import tm3
import string
import sys
import dot
if -1 != string.find(sys.argv[0], "tm3rescomp.py"):
tmDataList = []
nameOrNum = sys.argv[1]
resList = sys.argv[2]
for filename in sys.argv[3:]:
tmDataList.append(tm3.tmTreeFromFile(filename))
colName = "Residue Number List"
if nameOrNum == "name":
colName = "Residue Name List"
dotData = dot.dotResidues(tmDataList, resList, colNameIn=colName, penalty=3.0)
#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",
"Area of Biggest Mouth", "Diameter of Biggest Mouth", "mean height"],
10000000, 1000, 50,
resCols=["Atom Name List"], sizeColName="Volume",
sizeMin=-1., sizeMax=10000000000,
#!/usr/bin/env python
#reports pockets with highest overlap with the set of residues
import tm3
import string
import sys
import statistics
import dot
if -1 != string.find(sys.argv[0], "tm3residues.py"):
prefix = "temp"
tmDataList = []
nameOrNum = sys.argv[1]
resList = sys.argv[2]
for filename in sys.argv[3:]:
tmDataList.append(tm3.tmTreeFromFile(filename))
colName = "Residue Number List"
if nameOrNum == "name":
colName = "Residue Name List"
dotData = dot.dotResidues(
tmDataList, resList, colNameIn=colName, printHelpful=False)
dotData.printHelpful(prefix)
dotData.write(prefix + ".dot")
dotData.writeGdl(prefix + ".gdl", force=False)
print "dot -Tpng "+prefix+".dot > "+prefix+".png"
print "output files written to " + prefix + ".tab.txt and " + prefix + \
".animation.py"
