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rdkit/Code/GraphMol/Wrap/rough_test.py
Ric 3b2916c9a4 Fixes #5172 (#5181) 
* add test

* fix LogStateSetter

* fix BlockLogs() usage in Draw module

* allow BlockLogs() as a contestmgr

* move test to more suitable location

* guarantee log restoration on __exit__

* skip test if logs cannot be grabbed before block
2022-04-12 05:57:25 +02:00

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#
# Copyright (C) 2003-2021 Greg Landrum and other RDKit contributors
# All Rights Reserved
#
""" This is a rough coverage test of the python wrapper
it's intended to be shallow, but broad
"""
import doctest
import gc
import gzip
import logging
import os
import sys
import tempfile
import unittest
from contextlib import contextmanager
from datetime import datetime, timedelta
from io import StringIO
import rdkit.Chem.rdDepictor
from rdkit import Chem, DataStructs, RDConfig, __version__, rdBase
from rdkit.Chem import rdqueries
# Boost functions are NOT found by doctest, this "fixes" them
# by adding the doctests to a fake module
import importlib.util
spec = importlib.util.spec_from_loader("TestReplaceCore", loader=None)
TestReplaceCore = importlib.util.module_from_spec(spec)
code = """
from rdkit.Chem import ReplaceCore
def ReplaceCore(*a, **kw):
'''%s
'''
return Chem.ReplaceCore(*a, **kw)
""" % "\n".join([x.lstrip() for x in Chem.ReplaceCore.__doc__.split("\n")])
exec(code, TestReplaceCore.__dict__)
@contextmanager
def log_to_python(level=None):
"""
Temporarily redirect logging to Python streams, optionally
setting a specific log level.
"""
rdBase.LogToPythonLogger()
pylog = logging.getLogger("rdkit")
if level is not None:
original_level = pylog.level
pylog.setLevel(level)
yield pylog
if level is not None:
pylog.setLevel(original_level)
rdBase.LogToCppStreams()
@contextmanager
def capture_logging(level=None):
"""
Temporarily redirect logging to a Python StringIO, optionally
setting a specific log level.
"""
log_stream = StringIO()
stream_handler = logging.StreamHandler(stream=log_stream)
with log_to_python(level) as pylog:
pylog.addHandler(stream_handler)
yield log_stream
pylog.removeHandler(stream_handler)
def load_tests(loader, tests, ignore):
tests.addTests(doctest.DocTestSuite(TestReplaceCore))
return tests
def feq(v1, v2, tol2=1e-4):
return abs(v1 - v2) <= tol2
def getTotalFormalCharge(mol):
totalFormalCharge = 0
for atom in mol.GetAtoms():
totalFormalCharge += atom.GetFormalCharge()
return totalFormalCharge
def cmpFormalChargeBondOrder(self, mol1, mol2):
self.assertEqual(mol1.GetNumAtoms(), mol2.GetNumAtoms())
self.assertEqual(mol1.GetNumBonds(), mol2.GetNumBonds())
for i in range(mol1.GetNumAtoms()):
self.assertEqual(
mol1.GetAtomWithIdx(i).GetFormalCharge(),
mol2.GetAtomWithIdx(i).GetFormalCharge())
for i in range(mol1.GetNumBonds()):
self.assertEqual(mol1.GetBondWithIdx(i).GetBondType(), mol2.GetBondWithIdx(i).GetBondType())
def setResidueFormalCharge(mol, res, fc):
for query in res:
matches = mol.GetSubstructMatches(query)
for match in matches:
mol.GetAtomWithIdx(match[-1]).SetFormalCharge(fc)
def getBtList2(resMolSuppl):
btList2 = []
while (not resMolSuppl.atEnd()):
resMol = next(resMolSuppl)
bt = []
for bond in resMol.GetBonds():
bt.append(int(bond.GetBondTypeAsDouble()))
btList2.append(bt)
for i in range(len(btList2)):
same = True
for j in range(len(btList2[i])):
if (not i):
continue
if (same):
same = (btList2[i][j] == btList2[i - 1][j])
if (i and same):
return None
return btList2
class TestCase(unittest.TestCase):
def test0Except(self):
with self.assertRaises(IndexError):
Chem.tossit()
def test1Table(self):
tbl = Chem.GetPeriodicTable()
self.assertTrue(tbl)
self.assertTrue(feq(tbl.GetAtomicWeight(6), 12.011))
self.assertTrue(feq(tbl.GetAtomicWeight("C"), 12.011))
self.assertTrue(tbl.GetAtomicNumber('C') == 6)
self.assertTrue(feq(tbl.GetRvdw(6), 1.7))
self.assertTrue(feq(tbl.GetRvdw("C"), 1.7))
self.assertTrue(feq(tbl.GetRcovalent(6), 0.680))
self.assertTrue(feq(tbl.GetRcovalent("C"), 0.680))
self.assertTrue(tbl.GetDefaultValence(6) == 4)
self.assertTrue(tbl.GetDefaultValence("C") == 4)
self.assertTrue(tuple(tbl.GetValenceList(6)) == (4, ))
self.assertTrue(tuple(tbl.GetValenceList("C")) == (4, ))
self.assertTrue(tuple(tbl.GetValenceList(16)) == (2, 4, 6))
self.assertTrue(tuple(tbl.GetValenceList("S")) == (2, 4, 6))
self.assertTrue(tbl.GetNOuterElecs(6) == 4)
self.assertTrue(tbl.GetNOuterElecs("C") == 4)
self.assertTrue(tbl.GetMostCommonIsotope(6) == 12)
self.assertTrue(tbl.GetMostCommonIsotope('C') == 12)
self.assertTrue(tbl.GetMostCommonIsotopeMass(6) == 12.0)
self.assertTrue(tbl.GetMostCommonIsotopeMass('C') == 12.0)
self.assertTrue(tbl.GetAbundanceForIsotope(6, 12) == 98.93)
self.assertTrue(tbl.GetAbundanceForIsotope('C', 12) == 98.93)
self.assertTrue(feq(tbl.GetRb0(6), 0.77))
self.assertTrue(feq(tbl.GetRb0("C"), 0.77))
self.assertTrue(tbl.GetElementSymbol(6) == 'C')
def test2Atom(self):
atom = Chem.Atom(6)
self.assertTrue(atom)
self.assertTrue(atom.GetAtomicNum() == 6)
atom.SetAtomicNum(8)
self.assertTrue(atom.GetAtomicNum() == 8)
atom = Chem.Atom("C")
self.assertTrue(atom)
self.assertTrue(atom.GetAtomicNum() == 6)
def test3Bond(self):
# No longer relevant, bonds are not constructible from Python
pass
def test4Mol(self):
mol = Chem.Mol()
self.assertTrue(mol)
def test5Smiles(self):
mol = Chem.MolFromSmiles('n1ccccc1')
self.assertTrue(mol)
self.assertTrue(mol.GetNumAtoms() == 6)
self.assertTrue(mol.GetNumAtoms(1) == 6)
self.assertTrue(mol.GetNumAtoms(0) == 11)
at = mol.GetAtomWithIdx(2)
self.assertTrue(at.GetAtomicNum() == 6)
at = mol.GetAtomWithIdx(0)
self.assertTrue(at.GetAtomicNum() == 7)
def _test6Bookmarks(self):
mol = Chem.MolFromSmiles('n1ccccc1')
self.assertTrue(mol)
self.assertTrue(not mol.HasAtomBookmark(0))
mol.SetAtomBookmark(mol.GetAtomWithIdx(0), 0)
mol.SetAtomBookmark(mol.GetAtomWithIdx(1), 1)
self.assertTrue(mol.HasAtomBookmark(0))
self.assertTrue(mol.HasAtomBookmark(1))
if 1:
self.assertTrue(not mol.HasBondBookmark(0))
self.assertTrue(not mol.HasBondBookmark(1))
mol.SetBondBookmark(mol.GetBondWithIdx(0), 0)
mol.SetBondBookmark(mol.GetBondWithIdx(1), 1)
self.assertTrue(mol.HasBondBookmark(0))
self.assertTrue(mol.HasBondBookmark(1))
at = mol.GetAtomWithBookmark(0)
self.assertTrue(at)
self.assertTrue(at.GetAtomicNum() == 7)
mol.ClearAtomBookmark(0)
self.assertTrue(not mol.HasAtomBookmark(0))
self.assertTrue(mol.HasAtomBookmark(1))
mol.ClearAllAtomBookmarks()
self.assertTrue(not mol.HasAtomBookmark(0))
self.assertTrue(not mol.HasAtomBookmark(1))
mol.SetAtomBookmark(mol.GetAtomWithIdx(1), 1)
if 1:
self.assertTrue(mol.HasBondBookmark(0))
self.assertTrue(mol.HasBondBookmark(1))
bond = mol.GetBondWithBookmark(0)
self.assertTrue(bond)
mol.ClearBondBookmark(0)
self.assertTrue(not mol.HasBondBookmark(0))
self.assertTrue(mol.HasBondBookmark(1))
mol.ClearAllBondBookmarks()
self.assertTrue(not mol.HasBondBookmark(0))
self.assertTrue(not mol.HasBondBookmark(1))
self.assertTrue(mol.HasAtomBookmark(1))
def test7Atom(self):
mol = Chem.MolFromSmiles('n1ccccc1C[CH2-]')
self.assertTrue(mol)
Chem.SanitizeMol(mol)
a0 = mol.GetAtomWithIdx(0)
a1 = mol.GetAtomWithIdx(1)
a6 = mol.GetAtomWithIdx(6)
a7 = mol.GetAtomWithIdx(7)
self.assertTrue(a0.GetAtomicNum() == 7)
self.assertTrue(a0.GetSymbol() == 'N')
self.assertTrue(a0.GetIdx() == 0)
aList = [a0, a1, a6, a7]
self.assertTrue(a0.GetDegree() == 2)
self.assertTrue(a1.GetDegree() == 2)
self.assertTrue(a6.GetDegree() == 2)
self.assertTrue(a7.GetDegree() == 1)
self.assertTrue([x.GetDegree() for x in aList] == [2, 2, 2, 1])
self.assertTrue([x.GetTotalNumHs() for x in aList] == [0, 1, 2, 2])
self.assertTrue([x.GetNumImplicitHs() for x in aList] == [0, 1, 2, 0])
self.assertTrue([x.GetExplicitValence() for x in aList] == [3, 3, 2, 3])
self.assertTrue([x.GetImplicitValence() for x in aList] == [0, 1, 2, 0])
self.assertTrue([x.GetFormalCharge() for x in aList] == [0, 0, 0, -1])
self.assertTrue([x.GetNoImplicit() for x in aList] == [0, 0, 0, 1])
self.assertTrue([x.GetNumExplicitHs() for x in aList] == [0, 0, 0, 2])
self.assertTrue([x.GetIsAromatic() for x in aList] == [1, 1, 0, 0])
self.assertTrue([x.GetHybridization() for x in aList] == [
Chem.HybridizationType.SP2, Chem.HybridizationType.SP2, Chem.HybridizationType.SP3,
Chem.HybridizationType.SP3
], [x.GetHybridization() for x in aList])
def test8Bond(self):
mol = Chem.MolFromSmiles('n1ccccc1CC(=O)O')
self.assertTrue(mol)
Chem.SanitizeMol(mol)
# note bond numbering is funny because of ring closure
b0 = mol.GetBondWithIdx(0)
b6 = mol.GetBondWithIdx(6)
b7 = mol.GetBondWithIdx(7)
b8 = mol.GetBondWithIdx(8)
bList = [b0, b6, b7, b8]
self.assertTrue(
[x.GetBondType() for x in bList] ==
[Chem.BondType.AROMATIC, Chem.BondType.SINGLE, Chem.BondType.DOUBLE, Chem.BondType.SINGLE])
self.assertTrue([x.GetIsAromatic() for x in bList] == [1, 0, 0, 0])
self.assertEqual(bList[0].GetBondTypeAsDouble(), 1.5)
self.assertEqual(bList[1].GetBondTypeAsDouble(), 1.0)
self.assertEqual(bList[2].GetBondTypeAsDouble(), 2.0)
self.assertTrue([x.GetIsConjugated() != 0 for x in bList] == [1, 0, 1, 1],
[x.GetIsConjugated() != 0 for x in bList])
self.assertTrue([x.GetBeginAtomIdx() for x in bList] == [0, 6, 7, 7],
[x.GetBeginAtomIdx() for x in bList])
self.assertTrue([x.GetBeginAtom().GetIdx() for x in bList] == [0, 6, 7, 7])
self.assertTrue([x.GetEndAtomIdx() for x in bList] == [1, 7, 8, 9])
self.assertTrue([x.GetEndAtom().GetIdx() for x in bList] == [1, 7, 8, 9])
def test9Smarts(self):
query1 = Chem.MolFromSmarts('C(=O)O')
self.assertTrue(query1)
query2 = Chem.MolFromSmarts('C(=O)[O,N]')
self.assertTrue(query2)
query3 = Chem.MolFromSmarts('[$(C(=O)O)]')
self.assertTrue(query3)
mol = Chem.MolFromSmiles('CCC(=O)O')
self.assertTrue(mol)
self.assertTrue(mol.HasSubstructMatch(query1))
self.assertTrue(mol.HasSubstructMatch(query2))
self.assertTrue(mol.HasSubstructMatch(query3))
mol = Chem.MolFromSmiles('CCC(=O)N')
self.assertTrue(mol)
self.assertTrue(not mol.HasSubstructMatch(query1))
self.assertTrue(mol.HasSubstructMatch(query2))
self.assertTrue(not mol.HasSubstructMatch(query3))
