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rdkit/Code/ForceField/Wrap/testConstraints.py

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import os
import sys
import unittest
from multiprocessing import Process, Value
from time import sleep
from rdkit import Chem, RDConfig
from rdkit.Chem import ChemicalForceFields, rdMolTransforms
class OptSafe:
def __init__(self):
self.minInfLoop = """minInfLoop
RDKit 3D
7 5 0 0 0 0 0 0 0 0999 V2000
1.7321 -0.5000 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0
0.8660 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 -0.5000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
0.5000 -1.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.8660 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.5000 0.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.2321 -0.5000 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
3 4 1 0 0 0 0
3 5 1 0 0 0 0
3 6 1 0 0 0 0
M CHG 2 3 1 7 -1
M END"""
def uffOptFunc(self, v, mol):
ff = ChemicalForceFields.UFFGetMoleculeForceField(mol)
try:
ff.Minimize()
except RuntimeError:
pass
v.value = True
return
def mmffOptFunc(self, v, mol):
mp = ChemicalForceFields.MMFFGetMoleculeProperties(mol)
ff = ChemicalForceFields.MMFFGetMoleculeForceField(mol, mp)
try:
ff.Minimize()
except RuntimeError:
pass
v.value = True
return
def opt(self, mol, optFunc):
OPT_SLEEP_SEC = 0.2
MAX_OPT_SLEEP_SEC = 3
v = Value('b', False)
optProcess = Process(target=optFunc, args=(v, mol))
optProcess.start()
s = 0.0
while ((s < MAX_OPT_SLEEP_SEC) and (not v.value)):
s += OPT_SLEEP_SEC
sleep(OPT_SLEEP_SEC)
if (not v.value):
sys.stderr.write('Killing Minimize() or it will loop indefinitely\n')
optProcess.terminate()
optProcess.join()
return bool(v.value)
class TestCase(unittest.TestCase):
def setUp(self):
self.molB = """butane
RDKit 3D
butane
17 16 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.4280 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.7913 -0.2660 0.9927 H 0 0 0 0 0 0 0 0 0 0 0 0
1.9040 1.3004 -0.3485 C 0 0 0 0 0 0 0 0 0 0 0 0
1.5407 2.0271 0.3782 H 0 0 0 0 0 0 0 0 0 0 0 0
1.5407 1.5664 -1.3411 H 0 0 0 0 0 0 0 0 0 0 0 0
3.3320 1.3004 -0.3485 C 0 0 0 0 0 0 0 0 0 0 0 0
3.6953 1.5162 -1.3532 H 0 0 0 0 0 0 0 0 0 0 0 0
3.8080 0.0192 0.0649 C 0 0 0 0 0 0 0 0 0 0 0 0
3.4447 -0.7431 -0.6243 H 0 0 0 0 0 0 0 0 0 0 0 0
3.4447 -0.1966 1.0697 H 0 0 0 0 0 0 0 0 0 0 0 0
4.8980 0.0192 0.0649 H 0 0 0 0 0 0 0 0 0 0 0 0
3.6954 2.0627 0.3408 H 0 0 0 0 0 0 0 0 0 0 0 0
1.7913 -0.7267 -0.7267 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.3633 0.7267 0.7267 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.3633 -0.9926 0.2660 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.3633 0.2660 -0.9926 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 15 1 0 0 0 0
1 16 1 0 0 0 0
1 17 1 0 0 0 0
2 3 1 0 0 0 0
2 4 1 0 0 0 0
2 14 1 0 0 0 0
4 5 1 0 0 0 0
4 6 1 0 0 0 0
4 7 1 0 0 0 0
7 8 1 0 0 0 0
7 9 1 0 0 0 0
7 13 1 0 0 0 0
9 10 1 0 0 0 0
9 11 1 0 0 0 0
9 12 1 0 0 0 0
M END"""
def testUFFMinInfLoop(self):
os = OptSafe()
m = Chem.MolFromMolBlock(os.minInfLoop)
self.assertTrue(m)
ok = False
try:
ok = os.opt(m, os.uffOptFunc)
except RuntimeError:
ok = True
pass
self.assertTrue(ok)
def testUFFDistanceConstraints(self):
m = Chem.MolFromMolBlock(self.molB, True, False)
ff = ChemicalForceFields.UFFGetMoleculeForceField(m)
self.assertTrue(ff)
ff.UFFAddDistanceConstraint(1, 3, False, 2.0, 2.0, 1.0e5)
