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# $Id$
#
# Copyright (C) 2004 Rational Discovery LLC
# All Rights Reserved
#
from rdkit import RDConfig
import os, sys
import unittest
from rdkit import Chem
from rdkit import Geometry
from rdkit.Geometry import Point3D
def feq(v1, v2, tol2=1e-4):
return abs(v1 - v2) <= tol2
def ptEq(pt1, pt2, tol=1e-4):
return feq(pt1.x, pt2.x, tol) and feq(pt1.y, pt2.y, tol) and feq(pt1.z, pt2.z, tol)
def addConf(mol):
conf = Chem.Conformer(mol.GetNumAtoms())
for i in range(mol.GetNumAtoms()):
conf.SetAtomPosition(i, (0., 0., 0.))
mol.AddConformer(conf)
mb = Chem.MolToMolBlock(mol)
mb = Chem.MolToMolBlock(mol)
class TestCase(unittest.TestCase):
def setUp(self):
pass
def test0Conformers(self):
"""Test the conformer data structure"""
mol = Chem.MolFromSmiles("CC")
conf = Chem.Conformer(2)
conf.SetAtomPosition(0, (-0.5, 0.0, 0.0))
conf.SetAtomPosition(1, (1.0, 0.0, 0.0))
conf.SetId(0)
cid = mol.AddConformer(conf)
self.assertTrue(cid == 0)
conf2 = mol.GetConformer(0)
self.assertTrue(conf2.GetId() == cid)
pt1 = conf2.GetAtomPosition(0)
self.assertTrue(ptEq(pt1, Point3D(-0.5, 0.0, 0.0)))
pt2 = conf2.GetAtomPosition(1)
self.assertTrue(ptEq(pt2, Point3D(1.0, 0.0, 0.0)))
#changing conf should not change conf2 - related to issue 217
conf.SetAtomPosition(1, Point3D(2.0, 0.0, 0.0))
pt2 = conf2.GetAtomPosition(1)
self.assertTrue(feq(pt2[0], 1.0))
conf = Chem.Conformer(2)
conf.SetAtomPosition(0, Point3D(-0.5, 0.0, 0.0))
conf.SetAtomPosition(1, Point3D(1.0, 0.0, 0.0))
conf.SetId(2)
cid = mol.AddConformer(conf, 0)
self.assertTrue(cid == 2)
conf3 = mol.GetConformer(2)
def test0AddHds(self):
mol = Chem.MolFromSmiles("CC")
conf = Chem.Conformer(1)
conf.SetAtomPosition(0, Point3D(-0.5, 0.0, 0.0))
conf.SetAtomPosition(1, Point3D(1.0, 0.0, 0.0))
cid = mol.AddConformer(conf)
conf2 = mol.GetConformer()
self.assertTrue(conf2.GetNumAtoms() == 2)
nmol = Chem.AddHs(mol, 0, 1)
conf3 = nmol.GetConformer()
self.assertTrue(conf3.GetNumAtoms() == 8)
self.assertTrue(conf2.GetNumAtoms() == 2)
targetCoords = [[-0.5, 0.0, 0.0], [1.0, 0.0, 0.0], [-0.8667, 0.0, 1.03709],
[-0.8667, 0.8981, -0.5185], [-0.8667, -0.8981, -0.5185], [1.3667, 0.0, -1.0371],
[1.36667, 0.8981, 0.5185], [1.36667, -0.8981, 0.5185]]
for i in range(8):
pt = conf3.GetAtomPosition(i)
self.assertTrue(ptEq(pt, Point3D(*tuple(targetCoords[i]))))
def test2Issue217(self):
smi = 'c1ccccc1'
m = Chem.MolFromSmiles(smi)
addConf(m)
self.assertTrue(m.GetNumConformers() == 1)
mb2 = Chem.MolToMolBlock(m)
def test3Exceptions(self):
smi = 'c1ccccc1'
m = Chem.MolFromSmiles(smi)
addConf(m)
self.assertTrue(m.GetNumConformers() == 1)
self.assertRaises(ValueError, lambda: m.GetConformer(2))
def test4ConfTuple(self):
smi = 'c1ccccc1'
m = Chem.MolFromSmiles(smi)
for i in range(10):
addConf(m)
confs = m.GetConformers()
self.assertTrue(len(confs) == 10)
for conf in confs:
for i in range(6):
pt = conf.GetAtomPosition(i)
self.assertTrue(ptEq(pt, Point3D(0.0, 0.0, 0.0)))
m.RemoveAllConformers()
self.assertTrue(m.GetNumConformers() == 0)
confs = m.GetConformers()
self.assertTrue(confs == ())
def test5PositionsArray(self):
smi = 'c1ccccc1'
m = Chem.MolFromSmiles(smi)
addConf(m)
confs = m.GetConformers()
self.assertTrue(len(confs) == 1)
for conf in confs:
pos = conf.GetPositions()
self.assertTrue(pos.shape, (6, 3))
m.RemoveAllConformers()
self.assertTrue(m.GetNumConformers() == 0)
confs = m.GetConformers()
self.assertTrue(confs == ())
if __name__ == '__main__':
unittest.main()
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