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from rdkit import Chem
from rdkit.Chem import ChemicalForceFields
from rdkit import RDConfig
import unittest
import os
def feq(v1,v2,tol2=1e-4):
return abs(v1-v2)<=tol2
class TestCase(unittest.TestCase):
def setUp(self) :
self.dirName=os.path.join(RDConfig.RDBaseDir,'Code','GraphMol',
'ForceFieldHelpers','UFF','test_data')
def test1(self) :
fName = os.path.join(self.dirName,'benzene.mol')
m = Chem.MolFromMolFile(fName)
self.failIf(ChemicalForceFields.UFFOptimizeMolecule(m))
# make sure that keyword arguments work:
m = Chem.MolFromMolFile(fName)
self.failUnless(ChemicalForceFields.UFFOptimizeMolecule(m,maxIters=1))
m = Chem.MolFromMolFile(fName)
self.failIf(ChemicalForceFields.UFFOptimizeMolecule(m,vdwThresh=2.0))
m = Chem.MolFromMolFile(fName)
self.failIf(ChemicalForceFields.UFFOptimizeMolecule(m,confId=-1))
m = Chem.MolFromMolFile(fName)
self.failUnlessRaises(ValueError,lambda :ChemicalForceFields.UFFOptimizeMolecule(m,confId=1))
def test2(self) :
fName = os.path.join(self.dirName,'benzene.mol')
m = Chem.MolFromMolFile(fName)
ff = ChemicalForceFields.UFFGetMoleculeForceField(m)
self.failUnless(ff)
e1 = ff.CalcEnergy()
r = ff.Minimize()
self.failUnless(r==0)
e2 = ff.CalcEnergy()
self.failUnless(e2<e1);
# test keyword args:
r = ff.Minimize(forceTol=1e-8)
self.failUnless(r==0)
# test keyword args:
r = ff.Minimize(energyTol=1e-3)
self.failUnless(r==0)
def test3(self) :
molB = """
4 4 0 0 0 0 0 0 0 0999 V2000
-0.8500 0.4512 -0.6671 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3307 -0.9436 -0.3641 C 0 0 0 0 0 0 0 0 0 0 0 0
0.6796 -0.4074 0.5894 C 0 0 0 0 0 0 0 0 0 0 0 0
0.5011 0.8998 -0.1231 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 0
3 4 1 0
1 4 1 0
M END"""
m = Chem.MolFromMolBlock(molB)
ff = ChemicalForceFields.UFFGetMoleculeForceField(m)
self.failUnless(ff)
e1 = ff.CalcEnergy()
r = ff.Minimize()
self.failUnless(r==0)
e2 = ff.CalcEnergy()
self.failUnless(e2<e1);
def test4(self) :
m = Chem.MolFromSmiles('[Cu](C)(C)(C)(C)C')
self.failIf(ChemicalForceFields.UFFHasAllMoleculeParams(m))
m = Chem.MolFromSmiles('C(C)(C)(C)C')
self.failUnless(ChemicalForceFields.UFFHasAllMoleculeParams(m))
def test5(self) :
fName = os.path.join(self.dirName,'benzene.mol')
m = Chem.MolFromMolFile(fName)
self.failIf(ChemicalForceFields.MMFFOptimizeMolecule(m))
# make sure that keyword arguments work:
m = Chem.MolFromMolFile(fName)
self.failUnless(ChemicalForceFields.MMFFOptimizeMolecule(m, maxIters = 1))
m = Chem.MolFromMolFile(fName)
self.failIf(ChemicalForceFields.MMFFOptimizeMolecule(m, nonBondedThresh = 2.0))
m = Chem.MolFromMolFile(fName)
self.failIf(ChemicalForceFields.MMFFOptimizeMolecule(m, confId = -1))
m = Chem.MolFromMolFile(fName)
self.failUnlessRaises(ValueError, lambda :ChemicalForceFields.MMFFOptimizeMolecule(m, confId = 1))
def test6(self) :
fName = os.path.join(self.dirName, 'benzene.mol')
m = Chem.MolFromMolFile(fName)
mp = ChemicalForceFields.MMFFGetMoleculeProperties(m)
ff = ChemicalForceFields.MMFFGetMoleculeForceField(m, mp)
self.failUnless(ff)
e1 = ff.CalcEnergy()
r = ff.Minimize()
self.failUnless(r == 0)
e2 = ff.CalcEnergy()
self.failUnless(e2 < e1);
# test keyword args:
r = ff.Minimize(forceTol = 1.0e-8)
self.failUnless(r == 0)
# test keyword args:
r = ff.Minimize(energyTol = 1.0e-3)
self.failUnless(r == 0)
def test7(self) :
molB = """
4 4 0 0 0 0 0 0 0 0999 V2000
-0.8500 0.4512 -0.6671 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3307 -0.9436 -0.3641 C 0 0 0 0 0 0 0 0 0 0 0 0
0.6796 -0.4074 0.5894 C 0 0 0 0 0 0 0 0 0 0 0 0
0.5011 0.8998 -0.1231 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 0
3 4 1 0
1 4 1 0
M END"""
m = Chem.MolFromMolBlock(molB)
mp = ChemicalForceFields.MMFFGetMoleculeProperties(m)
ff = ChemicalForceFields.MMFFGetMoleculeForceField(m, mp)
self.failUnless(ff)
e1 = ff.CalcEnergy()
r = ff.Minimize()
self.failUnless(r == 0)
e2 = ff.CalcEnergy()
self.failUnless(e2 < e1);
def test8(self) :
m = Chem.MolFromSmiles('[Cu](C)(C)(C)(C)C')
self.failIf(ChemicalForceFields.MMFFHasAllMoleculeParams(m))
m = Chem.MolFromSmiles('C(C)(C)(C)C')
self.failUnless(ChemicalForceFields.MMFFHasAllMoleculeParams(m))
if __name__== '__main__':
unittest.main()
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