r = ff.Minimize()
self.assertTrue(r == 0)
conf = m.GetConformer()
dist = rdMolTransforms.GetBondLength(conf, 1, 3)
self.assertTrue(dist > 1.99)
ff = ChemicalForceFields.UFFGetMoleculeForceField(m)
self.assertTrue(ff)
ff.UFFAddDistanceConstraint(1, 3, True, -0.2, 0.2, 1.0e5)
r = ff.Minimize()
self.assertTrue(r == 0)
conf = m.GetConformer()
dist = rdMolTransforms.GetBondLength(conf, 1, 3)
self.assertTrue(dist > 1.79)
def testUFFAngleConstraints(self):
m = Chem.MolFromMolBlock(self.molB, True, False)
ff = ChemicalForceFields.UFFGetMoleculeForceField(m)
self.assertTrue(ff)
ff.UFFAddAngleConstraint(1, 3, 6, False, 90.0, 90.0, 100.0)
r = ff.Minimize()
self.assertTrue(r == 0)
conf = m.GetConformer()
angle = rdMolTransforms.GetAngleDeg(conf, 1, 3, 6)
self.assertAlmostEqual(angle, 90, delta=0.1)
ff = ChemicalForceFields.UFFGetMoleculeForceField(m)
self.assertTrue(ff)
ff.UFFAddAngleConstraint(1, 3, 6, True, -10.0, 10.0, 100.0)
r = ff.Minimize()
self.assertTrue(r == 0)
conf = m.GetConformer()
angle = rdMolTransforms.GetAngleDeg(conf, 1, 3, 6)
self.assertAlmostEqual(angle, 100, delta=0.1)
def testUFFTorsionConstraints(self):
m = Chem.MolFromMolBlock(self.molB, True, False)
conf = m.GetConformer()
rdMolTransforms.SetDihedralDeg(conf, 1, 3, 6, 8, 15.0)
ff = ChemicalForceFields.UFFGetMoleculeForceField(m)
self.assertTrue(ff)
ff.UFFAddTorsionConstraint(1, 3, 6, 8, False, 10.0, 20.0, 100.0)
r = ff.Minimize()
self.assertTrue(r == 0)
dihedral = rdMolTransforms.GetDihedralDeg(conf, 1, 3, 6, 8)
self.assertAlmostEqual(dihedral, 20, delta=0.1)
rdMolTransforms.SetDihedralDeg(conf, 1, 3, 6, 8, -30.0)
ff = ChemicalForceFields.UFFGetMoleculeForceField(m)
self.assertTrue(ff)
ff.UFFAddTorsionConstraint(1, 3, 6, 8, True, -10.0, 8.0, 100.0)
r = ff.Minimize()
self.assertTrue(r == 0)
conf = m.GetConformer()
dihedral = rdMolTransforms.GetDihedralDeg(conf, 1, 3, 6, 8)
self.assertAlmostEqual(dihedral, -40, delta=0.1)
rdMolTransforms.SetDihedralDeg(conf, 1, 3, 6, 8, -10.0)
ff = ChemicalForceFields.UFFGetMoleculeForceField(m)
self.assertTrue(ff)
ff.UFFAddTorsionConstraint(1, 3, 6, 8, False, -10.0, 8.0, 1.0e6)
r = ff.Minimize(500)
self.assertTrue(r == 0)
conf = m.GetConformer()
dihedral = rdMolTransforms.GetDihedralDeg(conf, 1, 3, 6, 8)
self.assertAlmostEqual(dihedral, -10, delta=0.1)
def testUFFPositionConstraints(self):
m = Chem.MolFromMolBlock(self.molB, True, False)
ff = ChemicalForceFields.UFFGetMoleculeForceField(m)
self.assertTrue(ff)
conf = m.GetConformer()
p = conf.GetAtomPosition(1)
ff.UFFAddPositionConstraint(1, 0.3, 1.0e5)
r = ff.Minimize()
self.assertTrue(r == 0)
q = conf.GetAtomPosition(1)
self.assertTrue((p - q).Length() < 0.3)
def testUFFFixedAtoms(self):
m = Chem.MolFromMolBlock(self.molB, True, False)
ff = ChemicalForceFields.UFFGetMoleculeForceField(m)
self.assertTrue(ff)
conf = m.GetConformer()
fp = conf.GetAtomPosition(1)
ff.AddFixedPoint(1)
r = ff.Minimize()
self.assertTrue(r == 0)
fq = conf.GetAtomPosition(1)
self.assertTrue((fp - fq).Length() < 0.01)
def testMMFFMinInfLoop(self):
os = OptSafe()
m = Chem.MolFromMolBlock(os.minInfLoop)
self.assertTrue(m)
ok = False
try:
ok = os.opt(m, os.mmffOptFunc)
except RuntimeError:
ok = True
pass
self.assertTrue(ok)
def testMMFFDistanceConstraints(self):
m = Chem.MolFromMolBlock(self.molB, True, False)
mp = ChemicalForceFields.MMFFGetMoleculeProperties(m)
ff = ChemicalForceFields.MMFFGetMoleculeForceField(m, mp)
self.assertTrue(ff)