def test10Iterators(self):
mol = Chem.MolFromSmiles('CCOC')
self.assertTrue(mol)
for atom in mol.GetAtoms():
self.assertTrue(atom)
ats = mol.GetAtoms()
ats[1]
with self.assertRaisesRegex(IndexError, ""):
ats[12]
for bond in mol.GetBonds():
self.assertTrue(bond)
bonds = mol.GetBonds()
bonds[1]
with self.assertRaisesRegex(IndexError, ""):
bonds[12]
def test11MolOps(self):
mol = Chem.MolFromSmiles('C1=CC=C(C=C1)P(C2=CC=CC=C2)C3=CC=CC=C3')
self.assertTrue(mol)
smi = Chem.MolToSmiles(mol)
Chem.SanitizeMol(mol)
nr = Chem.GetSymmSSSR(mol)
self.assertTrue((len(nr) == 3))
def test12Smarts(self):
query1 = Chem.MolFromSmarts('C(=O)O')
self.assertTrue(query1)
query2 = Chem.MolFromSmarts('C(=O)[O,N]')
self.assertTrue(query2)
query3 = Chem.MolFromSmarts('[$(C(=O)O)]')
self.assertTrue(query3)
mol = Chem.MolFromSmiles('CCC(=O)O')
self.assertTrue(mol)
self.assertTrue(mol.HasSubstructMatch(query1))
self.assertTrue(mol.GetSubstructMatch(query1) == (2, 3, 4))
self.assertTrue(mol.HasSubstructMatch(query2))
self.assertTrue(mol.GetSubstructMatch(query2) == (2, 3, 4))
self.assertTrue(mol.HasSubstructMatch(query3))
self.assertTrue(mol.GetSubstructMatch(query3) == (2, ))
mol = Chem.MolFromSmiles('CCC(=O)N')
self.assertTrue(mol)
self.assertTrue(not mol.HasSubstructMatch(query1))
self.assertTrue(not mol.GetSubstructMatch(query1))
self.assertTrue(mol.HasSubstructMatch(query2))
self.assertTrue(mol.GetSubstructMatch(query2) == (2, 3, 4))
self.assertTrue(not mol.HasSubstructMatch(query3))
mol = Chem.MolFromSmiles('OC(=O)CC(=O)O')
self.assertTrue(mol)
self.assertTrue(mol.HasSubstructMatch(query1))
self.assertTrue(mol.GetSubstructMatch(query1) == (1, 2, 0))
self.assertTrue(mol.GetSubstructMatches(query1) == ((1, 2, 0), (4, 5, 6)))
self.assertTrue(mol.HasSubstructMatch(query2))
self.assertTrue(mol.GetSubstructMatch(query2) == (1, 2, 0))
self.assertTrue(mol.GetSubstructMatches(query2) == ((1, 2, 0), (4, 5, 6)))
self.assertTrue(mol.HasSubstructMatch(query3))
self.assertTrue(mol.GetSubstructMatches(query3) == ((1, ), (4, )))
def test13Smarts(self):
# previous smarts problems:
query = Chem.MolFromSmarts('N(=,-C)')
self.assertTrue(query)
mol = Chem.MolFromSmiles('N#C')
self.assertTrue(not mol.HasSubstructMatch(query))
mol = Chem.MolFromSmiles('N=C')
self.assertTrue(mol.HasSubstructMatch(query))
mol = Chem.MolFromSmiles('NC')
self.assertTrue(mol.HasSubstructMatch(query))
query = Chem.MolFromSmarts('[Cl,$(O)]')
mol = Chem.MolFromSmiles('C(=O)O')
self.assertTrue(len(mol.GetSubstructMatches(query)) == 2)
mol = Chem.MolFromSmiles('C(=N)N')
self.assertTrue(len(mol.GetSubstructMatches(query)) == 0)
query = Chem.MolFromSmarts('[$([O,S]-[!$(*=O)])]')
mol = Chem.MolFromSmiles('CC(S)C(=O)O')
self.assertTrue(len(mol.GetSubstructMatches(query)) == 1)
mol = Chem.MolFromSmiles('C(=O)O')
self.assertTrue(len(mol.GetSubstructMatches(query)) == 0)
def test14Hs(self):
m = Chem.MolFromSmiles('CC(=O)[OH]')
self.assertEqual(m.GetNumAtoms(), 4)
m2 = Chem.AddHs(m)
self.assertEqual(m2.GetNumAtoms(), 8)
m2 = Chem.RemoveHs(m2)
self.assertEqual(m2.GetNumAtoms(), 4)
m = Chem.MolFromSmiles('CC[H]', False)
self.assertEqual(m.GetNumAtoms(), 3)
m2 = Chem.MergeQueryHs(m)
self.assertEqual(m2.GetNumAtoms(), 2)
self.assertTrue(m2.GetAtomWithIdx(1).HasQuery())
m = Chem.MolFromSmiles('CC[H]', False)
self.assertEqual(m.GetNumAtoms(), 3)
m1 = Chem.RemoveHs(m)
self.assertEqual(m1.GetNumAtoms(), 2)
self.assertEqual(m1.GetAtomWithIdx(1).GetNumExplicitHs(), 0)
m1 = Chem.RemoveHs(m, updateExplicitCount=True)
self.assertEqual(m1.GetNumAtoms(), 2)
self.assertEqual(m1.GetAtomWithIdx(1).GetNumExplicitHs(), 1)
# test merging of mapped hydrogens
m = Chem.MolFromSmiles('CC[H]', False)
m.GetAtomWithIdx(2).SetProp("molAtomMapNumber", "1")
self.assertEqual(m.GetNumAtoms(), 3)
m2 = Chem.MergeQueryHs(m, mergeUnmappedOnly=True)
self.assertTrue(m2 is not None)
self.assertEqual(m2.GetNumAtoms(), 3)
self.assertFalse(m2.GetAtomWithIdx(1).HasQuery())
# here the hydrogen is unmapped
# should be the same as merging all hydrogens
m = Chem.MolFromSmiles('CC[H]', False)
m.GetAtomWithIdx(1).SetProp("molAtomMapNumber", "1")
self.assertEqual(m.GetNumAtoms(), 3)
m2 = Chem.MergeQueryHs(m, mergeUnmappedOnly=True)
self.assertTrue(m2 is not None)
self.assertEqual(m2.GetNumAtoms(), 2)
self.assertTrue(m2.GetAtomWithIdx(1).HasQuery())
# test github758
m = Chem.MolFromSmiles('CCC')
self.assertEqual(m.GetNumAtoms(), 3)
m = Chem.AddHs(m, onlyOnAtoms=(0, 2))
self.assertEqual(m.GetNumAtoms(), 9)
self.assertEqual(m.GetAtomWithIdx(0).GetDegree(), 4)
self.assertEqual(m.GetAtomWithIdx(2).GetDegree(), 4)
self.assertEqual(m.GetAtomWithIdx(1).GetDegree(), 2)
def test15Neighbors(self):
m = Chem.MolFromSmiles('CC(=O)[OH]')
self.assertTrue(m.GetNumAtoms() == 4)
a = m.GetAtomWithIdx(1)
ns = a.GetNeighbors()
self.assertTrue(len(ns) == 3)
bs = a.GetBonds()
self.assertTrue(len(bs) == 3)
for b in bs:
try:
a2 = b.GetOtherAtom(a)
except Exception:
a2 = None
self.assertTrue(a2)
self.assertTrue(len(bs) == 3)
def test16Pickle(self):
import pickle
m = Chem.MolFromSmiles('C1=CN=CC=C1')
pkl = pickle.dumps(m)
m2 = pickle.loads(pkl)
self.assertTrue(type(m2) == Chem.Mol)
smi1 = Chem.MolToSmiles(m)
smi2 = Chem.MolToSmiles(m2)
self.assertTrue(smi1 == smi2)
pkl = pickle.dumps(Chem.RWMol(m))
m2 = pickle.loads(pkl)
self.assertTrue(type(m2) == Chem.RWMol)
smi1 = Chem.MolToSmiles(m)
smi2 = Chem.MolToSmiles(m2)
self.assertTrue(smi1 == smi2)
def test16Props(self):
m = Chem.MolFromSmiles('C1=CN=CC=C1')
self.assertTrue(not m.HasProp('prop1'))
self.assertTrue(not m.HasProp('prop2'))
self.assertTrue(not m.HasProp('prop2'))
m.SetProp('prop1', 'foob')
self.assertTrue(not m.HasProp('prop2'))
self.assertTrue(m.HasProp('prop1'))
self.assertTrue(m.GetProp('prop1') == 'foob')
self.assertTrue(not m.HasProp('propo'))
try:
m.GetProp('prop2')
except KeyError:
ok = 1
else:
ok = 0
self.assertTrue(ok)
# test computed properties
m.SetProp('cprop1', 'foo', 1)
m.SetProp('cprop2', 'foo2', 1)
m.ClearComputedProps()
self.assertTrue(not m.HasProp('cprop1'))
self.assertTrue(not m.HasProp('cprop2'))
m.SetDoubleProp("a", 2.0)
self.assertTrue(m.GetDoubleProp("a") == 2.0)
try:
self.assertTrue(m.GetIntProp("a") == 2.0)
raise Exception("Expected runtime exception")
except ValueError:
pass
try:
self.assertTrue(m.GetUnsignedProp("a") == 2.0)
raise Exception("Expected runtime exception")
except ValueError:
pass
m.SetDoubleProp("a", -2)
self.assertTrue(m.GetDoubleProp("a") == -2.0)
m.SetIntProp("a", -2)
self.assertTrue(m.GetIntProp("a") == -2)
try:
m.SetUnsignedProp("a", -2)
raise Exception("Expected failure with negative unsigned number")
except OverflowError:
pass
m.SetBoolProp("a", False)
self.assertFalse(m.GetBoolProp("a"))
self.assertEqual(m.GetPropsAsDict(), {'a': False, 'prop1': 'foob'})
m.SetDoubleProp("b", 1000.0)
m.SetUnsignedProp("c", 2000)
m.SetIntProp("d", -2)
m.SetUnsignedProp("e", 2, True)
self.assertEqual(m.GetPropsAsDict(False, True), {
'a': False,
'c': 2000,
'b': 1000.0,
'e': 2,
'd': -2,
'prop1': 'foob'
})
m = Chem.MolFromSmiles('C1=CN=CC=C1')
m.SetProp("int", "1000")
m.SetProp("double", "10000.123")
self.assertEqual(m.GetPropsAsDict(), {"int": 1000, "double": 10000.123})
self.assertEqual(type(m.GetPropsAsDict()['int']), int)
self.assertEqual(type(m.GetPropsAsDict()['double']), float)
def test17Kekulize(self):
m = Chem.MolFromSmiles('c1ccccc1')
smi = Chem.MolToSmiles(m)
self.assertTrue(smi == 'c1ccccc1')
Chem.Kekulize(m)
smi = Chem.MolToSmiles(m)
self.assertTrue(smi == 'c1ccccc1')
m = Chem.MolFromSmiles('c1ccccc1')
smi = Chem.MolToSmiles(m)
self.assertTrue(smi == 'c1ccccc1')
Chem.Kekulize(m, 1)
smi = Chem.MolToSmiles(m)
self.assertTrue(smi == 'C1=CC=CC=C1', smi)
def test18Paths(self):
m = Chem.MolFromSmiles("C1CC2C1CC2")
#self.assertTrue(len(Chem.FindAllPathsOfLengthN(m,1,useBonds=1))==7)
#print(Chem.FindAllPathsOfLengthN(m,3,useBonds=0))
self.assertTrue(
len(Chem.FindAllPathsOfLengthN(m, 2, useBonds=1)) == 10,
Chem.FindAllPathsOfLengthN(m, 2, useBonds=1))
self.assertTrue(len(Chem.FindAllPathsOfLengthN(m, 3, useBonds=1)) == 14)
m = Chem.MolFromSmiles('C1CC1C')
self.assertTrue(m)
self.assertTrue(len(Chem.FindAllPathsOfLengthN(m, 1, useBonds=1)) == 4)
self.assertTrue(len(Chem.FindAllPathsOfLengthN(m, 2, useBonds=1)) == 5)
self.assertTrue(
len(Chem.FindAllPathsOfLengthN(m, 3, useBonds=1)) == 3,
Chem.FindAllPathsOfLengthN(m, 3, useBonds=1))
self.assertTrue(
len(Chem.FindAllPathsOfLengthN(m, 4, useBonds=1)) == 1,
Chem.FindAllPathsOfLengthN(m, 4, useBonds=1))
self.assertTrue(
len(Chem.FindAllPathsOfLengthN(m, 5, useBonds=1)) == 0,
Chem.FindAllPathsOfLengthN(m, 5, useBonds=1))
#
# Hexane example from Hall-Kier Rev.Comp.Chem. paper
# Rev. Comp. Chem. vol 2, 367-422, (1991)
#
m = Chem.MolFromSmiles("CCCCCC")
self.assertTrue(len(Chem.FindAllPathsOfLengthN(m, 1, useBonds=1)) == 5)
self.assertTrue(len(Chem.FindAllPathsOfLengthN(m, 2, useBonds=1)) == 4)
self.assertTrue(len(Chem.FindAllPathsOfLengthN(m, 3, useBonds=1)) == 3)
m = Chem.MolFromSmiles("CCC(C)CC")
self.assertTrue(len(Chem.FindAllPathsOfLengthN(m, 1, useBonds=1)) == 5)
self.assertTrue(len(Chem.FindAllPathsOfLengthN(m, 2, useBonds=1)) == 5)
self.assertTrue(
len(Chem.FindAllPathsOfLengthN(m, 3, useBonds=1)) == 4,
Chem.FindAllPathsOfLengthN(m, 3, useBonds=1))
m = Chem.MolFromSmiles("CCCC(C)C")
self.assertTrue(len(Chem.FindAllPathsOfLengthN(m, 1, useBonds=1)) == 5)
self.assertTrue(len(Chem.FindAllPathsOfLengthN(m, 2, useBonds=1)) == 5)
self.assertTrue(len(Chem.FindAllPathsOfLengthN(m, 3, useBonds=1)) == 3)
m = Chem.MolFromSmiles("CC(C)C(C)C")
self.assertTrue(len(Chem.FindAllPathsOfLengthN(m, 1, useBonds=1)) == 5)
self.assertTrue(len(Chem.FindAllPathsOfLengthN(m, 2, useBonds=1)) == 6)
self.assertTrue(len(Chem.FindAllPathsOfLengthN(m, 3, useBonds=1)) == 4)
m = Chem.MolFromSmiles("CC(C)(C)CC")
self.assertTrue(len(Chem.FindAllPathsOfLengthN(m, 1, useBonds=1)) == 5)
self.assertTrue(len(Chem.FindAllPathsOfLengthN(m, 2, useBonds=1)) == 7)
self.assertTrue(
len(Chem.FindAllPathsOfLengthN(m, 3, useBonds=1)) == 3,
Chem.FindAllPathsOfLengthN(m, 3, useBonds=1))
m = Chem.MolFromSmiles("C1CCCCC1")
