths
tstFile = open(tstFileName, 'a')
tstFile.write("POINT_TRAVEL_DEPTH_REPORT\n")
for line in volumePointDepths:
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 POINT_TRAVEL_DEPTH_REPORT\n")
tstFile.close()
#save tracebacks into tstData
tracebackArray = [] # format is end, dist, list of starts
tracebackKeys = traceback.keys()
tracebackKeys.sort()
for endkey in tracebackKeys:
startList, end, dist = traceback[endkey]
tbLine = [end[0], end[1], end[2], dist]
for start in startList:
tbLine.append(start[0])
tbLine.append(start[1])
tbLine.append(start[2])
tracebackArray.append(tbLine)
tstD.dict['TRACEBACK_LIST'] = tracebackArray
#now write to file
tstFile = open(tstFileName, 'a')
tstFile.write("TRACEBACK_LIST\n")
for line in tracebackArray:
lineOut = " "
for count in xrange(0, len(line)):
lineOut += "%+9.4f " % line[count]
noPlusLine = string.replace(lineOut, "+", " ")
tstFile.write(noPlusLine)
tstFile.write("\n")
tstFile.write("END TRACEBACK_LIST\n")
tstFile.close()
def tstTravelDepthRun(tstD, phiData, tstFileName="temp.tst"):
if 'CONVEX_HULL_TRI_POINT_LIST' not in tstD.dict.keys():
print "Run tstConvexHull.py on this tst data file first."
sys.exit(1)
#these sets are useful to construct
convexHullPoints = set()
for record in tstD.dict['CONVEX_HULL_TRI_POINT_LIST']:
convexHullPoints.update(record[1:])
gridD, mins, maxs = grid.makeTrimmedGridFromPhi(
phiData, tstD.dict['POINT_XYZ'], convexHullPoints, 0.6, -2.0, -1.0)
gridSize = 1.0/phiData.scale
del phiData # no longer needed in this function, so delete this reference
#tstdebug.debugGridCountVals(gridD)
#do the biggest disjoint set of tris/points stuff
allPoints, allTris, cavPoints, cavTris = cavity.assumeNoCavities(
tstD.dict['POINT_XYZ'], tstD.dict['TRIANGLE_POINT'],
tstD.dict['POINT_NEIGHBOR'])
convexTriTuples = geometry.cacheTriangle(
tstD.dict['CONVEX_HULL_TRI_POINT_LIST'], tstD.dict['POINT_XYZ'])
#grid encoding -1 = outside ch, 0 = between ch, ms, -2 = inside ms
#this function marks cavities as interior
#cavities now removed already
#cavTriTuples = geometry.cacheTriangle( \
# tstD.dict['TRIANGLE_POINT'], tstD.dict['POINT_XYZ'], cavTris)
#orstHelper.decideInside(gridD, cavTriTuples, cavPoints, \
# tstD.dict['POINT_TRIANGLE'], tstD.dict['POINT_XYZ'], \
# tstD.dict['TRIANGLE_POINT'], -2, -1)
#-2 inside everything, -1 only valid to change
#tstdebug.debugGridCountVals(gridD)
#this marks the editable volume between the two surfaces
orstHelper.decideInside(
gridD, convexTriTuples, convexHullPoints,
tstD.dict['CONVEX_HULL_POINT_TRI_LIST'], tstD.dict['POINT_XYZ'],
tstD.dict['CONVEX_HULL_TRI_POINT_LIST'], 0, -1, 2)
#0 inside convex hull, -1 outside (only valid to change), 2 = max tris
#tstdebug.debugGridCountVals(gridD)
#following lines make files that allow visual debugging in pymol
#tstdebug.debugGrid(gridD, "debug.grid." + str(gridSize) + ".py")
#tstdebug.debugGridNoBlue(gridD, "debug.grid.nb." + str(gridSize) + ".py")
#tstdebug.debugGridJustGreen(gridD, "debug.grid.jg." + str(gridSize) + ".py")
#now...
#here's the (relatively simple) surface travel distance calculation finally
# assign following encoding -1 = outside ch, 0 = on border,
# pos ints = dist from border, -2 = far inside ms,
# other neg ints = -(dist)-3
#whole algorithm wrapped into big function...
extraEdges, surfaceEdgeBoxes = grid.findLongSurfEdges(
tstD.dict['POINT_XYZ'], tstD.dict['POINT_NEIGHBOR'], gridSize, mins, maxs)
volumePoints = False
if 'POINT_TRAVEL_DEPTH_CHECK' in tstD.dict.keys():
volumePoints = tstD.dict['POINT_TRAVEL_DEPTH_CHECK']
pointTravelDist, traceback, volumePointDepths = \
travelDistNoMesh.calcTravelDist(
gridD, tstD.dict['POINT_XYZ'], gridSize, mins, maxs, allPoints,
extraEdges, surfaceEdgeBoxes, tstFileName, volumePoints)
#tstdebug.debugGridCountVals(gridD)
#transform grid to actual travel distance
maxTD = grid.finalizeGridTravelDist(gridD, gridSize)
#more pymol debugging if desired
#tstdebug.debugTravelGrid(
# gridD, "debug.travel.grid." + str(gridSize) + ".py", maximumTD)
#tstdebug.debugTravelSurfGrid(
# gridD, "debug.travel.surf.grid." + str(gridSize) + ".py",
# extraEdges, mins, maxs, gridSize, maximumTD)
#save data into tstD
tstD.dict['DEPTH_TRAVEL_DIST'] = pointTravelDist
#save tracebacks into tstD
tracebackArray = [] # format is end, dist, list of starts
tracebackKeys = traceback.keys()
tracebackKeys.sort()
for endkey in tracebackKeys:
startList, end, dist = traceback[endkey]
tbLine = [end[0], end[1], end[2], dist]
for start in startList:
tbLine.append(start[0])
tbLine.append(start[1])
tbLine.append(start[2])
tracebackArray.append(tbLine)
tstD.dict['TRACEBACK_LIST'] = tracebackArray
phiDataOut = phi()
phiDataOut.createFromGrid(
gridD, gridSize, toplabel="travel depth", defaultValue=maxTD)
return gridD, phiDataOut, volumePointDepths