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from rdkit import RDConfig
import os,sys,math
import unittest
from rdkit import DataStructs
from rdkit import Chem
from rdkit.Geometry import rdGeometry as geom
from rdkit.Chem import rdMolTransforms as rdmt
def feq(v1, v2, tol=1.0e-4):
return abs(v1-v2) < tol
def ptEq(pt, tpt, tol=0.0001):
pt -= tpt
return feq(pt.Length(), 0.0)
class TestCase(unittest.TestCase):
def setUp(self) :
pass
def test1Canonicalization(self) :
mol = Chem.MolFromSmiles("C")
conf = Chem.Conformer(1)
conf.SetAtomPosition(0, (4.0, 5.0, 6.0))
mol.AddConformer(conf,1)
conf = mol.GetConformer()
pt = rdmt.ComputeCentroid(conf)
self.failUnless(ptEq(pt, geom.Point3D(4.0, 5.0, 6.0)))
fileN = os.path.join(RDConfig.RDBaseDir,'Code','GraphMol','MolTransforms',
'test_data','1oir.mol')
m = Chem.MolFromMolFile(fileN)
cpt = rdmt.ComputeCentroid(m.GetConformer())
trans = rdmt.ComputeCanonicalTransform(m.GetConformer(), cpt)
trans2 = rdmt.ComputeCanonicalTransform(m.GetConformer())
for i in range(4):
for j in range(4) :
self.failUnless(feq(trans[i,j], trans2[i, j]))
rdmt.TransformConformer(m.GetConformer(), trans2)
m2 = Chem.MolFromMolFile(fileN)
rdmt.CanonicalizeConformer(m2.GetConformer())
nats = m.GetNumAtoms()
cnf1 = m.GetConformer()
cnf2 = m2.GetConformer()
for i in range(nats):
p1 = list(cnf1.GetAtomPosition(i))
p2 = list(cnf2.GetAtomPosition(i))
self.failUnless(feq(p1[0],p2[0]))
self.failUnless(feq(p1[1],p2[1]))
self.failUnless(feq(p1[2],p2[2]))
m3 = Chem.MolFromMolFile(fileN)
rdmt.CanonicalizeMol(m3)
cnf1 = m.GetConformer()
cnf2 = m3.GetConformer()
for i in range(nats):
p1 = list(cnf1.GetAtomPosition(i))
p2 = list(cnf2.GetAtomPosition(i))
self.failUnless(feq(p1[0],p2[0]))
self.failUnless(feq(p1[1],p2[1]))
self.failUnless(feq(p1[2],p2[2]))
def testGetSetBondLength(self):
file = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'MolTransforms',
'test_data', '3-cyclohexylpyridine.mol')
m = Chem.MolFromMolFile(file, True, False)
conf = m.GetConformer()
dist = rdmt.GetBondLength(conf, 0, 19)
self.failUnlessAlmostEqual(dist, 1.36, 2)
rdmt.SetBondLength(conf, 0, 19, 2.5)
dist = rdmt.GetBondLength(conf, 0, 19)
self.failUnlessAlmostEqual(dist, 2.5, 1)
rdmt.SetBondLength(conf, 19, 0, 3.0)
dist = rdmt.GetBondLength(conf, 0, 19)
self.failUnlessAlmostEqual(dist, 3.0, 1)
def testGetSetAngle(self):
file = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'MolTransforms',
'test_data', '3-cyclohexylpyridine.mol')
m = Chem.MolFromMolFile(file, True, False)
conf = m.GetConformer()
angle = rdmt.GetAngleDeg(conf, 0, 19, 21)
self.failUnlessAlmostEqual(angle, 109.7, 1)
rdmt.SetAngleDeg(conf, 0, 19, 21, 125.0)
angle = rdmt.GetAngleDeg(conf, 0, 19, 21);
self.failUnlessAlmostEqual(angle, 125.0, 1)
rdmt.SetAngleRad(conf, 21, 19, 0, math.pi / 2.)
angle = rdmt.GetAngleRad(conf, 0, 19, 21)
self.failUnlessAlmostEqual(angle, math.pi / 2., 1)
angle = rdmt.GetAngleDeg(conf, 0, 19, 21)
self.failUnlessAlmostEqual(angle, 90.0, 1)
def testGetSetDihedral(self):
file = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'MolTransforms',
'test_data', '3-cyclohexylpyridine.mol')
m = Chem.MolFromMolFile(file, True, False)
conf = m.GetConformer()
dihedral = rdmt.GetDihedralDeg(conf, 0, 19, 21, 24)
self.failUnlessAlmostEqual(dihedral, 176.05, 2)
rdmt.SetDihedralDeg(conf, 8, 0, 19, 21, 65.0)
dihedral = rdmt.GetDihedralDeg(conf, 8, 0, 19, 21)
self.failUnlessAlmostEqual(dihedral, 65.0, 1)
rdmt.SetDihedralDeg(conf, 8, 0, 19, 21, -130.0)
dihedral = rdmt.GetDihedralDeg(conf, 8, 0, 19, 21)
self.failUnlessAlmostEqual(dihedral, -130.0, 1)
rdmt.SetDihedralRad(conf, 21, 19, 0, 8, -2. / 3. * math.pi)
dihedral = rdmt.GetDihedralRad(conf, 8, 0, 19, 21)
self.failUnlessAlmostEqual(dihedral, -2. / 3. * math.pi, 1)
dihedral = rdmt.GetDihedralDeg(conf, 8, 0, 19, 21)
self.failUnlessAlmostEqual(dihedral, -120.0, 1)
if __name__=="__main__":
unittest.main()
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