self.assertTrue(len(Chem.FindAllPathsOfLengthN(m, 1, useBonds=1)) == 6)
self.assertTrue(len(Chem.FindAllPathsOfLengthN(m, 2, useBonds=1)) == 6)
self.assertTrue(len(Chem.FindAllPathsOfLengthN(m, 3, useBonds=1)) == 6)
m = Chem.MolFromSmiles("C1CC2C1CC2")
self.assertTrue(len(Chem.FindAllPathsOfLengthN(m, 1, useBonds=1)) == 7)
self.assertTrue(
len(Chem.FindAllPathsOfLengthN(m, 2, useBonds=1)) == 10,
Chem.FindAllPathsOfLengthN(m, 2, useBonds=1))
self.assertTrue(len(Chem.FindAllPathsOfLengthN(m, 3, useBonds=1)) == 14)
m = Chem.MolFromSmiles("CC2C1CCC12")
self.assertTrue(len(Chem.FindAllPathsOfLengthN(m, 1, useBonds=1)) == 7)
self.assertTrue(len(Chem.FindAllPathsOfLengthN(m, 2, useBonds=1)) == 11)
# FIX: this result disagrees with the paper (which says 13),
# but it seems right
self.assertTrue(
len(Chem.FindAllPathsOfLengthN(m, 3, useBonds=1)) == 15,
Chem.FindAllPathsOfLengthN(m, 3, useBonds=1))
def test19Subgraphs(self):
m = Chem.MolFromSmiles('C1CC1C')
self.assertTrue(m)
self.assertTrue(len(Chem.FindAllSubgraphsOfLengthN(m, 1, 0)) == 4)
self.assertTrue(len(Chem.FindAllSubgraphsOfLengthN(m, 2)) == 5)
self.assertTrue(len(Chem.FindAllSubgraphsOfLengthN(m, 3)) == 4)
self.assertTrue(len(Chem.FindAllSubgraphsOfLengthN(m, 4)) == 1)
self.assertTrue(len(Chem.FindAllSubgraphsOfLengthN(m, 5)) == 0)
#
# Hexane example from Hall-Kier Rev.Comp.Chem. paper
# Rev. Comp. Chem. vol 2, 367-422, (1991)
#
m = Chem.MolFromSmiles("CCCCCC")
self.assertTrue(len(Chem.FindAllSubgraphsOfLengthN(m, 1)) == 5)
self.assertTrue(len(Chem.FindAllSubgraphsOfLengthN(m, 2)) == 4)
self.assertTrue(len(Chem.FindAllSubgraphsOfLengthN(m, 3)) == 3)
l = Chem.FindAllSubgraphsOfLengthMToN(m, 1, 3)
self.assertEqual(len(l), 3)
self.assertEqual(len(l[0]), 5)
self.assertEqual(len(l[1]), 4)
self.assertEqual(len(l[2]), 3)
self.assertRaises(ValueError, lambda: Chem.FindAllSubgraphsOfLengthMToN(m, 4, 3))
m = Chem.MolFromSmiles("CCC(C)CC")
self.assertTrue(len(Chem.FindAllSubgraphsOfLengthN(m, 1)) == 5)
self.assertTrue(len(Chem.FindAllSubgraphsOfLengthN(m, 2)) == 5)
self.assertTrue(len(Chem.FindAllSubgraphsOfLengthN(m, 3)) == 5)
m = Chem.MolFromSmiles("CCCC(C)C")
self.assertTrue(len(Chem.FindAllSubgraphsOfLengthN(m, 1)) == 5)
self.assertTrue(len(Chem.FindAllSubgraphsOfLengthN(m, 2)) == 5)
self.assertTrue(len(Chem.FindAllSubgraphsOfLengthN(m, 3)) == 4)
m = Chem.MolFromSmiles("CC(C)C(C)C")
self.assertTrue(len(Chem.FindAllSubgraphsOfLengthN(m, 1)) == 5)
self.assertTrue(len(Chem.FindAllSubgraphsOfLengthN(m, 2)) == 6)
self.assertTrue(len(Chem.FindAllSubgraphsOfLengthN(m, 3)) == 6)
m = Chem.MolFromSmiles("CC(C)(C)CC")
self.assertTrue(len(Chem.FindAllSubgraphsOfLengthN(m, 1)) == 5)
self.assertTrue(len(Chem.FindAllSubgraphsOfLengthN(m, 2)) == 7)
self.assertTrue(
len(Chem.FindAllSubgraphsOfLengthN(m, 3)) == 7, Chem.FindAllSubgraphsOfLengthN(m, 3))
m = Chem.MolFromSmiles("C1CCCCC1")
self.assertTrue(len(Chem.FindAllSubgraphsOfLengthN(m, 1)) == 6)
self.assertTrue(len(Chem.FindAllSubgraphsOfLengthN(m, 2)) == 6)
self.assertTrue(len(Chem.FindAllSubgraphsOfLengthN(m, 3)) == 6)
#self.assertTrue(len(Chem.FindUniqueSubgraphsOfLengthN(m,1))==1)
self.assertTrue(len(Chem.FindUniqueSubgraphsOfLengthN(m, 2)) == 1)
self.assertTrue(len(Chem.FindUniqueSubgraphsOfLengthN(m, 3)) == 1)
m = Chem.MolFromSmiles("C1CC2C1CC2")
self.assertTrue(len(Chem.FindAllSubgraphsOfLengthN(m, 1)) == 7)
self.assertTrue(len(Chem.FindAllSubgraphsOfLengthN(m, 2)) == 10)
self.assertTrue(len(Chem.FindAllSubgraphsOfLengthN(m, 3)) == 16)
m = Chem.MolFromSmiles("CC2C1CCC12")
self.assertTrue(len(Chem.FindAllSubgraphsOfLengthN(m, 1)) == 7)
self.assertTrue(len(Chem.FindAllSubgraphsOfLengthN(m, 2)) == 11)
self.assertTrue(
len(Chem.FindAllSubgraphsOfLengthN(m, 3)) == 18, len(Chem.FindAllSubgraphsOfLengthN(m, 3)))
def test20IsInRing(self):
m = Chem.MolFromSmiles('C1CCC1C')
self.assertTrue(m)
self.assertTrue(m.GetAtomWithIdx(0).IsInRingSize(4))
self.assertTrue(m.GetAtomWithIdx(1).IsInRingSize(4))
self.assertTrue(m.GetAtomWithIdx(2).IsInRingSize(4))
self.assertTrue(m.GetAtomWithIdx(3).IsInRingSize(4))
self.assertTrue(not m.GetAtomWithIdx(4).IsInRingSize(4))
self.assertTrue(not m.GetAtomWithIdx(0).IsInRingSize(3))
self.assertTrue(not m.GetAtomWithIdx(1).IsInRingSize(3))
self.assertTrue(not m.GetAtomWithIdx(2).IsInRingSize(3))
self.assertTrue(not m.GetAtomWithIdx(3).IsInRingSize(3))
self.assertTrue(not m.GetAtomWithIdx(4).IsInRingSize(3))
self.assertTrue(m.GetBondWithIdx(0).IsInRingSize(4))
self.assertTrue(not m.GetBondWithIdx(3).IsInRingSize(4))
self.assertTrue(not m.GetBondWithIdx(0).IsInRingSize(3))
self.assertTrue(not m.GetBondWithIdx(3).IsInRingSize(3))
def test21Robustification(self):
ok = False
# FIX: at the moment I can't figure out how to catch the
# actual exception that BPL is throwing when it gets
# invalid arguments (Boost.Python.ArgumentError)
try:
Chem.MolFromSmiles('C=O').HasSubstructMatch(Chem.MolFromSmarts('fiib'))
#except ValueError:
# ok=True
except Exception:
ok = True
self.assertTrue(ok)
def test22DeleteSubstruct(self):
query = Chem.MolFromSmarts('C(=O)O')
mol = Chem.MolFromSmiles('CCC(=O)O')
nmol = Chem.DeleteSubstructs(mol, query)
self.assertTrue(Chem.MolToSmiles(nmol) == 'CC')
mol = Chem.MolFromSmiles('CCC(=O)O.O=CO')
# now delete only fragments
nmol = Chem.DeleteSubstructs(mol, query, 1)
self.assertTrue(Chem.MolToSmiles(nmol) == 'CCC(=O)O', Chem.MolToSmiles(nmol))
mol = Chem.MolFromSmiles('CCC(=O)O.O=CO')
nmol = Chem.DeleteSubstructs(mol, query, 0)
self.assertTrue(Chem.MolToSmiles(nmol) == 'CC')
mol = Chem.MolFromSmiles('CCCO')
nmol = Chem.DeleteSubstructs(mol, query, 0)
self.assertTrue(Chem.MolToSmiles(nmol) == 'CCCO')
# Issue 96 prevented this from working:
mol = Chem.MolFromSmiles('CCC(=O)O.O=CO')
nmol = Chem.DeleteSubstructs(mol, query, 1)
self.assertTrue(Chem.MolToSmiles(nmol) == 'CCC(=O)O')
nmol = Chem.DeleteSubstructs(nmol, query, 1)
self.assertTrue(Chem.MolToSmiles(nmol) == 'CCC(=O)O')
nmol = Chem.DeleteSubstructs(nmol, query, 0)
self.assertTrue(Chem.MolToSmiles(nmol) == 'CC')
def test23MolFileParsing(self):
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'triazine.mol')
#fileN = "../FileParsers/test_data/triazine.mol"
with open(fileN, 'r') as inF:
inD = inF.read()
m1 = Chem.MolFromMolBlock(inD)
self.assertTrue(m1 is not None)
self.assertTrue(m1.GetNumAtoms() == 9)
m1 = Chem.MolFromMolFile(fileN)
self.assertTrue(m1 is not None)
self.assertTrue(m1.GetNumAtoms() == 9)
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'triazine.mof')
self.assertRaises(IOError, lambda: Chem.MolFromMolFile(fileN))
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'list-query.mol')
query = Chem.MolFromMolFile(fileN)
smi = Chem.MolToSmiles(query)
self.assertEqual(smi, 'c1ccccc1')
smi = Chem.MolToSmarts(query)
self.assertEqual(smi, '[#6]1:[#6]:[#6]:[#6]:[#6]:[#6,#7,#15]:1', smi)
query = Chem.MolFromMolFile(fileN, sanitize=False)
smi = Chem.MolToSmiles(query)
self.assertEqual(smi, 'C1=CC=CC=C1')
query.UpdatePropertyCache()
smi = Chem.MolToSmarts(query)
self.assertEqual(smi, '[#6]1=[#6]-[#6]=[#6]-[#6]=[#6,#7,#15]-1')
smi = "C1=CC=CC=C1"
mol = Chem.MolFromSmiles(smi, 0)
self.assertTrue(mol.HasSubstructMatch(query))
Chem.SanitizeMol(mol)
self.assertTrue(not mol.HasSubstructMatch(query))
mol = Chem.MolFromSmiles('N1=CC=CC=C1', 0)
self.assertTrue(mol.HasSubstructMatch(query))
mol = Chem.MolFromSmiles('S1=CC=CC=C1', 0)
self.assertTrue(not mol.HasSubstructMatch(query))
mol = Chem.MolFromSmiles('P1=CC=CC=C1', 0)
self.assertTrue(mol.HasSubstructMatch(query))
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'issue123.mol')
mol = Chem.MolFromMolFile(fileN)
self.assertTrue(mol)
self.assertEqual(mol.GetNumAtoms(), 23)
mol = Chem.MolFromMolFile(fileN, removeHs=False)
self.assertTrue(mol)
self.assertEqual(mol.GetNumAtoms(), 39)
# test23 was for Chem.DaylightFingerprint, which is deprecated
def test24RDKFingerprint(self):
from rdkit import DataStructs
m1 = Chem.MolFromSmiles('C1=CC=CC=C1')
fp1 = Chem.RDKFingerprint(m1)
self.assertTrue(len(fp1) == 2048)
m2 = Chem.MolFromSmiles('C1=CC=CC=C1')
fp2 = Chem.RDKFingerprint(m2)
tmp = DataStructs.TanimotoSimilarity(fp1, fp2)
self.assertTrue(tmp == 1.0, tmp)
m2 = Chem.MolFromSmiles('C1=CC=CC=N1')
fp2 = Chem.RDKFingerprint(m2)
self.assertTrue(len(fp2) == 2048)
tmp = DataStructs.TanimotoSimilarity(fp1, fp2)
self.assertTrue(tmp < 1.0, tmp)
self.assertTrue(tmp > 0.0, tmp)
fp3 = Chem.RDKFingerprint(m1, tgtDensity=0.3)
self.assertTrue(len(fp3) < 2048)
m1 = Chem.MolFromSmiles('C1=CC=CC=C1')
fp1 = Chem.RDKFingerprint(m1)
m2 = Chem.MolFromSmiles('C1=CC=CC=N1')
fp2 = Chem.RDKFingerprint(m2)
self.assertNotEqual(fp1, fp2)
atomInvariants = [1] * 6
fp1 = Chem.RDKFingerprint(m1, atomInvariants=atomInvariants)
fp2 = Chem.RDKFingerprint(m2, atomInvariants=atomInvariants)
self.assertEqual(fp1, fp2)
m2 = Chem.MolFromSmiles('C1CCCCN1')
fp1 = Chem.RDKFingerprint(m1, atomInvariants=atomInvariants, useBondOrder=False)
fp2 = Chem.RDKFingerprint(m2, atomInvariants=atomInvariants, useBondOrder=False)
self.assertEqual(fp1, fp2)
# rooted at atom
m1 = Chem.MolFromSmiles('CCCCCO')
fp1 = Chem.RDKFingerprint(m1, 1, 4, nBitsPerHash=1, fromAtoms=[0])
self.assertEqual(fp1.GetNumOnBits(), 4)
m1 = Chem.MolFromSmiles('CCCCCO')
fp1 = Chem.RDKFingerprint(m1, 1, 4, nBitsPerHash=1, fromAtoms=[0, 5])
self.assertEqual(fp1.GetNumOnBits(), 8)
# test sf.net issue 270:
fp1 = Chem.RDKFingerprint(m1, atomInvariants=[x.GetAtomicNum() + 10 for x in m1.GetAtoms()])
# atomBits
m1 = Chem.MolFromSmiles('CCCO')
l = []
fp1 = Chem.RDKFingerprint(m1, minPath=1, maxPath=2, nBitsPerHash=1, atomBits=l)
self.assertEqual(fp1.GetNumOnBits(), 4)
self.assertEqual(len(l), m1.GetNumAtoms())
self.assertEqual(len(l[0]), 2)
self.assertEqual(len(l[1]), 3)
self.assertEqual(len(l[2]), 4)
self.assertEqual(len(l[3]), 2)
def test25SDMolSupplier(self):
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'NCI_aids_few.sdf')
#fileN = "../FileParsers/test_data/NCI_aids_few.sdf"
sdSup = Chem.SDMolSupplier(fileN)
molNames = [
"48", "78", "128", "163", "164", "170", "180", "186", "192", "203", "210", "211", "213",
"220", "229", "256"
]
