self.planeD2 = planeD2
self.planeD3 = planeD3
def measure(self, structure):
try:
point = lookup(self.pointD, structure).center
plane1 = lookup(self.planeD1, structure).center
plane2 = lookup(self.planeD2, structure).center
plane3 = lookup(self.planeD3, structure).center
return signedPointPlaneDistance(point, plane1, plane2, plane3)
except AttributeError, ae:
print str(ae)
filename = sys.argv[1]
pdbdir = sys.argv[2]
def parse(line):
pdbid, chain, start, stop = line.split(".")
return ExampleDescription(pdbid, chain, start, stop)
metal = constructSelection(chainType="Ligand", residuePosition=1, atomName="CA")
o1 = constructSelection(chainType="Protein", residuePosition=1, atomName="O")
o2 = constructSelection(chainType="Protein", residuePosition=3, atomName="O")
o3 = constructSelection(chainType="Protein", residuePosition=6, atomName="O")
measure = PointPlaneDistanceMeasure(metal, o1, o2, o3)
for e in generateExamples(filename, pdbdir, parse):
# XXX hack!
print measure.measure(e[0][0])
print str(ae)
filename = sys.argv[1]
pdbdir = sys.argv[2]
def parse(line):
bits = line.split("\t")
pdbid, chain = bits[0].split(".")
start, stop = bits[1].split("-")
ligands = eval(bits[-1])
for lig in ligands:
name = lig[0:3]
if name == "HOH":
ligand_num = lig[3:]
break
return ExampleDescription(pdbid, chain, start, stop, ligand_num)
hoh = constructSelection(chainType="Water", residuePosition=1, atomName="O")
o1 = constructSelection(chainType="Protein", residuePosition=1, atomName="O")
o2 = constructSelection(chainType="Protein", residuePosition=2, atomName="O")
o3 = constructSelection(chainType="Protein", residuePosition=3, atomName="O")
measure = OXOMeasure(hoh, o1, o2, o3)
for e in generateExamples(filename, pdbdir, parse):
try:
# XXX hack!
print "%s\t%s\t%s" % (e, e[0][0].residueRange, measure.measure(e))
except Exception, ex:
sys.stderr.write("%s in %s\n" % (str(ex), e))
# test the list reader
import sys
from Tailor.Engine import TmpDistanceMeasure, constructSelection
from Tailor.Description import ChainDescription
from Tailor.ResultParser import ExampleDescription, generateExamples
filename = sys.argv[1]
pdbdir = sys.argv[2]
def parse(line):
pdbid, chain, start, stop = line.split(".")
return ExampleDescription(pdbid, chain, start, stop)
abstractDescription = ChainDescription({"chainID": " "})
abstractDescription.createResidues(3)
o = constructSelection(residuePosition=1, atomName="O")
n = constructSelection(residuePosition=3, atomName="N")
measures = [TmpDistanceMeasure(o, n)]
for e in generateExamples(filename, pdbdir, parse):
for measure in measures:
# XXX hack!
print measure.measure(e[0][0])