def CalculateTorsionAngles(mol, tors_list, tors_list_rings, confId=-1):
""" Calculate the torsion angles for a list of non-ring and
a list of ring torsions.
Arguments:
- mol: the molecule of interest
- tors_list: list of non-ring torsions
- tors_list_rings: list of ring torsions
- confId: index of the conformation (default: first conformer)
Return: list of torsion angles
"""
torsions = []
conf = mol.GetConformer(confId)
for t, maxdev in tors_list:
if len(t) == 1:
t = t[0]
p1, p2, p3, p4 = _getTorsionAtomPositions(t, conf)
tors = (Geometry.ComputeSignedDihedralAngle(p1, p2, p3, p4) /
math.pi) * 180.0
if tors < 0: tors += 360.0 # angle between 0 and 360
else:
# loop over torsions and take minimum
tors = 360.0
for t2 in t:
p1, p2, p3, p4 = _getTorsionAtomPositions(t2, conf)
tmp = (Geometry.ComputeSignedDihedralAngle(p1, p2, p3, p4) /
math.pi) * 180.0
if tmp < 0: tmp += 360.0 # angle between 0 and 360
if tmp < tors: tors = tmp
torsions.append((tors, maxdev))
# rings
for t, maxdev in tors_list_rings:
num = len(t)
# loop over torsions and sum them up
tors = 0
for t2 in t:
p1, p2, p3, p4 = _getTorsionAtomPositions(t2, conf)
tmp = abs(
(Geometry.ComputeSignedDihedralAngle(p1, p2, p3, p4) / math.pi)
* 180.0)
tors += tmp
tors /= num
torsions.append((tors, maxdev))
return torsions
def CalculateTorsionAngles(mol, tors_list, tors_list_rings, confId=-1):
""" Calculate the torsion angles for a list of non-ring and
a list of ring torsions.
Arguments:
- mol: the molecule of interest
- tors_list: list of non-ring torsions
- tors_list_rings: list of ring torsions
- confId: index of the conformation (default: first conformer)
Return: list of torsion angles
"""
torsions = []
conf = mol.GetConformer(confId)
for quartets, maxdev in tors_list:
tors = []
# loop over torsions and calculate angle
for atoms in quartets:
p1, p2, p3, p4 = _getTorsionAtomPositions(atoms, conf)
tmpTors = (Geometry.ComputeSignedDihedralAngle(p1, p2, p3, p4) /
math.pi) * 180.0
if tmpTors < 0: tmpTors += 360.0 # angle between 0 and 360
tors.append(tmpTors)
torsions.append((tors, maxdev))
# rings
for quartets, maxdev in tors_list_rings:
num = len(quartets)
# loop over torsions and sum them up
tors = 0
for atoms in quartets:
p1, p2, p3, p4 = _getTorsionAtomPositions(atoms, conf)
tmpTors = abs(
(Geometry.ComputeSignedDihedralAngle(p1, p2, p3, p4) / math.pi)
* 180.0)
tors += tmpTors
tors /= num
torsions.append(([tors], maxdev))
return torsions