chgs192 = {8: 1, 11: 1, 15: -1, 18: -1, 20: 1, 21: 1, 23: -1, 25: -1}
i = 0
for mol in sdSup:
self.assertTrue(mol)
self.assertTrue(mol.GetProp("_Name") == molNames[i])
i += 1
if (mol.GetProp("_Name") == "192"):
# test parsed charges on one of the molecules
for id in chgs192.keys():
self.assertTrue(mol.GetAtomWithIdx(id).GetFormalCharge() == chgs192[id])
self.assertRaises(StopIteration, lambda: next(sdSup))
sdSup.reset()
ns = [mol.GetProp("_Name") for mol in sdSup]
self.assertTrue(ns == molNames)
sdSup = Chem.SDMolSupplier(fileN, 0)
for mol in sdSup:
self.assertTrue(not mol.HasProp("numArom"))
sdSup = Chem.SDMolSupplier(fileN)
self.assertTrue(len(sdSup) == 16)
mol = sdSup[5]
self.assertTrue(mol.GetProp("_Name") == "170")
# test handling of H removal:
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'withHs.sdf')
sdSup = Chem.SDMolSupplier(fileN)
m = next(sdSup)
self.assertTrue(m)
self.assertTrue(m.GetNumAtoms() == 23)
m = next(sdSup)
self.assertTrue(m)
self.assertTrue(m.GetNumAtoms() == 28)
sdSup = Chem.SDMolSupplier(fileN, removeHs=False)
m = next(sdSup)
self.assertTrue(m)
self.assertTrue(m.GetNumAtoms() == 39)
m = next(sdSup)
self.assertTrue(m)
self.assertTrue(m.GetNumAtoms() == 30)
with open(fileN, 'rb') as dFile:
d = dFile.read()
sdSup.SetData(d)
m = next(sdSup)
self.assertTrue(m)
self.assertTrue(m.GetNumAtoms() == 23)
m = next(sdSup)
self.assertTrue(m)
self.assertTrue(m.GetNumAtoms() == 28)
sdSup.SetData(d, removeHs=False)
m = next(sdSup)
self.assertTrue(m)
self.assertTrue(m.GetNumAtoms() == 39)
m = next(sdSup)
self.assertTrue(m)
self.assertTrue(m.GetNumAtoms() == 30)
# test strictParsing1:
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'strictLax1.sdf')
#strict from file
sdSup = Chem.SDMolSupplier(fileN, strictParsing=True)
i = 0
for mol in sdSup:
self.assertTrue(mol.HasProp("_Name"))
if (i == 0):
self.assertTrue(not mol.HasProp("ID"))
self.assertTrue(not mol.HasProp("ANOTHER_PROPERTY"))
i += 1
self.assertTrue(i == 2)
#lax from file
sdSup = Chem.SDMolSupplier(fileN, strictParsing=False)
i = 0
for mol in sdSup:
self.assertTrue(mol.HasProp("_Name"))
self.assertTrue(mol.HasProp("ID"))
self.assertTrue(mol.HasProp("ANOTHER_PROPERTY"))
i += 1
self.assertTrue(i == 2)
#strict from text
with open(fileN, 'rb') as dFile:
d = dFile.read()
sdSup = Chem.SDMolSupplier()
sdSup.SetData(d, strictParsing=True)
i = 0
for mol in sdSup:
self.assertTrue(mol.HasProp("_Name"))
if (i == 0):
self.assertTrue(not mol.HasProp("ID"))
self.assertTrue(not mol.HasProp("ANOTHER_PROPERTY"))
i += 1
self.assertTrue(i == 2)
#lax from text
sdSup = Chem.SDMolSupplier()
sdSup.SetData(d, strictParsing=False)
i = 0
for mol in sdSup:
self.assertTrue(mol.HasProp("_Name"))
self.assertTrue(mol.HasProp("ID"))
self.assertTrue(mol.HasProp("ANOTHER_PROPERTY"))
i += 1
self.assertTrue(i == 2)
# test strictParsing2:
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'strictLax2.sdf')
#strict from file
sdSup = Chem.SDMolSupplier(fileN, strictParsing=True)
i = 0
for mol in sdSup:
self.assertTrue(mol.HasProp("_Name"))
self.assertTrue(mol.HasProp("ID"))
self.assertTrue(mol.GetProp("ID") == "Lig1")
self.assertTrue(mol.HasProp("ANOTHER_PROPERTY"))
self.assertTrue(
mol.GetProp("ANOTHER_PROPERTY") == "No blank line before dollars\n"
"$$$$\n"
"Structure1\n"
"csChFnd70/05230312262D")
i += 1
self.assertTrue(i == 1)
#lax from file
sdSup = Chem.SDMolSupplier(fileN, strictParsing=False)
i = 0
for mol in sdSup:
self.assertTrue(mol.HasProp("_Name"))
self.assertTrue(mol.HasProp("ID"))
self.assertTrue(mol.GetProp("ID") == "Lig2")
self.assertTrue(mol.HasProp("ANOTHER_PROPERTY"))
self.assertTrue(mol.GetProp("ANOTHER_PROPERTY") == "Value2")
i += 1
self.assertTrue(i == 1)
#strict from text
with open(fileN, 'rb') as dFile:
d = dFile.read()
sdSup = Chem.SDMolSupplier()
sdSup.SetData(d, strictParsing=True)
i = 0
for mol in sdSup:
self.assertTrue(mol.HasProp("_Name"))
self.assertTrue(mol.HasProp("ID"))
self.assertTrue(mol.GetProp("ID") == "Lig1")
self.assertTrue(mol.HasProp("ANOTHER_PROPERTY"))
self.assertTrue(
mol.GetProp("ANOTHER_PROPERTY") == "No blank line before dollars\n"
"$$$$\n"
"Structure1\n"
"csChFnd70/05230312262D")
i += 1
self.assertTrue(i == 1)
#lax from text
sdSup = Chem.SDMolSupplier()
sdSup.SetData(d, strictParsing=False)
i = 0
for mol in sdSup:
self.assertTrue(mol.HasProp("_Name"))
self.assertTrue(mol.HasProp("ID"))
self.assertTrue(mol.GetProp("ID") == "Lig2")
self.assertTrue(mol.HasProp("ANOTHER_PROPERTY"))
self.assertTrue(mol.GetProp("ANOTHER_PROPERTY") == "Value2")
i += 1
self.assertTrue(i == 1)
def test26SmiMolSupplier(self):
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'first_200.tpsa.csv')
#fileN = "../FileParsers/test_data/first_200.tpsa.csv"
smiSup = Chem.SmilesMolSupplier(fileN, ",", 0, -1)
mol = smiSup[16]
self.assertTrue(mol.GetProp("TPSA") == "46.25")
mol = smiSup[8]
self.assertTrue(mol.GetProp("TPSA") == "65.18")
self.assertTrue(len(smiSup) == 200)
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'fewSmi.csv')
#fileN = "../FileParsers/test_data/fewSmi.csv"
smiSup = Chem.SmilesMolSupplier(fileN, delimiter=",", smilesColumn=1, nameColumn=0, titleLine=0)
names = ["1", "2", "3", "4", "5", "6", "7", "8", "9", "10"]
i = 0
for mol in smiSup:
self.assertTrue(mol.GetProp("_Name") == names[i])
i += 1
mol = smiSup[3]
self.assertTrue(mol.GetProp("_Name") == "4")
self.assertTrue(mol.GetProp("Column_2") == "82.78")
# and test doing a supplier from text:
with open(fileN, 'r') as inF:
inD = inF.read()
smiSup.SetData(inD, delimiter=",", smilesColumn=1, nameColumn=0, titleLine=0)
names = ["1", "2", "3", "4", "5", "6", "7", "8", "9", "10"]
i = 0
# iteration interface:
for mol in smiSup:
self.assertTrue(mol.GetProp("_Name") == names[i])
i += 1
self.assertTrue(i == 10)
# random access:
mol = smiSup[3]
self.assertTrue(len(smiSup) == 10)
self.assertTrue(mol.GetProp("_Name") == "4")
self.assertTrue(mol.GetProp("Column_2") == "82.78")
# issue 113:
smiSup.SetData(inD, delimiter=",", smilesColumn=1, nameColumn=0, titleLine=0)
self.assertTrue(len(smiSup) == 10)
# and test failure handling:
inD = """mol-1,CCC
mol-2,CCCC
mol-3,fail
mol-4,CCOC
"""
smiSup.SetData(inD, delimiter=",", smilesColumn=1, nameColumn=0, titleLine=0)
# there are 4 entries in the supplier:
self.assertTrue(len(smiSup) == 4)
# but the 3rd is a None:
self.assertTrue(smiSup[2] is None)
text="Id SMILES Column_2\n"+\
"mol-1 C 1.0\n"+\
"mol-2 CC 4.0\n"+\
"mol-4 CCCC 16.0"
smiSup.SetData(text, delimiter=" ", smilesColumn=1, nameColumn=0, titleLine=1)
self.assertTrue(len(smiSup) == 3)
self.assertTrue(smiSup[0])
self.assertTrue(smiSup[1])
self.assertTrue(smiSup[2])
m = [x for x in smiSup]
self.assertTrue(smiSup[2])
self.assertTrue(len(m) == 3)
self.assertTrue(m[0].GetProp("Column_2") == "1.0")
# test simple parsing and Issue 114:
smis = ['CC', 'CCC', 'CCOC', 'CCCOCC', 'CCCOCCC']
inD = '\n'.join(smis)
smiSup.SetData(inD, delimiter=",", smilesColumn=0, nameColumn=-1, titleLine=0)
self.assertTrue(len(smiSup) == 5)
m = [x for x in smiSup]
self.assertTrue(smiSup[4])
self.assertTrue(len(m) == 5)
# order dependence:
smiSup.SetData(inD, delimiter=",", smilesColumn=0, nameColumn=-1, titleLine=0)
self.assertTrue(smiSup[4])
self.assertTrue(len(smiSup) == 5)
# this was a nasty BC:
# asking for a particular entry with a higher index than what we've
# already seen resulted in a duplicate:
smis = ['CC', 'CCC', 'CCOC', 'CCCCOC']
inD = '\n'.join(smis)
smiSup.SetData(inD, delimiter=",", smilesColumn=0, nameColumn=-1, titleLine=0)
m = next(smiSup)
m = smiSup[3]
self.assertTrue(len(smiSup) == 4)
with self.assertRaisesRegex(Exception, ""):
smiSup[4]
smiSup.SetData(inD, delimiter=",", smilesColumn=0, nameColumn=-1, titleLine=0)
with self.assertRaisesRegex(Exception, ""):
smiSup[4]
sys.stderr.write(
'>>> This may result in an infinite loop. It should finish almost instantly\n')
self.assertEqual(len(smiSup), 4)
sys.stderr.write('<<< OK, it finished.\n')
def test27SmilesWriter(self):
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'fewSmi.csv')
#fileN = "../FileParsers/test_data/fewSmi.csv"
smiSup = Chem.SmilesMolSupplier(fileN, delimiter=",", smilesColumn=1, nameColumn=0, titleLine=0)
propNames = []
propNames.append("Column_2")
ofile = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'Wrap', 'test_data',
'outSmiles.txt')
writer = Chem.SmilesWriter(ofile)
writer.SetProps(propNames)
for mol in smiSup:
writer.write(mol)
writer.flush()
def test28SmilesReverse(self):
names = ["1", "2", "3", "4", "5", "6", "7", "8", "9", "10"]
props = [
"34.14", "25.78", "106.51", "82.78", "60.16", "87.74", "37.38", "77.28", "65.18", "0.00"
]
ofile = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'Wrap', 'test_data',
'outSmiles.txt')
#ofile = "test_data/outSmiles.csv"
smiSup = Chem.SmilesMolSupplier(ofile)
i = 0
for mol in smiSup:
#print([repr(x) for x in mol.GetPropNames()])
self.assertTrue(mol.GetProp("_Name") == names[i])
self.assertTrue(mol.GetProp("Column_2") == props[i])
i += 1
def writerSDFile(self):
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'NCI_aids_few.sdf')
#fileN = "../FileParsers/test_data/NCI_aids_few.sdf"
ofile = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'Wrap', 'test_data',
'outNCI_few.sdf')
writer = Chem.SDWriter(ofile)
sdSup = Chem.SDMolSupplier(fileN)
for mol in sdSup:
writer.write(mol)
writer.flush()
def test29SDWriterLoop(self):
self.writerSDFile()
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'Wrap', 'test_data',
'outNCI_few.sdf')
sdSup = Chem.SDMolSupplier(fileN)
molNames = [
"48", "78", "128", "163", "164", "170", "180", "186", "192", "203", "210", "211", "213",
"220", "229", "256"
]
chgs192 = {8: 1, 11: 1, 15: -1, 18: -1, 20: 1, 21: 1, 23: -1, 25: -1}
i = 0
for mol in sdSup:
#print('mol:',mol)
#print('\t',molNames[i])
self.assertTrue(mol.GetProp("_Name") == molNames[i])
i += 1
if (mol.GetProp("_Name") == "192"):
# test parsed charges on one of the molecules
for id in chgs192.keys():
self.assertTrue(mol.GetAtomWithIdx(id).GetFormalCharge() == chgs192[id])
def test30Issues109and110(self):
""" issues 110 and 109 were both related to handling of explicit Hs in
SMILES input.
