def meshConstruct(
tstD, phiData, tstFileName="temp.tst", borderSize=2,
threshold="auto", cavities=False):
'''returns a phi and a grid, modifies tstD in place.'''
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, -1.0, borderSize)
gridSize = 1.0 / phiData.scale
del phiData # no longer needed in this function, so delete this reference
#needs border = 2 so all surface points have a grid point on either side...
#tstdebug.debugGridCountVals(gridD)
#tstdebug.debugGridNoBlue(gridD, "debug.phigrid.py")
#do the biggest disjoint set of tris/points stuff
if not cavities:
allPoints, allTris, cavPoints, cavTris = cavity.assumeNoCavities(
tstD.dict['POINT_XYZ'], tstD.dict['TRIANGLE_POINT'],
tstD.dict['POINT_NEIGHBOR'])
cavPointLists = False
else:
allPoints, allCavPoints, cavPointLists = \
cavity.findBiggestDisjointSetsBreakCavities(
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'])
#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
#grid encoding -1 = outside ch, 0 = between ch, ms, -2 = inside ms
#tstdebug.debugGridNoBlue(gridD, "debug.phigrid.py")
meshData = mesh.mesh(
gridD, tstD.dict['POINT_XYZ'], tstD.dict['POINT_NEIGHBOR'],
gridSize, -1, -2, 0, allPoints, cavPointLists)
#now mesh is initialized
return meshData, gridD
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
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 tstCavityRemoval(
tstFileName, tstFileNameOut, phiFileName=False, phiFileNameOut=False):
oldTst = tstdata.tstDataWritable(tstFileName) # read the file into the struct
allPoints, allTris, cavPoints, cavTris = findBiggestDisjointSets(
oldTst.dict['POINT_XYZ'], oldTst.dict['TRIANGLE_POINT'],
oldTst.dict['POINT_NEIGHBOR'])
#print len(allPoints), len(allTris), len(cavPoints), len(cavTris) #debug
#now remove everything that isn't allPoints and allTris
#first generate maps from old numbering to new numbering
mapPoints = makeMapLists(oldTst.dict['POINT_XYZ'], allPoints)
mapTris = makeMapLists(oldTst.dict['TRIANGLE_POINT'], allTris)
#ugh. phi map.
phiData = sharp_phi.phi(phiFileName) # read in the phimap if possible
gridD = grid.makeGridFromPhi(phiData, False)
#the False just makes it copy values
mins, maxs = phiData.getMinsMaxs()
maxVal = phiData.getMaxValues()
gridSize = 1.0/phiData.scale
#this function marks cavities as interior
cavTriTuples = geometry.cacheTriangle(
oldTst.dict['TRIANGLE_POINT'], oldTst.dict['POINT_XYZ'], cavTris)
#have to do this now before oldTst gets modified
orstHelper.decideInside(
gridD, cavTriTuples, cavPoints,
oldTst.dict['POINT_TRIANGLE'], oldTst.dict['POINT_XYZ'],
oldTst.dict['TRIANGLE_POINT'], maxVal)
#change anything inside cavities to max..
#now piece-by-piece fix each entry
newTN = replaceEntry(
oldTst.dict['TRIANGLE_NEIGHBOR'], mapTris, [mapTris, mapTris, mapTris])
oldTst.dict['TRIANGLE_NEIGHBOR'] = newTN
newPX = replaceEntry(
oldTst.dict['POINT_XYZ'], mapPoints, [False, False, False])
oldTst.dict['POINT_XYZ'] = newPX
newTP = replaceEntry(
oldTst.dict['TRIANGLE_POINT'], mapTris, [mapPoints, mapPoints, mapPoints])
oldTst.dict['TRIANGLE_POINT'] = newTP
newPT = replaceEntry(
oldTst.dict['POINT_TRIANGLE'], mapPoints, [False, mapTris],
extendToEnd=True)
oldTst.dict['POINT_TRIANGLE'] = newPT
newPN = replaceEntry(
oldTst.dict['POINT_NEIGHBOR'], mapPoints, [False, mapPoints],
extendToEnd=True)
oldTst.dict['POINT_NEIGHBOR'] = newPN
newNX = replaceEntry(
oldTst.dict['NORM_XYZ'], mapPoints, [False, False, False])
oldTst.dict['NORM_XYZ'] = newNX
newPPR = replaceEntry(oldTst.dict['POINT_PDB_RECORD'], mapPoints, [False])
oldTst.dict['POINT_PDB_RECORD'] = newPPR
newTPR = replaceEntry(oldTst.dict['TRIANGLE_PDB_RECORD'], mapTris, [False])
oldTst.dict['TRIANGLE_PDB_RECORD'] = newTPR
#don't touch PDB_RECORD...
newCX = replaceEntry(oldTst.dict['CURVATURE_XYZ'], mapPoints, [False])
oldTst.dict['CURVATURE_XYZ'] = newCX
newPX = replaceEntry(oldTst.dict['PROPERTY_XYZ'], mapPoints, [False])
oldTst.dict['PROPERTY_XYZ'] = newPX
#now write it back out...should probably tag it somehow....hmmm
oldTst.write(tstFileNameOut)
#write phi map
phiDataOut = sharp_phi.phi()
phiDataOut.createFromGrid(
gridD, gridSize, toplabel=phiData.toplabel,
head=phiData.head, title=phiData.title, botlabel=phiData.botlabel)
phiDataOut.write(phiFileNameOut)