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from rdkit import Chem
from rdkit.Chem import rdDistGeom,ChemicalForceFields,rdMolAlign
from rdkit import RDConfig
import unittest
import os,copy
import cPickle as pickle
import math
import numpy
from rdkit.Geometry import rdGeometry as geom
from rdkit.RDLogger import logger
logger=logger()
def feq(v1, v2, tol=1.e-4) :
return abs(v1-v2) < tol
def lstEq(l1, l2, tol=1.0e-4) :
ln = len(l1)
if (ln != len(l2) ) :
return 0
for i in range(ln) :
if abs(l1[i] - l2[i]) > tol :
return 0
return 1
def compareWithOld(smilesFile, sdFile) :
smiSup = Chem.SmilesMolSupplier(smilesFile, ",", 0, -1)
sdsup = Chem.SDMolSupplier(sdFile)
im = 0
for mol in smiSup :
cid = rdDistGeom.EmbedMolecule(mol, 10,1)
omol = sdsup[im]
assert cid == 0
conf = mol.GetConformer(0)
oconf = omol.GetConformer()
nat = mol.GetNumAtoms()
for i in range(nat) :
#atm = mol.GetAtomWithIdx(i)
#oatm = omol.GetAtomWithIdx(i)
pos = conf.GetAtomPosition(i)
opos = oconf.GetAtomPosition(i)
if not lstEq(pos, opos):
return 0
im += 1
return 1
def compareMatrices(bm1, bm2, map, tol=1.0e-5) :
N = numpy.shape(bm1)[0]
for i in range(1,N):
for j in range(i):
l, m = map[i], map[j]
if (l < m) :
l, m = m,l
if (abs(bm1[l,m] - bm2[i,j]) > tol):
return 0
if (abs(bm1[m,l] - bm2[j,i]) > tol):
return 0
return 1
def compareOrder(smi1, smi2, tol=1.0e-5) :
m1 = Chem.MolFromSmiles(smi1)
m2 = Chem.MolFromSmiles(smi2)
bm1 = rdDistGeom.GetMoleculeBoundsMatrix(m1)
bm2 = rdDistGeom.GetMoleculeBoundsMatrix(m2)
map = m1.GetSubstructMatch(m2)
return compareMatrices(bm1, bm2,map, tol)
def computeDist(lst1, lst2):
res = 0.0
for i, val in enumerate(lst1):
res += (val - lst2[i])*(val - lst2[i])
res = math.sqrt(res)
return res
def computeChiralVol(pt1, pt2, pt3, pt4):
v1 = pt1 - pt4
v2 = pt2 - pt4
v3 = pt3 - pt4
cp = v2.CrossProduct(v3)
vol = v1.DotProduct(cp)
return vol
class TestCase(unittest.TestCase) :
def setUp(self):
pass
def _test0Cdk2(self):
fileN = os.path.join(RDConfig.RDBaseDir,'Code','GraphMol','DistGeomHelpers',
'test_data','cis_trans_cases.csv')
ofile = os.path.join(RDConfig.RDBaseDir,'Code','GraphMol','DistGeomHelpers',
'test_data','embedDistOpti.sdf')
self.failUnless(compareWithOld(fileN, ofile))
def test1Small(self):
#writer = Chem.SDWriter("test.sdf")
# single double and tripple atoms cases should not fail
mol = Chem.MolFromSmiles('O')
rdDistGeom.EmbedMolecule(mol,10,1)
conf = mol.GetConformer()
self.failUnless(lstEq(conf.GetAtomPosition(0), [0.0, 0.0, 0.0]))
#writer.write(mol)
mol = Chem.MolFromSmiles('CO')
rdDistGeom.EmbedMolecule(mol, 10,1)
conf = mol.GetConformer()
self.failUnless(lstEq(conf.GetAtomPosition(0), [0.71308, 0.0, 0.0]))
self.failUnless(lstEq(conf.GetAtomPosition(1), [-0.71308, 0.0, 0.0]))
#writer.write(mol)
mol = Chem.MolFromSmiles('CCC')