"""
m1 = Chem.MolFromSmiles('N12[CH](SC(C)(C)[CH]1C(O)=O)[CH](C2=O)NC(=O)[CH](N)c3ccccc3')
self.assertTrue(m1.GetNumAtoms() == 24)
m2 = Chem.MolFromSmiles(
'C1C=C([CH](N)C(=O)N[C]2([H])[C]3([H])SC(C)(C)[CH](C(=O)O)N3C(=O)2)C=CC=1')
self.assertTrue(m2.GetNumAtoms() == 24)
smi1 = Chem.MolToSmiles(m1)
smi2 = Chem.MolToSmiles(m2)
self.assertTrue(smi1 == smi2)
m1 = Chem.MolFromSmiles('[H]CCl')
self.assertTrue(m1.GetNumAtoms() == 2)
self.assertTrue(m1.GetAtomWithIdx(0).GetNumExplicitHs() == 1)
m1 = Chem.MolFromSmiles('[H][CH2]Cl')
self.assertTrue(m1.GetNumAtoms() == 2)
self.assertTrue(m1.GetAtomWithIdx(0).GetNumExplicitHs() == 3)
m2 = Chem.AddHs(m1)
self.assertTrue(m2.GetNumAtoms() == 5)
m2 = Chem.RemoveHs(m2)
self.assertTrue(m2.GetNumAtoms() == 2)
def test31ChiralitySmiles(self):
m1 = Chem.MolFromSmiles('F[C@](Br)(I)Cl')
self.assertTrue(m1 is not None)
self.assertTrue(m1.GetNumAtoms() == 5)
self.assertTrue(Chem.MolToSmiles(m1, 1) == 'F[C@](Cl)(Br)I', Chem.MolToSmiles(m1, 1))
m1 = Chem.MolFromSmiles('CC1C[C@@]1(Cl)F')
self.assertTrue(m1 is not None)
self.assertTrue(m1.GetNumAtoms() == 6)
self.assertTrue(Chem.MolToSmiles(m1, 1) == 'CC1C[C@]1(F)Cl', Chem.MolToSmiles(m1, 1))
m1 = Chem.MolFromSmiles('CC1C[C@]1(Cl)F')
self.assertTrue(m1 is not None)
self.assertTrue(m1.GetNumAtoms() == 6)
self.assertTrue(Chem.MolToSmiles(m1, 1) == 'CC1C[C@@]1(F)Cl', Chem.MolToSmiles(m1, 1))
def test31aChiralitySubstructs(self):
m1 = Chem.MolFromSmiles('CC1C[C@@]1(Cl)F')
self.assertTrue(m1 is not None)
self.assertTrue(m1.GetNumAtoms() == 6)
self.assertTrue(Chem.MolToSmiles(m1, 1) == 'CC1C[C@]1(F)Cl', Chem.MolToSmiles(m1, 1))
m2 = Chem.MolFromSmiles('CC1C[C@]1(Cl)F')
self.assertTrue(m2 is not None)
self.assertTrue(m2.GetNumAtoms() == 6)
self.assertTrue(Chem.MolToSmiles(m2, 1) == 'CC1C[C@@]1(F)Cl', Chem.MolToSmiles(m2, 1))
self.assertTrue(m1.HasSubstructMatch(m1))
self.assertTrue(m1.HasSubstructMatch(m2))
self.assertTrue(m1.HasSubstructMatch(m1, useChirality=True))
self.assertTrue(not m1.HasSubstructMatch(m2, useChirality=True))
def _test32MolFilesWithChirality(self):
inD = """chiral1.mol
ChemDraw10160313232D
5 4 0 0 0 0 0 0 0 0999 V2000
0.0553 0.6188 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
0.0553 -0.2062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7697 -0.6188 0.0000 I 0 0 0 0 0 0 0 0 0 0 0 0
-0.6592 -0.6188 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0
-0.7697 -0.2062 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 0
2 4 1 1
2 5 1 0
M END
"""
m1 = Chem.MolFromMolBlock(inD)
self.assertTrue(m1 is not None)
self.assertTrue(m1.GetNumAtoms() == 5)
self.assertTrue(smi == 'F[C@](Cl)(Br)I', smi)
inD = """chiral2.cdxml
ChemDraw10160314052D
5 4 0 0 0 0 0 0 0 0999 V2000
0.0553 0.6188 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
0.0553 -0.2062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7697 -0.6188 0.0000 I 0 0 0 0 0 0 0 0 0 0 0 0
-0.6592 -0.6188 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0
-0.7697 -0.2062 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 0
2 4 1 6
2 5 1 0
M END
"""
m1 = Chem.MolFromMolBlock(inD)
self.assertTrue(m1 is not None)
self.assertTrue(m1.GetNumAtoms() == 5)
self.assertTrue(Chem.MolToSmiles(m1, 1) == 'F[C@@](Cl)(Br)I')
inD = """chiral1.mol
ChemDraw10160313232D
5 4 0 0 0 0 0 0 0 0999 V2000
0.0553 0.6188 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
0.0553 -0.2062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7697 -0.2062 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
-0.6592 -0.6188 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0
0.7697 -0.6188 0.0000 I 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 0
2 4 1 1
2 5 1 0
M END
"""
m1 = Chem.MolFromMolBlock(inD)
self.assertTrue(m1 is not None)
self.assertTrue(m1.GetNumAtoms() == 5)
self.assertTrue(Chem.MolToSmiles(m1, 1) == 'F[C@](Cl)(Br)I')
inD = """chiral1.mol
ChemDraw10160313232D
5 4 0 0 0 0 0 0 0 0999 V2000
0.0553 -0.2062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7697 -0.2062 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
-0.6592 -0.6188 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0
0.7697 -0.6188 0.0000 I 0 0 0 0 0 0 0 0 0 0 0 0
0.0553 0.6188 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
1 3 1 1
1 4 1 0
1 5 1 0
M END
"""
m1 = Chem.MolFromMolBlock(inD)
self.assertTrue(m1 is not None)
self.assertTrue(m1.GetNumAtoms() == 5)
self.assertTrue(Chem.MolToSmiles(m1, 1) == 'F[C@](Cl)(Br)I')
inD = """chiral3.mol
ChemDraw10160314362D
4 3 0 0 0 0 0 0 0 0999 V2000
0.4125 0.6188 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
0.4125 -0.2062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3020 -0.6188 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0
-0.4125 -0.2062 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 1
2 4 1 0
M END
"""
m1 = Chem.MolFromMolBlock(inD)
self.assertTrue(m1 is not None)
self.assertTrue(m1.GetNumAtoms() == 4)
self.assertTrue(Chem.MolToSmiles(m1, 1) == 'F[C@H](Cl)Br')
inD = """chiral4.mol
ChemDraw10160314362D
4 3 0 0 0 0 0 0 0 0999 V2000
0.4125 0.6188 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
0.4125 -0.2062 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-0.3020 -0.6188 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0
-0.4125 -0.2062 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 1
2 4 1 0
M END
"""
m1 = Chem.MolFromMolBlock(inD)
self.assertTrue(m1 is not None)
self.assertTrue(m1.GetNumAtoms() == 4)
self.assertTrue(Chem.MolToSmiles(m1, 1) == 'FN(Cl)Br')
inD = """chiral5.mol
ChemDraw10160314362D
4 3 0 0 0 0 0 0 0 0999 V2000
0.4125 0.6188 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
0.4125 -0.2062 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-0.3020 -0.6188 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0
-0.4125 -0.2062 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 1
2 4 1 0
M CHG 1 2 1
M END
"""
m1 = Chem.MolFromMolBlock(inD)
self.assertTrue(m1 is not None)
self.assertTrue(m1.GetNumAtoms() == 4)
self.assertTrue(Chem.MolToSmiles(m1, 1) == 'F[N@H+](Cl)Br')
inD = """Case 10-14-3
ChemDraw10140308512D
4 3 0 0 0 0 0 0 0 0999 V2000
-0.8250 -0.4125 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.8250 -0.4125 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.4125 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 0
2 4 1 1
M END
"""
m1 = Chem.MolFromMolBlock(inD)
self.assertTrue(m1 is not None)
self.assertTrue(m1.GetNumAtoms() == 4)
self.assertTrue(Chem.MolToSmiles(m1, 1) == 'F[C@H](Cl)Br')
inD = """Case 10-14-4
ChemDraw10140308512D
4 3 0 0 0 0 0 0 0 0999 V2000
-0.8250 -0.4125 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.8250 -0.4125 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.4125 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 1
2 4 1 0
M END
"""
m1 = Chem.MolFromMolBlock(inD)
self.assertTrue(m1 is not None)
self.assertTrue(m1.GetNumAtoms() == 4)
self.assertTrue(Chem.MolToSmiles(m1, 1) == 'F[C@H](Cl)Br')
inD = """chiral4.mol
ChemDraw10160315172D
6 6 0 0 0 0 0 0 0 0999 V2000
-0.4422 0.1402 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.4422 -0.6848 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.2723 -0.2723 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.8547 0.8547 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.6848 0.4422 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
0.8547 -0.8547 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 0
3 1 1 0
1 4 1 0
3 5 1 1
3 6 1 0
M END
"""
m1 = Chem.MolFromMolBlock(inD)
self.assertTrue(m1 is not None)
self.assertTrue(m1.GetNumAtoms() == 6)
self.assertTrue(Chem.MolToSmiles(m1, 1) == 'CC1C[C@@]1(F)Cl', Chem.MolToSmiles(m1, 1))
inD = """chiral4.mol
ChemDraw10160315172D
6 6 0 0 0 0 0 0 0 0999 V2000
-0.4422 0.1402 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.4422 -0.6848 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.2723 -0.2723 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.8547 0.8547 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.6848 0.4422 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
0.8547 -0.8547 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 0
3 1 1 0
1 4 1 0
3 5 1 6
3 6 1 0
M END
"""
m1 = Chem.MolFromMolBlock(inD)
self.assertTrue(m1 is not None)
self.assertTrue(m1.GetNumAtoms() == 6)
self.assertTrue(Chem.MolToSmiles(m1, 1) == 'CC1C[C@]1(F)Cl', Chem.MolToSmiles(m1, 1))
def test33Issue65(self):
""" issue 65 relates to handling of [H] in SMARTS
"""
m1 = Chem.MolFromSmiles('OC(O)(O)O')
m2 = Chem.MolFromSmiles('OC(O)O')
m3 = Chem.MolFromSmiles('OCO')
q1 = Chem.MolFromSmarts('OC[H]', 1)
q2 = Chem.MolFromSmarts('O[C;H1]', 1)
q3 = Chem.MolFromSmarts('O[C;H1][H]', 1)
self.assertTrue(not m1.HasSubstructMatch(q1))
self.assertTrue(not m1.HasSubstructMatch(q2))
self.assertTrue(not m1.HasSubstructMatch(q3))
self.assertTrue(m2.HasSubstructMatch(q1))
self.assertTrue(m2.HasSubstructMatch(q2))
self.assertTrue(m2.HasSubstructMatch(q3))
self.assertTrue(m3.HasSubstructMatch(q1))
self.assertTrue(not m3.HasSubstructMatch(q2))
self.assertTrue(not m3.HasSubstructMatch(q3))
m1H = Chem.AddHs(m1)
m2H = Chem.AddHs(m2)
m3H = Chem.AddHs(m3)
q1 = Chem.MolFromSmarts('OC[H]')
q2 = Chem.MolFromSmarts('O[C;H1]')
q3 = Chem.MolFromSmarts('O[C;H1][H]')
self.assertTrue(not m1H.HasSubstructMatch(q1))
self.assertTrue(not m1H.HasSubstructMatch(q2))
self.assertTrue(not m1H.HasSubstructMatch(q3))
#m2H.Debug()
self.assertTrue(m2H.HasSubstructMatch(q1))
self.assertTrue(m2H.HasSubstructMatch(q2))
self.assertTrue(m2H.HasSubstructMatch(q3))
self.assertTrue(m3H.HasSubstructMatch(q1))
self.assertTrue(not m3H.HasSubstructMatch(q2))
self.assertTrue(not m3H.HasSubstructMatch(q3))
def test34Issue124(self):
""" issue 124 relates to calculation of the distance matrix
"""
m = Chem.MolFromSmiles('CC=C')
d = Chem.GetDistanceMatrix(m, 0)
self.assertTrue(feq(d[0, 1], 1.0))
self.assertTrue(feq(d[0, 2], 2.0))
