#!/usr/bin/env python
import tm3
import string
import sys
def deleteLeaves(tmData, attributeName, threshold):
column = tmData.attributeTitles.index(attributeName)
for node in tmData.bottomUpTraversal():
if node in tmData.tree: # may have already been merged
if tmData.isLeaf(node.getId()):
if node.attributes[column] < threshold:
tmData.deleteLeaf(node.getId())
#main is only run for testing import of tm3 from commandline
if -1 != string.find(sys.argv[0], "tm3filterVolumeJustThreshold.py"):
try:
threshold = float(sys.argv[1])
if 2 == len(sys.argv):
print "no input files specified"
else:
for filename in sys.argv[2:]:
tmData = tm3.tmTreeFromFile(filename)
deleteLeaves(tmData, "Volume", threshold)
tmData.write(filename+".v"+str(threshold)+".jt.tm3")
except (TypeError, IndexError):
print "tm3filterVolumeJustThreshold.py threshold file [more files]"
#!/usr/bin/env python
# compares the roots of the trees passed in
import tm3
import string
import sys
import dot
if -1 != string.find(sys.argv[0], "tm3rootcomp.py"):
tmDataList = []
for filename in sys.argv[1:]:
tmDataList.append(tm3.tmTreeFromFile(filename))
dotData = dot.dotRoot(tmDataList)
# print dotData.treeToBestNode
# dotData.write("temp.dot")
# dotData.writeGdl("temp.gdl", force=False)
# print "dot -Tpng temp.dot > temp.png"
print "output file also written to temp.tab.txt and temp.animation.py"
matchList = tm3.findSimilarNodes(
tmDataList,
[
"Surface Area",
"Volume",
"height",
# "mean absolute Curvature",
"mean Curvature",
"mouths",
"longest dimension",
"middle dimension",
"short dimension",
import tm3
import string
import sys
def animateScript(tmData, tstData, sortCol, outName):
'''sort by threshold, make a script to open and display each pocket in turn'''
nodes = tmData.idNode.values()
nodes.sort(
lambda xList, yList: cmp(
xList.attributes[sortCol], yList.attributes[sortCol]))
nodes.reverse() # sorted high to low now
print "from pymol import cmd"
print 'cmd.do("delete all")'
print 'cmd.do("tstOpen ' + tstData + '")'
print 'cmd.do("tstDraw surf=pdb")'
print 'cmd.do("color grey")'
for index, node in enumerate(nodes):
print 'cmd.do("turn x,1")'
print 'cmd.do("tstDraw group=', str(node.getId()), '")'
if index % 5 == 0:
print 'cmd.do("ray")'
print 'cmd.do("png ', str(outName + string.zfill(index, 6)+'.png') + '")'
print 'cmd.do("ray")'
print 'cmd.do("png ', str(outName + string.zfill(index+1, 6)+'.png') + '")'
if -1 != string.find(sys.argv[0], "tm3animatepockets.py"):
tmData = tm3.tmTreeFromFile(sys.argv[1])
tstData = sys.argv[1].replace(".tree.tm3", "")
animateScript(tmData, tstData, 3, tstData+".movie.turn.")