rdDistGeom.EmbedMolecule(mol,10,1)
conf = mol.GetConformer()
self.failUnless(lstEq(conf.GetAtomPosition(0), [-1.21676, -0.2989, 0.0]))
self.failUnless(lstEq(conf.GetAtomPosition(1), [-0.00604, 0.59337, 0.0]))
self.failUnless(lstEq(conf.GetAtomPosition(2), [1.22281, -0.29446, 0.0]))
#writer.write(mol)
mol = Chem.MolFromSmiles('O=C=O')
rdDistGeom.EmbedMolecule(mol,10,1)
conf = mol.GetConformer()
#writer.write(mol)
self.failUnless(lstEq(conf.GetAtomPosition(0), [-1.2591, -0.06189, 0.0]))
self.failUnless(lstEq(conf.GetAtomPosition(1), [-0.00408, 0.12317, 0.0]))
self.failUnless(lstEq(conf.GetAtomPosition(2), [1.26318, -0.061288, 0.0]))
mol = Chem.MolFromSmiles('C=C=C=C')
rdDistGeom.EmbedMolecule(mol,10,1)
conf = mol.GetConformer()
#writer.write(mol)
d1 = computeDist(conf.GetAtomPosition(0), conf.GetAtomPosition(1))
self.failUnless(feq(d1, 1.31, 0.01))
d2 = computeDist(conf.GetAtomPosition(0), conf.GetAtomPosition(2))
self.failUnless(feq(d2, 2.59, 0.05))
d3 = computeDist(conf.GetAtomPosition(0), conf.GetAtomPosition(3))
self.failUnless(feq(d3, 3.84, 0.1))
d4 = computeDist(conf.GetAtomPosition(1), conf.GetAtomPosition(2))
self.failUnless(feq(d4, 1.29, 0.01))
d5 = computeDist(conf.GetAtomPosition(1), conf.GetAtomPosition(3))
self.failUnless(feq(d5, 2.54, 0.1))
d6 = computeDist(conf.GetAtomPosition(2), conf.GetAtomPosition(3))
self.failUnless(feq(d6, 1.31, 0.01))
def test2Utils(self):
mol = Chem.MolFromSmiles('CC')
bm = rdDistGeom.GetMoleculeBoundsMatrix(mol)
self.failUnless(bm[1,0]>0)
self.failUnless(bm[0,1]>0)
self.failUnless(bm[0,1]>=bm[1,0])
self.failUnless(bm[1,0]<1.510)
self.failUnless(bm[0,1]>1.510)
def test3MultiConf(self):
mol = Chem.MolFromSmiles("CC(C)(C)c(cc12)n[n]2C(=O)/C=C(N1)/COC")
cids = rdDistGeom.EmbedMultipleConfs(mol,10,maxAttempts=30,randomSeed=100)
energies = [90.05, 77.35, 91.45, 81.82, 81.60, 75.65, 86.50,
80.35, 80.55, 73.73]
nenergies = []
for cid in cids:
ff = ChemicalForceFields.UFFGetMoleculeForceField(mol, 10.0, cid)
ee = ff.CalcEnergy()
nenergies.append(ee)
#print ['%.2f'%x for x in nenergies]
#print nenergies
self.failUnless(lstEq(energies, nenergies,tol=1e-2))
def test4OrderDependence(self) :
self.failUnless(compareOrder("CC(C)(C)C(=O)NC(C1)CC(N2C)CCC12",
"CN1C2CCC1CC(NC(=O)C(C)(C)C)C2"))
#issue 230
self.failUnless(compareOrder("C#CC(C)(C)N(CN1)C\N=C/1SC",
"CSC1=NCN(C(C)(C)C#C)CN1"))
#issue 232
self.failUnless(compareOrder("CC(C)(C)C(=O)NC(C1)CC(N2C)CCC12",
"CN1C2CCC1CC(NC(=O)C(C)(C)C)C2"))
def test5Issue285(self):
m = Chem.MolFromSmiles('CNC=O')
cs = rdDistGeom.EmbedMultipleConfs(m,10)
for i,ci in enumerate(cs):
for j in range(i+1,len(cs)):
cj = cs[j]
self.failUnless(Chem.MolToMolBlock(m,confId=ci)!=Chem.MolToMolBlock(m,confId=cj))
def test6RmsPruning(self):
smiles = ['CC(C)CC(NC(C1[N+]CCC1)=O)C([O-])=O',