# force an update:
d = Chem.GetDistanceMatrix(m, 1, 0, 1)
self.assertTrue(feq(d[0, 1], 1.0))
self.assertTrue(feq(d[0, 2], 1.5))
def test35ChiralityPerception(self):
""" Test perception of chirality and CIP encoding
"""
m = Chem.MolFromSmiles('F[C@]([C@])(Cl)Br')
Chem.AssignStereochemistry(m, 1)
self.assertTrue(m.GetAtomWithIdx(1).HasProp('_CIPCode'))
self.assertFalse(m.GetAtomWithIdx(2).HasProp('_CIPCode'))
Chem.RemoveStereochemistry(m)
self.assertFalse(m.GetAtomWithIdx(1).HasProp('_CIPCode'))
m = Chem.MolFromSmiles('F[C@H](C)C')
Chem.AssignStereochemistry(m, 1)
self.assertTrue(m.GetAtomWithIdx(1).GetChiralTag() == Chem.ChiralType.CHI_UNSPECIFIED)
self.assertFalse(m.GetAtomWithIdx(1).HasProp('_CIPCode'))
m = Chem.MolFromSmiles('F\\C=C/Cl')
self.assertTrue(m.GetBondWithIdx(0).GetStereo() == Chem.BondStereo.STEREONONE)
self.assertTrue(m.GetBondWithIdx(1).GetStereo() == Chem.BondStereo.STEREOZ)
atoms = m.GetBondWithIdx(1).GetStereoAtoms()
self.assertTrue(0 in atoms)
self.assertTrue(3 in atoms)
self.assertTrue(m.GetBondWithIdx(2).GetStereo() == Chem.BondStereo.STEREONONE)
Chem.RemoveStereochemistry(m)
self.assertTrue(m.GetBondWithIdx(1).GetStereo() == Chem.BondStereo.STEREONONE)
m = Chem.MolFromSmiles('F\\C=CCl')
self.assertTrue(m.GetBondWithIdx(1).GetStereo() == Chem.BondStereo.STEREONONE)
def checkDefaultBondProperties(self, m):
for bond in m.GetBonds():
self.assertIn(bond.GetBondType(), [Chem.BondType.SINGLE, Chem.BondType.DOUBLE])
self.assertEqual(bond.GetBondDir(), Chem.BondDir.NONE)
self.assertEqual(list(bond.GetStereoAtoms()), [])
self.assertEqual(bond.GetStereo(), Chem.BondStereo.STEREONONE)
def assertHasDoubleBondStereo(self, smi):
m = Chem.MolFromSmiles(smi)
self.checkDefaultBondProperties(m)
Chem.FindPotentialStereoBonds(m)
for bond in m.GetBonds():
self.assertIn(bond.GetBondType(), [Chem.BondType.SINGLE, Chem.BondType.DOUBLE])
self.assertEqual(bond.GetBondDir(), Chem.BondDir.NONE)
if bond.GetBondType() == Chem.BondType.DOUBLE:
self.assertEqual(bond.GetStereo(), Chem.BondStereo.STEREOANY)
self.assertEqual(len(list(bond.GetStereoAtoms())), 2)
else:
self.assertEqual(list(bond.GetStereoAtoms()), [])
self.assertEqual(bond.GetStereo(), Chem.BondStereo.STEREONONE)
def testFindPotentialStereoBonds(self):
self.assertHasDoubleBondStereo("FC=CF")
self.assertHasDoubleBondStereo("FC(Cl)=C(Br)I")
self.assertHasDoubleBondStereo("FC=CC=CC=CCl")
self.assertHasDoubleBondStereo("C1CCCCC1C=CC1CCCCC1")
def assertDoesNotHaveDoubleBondStereo(self, smi):
m = Chem.MolFromSmiles(smi)
self.checkDefaultBondProperties(m)
Chem.FindPotentialStereoBonds(m)
self.checkDefaultBondProperties(m)
def testFindPotentialStereoBondsShouldNotFindThisDoubleBondAsStereo(self):
self.assertDoesNotHaveDoubleBondStereo("FC(F)=CF")
self.assertDoesNotHaveDoubleBondStereo("C=C")
self.assertDoesNotHaveDoubleBondStereo("C1CCCCC1C(C1CCCCC1)=CC1CCCCC1")
def assertDoubleBondStereo(self, smi, stereo):
mol = Chem.MolFromSmiles(smi)
bond = mol.GetBondWithIdx(1)
self.assertEqual(bond.GetBondType(), Chem.BondType.DOUBLE)
self.assertEqual(bond.GetStereo(), stereo)
self.assertEqual(list(bond.GetStereoAtoms()), [0, 3])
def allStereoBonds(self, bonds):
for bond in bonds:
self.assertEqual(len(list(bond.GetStereoAtoms())), 2)
def testBondSetStereo(self):
for testAssignStereo in [False, True]:
mol = Chem.MolFromSmiles("FC=CF")
Chem.FindPotentialStereoBonds(mol)
for bond in mol.GetBonds():
if (bond.GetBondType() == Chem.BondType.DOUBLE
and bond.GetStereo() == Chem.BondStereo.STEREOANY):
break
self.assertEqual(bond.GetBondType(), Chem.BondType.DOUBLE)
self.assertEqual(bond.GetStereo(), Chem.BondStereo.STEREOANY)
self.assertEqual(list(bond.GetStereoAtoms()), [0, 3])
bond.SetStereo(Chem.BondStereo.STEREOTRANS)
self.assertEqual(bond.GetStereo(), Chem.BondStereo.STEREOTRANS)
if testAssignStereo: # should be invariant of Chem.AssignStereochemistry being called
Chem.AssignStereochemistry(mol, force=True)
smi = Chem.MolToSmiles(mol, isomericSmiles=True)
self.allStereoBonds([bond])
self.assertEqual(smi, "F/C=C/F")
self.assertDoubleBondStereo(smi, Chem.BondStereo.STEREOE)
bond.SetStereo(Chem.BondStereo.STEREOCIS)
self.assertEqual(bond.GetStereo(), Chem.BondStereo.STEREOCIS)
if testAssignStereo:
Chem.AssignStereochemistry(mol, force=True)
smi = Chem.MolToSmiles(mol, isomericSmiles=True)
self.allStereoBonds([bond])
self.assertEqual(smi, r"F/C=C\F")
self.assertDoubleBondStereo(smi, Chem.BondStereo.STEREOZ)
def recursive_enumerate_stereo_bonds(self, mol, done_bonds, bonds):
if not bonds:
yield done_bonds, Chem.Mol(mol)
return
bond = bonds[0]
child_bonds = bonds[1:]
self.assertEqual(len(list(bond.GetStereoAtoms())), 2)
bond.SetStereo(Chem.BondStereo.STEREOTRANS)
for isomer in self.recursive_enumerate_stereo_bonds(mol, done_bonds + [Chem.BondStereo.STEREOE],
child_bonds):
yield isomer
self.assertEqual(len(list(bond.GetStereoAtoms())), 2)
bond.SetStereo(Chem.BondStereo.STEREOCIS)
for isomer in self.recursive_enumerate_stereo_bonds(mol, done_bonds + [Chem.BondStereo.STEREOZ],
child_bonds):
yield isomer
def testBondSetStereoDifficultCase(self):
unspec_smiles = "CCC=CC(CO)=C(C)CC"
mol = Chem.MolFromSmiles(unspec_smiles)
Chem.FindPotentialStereoBonds(mol)
stereo_bonds = []
for bond in mol.GetBonds():
if bond.GetStereo() == Chem.BondStereo.STEREOANY:
stereo_bonds.append(bond)
isomers = set()
for bond_stereo, isomer in self.recursive_enumerate_stereo_bonds(mol, [], stereo_bonds):
self.allStereoBonds(stereo_bonds)
isosmi = Chem.MolToSmiles(isomer, isomericSmiles=True)
self.allStereoBonds(stereo_bonds)
self.assertNotIn(isosmi, isomers)
isomers.add(isosmi)
isomol = Chem.MolFromSmiles(isosmi)
round_trip_stereo = [
b.GetStereo() for b in isomol.GetBonds() if b.GetStereo() != Chem.BondStereo.STEREONONE
]
self.assertEqual(bond_stereo, round_trip_stereo)
self.assertEqual(len(isomers), 4)
def getNumUnspecifiedBondStereo(self, smi):
mol = Chem.MolFromSmiles(smi)
Chem.FindPotentialStereoBonds(mol)
count = 0
for bond in mol.GetBonds():
if bond.GetStereo() == Chem.BondStereo.STEREOANY:
count += 1
return count
def testBondSetStereoReallyDifficultCase(self):
# this one is much trickier because a double bond can gain and
# lose it's stereochemistry based upon whether 2 other double
# bonds have the same or different stereo chemistry.
unspec_smiles = "CCC=CC(C=CCC)=C(CO)CC"
mol = Chem.MolFromSmiles(unspec_smiles)
Chem.FindPotentialStereoBonds(mol)
stereo_bonds = []
for bond in mol.GetBonds():
if bond.GetStereo() == Chem.BondStereo.STEREOANY:
stereo_bonds.append(bond)
self.assertEqual(len(stereo_bonds), 2)
isomers = set()
for bond_stereo, isomer in self.recursive_enumerate_stereo_bonds(mol, [], stereo_bonds):
isosmi = Chem.MolToSmiles(isomer, isomericSmiles=True)
isomers.add(isosmi)
self.assertEqual(len(isomers), 3)
# one of these then gains a new stereo bond due to the
# introduction of a new symmetry
counts = {}
for isosmi in isomers:
num_unspecified = self.getNumUnspecifiedBondStereo(isosmi)
counts[num_unspecified] = counts.get(num_unspecified, 0) + 1
# 2 of the isomers don't have any unspecified bond stereo centers
# left, 1 does
self.assertEqual(counts, {0: 2, 1: 1})
def assertBondSetStereoIsAlwaysEquivalent(self, all_smiles, desired_stereo, bond_idx):
refSmiles = None
for smi in all_smiles:
mol = Chem.MolFromSmiles(smi)
doubleBond = None
for bond in mol.GetBonds():
if bond.GetBondType() == Chem.BondType.DOUBLE:
doubleBond = bond
self.assertTrue(doubleBond is not None)
Chem.FindPotentialStereoBonds(mol)
doubleBond.SetStereo(desired_stereo)
isosmi = Chem.MolToSmiles(mol, isomericSmiles=True)
if refSmiles is None:
refSmiles = isosmi
self.assertEqual(refSmiles, isosmi)
def testBondSetStereoAllHalogens(self):
# can't get much more brutal than this test
from itertools import combinations, permutations
halogens = ['F', 'Cl', 'Br', 'I']
# binary double bond stereo
for unique_set in combinations(halogens, 2):
all_smiles = []
for fmt in ['%sC=C%s', 'C(%s)=C%s']:
for ordering in permutations(unique_set):
all_smiles.append(fmt % ordering)
#print(fmt, all_smiles)
for desired_stereo in [Chem.BondStereo.STEREOTRANS, Chem.BondStereo.STEREOCIS]:
self.assertBondSetStereoIsAlwaysEquivalent(all_smiles, desired_stereo, 1)
# tertiary double bond stereo
for unique_set in combinations(halogens, 3):
for mono_side in unique_set:
halogens_left = list(unique_set)
halogens_left.remove(mono_side)
for binary_side in combinations(halogens_left, 2):
all_smiles = []
for binary_side_permutation in permutations(binary_side):
all_smiles.append('%sC=C(%s)%s' % ((mono_side, ) + binary_side_permutation))
all_smiles.append('C(%s)=C(%s)%s' % ((mono_side, ) + binary_side_permutation))
all_smiles.append('%sC(%s)=C%s' % (binary_side_permutation + (mono_side, )))
all_smiles.append('C(%s)(%s)=C%s' % (binary_side_permutation + (mono_side, )))
#print(all_smiles)
for desired_stereo in [Chem.BondStereo.STEREOTRANS, Chem.BondStereo.STEREOCIS]:
self.assertBondSetStereoIsAlwaysEquivalent(all_smiles, desired_stereo, 1)
# quaternary double bond stereo
for unique_ordering in permutations(halogens):
left_side = unique_ordering[:2]
rght_side = unique_ordering[2:]
all_smiles = []
for left_side_permutation in permutations(left_side):
for rght_side_permutation in permutations(rght_side):
for smifmt in ['%sC(%s)=C(%s)%s', 'C(%s)(%s)=C(%s)%s']:
all_smiles.append(smifmt % (left_side_permutation + rght_side_permutation))
#print(all_smiles)
for desired_stereo in [Chem.BondStereo.STEREOTRANS, Chem.BondStereo.STEREOCIS]:
self.assertBondSetStereoIsAlwaysEquivalent(all_smiles, desired_stereo, 1)
def testBondSetStereoAtoms(self):
# use this difficult molecule that only generates 4 isomers, but
# assume all double bonds are stereo!
unspec_smiles = "CCC=CC(C=CCC)=C(CO)CC"
mol = Chem.MolFromSmiles(unspec_smiles)
def getNbr(atom, exclude):
for nbr in atom.GetNeighbors():
if nbr.GetIdx() not in exclude:
return nbr
raise ValueError("No neighbor found!")