ff.MMFFAddDistanceConstraint(1, 3, False, 2.0, 2.0, 1.0e5)
r = ff.Minimize()
self.assertTrue(r == 0)
conf = m.GetConformer()
dist = rdMolTransforms.GetBondLength(conf, 1, 3)
self.assertTrue(dist > 1.99)
ff = ChemicalForceFields.MMFFGetMoleculeForceField(m, mp)
self.assertTrue(ff)
ff.MMFFAddDistanceConstraint(1, 3, True, -0.2, 0.2, 1.0e5)
r = ff.Minimize()
self.assertTrue(r == 0)
conf = m.GetConformer()
dist = rdMolTransforms.GetBondLength(conf, 1, 3)
self.assertTrue(dist > 1.79)
def testMMFFAngleConstraints(self):
m = Chem.MolFromMolBlock(self.molB, True, False)
mp = ChemicalForceFields.MMFFGetMoleculeProperties(m)
ff = ChemicalForceFields.MMFFGetMoleculeForceField(m, mp)
self.assertTrue(ff)
ff.MMFFAddAngleConstraint(1, 3, 6, False, 90.0, 90.0, 100.0)
r = ff.Minimize()
self.assertTrue(r == 0)
conf = m.GetConformer()
angle = rdMolTransforms.GetAngleDeg(conf, 1, 3, 6)
self.assertAlmostEqual(angle, 90, delta=0.1)
ff = ChemicalForceFields.MMFFGetMoleculeForceField(m, mp)
self.assertTrue(ff)
ff.MMFFAddAngleConstraint(1, 3, 6, True, -10.0, 10.0, 100.0)
r = ff.Minimize()
self.assertTrue(r == 0)
conf = m.GetConformer()
angle = rdMolTransforms.GetAngleDeg(conf, 1, 3, 6)
self.assertAlmostEqual(angle, 100, delta=0.1)
def testMMFFTorsionConstraints(self):
m = Chem.MolFromMolBlock(self.molB, True, False)
conf = m.GetConformer()
rdMolTransforms.SetDihedralDeg(conf, 1, 3, 6, 8, 15.0)
mp = ChemicalForceFields.MMFFGetMoleculeProperties(m)
ff = ChemicalForceFields.MMFFGetMoleculeForceField(m, mp)
self.assertTrue(ff)
ff.MMFFAddTorsionConstraint(1, 3, 6, 8, False, 10.0, 20.0, 100.0)
r = ff.Minimize()
self.assertTrue(r == 0)
dihedral = rdMolTransforms.GetDihedralDeg(conf, 1, 3, 6, 8)
self.assertAlmostEqual(dihedral, 20, delta=0.1)
rdMolTransforms.SetDihedralDeg(conf, 1, 3, 6, 8, -30.0)
ff = ChemicalForceFields.MMFFGetMoleculeForceField(m, mp)
self.assertTrue(ff)
ff.MMFFAddTorsionConstraint(1, 3, 6, 8, True, -10.0, 8.0, 100.0)
r = ff.Minimize()
self.assertTrue(r == 0)
conf = m.GetConformer()
dihedral = rdMolTransforms.GetDihedralDeg(conf, 1, 3, 6, 8)
self.assertAlmostEqual(dihedral, -40, delta=0.1)
rdMolTransforms.SetDihedralDeg(conf, 1, 3, 6, 8, -10.0)
ff = ChemicalForceFields.MMFFGetMoleculeForceField(m, mp)
self.assertTrue(ff)
ff.MMFFAddTorsionConstraint(1, 3, 6, 8, False, -10.0, 8.0, 100.0)
r = ff.Minimize(1000)
self.assertTrue(r == 0)
conf = m.GetConformer()
dihedral = rdMolTransforms.GetDihedralDeg(conf, 1, 3, 6, 8)
self.assertAlmostEqual(dihedral, -10, delta=0.1)
def testMMFFPositionConstraints(self):
m = Chem.MolFromMolBlock(self.molB, True, False)
mp = ChemicalForceFields.MMFFGetMoleculeProperties(m)
ff = ChemicalForceFields.MMFFGetMoleculeForceField(m, mp)
self.assertTrue(ff)
conf = m.GetConformer()
p = conf.GetAtomPosition(1)
ff.MMFFAddPositionConstraint(1, 0.3, 1.0e5)
r = ff.Minimize()
self.assertTrue(r == 0)
q = conf.GetAtomPosition(1)
self.assertTrue((p - q).Length() < 0.3)
def testMMFFFixedAtoms(self):
m = Chem.MolFromMolBlock(self.molB, True, False)
mp = ChemicalForceFields.MMFFGetMoleculeProperties(m)
ff = ChemicalForceFields.MMFFGetMoleculeForceField(m, mp)
self.assertTrue(ff)
conf = m.GetConformer()
fp = conf.GetAtomPosition(1)
ff.AddFixedPoint(1)
r = ff.Minimize()
self.assertTrue(r == 0)
fq = conf.GetAtomPosition(1)
self.assertTrue((fp - fq).Length() < 0.01)
if __name__ == '__main__':
unittest.main()
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