'CC(NC(CO)C(O)c1ccc([N+]([O-])=O)cc1)=O',
'CC([N+])C(NC(C)C(N1C(C=O)CCC1)=O)=O',
'CC(NC1C(O)C=C(C([O-])=O)OC1C(O)C(O)CO)=O',
'CCCC=C(NC(C1CC1(C)C)=O)C([O-])=O',
'OCC(O)C(O)C(Cn1c2c(cc(C)c(C)c2)nc-2c(=O)[nH]c(=O)nc12)O']
nconfs = []
expected = [5, 8, 8, 5, 6, 4]
for smi in smiles:
mol = Chem.MolFromSmiles(smi)
cids = rdDistGeom.EmbedMultipleConfs(mol, 50, maxAttempts=30,
randomSeed=100, pruneRmsThresh=1.5)
nconfs.append(len(cids))
d = [abs(x-y) for x,y in zip(expected,nconfs)]
self.failUnless(max(d)<=1)
def test6Chirality(self):
# turn on chirality and we should get chiral volume that is pretty consistent and
# positive
tgtVol=14.0
smiles = "Cl[C@](C)(F)Br"
mol = Chem.MolFromSmiles(smiles)
cids = rdDistGeom.EmbedMultipleConfs(mol, 10, maxAttempts=30,
randomSeed=100)
self.failUnless(len(cids)==10)
for cid in cids:
conf = mol.GetConformer(cid)
vol = computeChiralVol(conf.GetAtomPosition(0),
conf.GetAtomPosition(2),
conf.GetAtomPosition(3),
conf.GetAtomPosition(4))
self.failUnless(abs(vol-tgtVol)<1)
# turn of chirality and now we should see both chiral forms
smiles = "ClC(C)(F)Br"
mol = Chem.MolFromSmiles(smiles)
cids = rdDistGeom.EmbedMultipleConfs(mol, 10, maxAttempts=30,
randomSeed=120)
self.failUnless(len(cids)==10)
nPos=0
nNeg=0
for cid in cids:
conf = mol.GetConformer(cid)
vol = computeChiralVol(conf.GetAtomPosition(0),
conf.GetAtomPosition(2),
conf.GetAtomPosition(3),
conf.GetAtomPosition(4))
self.failUnless(abs(vol-tgtVol)<1 or abs(vol+tgtVol)<1)
if vol<0: nNeg+=1
else: nPos+=1
self.failUnless(nPos>0)
self.failUnless(nNeg>0)
tgtVol=5.0
for i in range(10):
smiles = "Cl[C@H](F)Br"
mol = Chem.MolFromSmiles(smiles)
ci = rdDistGeom.EmbedMolecule(mol, 30, (i+1)*10)
conf = mol.GetConformer(ci)
vol = computeChiralVol(conf.GetAtomPosition(0),
conf.GetAtomPosition(1),
conf.GetAtomPosition(2),
conf.GetAtomPosition(3))
self.failUnless(abs(vol-tgtVol)<1,"%s %s"%(vol,tgtVol))
tgtVol=3.5
expected = [-3.62, -3.67, -3.72, 3.91, 3.95, 3.98, 3.90, 3.94, 3.98, 3.91]
nPos=0
nNeg=0
for i in range(10):
smiles = "ClC(F)Br"
mol = Chem.MolFromSmiles(smiles)
ci = rdDistGeom.EmbedMolecule(mol, 30, (i+1)*10)
conf = mol.GetConformer(ci)
vol = computeChiralVol(conf.GetAtomPosition(0),
conf.GetAtomPosition(1),
conf.GetAtomPosition(2),
conf.GetAtomPosition(3))
self.failUnless(abs(vol-tgtVol)<1 or abs(vol+tgtVol)<1)
if vol<0: nNeg+=1
else: nPos+=1
self.failUnless(nPos>0)
self.failUnless(nNeg>0)
smiles = "Cl[C@H](F)Br"
m = Chem.MolFromSmiles(smiles)
mol = Chem.AddHs(m)
cids = rdDistGeom.EmbedMultipleConfs(mol, 10, maxAttempts=30,
randomSeed=100)
self.failUnless(len(cids)==10)
tgtVol=10.5
for cid in cids:
conf = mol.GetConformer(cid)
vol = computeChiralVol(conf.GetAtomPosition(0),
conf.GetAtomPosition(2),
conf.GetAtomPosition(3),
conf.GetAtomPosition(4))
self.failUnless(abs(vol-tgtVol)<2.)