double_bonds = []
for bond in mol.GetBonds():
if bond.GetBondType() == 2:
double_bonds.append(bond)
exclude = {bond.GetBeginAtomIdx(), bond.GetEndAtomIdx()}
bgnNbr = getNbr(bond.GetBeginAtom(), exclude)
endNbr = getNbr(bond.GetEndAtom(), exclude)
bond.SetStereoAtoms(bgnNbr.GetIdx(), endNbr.GetIdx())
self.assertEqual(len(double_bonds), 3)
import itertools
stereos = [Chem.BondStereo.STEREOE, Chem.BondStereo.STEREOZ]
isomers = set()
for stereo_config in itertools.product(stereos, repeat=len(double_bonds)):
for bond, stereo in zip(double_bonds, stereo_config):
bond.SetStereo(stereo)
smi = Chem.MolToSmiles(mol, True)
isomers.add(smi)
# the dependent double bond stereo isn't picked up by this, should it?
self.assertEqual(len(isomers), 6)
# round tripping them through one more time does pick up the dependency, so meh?
round_trip_isomers = set()
for smi in isomers:
isosmi = Chem.MolToSmiles(Chem.MolFromSmiles(smi), True)
round_trip_isomers.add(isosmi)
self.assertEqual(len(round_trip_isomers), 4)
def test36SubstructMatchStr(self):
""" test the _SubstructMatchStr function """
query = Chem.MolFromSmarts('[n,p]1ccccc1')
self.assertTrue(query)
mol = Chem.MolFromSmiles('N1=CC=CC=C1')
self.assertTrue(mol.HasSubstructMatch(query))
self.assertTrue(Chem._HasSubstructMatchStr(mol.ToBinary(), query))
mol = Chem.MolFromSmiles('S1=CC=CC=C1')
self.assertTrue(not Chem._HasSubstructMatchStr(mol.ToBinary(), query))
self.assertTrue(not mol.HasSubstructMatch(query))
mol = Chem.MolFromSmiles('P1=CC=CC=C1')
self.assertTrue(mol.HasSubstructMatch(query))
self.assertTrue(Chem._HasSubstructMatchStr(mol.ToBinary(), query))
def test37SanitException(self):
mol = Chem.MolFromSmiles('CC(C)(C)(C)C', 0)
self.assertTrue(mol)
self.assertRaises(ValueError, lambda: Chem.SanitizeMol(mol))
def test38TDTSuppliers(self):
data = """$SMI<Cc1nnc(N)nc1C>
CAS<17584-12-2>
|
$SMI<Cc1n[nH]c(=O)nc1N>
CAS<~>
|
$SMI<Cc1n[nH]c(=O)[nH]c1=O>
CAS<932-53-6>
|
$SMI<Cc1nnc(NN)nc1O>
CAS<~>
|"""
suppl = Chem.TDTMolSupplier()
suppl.SetData(data, "CAS")
i = 0
for mol in suppl:
self.assertTrue(mol)
self.assertTrue(mol.GetNumAtoms())
self.assertTrue(mol.HasProp("CAS"))
self.assertTrue(mol.HasProp("_Name"))
self.assertTrue(mol.GetProp("CAS") == mol.GetProp("_Name"))
self.assertTrue(mol.GetNumConformers() == 0)
i += 1
self.assertTrue(i == 4)
self.assertTrue(len(suppl) == 4)
def test38Issue266(self):
""" test issue 266: generation of kekulized smiles"""
mol = Chem.MolFromSmiles('c1ccccc1')
Chem.Kekulize(mol)
smi = Chem.MolToSmiles(mol)
self.assertTrue(smi == 'c1ccccc1')
smi = Chem.MolToSmiles(mol, kekuleSmiles=True)
self.assertTrue(smi == 'C1=CC=CC=C1')
def test39Issue273(self):
""" test issue 273: MolFileComments and MolFileInfo props ending up in SD files
"""
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'Wrap', 'test_data',
'outNCI_few.sdf')
suppl = Chem.SDMolSupplier(fileN)
ms = [x for x in suppl]
for m in ms:
self.assertTrue(m.HasProp('_MolFileInfo'))
self.assertTrue(m.HasProp('_MolFileComments'))
fName = tempfile.NamedTemporaryFile(suffix='.sdf', delete=False).name
w = Chem.SDWriter(fName)
w.SetProps(ms[0].GetPropNames())
for m in ms:
w.write(m)
w = None
with open(fName, 'r') as txtFile:
txt = txtFile.read()
os.unlink(fName)
self.assertTrue(txt.find('MolFileInfo') == -1)
self.assertTrue(txt.find('MolFileComments') == -1)
def test40SmilesRootedAtAtom(self):
""" test the rootAtAtom functionality
"""
smi = 'CN(C)C'
m = Chem.MolFromSmiles(smi)
self.assertTrue(Chem.MolToSmiles(m) == 'CN(C)C')
self.assertTrue(Chem.MolToSmiles(m, rootedAtAtom=1) == 'N(C)(C)C')
def test41SetStreamIndices(self):
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'NCI_aids_few.sdf')
allIndices = []
ifs = open(fileN, 'rb')
addIndex = True
line = True
pos = 0
while (line):
if (addIndex):
pos = ifs.tell()
line = ifs.readline().decode('utf-8')
if (line):
if (addIndex):
allIndices.append(pos)
addIndex = (line[:4] == '$$$$')
ifs.close()
indices = allIndices
sdSup = Chem.SDMolSupplier(fileN)
molNames = [
"48", "78", "128", "163", "164", "170", "180", "186", "192", "203", "210", "211", "213",
"220", "229", "256"
]
sdSup._SetStreamIndices(indices)
self.assertTrue(len(sdSup) == 16)
mol = sdSup[5]
self.assertTrue(mol.GetProp("_Name") == "170")
i = 0
for mol in sdSup:
self.assertTrue(mol)
self.assertTrue(mol.GetProp("_Name") == molNames[i])
i += 1
ns = [mol.GetProp("_Name") for mol in sdSup]
self.assertTrue(ns == molNames)
# this can also be used to skip molecules in the file:
indices = [allIndices[0], allIndices[2], allIndices[5]]
sdSup._SetStreamIndices(indices)
self.assertTrue(len(sdSup) == 3)
mol = sdSup[2]
self.assertTrue(mol.GetProp("_Name") == "170")
# or to reorder them:
indices = [allIndices[0], allIndices[5], allIndices[2]]
sdSup._SetStreamIndices(indices)
self.assertTrue(len(sdSup) == 3)
mol = sdSup[1]
self.assertTrue(mol.GetProp("_Name") == "170")
def test42LifeTheUniverseAndEverything(self):
self.assertTrue(True)
def test43TplFileParsing(self):
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'cmpd2.tpl')
m1 = Chem.MolFromTPLFile(fileN)
self.assertTrue(m1 is not None)
self.assertTrue(m1.GetNumAtoms() == 12)
self.assertTrue(m1.GetNumConformers() == 2)
m1 = Chem.MolFromTPLFile(fileN, skipFirstConf=True)
self.assertTrue(m1 is not None)
self.assertTrue(m1.GetNumAtoms() == 12)
self.assertTrue(m1.GetNumConformers() == 1)
with open(fileN, 'r') as blockFile:
block = blockFile.read()
m1 = Chem.MolFromTPLBlock(block)
self.assertTrue(m1 is not None)
self.assertTrue(m1.GetNumAtoms() == 12)
self.assertTrue(m1.GetNumConformers() == 2)
def test44TplFileWriting(self):
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'cmpd2.tpl')
m1 = Chem.MolFromTPLFile(fileN)
self.assertTrue(m1 is not None)
self.assertTrue(m1.GetNumAtoms() == 12)
self.assertTrue(m1.GetNumConformers() == 2)
block = Chem.MolToTPLBlock(m1)
m1 = Chem.MolFromTPLBlock(block)
self.assertTrue(m1 is not None)
self.assertTrue(m1.GetNumAtoms() == 12)
self.assertTrue(m1.GetNumConformers() == 2)
def test45RingInfo(self):
""" test the RingInfo class
"""
smi = 'CNC'
m = Chem.MolFromSmiles(smi)
ri = m.GetRingInfo()
self.assertTrue(ri)
self.assertTrue(ri.NumRings() == 0)
self.assertFalse(ri.IsAtomInRingOfSize(0, 3))
self.assertFalse(ri.IsAtomInRingOfSize(1, 3))
self.assertFalse(ri.IsAtomInRingOfSize(2, 3))
self.assertFalse(ri.IsBondInRingOfSize(1, 3))
self.assertFalse(ri.IsBondInRingOfSize(2, 3))
if hasattr(Chem, 'FindRingFamilies'):
self.assertEquals(ri.AtomRingFamilies(), ())
if hasattr(Chem, 'FindRingFamilies'):
self.assertEquals(ri.BondRingFamilies(), ())
smi = 'C1CC2C1C2'
m = Chem.MolFromSmiles(smi)
ri = m.GetRingInfo()
self.assertTrue(ri)
self.assertEquals(ri.NumRings(), 2)
self.assertFalse(ri.IsAtomInRingOfSize(0, 3))
self.assertTrue(ri.IsAtomInRingOfSize(0, 4))
self.assertFalse(ri.IsBondInRingOfSize(0, 3))
self.assertTrue(ri.IsBondInRingOfSize(0, 4))
self.assertTrue(ri.IsAtomInRingOfSize(2, 4))
self.assertTrue(ri.IsAtomInRingOfSize(2, 3))
self.assertTrue(ri.IsBondInRingOfSize(2, 3))
self.assertTrue(ri.IsBondInRingOfSize(2, 4))
self.assertEqual(ri.AtomRings(), ((0, 3, 2, 1), (4, 3, 2)))
self.assertEqual(ri.BondRings(), ((4, 2, 1, 0), (3, 2, 5)))
self.assertEqual(len(ri.AtomMembers(2)), 2)
self.assertEqual(ri.AtomRingSizes(2), (4, 3))
self.assertEqual(ri.AtomRingSizes(99), ())
self.assertTrue(ri.AreAtomsInSameRing(2, 3))
self.assertFalse(ri.AreAtomsInSameRing(1, 4))
self.assertTrue(ri.AreAtomsInSameRingOfSize(2, 3, 3))
self.assertTrue(ri.AreAtomsInSameRingOfSize(2, 3, 4))
self.assertFalse(ri.AreAtomsInSameRingOfSize(2, 3, 5))
self.assertEqual(len(ri.BondMembers(2)), 2)
self.assertEqual(len(ri.BondMembers(0)), 1)
self.assertEqual(ri.BondRingSizes(2), (4, 3))
self.assertEqual(ri.BondRingSizes(0), (4, ))
self.assertEqual(ri.BondRingSizes(99), ())
self.assertTrue(ri.AreBondsInSameRing(1, 2))
self.assertTrue(ri.AreBondsInSameRing(2, 5))
self.assertFalse(ri.AreBondsInSameRing(1, 3))
self.assertTrue(ri.AreBondsInSameRingOfSize(1, 2, 4))
self.assertTrue(ri.AreBondsInSameRingOfSize(2, 5, 3))
self.assertFalse(ri.AreBondsInSameRingOfSize(1, 2, 3))
self.assertFalse(ri.AreBondsInSameRingOfSize(1, 3, 4))
if hasattr(Chem, 'FindRingFamilies'):
ri = m.GetRingInfo()
self.assertFalse(ri.AreRingFamiliesInitialized())
Chem.FindRingFamilies(m)
ri = m.GetRingInfo()
self.assertTrue(ri.AreRingFamiliesInitialized())
self.assertEquals(ri.NumRingFamilies(), 2)
self.assertEquals(sorted(ri.AtomRingFamilies()), [(0, 1, 2, 3), (2, 3, 4)])
self.assertEquals(sorted(ri.BondRingFamilies()), [(0, 1, 2, 4), (2, 3, 5)])
def test46ReplaceCore(self):
""" test the ReplaceCore functionality
"""
core = Chem.MolFromSmiles('C=O')
smi = 'CCC=O'
m = Chem.MolFromSmiles(smi)
r = Chem.ReplaceCore(m, core)
self.assertTrue(r)
self.assertEqual(Chem.MolToSmiles(r, True), '[1*]CC')
smi = 'C1CC(=O)CC1'
m = Chem.MolFromSmiles(smi)
r = Chem.ReplaceCore(m, core)
self.assertTrue(r)
self.assertEqual(Chem.MolToSmiles(r, True), '[1*]CCCC[2*]')
smi = 'C1CC(=N)CC1'
m = Chem.MolFromSmiles(smi)
r = Chem.ReplaceCore(m, core)
self.assertFalse(r)
# smiles, smarts, replaceDummies, labelByIndex, useChirality
expected = {
('C1O[C@@]1(OC)NC', 'C1O[C@]1(*)*', False, False, False): '[1*]OC.[2*]NC',
('C1O[C@@]1(OC)NC', 'C1O[C@]1(*)*', False, False, True): '[1*]NC.[2*]OC',
('C1O[C@@]1(OC)NC', 'C1O[C@]1(*)*', False, True, False): '[3*]OC.[4*]NC',
('C1O[C@@]1(OC)NC', 'C1O[C@]1(*)*', False, True, True): '[3*]NC.[4*]OC',
('C1O[C@@]1(OC)NC', 'C1O[C@]1(*)*', True, False, False): '[1*]C.[2*]C',
('C1O[C@@]1(OC)NC', 'C1O[C@]1(*)*', True, False, True): '[1*]C.[2*]C',
('C1O[C@@]1(OC)NC', 'C1O[C@]1(*)*', True, True, False): '[3*]C.[4*]C',
('C1O[C@@]1(OC)NC', 'C1O[C@]1(*)*', True, True, True): '[3*]C.[4*]C',
('C1O[C@]1(OC)NC', 'C1O[C@]1(*)*', False, False, False): '[1*]OC.[2*]NC',
('C1O[C@]1(OC)NC', 'C1O[C@]1(*)*', False, False, True): '[1*]OC.[2*]NC',
