def satisfiedBy(self, example):
try:
a = lookup(self.descriptionA, example).center
b = lookup(self.descriptionB, example).center
c = lookup(self.descriptionC, example).center
d = lookup(self.descriptionD, example).center
except DescriptionException:
return False
except AttributeError:
return False
t = torsion(a, b, c, d)
#print a, b, c, d
#print self.center -self.range, t, self.center + self.range
satisfied = self.center - self.range < t < self.center + self.range
if self.negated:
satisfied = not satisfied
if satisfied:
example.__dict__[self.name] = t
return satisfied # ho ho
else:
return False
def measure(self, structure):
try:
a = lookup(self.descriptionA, structure).center
b = lookup(self.descriptionB, structure).center
return distance(a, b)
except AttributeError, ae:
print "DISTANCE MEASURE FALIURE :", self.descriptionA, self.descriptionB, str(ae)
return 0.0
def satisfiedBy(self, example):
try:
donorAtomPosition = lookup(self.donorDescription, example).center
hydrogenAtomPosition = lookup(self.hydrogenDescription, example).center
acceptorAtomPosition = lookup(self.acceptorDescription, example).center
attachedAtomPosition = lookup(self.attachedDescription, example).center
except DescriptionException, d:
return False
def measure(self, structure):
try:
a = lookup(self.descriptionA, structure).center
b = lookup(self.descriptionB, structure).center
c = lookup(self.descriptionC, structure).center
return angle(a, b, c)
except AttributeError:
print "ANGLE MEASURE FALIURE :", self.descriptionA, self.descriptionB, self.descriptionC
return 0.0
def measure(self, structure):
try:
a = lookup(self.descriptionA, structure).center
b = lookup(self.descriptionB, structure).center
c = lookup(self.descriptionC, structure).center
d = lookup(self.descriptionD, structure).center
return torsion(a, b, c, d)
except AttributeError:
print "TORSION MEASURE FALIURE :", self.descriptionA, self.descriptionB, self.descriptionC, self.descriptionD
return 0.0
def measure(self, structure):
try:
donorAtom = lookup(self.donorDescription, structure)
hydrogenAtom = lookup(self.hydrogenDescription, structure)
acceptorAtom = lookup(self.acceptorDescription, structure)
attachedAtom = lookup(self.attachedDescription, structure)
#print donorAtom.toFullString(), hydrogenAtom.toFullString(), acceptorAtom.toFullString(), attachedAtom.toFullString()
except DescriptionException, d:
# better to re-raise some kind of error?
return (0,0,0)
def satisfiedBy(self, example):
try:
a = lookup(self.descriptionA, example).center
b = lookup(self.descriptionB, example).center
except DescriptionException:
sys.stderr.write("description exception")
return False
except AttributeError, e:
#dstr = "%s %s" % (self.descriptionA.to_str(), self.descriptionB.to_str())
#sys.stderr.write("attribute error %s for %s %s\n" % (e, dstr, example))
return False
def satisfiedBy(self, example):
try:
a = lookup(self.descriptionA, example).center
b = lookup(self.descriptionB, example).center
c = lookup(self.descriptionC, example).center
except DescriptionException:
return False
except AttributeError:
return False
aa = angle(a, b, c)
satisfied = self.center - self.range < aa < self.center + self.range
if self.negated:
satisfied = not satisfied
if satisfied:
chain.__dict__[self.name] = aa
return satisfied # ho ho
else:
return False