# let's try a little more complicated system
expectedV1 = -2.0
expectedV2 = -2.9
for i in range(5):
smi = "C1=CC=C(C=C1)[C@H](OC1=C[NH]N=C1)C(=O)[NH]C[C@H](Cl)C1=CC=NC=C1"
mol = Chem.MolFromSmiles(smi)
ci = rdDistGeom.EmbedMolecule(mol, 30, randomSeed=(i+1)*15)
ff = ChemicalForceFields.UFFGetMoleculeForceField(mol, 10.0, ci)
ff.Minimize()
conf = mol.GetConformer(ci)
vol1 = computeChiralVol(conf.GetAtomPosition(6),
conf.GetAtomPosition(3),
conf.GetAtomPosition(7),
conf.GetAtomPosition(13))
self.failUnless(abs(vol1-expectedV1)<1 or abs(vol1+expectedV1)<1)
if vol1<0: nNeg+=1
else: nPos+=1
vol2 = computeChiralVol(conf.GetAtomPosition(17),
conf.GetAtomPosition(16),
conf.GetAtomPosition(18),
conf.GetAtomPosition(19))
self.failUnless(abs(vol2-expectedV2)<1 or abs(vol2+expectedV2)<1)
# remove the chiral specification and we should see other chiral
# forms of the compound
expectedV1 = 2.0 #[-2.30, -2.31, -2.30, 2.30, -1.77]
expectedV2 = 2.8 #[2.90, 2.89, 2.69, -2.90, -2.93]
self.failUnless(nPos>0)
self.failUnless(nNeg>0)
for i in range(5):
smi = "C1=CC=C(C=C1)C(OC1=C[NH]N=C1)C(=O)[NH]CC(Cl)C1=CC=NC=C1"
mol = Chem.MolFromSmiles(smi)
ci = rdDistGeom.EmbedMolecule(mol, 30, (i+1)*10)
ff = ChemicalForceFields.UFFGetMoleculeForceField(mol, 10.0, ci)
ff.Minimize()
conf = mol.GetConformer(ci)
vol1 = computeChiralVol(conf.GetAtomPosition(6),
conf.GetAtomPosition(3),
conf.GetAtomPosition(7),
conf.GetAtomPosition(13))
vol2 = computeChiralVol(conf.GetAtomPosition(17),
conf.GetAtomPosition(16),
conf.GetAtomPosition(18),
conf.GetAtomPosition(19))
self.failUnless(abs(abs(vol1)-expectedV1)<1.0)
self.failUnless(abs(abs(vol2)-expectedV2)<1.0)
def test7ConstrainedEmbedding(self):
ofile = os.path.join(RDConfig.RDBaseDir,'Code','GraphMol','DistGeomHelpers',
'test_data','constrain1.sdf')
suppl = Chem.SDMolSupplier(ofile);
ref = suppl.next()
probe = copy.deepcopy(ref)
cMap={}
for i in range(5):
cMap[i]=ref.GetConformer().GetAtomPosition(i)
ci = rdDistGeom.EmbedMolecule(probe,coordMap=cMap,randomSeed=23)
self.failUnless(ci>-1);
algMap = zip(range(5),range(5))
ssd = rdMolAlign.AlignMol(probe,ref,atomMap=algMap)
print 'ssd:',ssd
self.failUnless(ssd<0.1)
if __name__ == '__main__':
unittest.main()
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