def __iter__(self):
"""Filter the constraints to be drawn.
"""
for aConstraint in self.constraints:
if aConstraint.getRange(self.rangeCutOff) in self.range:
if any(aResiNumber in self.residuesList for aResiNumber in aConstraint.ResiNumbers):
if aConstraint.isValid():
if aConstraint.setValueFromStructure():
aConstraint.setViolationState(self.cutOff)
if aConstraint.isSatisfied() in self.violationState:
yield aConstraint
else:
errors.add_error_message("Distance issue with constraint :\n" + aConstraint.definition)
else:
errors.add_error_message("Selection issue with constraint :\n" + aConstraint.definition)
def checkID(atomSet):
"""
"""
check = False
newName = ""
error_message = ""
if str(atomSet.resi_number) in pdb:
if atomSet.segid in (atom["segi"] for atom in pdb[str(atomSet.resi_number)]):
if atomSet.atoms in (atom["name"] for atom in pdb[str(atomSet.resi_number)]):
check = True
else:
if "*" not in atomSet.atoms:
if atomSet.atoms == "HN":
newName = "H"
elif atomSet.atoms == "H":
newName = "HN"
elif lastDigit.search(atomSet.atoms):
digit = lastDigit.search(atomSet.atoms).group()[0]
newName = digit + lastDigit.sub("", atomSet.atoms) # put final digit at the beginning
if newName in (atom["name"] for atom in pdb[str(atomSet.resi_number)]):
check = True
else:
error_message = "Atom name not found"
else:
nameRoot = atomSet.atoms.replace("*", "")
for aName in (atom["name"] for atom in pdb[str(atomSet.resi_number)]):
if nameRoot in aName:
check = True
break
if check is False:
error_message = "Atom name not found"
else:
error_message = "Wrong segment / chain"
else:
error_message = "Residue number not found"
if check is False:
errors.add_error_message(
"Can't find " + str(atomSet.atoms) + " in structure " + pdb["name"] + " because : " + error_message
)
if newName:
return {"valid": check, "NewData": {"atoms": newName}}
else:
return {"valid": check, "NewData": None}
def calcDistance(coord_init, coord_final):
""" Calculate distance according to :
((sum of all distances^-6)/number of distances)^-1/6
or (sum of all distances^-6)^-1/6
"""
result = None
if len(coord_init) and len(coord_final):
distance_list = (sqrt(sum((coord[0] - coord[1]) ** 2 for coord in zip(AtomA, AtomB))) for (AtomA, AtomB) in product(coord_init, coord_final))
try:
sum6 = sum(pow(distance, -6) for distance in distance_list)
if distance_method == 'ave6':
result = pow(sum6/len(distance_list), -1./6)
elif distance_method == 'sum6':
result = pow(sum6, -1./6)
except ValueError:
errors.add_error_message("Problem using coordinates : " +
str(coord_init) + " " +
str(coord_final) + "\n" +
" and distances list" +
str(distance_list) + "\n")
return result