('C1O[C@]1(OC)NC', 'C1O[C@]1(*)*', False, True, False): '[3*]OC.[4*]NC',
('C1O[C@]1(OC)NC', 'C1O[C@]1(*)*', False, True, True): '[3*]OC.[4*]NC',
('C1O[C@]1(OC)NC', 'C1O[C@]1(*)*', True, False, False): '[1*]C.[2*]C',
('C1O[C@]1(OC)NC', 'C1O[C@]1(*)*', True, False, True): '[1*]C.[2*]C',
('C1O[C@]1(OC)NC', 'C1O[C@]1(*)*', True, True, False): '[3*]C.[4*]C',
('C1O[C@]1(OC)NC', 'C1O[C@]1(*)*', True, True, True): '[3*]C.[4*]C',
}
for (smiles, smarts, replaceDummies, labelByIndex,
useChirality), expected_smiles in expected.items():
mol = Chem.MolFromSmiles(smiles)
core = Chem.MolFromSmarts(smarts)
nm = Chem.ReplaceCore(mol, core, replaceDummies=replaceDummies, labelByIndex=labelByIndex,
useChirality=useChirality)
if Chem.MolToSmiles(nm, True) != expected_smiles:
print(
"ReplaceCore(%r, %r, replaceDummies=%r, labelByIndex=%r, useChirality=%r" %
(smiles, smarts, replaceDummies, labelByIndex, useChirality), file=sys.stderr)
print("expected: %s\ngot: %s" % (expected_smiles, Chem.MolToSmiles(nm, True)),
file=sys.stderr)
self.assertEqual(expected_smiles, Chem.MolToSmiles(nm, True))
matchVect = mol.GetSubstructMatch(core, useChirality=useChirality)
nm = Chem.ReplaceCore(mol, core, matchVect, replaceDummies=replaceDummies,
labelByIndex=labelByIndex)
if Chem.MolToSmiles(nm, True) != expected_smiles:
print(
"ReplaceCore(%r, %r, %r, replaceDummies=%r, labelByIndex=%rr" %
(smiles, smarts, matchVect, replaceDummies, labelByIndex), file=sys.stderr)
print("expected: %s\ngot: %s" % (expected_smiles, Chem.MolToSmiles(nm, True)),
file=sys.stderr)
self.assertEqual(expected_smiles, Chem.MolToSmiles(nm, True))
mol = Chem.MolFromSmiles("C")
smarts = Chem.MolFromSmarts("C")
try:
Chem.ReplaceCore(mol, smarts, (3, ))
self.asssertFalse(True)
except Exception:
pass
mol = Chem.MolFromSmiles("C")
smarts = Chem.MolFromSmarts("C")
try:
Chem.ReplaceCore(mol, smarts, (0, 0))
self.asssertFalse(True)
except Exception:
pass
def test47RWMols(self):
""" test the RWMol class
"""
mol = Chem.MolFromSmiles('C1CCC1')
self.assertTrue(type(mol) == Chem.Mol)
for rwmol in [Chem.EditableMol(mol), Chem.RWMol(mol)]:
self.assertTrue(type(rwmol) in [Chem.EditableMol, Chem.RWMol])
newAt = Chem.Atom(8)
rwmol.ReplaceAtom(0, newAt)
self.assertTrue(Chem.MolToSmiles(rwmol.GetMol()) == 'C1COC1')
rwmol.RemoveBond(0, 1)
self.assertTrue(Chem.MolToSmiles(rwmol.GetMol()) == 'CCCO')
a = Chem.Atom(7)
idx = rwmol.AddAtom(a)
self.assertEqual(rwmol.GetMol().GetNumAtoms(), 5)
self.assertEqual(idx, 4)
idx = rwmol.AddBond(0, 4, order=Chem.BondType.SINGLE)
self.assertEqual(idx, 4)
self.assertTrue(Chem.MolToSmiles(rwmol.GetMol()) == 'CCCON')
rwmol.AddBond(4, 1, order=Chem.BondType.SINGLE)
self.assertTrue(Chem.MolToSmiles(rwmol.GetMol()) == 'C1CNOC1')
rwmol.RemoveAtom(3)
self.assertTrue(Chem.MolToSmiles(rwmol.GetMol()) == 'CCNO')
# practice shooting ourselves in the foot:
m = Chem.MolFromSmiles('c1ccccc1')
em = Chem.EditableMol(m)
em.RemoveAtom(0)
m2 = em.GetMol()
self.assertRaises(ValueError, lambda: Chem.SanitizeMol(m2))
m = Chem.MolFromSmiles('c1ccccc1')
em = Chem.EditableMol(m)
em.RemoveBond(0, 1)
m2 = em.GetMol()
self.assertRaises(ValueError, lambda: Chem.SanitizeMol(m2))
# boundary cases:
# removing non-existent bonds:
m = Chem.MolFromSmiles('c1ccccc1')
em = Chem.EditableMol(m)
em.RemoveBond(0, 2)
m2 = em.GetMol()
Chem.SanitizeMol(m2)
self.assertTrue(Chem.MolToSmiles(m2) == 'c1ccccc1')
# removing non-existent atoms:
m = Chem.MolFromSmiles('c1ccccc1')
em = Chem.EditableMol(m)
self.assertRaises(RuntimeError, lambda: em.RemoveAtom(12))
# confirm that an RWMol can be constructed without arguments
m = Chem.RWMol()
# test replaceAtom/Bond preserving properties
mol = Chem.MolFromSmiles('C1CCC1')
mol2 = Chem.MolFromSmiles('C1CCC1')
mol.GetAtomWithIdx(0).SetProp("foo", "bar")
mol.GetBondWithIdx(0).SetProp("foo", "bar")
newBond = mol2.GetBondWithIdx(0)
self.assertTrue(type(mol) == Chem.Mol)
for rwmol in [Chem.EditableMol(mol), Chem.RWMol(mol)]:
newAt = Chem.Atom(8)
rwmol.ReplaceAtom(0, newAt)
self.assertTrue(Chem.MolToSmiles(rwmol.GetMol()) == 'C1COC1')
self.assertFalse(rwmol.GetMol().GetAtomWithIdx(0).HasProp("foo"))
for rwmol in [Chem.EditableMol(mol), Chem.RWMol(mol)]:
newAt = Chem.Atom(8)
rwmol.ReplaceAtom(0, newAt, preserveProps=True)
self.assertTrue(Chem.MolToSmiles(rwmol.GetMol()) == 'C1COC1')
self.assertTrue(rwmol.GetMol().GetAtomWithIdx(0).HasProp("foo"))
self.assertEqual(rwmol.GetMol().GetAtomWithIdx(0).GetProp("foo"), "bar")
for rwmol in [Chem.EditableMol(mol), Chem.RWMol(mol)]:
rwmol.ReplaceBond(0, newBond)
self.assertTrue(Chem.MolToSmiles(rwmol.GetMol()) == 'C1CCC1')
self.assertFalse(rwmol.GetMol().GetBondWithIdx(0).HasProp("foo"))
for rwmol in [Chem.EditableMol(mol), Chem.RWMol(mol)]:
rwmol.ReplaceBond(0, newBond, preserveProps=True)
self.assertTrue(Chem.MolToSmiles(rwmol.GetMol()) == 'C1CCC1')
self.assertTrue(rwmol.GetMol().GetBondWithIdx(0).HasProp("foo"))
self.assertEqual(rwmol.GetMol().GetBondWithIdx(0).GetProp("foo"), "bar")
def test47SmartsPieces(self):
""" test the GetAtomSmarts and GetBondSmarts functions
"""
m = Chem.MolFromSmarts("[C,N]C")
self.assertTrue(m.GetAtomWithIdx(0).GetSmarts() == '[C,N]')
self.assertTrue(m.GetAtomWithIdx(1).GetSmarts() == 'C')
self.assertEqual(m.GetBondBetweenAtoms(0, 1).GetSmarts(), '')
m = Chem.MolFromSmarts("[$(C=O)]-O")
self.assertTrue(m.GetAtomWithIdx(0).GetSmarts() == '[$(C=O)]')
self.assertTrue(m.GetAtomWithIdx(1).GetSmarts() == 'O')
self.assertTrue(m.GetBondBetweenAtoms(0, 1).GetSmarts() == '-')
m = Chem.MolFromSmiles("CO")
self.assertTrue(m.GetAtomWithIdx(0).GetSmarts() == 'C')
self.assertTrue(m.GetAtomWithIdx(1).GetSmarts() == 'O')
self.assertTrue(m.GetBondBetweenAtoms(0, 1).GetSmarts() == '')
self.assertTrue(m.GetBondBetweenAtoms(0, 1).GetSmarts(allBondsExplicit=True) == '-')
m = Chem.MolFromSmiles("C=O")
self.assertTrue(m.GetAtomWithIdx(0).GetSmarts() == 'C')
self.assertTrue(m.GetAtomWithIdx(1).GetSmarts() == 'O')
self.assertTrue(m.GetBondBetweenAtoms(0, 1).GetSmarts() == '=')
m = Chem.MolFromSmiles('C[C@H](F)[15NH3+]')
self.assertEqual(m.GetAtomWithIdx(0).GetSmarts(), 'C')
self.assertEqual(m.GetAtomWithIdx(0).GetSmarts(allHsExplicit=True), '[CH3]')
self.assertEqual(m.GetAtomWithIdx(3).GetSmarts(), '[15NH3+]')
self.assertEqual(m.GetAtomWithIdx(3).GetSmarts(allHsExplicit=True), '[15NH3+]')
def test48Issue1928819(self):
""" test a crash involving looping directly over mol suppliers
"""
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'NCI_aids_few.sdf')
ms = [x for x in Chem.SDMolSupplier(fileN)]
self.assertEqual(len(ms), 16)
count = 0
for m in Chem.SDMolSupplier(fileN):
count += 1
self.assertEqual(count, 16)
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'fewSmi.csv')
count = 0
for m in Chem.SmilesMolSupplier(fileN, titleLine=False, smilesColumn=1, delimiter=','):
count += 1
self.assertEqual(count, 10)
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'acd_few.tdt')
count = 0
for m in Chem.TDTMolSupplier(fileN):
count += 1
self.assertEqual(count, 10)
def test49Issue1932365(self):
""" test aromatic Se and Te from smiles/smarts
"""
m = Chem.MolFromSmiles('c1ccc[se]1')
self.assertTrue(m)
self.assertTrue(m.GetAtomWithIdx(0).GetIsAromatic())
self.assertTrue(m.GetAtomWithIdx(4).GetIsAromatic())
m = Chem.MolFromSmiles('c1ccc[te]1')
self.assertTrue(m)
self.assertTrue(m.GetAtomWithIdx(0).GetIsAromatic())
self.assertTrue(m.GetAtomWithIdx(4).GetIsAromatic())
m = Chem.MolFromSmiles('C1=C[Se]C=C1')
self.assertTrue(m)
self.assertTrue(m.GetAtomWithIdx(0).GetIsAromatic())
self.assertTrue(m.GetAtomWithIdx(2).GetIsAromatic())
m = Chem.MolFromSmiles('C1=C[Te]C=C1')
self.assertTrue(m)
self.assertTrue(m.GetAtomWithIdx(0).GetIsAromatic())
self.assertTrue(m.GetAtomWithIdx(2).GetIsAromatic())
p = Chem.MolFromSmarts('[se]')
self.assertTrue(Chem.MolFromSmiles('c1ccc[se]1').HasSubstructMatch(p))
self.assertFalse(Chem.MolFromSmiles('C1=CCC[Se]1').HasSubstructMatch(p))
p = Chem.MolFromSmarts('[te]')
self.assertTrue(Chem.MolFromSmiles('c1ccc[te]1').HasSubstructMatch(p))
self.assertFalse(Chem.MolFromSmiles('C1=CCC[Te]1').HasSubstructMatch(p))
def test50Issue1968608(self):
""" test sf.net issue 1968608
"""
smarts = Chem.MolFromSmarts("[r5]")
mol = Chem.MolFromSmiles("N12CCC36C1CC(C(C2)=CCOC4CC5=O)C4C3N5c7ccccc76")
count = len(mol.GetSubstructMatches(smarts, uniquify=0))
self.assertTrue(count == 9)
def test51RadicalHandling(self):
""" test handling of atoms with radicals
"""
mol = Chem.MolFromSmiles("[C]C")
self.assertTrue(mol)
atom = mol.GetAtomWithIdx(0)
self.assertTrue(atom.GetNumRadicalElectrons() == 3)
self.assertTrue(atom.GetNoImplicit())
atom.SetNoImplicit(False)
atom.SetNumRadicalElectrons(1)
mol.UpdatePropertyCache()
self.assertTrue(atom.GetNumRadicalElectrons() == 1)
self.assertTrue(atom.GetNumImplicitHs() == 2)
mol = Chem.MolFromSmiles("[c]1ccccc1")
self.assertTrue(mol)
atom = mol.GetAtomWithIdx(0)
self.assertTrue(atom.GetNumRadicalElectrons() == 1)
self.assertTrue(atom.GetNoImplicit())
mol = Chem.MolFromSmiles("[n]1ccccc1")
self.assertTrue(mol)
atom = mol.GetAtomWithIdx(0)
self.assertTrue(atom.GetNumRadicalElectrons() == 0)
self.assertTrue(atom.GetNoImplicit())
def test52MolFrags(self):
""" test GetMolFrags functionality
"""
mol = Chem.MolFromSmiles("C.CC")
self.assertTrue(mol)
fs = Chem.GetMolFrags(mol)
self.assertTrue(len(fs) == 2)
self.assertTrue(len(fs[0]) == 1)
self.assertTrue(tuple(fs[0]) == (0, ))
self.assertTrue(len(fs[1]) == 2)
self.assertTrue(tuple(fs[1]) == (1, 2))
fs = Chem.GetMolFrags(mol, True)
self.assertTrue(len(fs) == 2)
self.assertTrue(fs[0].GetNumAtoms() == 1)
self.assertTrue(fs[1].GetNumAtoms() == 2)
mol = Chem.MolFromSmiles("CCC")
self.assertTrue(mol)
fs = Chem.GetMolFrags(mol)
self.assertTrue(len(fs) == 1)
self.assertTrue(len(fs[0]) == 3)
self.assertTrue(tuple(fs[0]) == (0, 1, 2))
fs = Chem.GetMolFrags(mol, True)
self.assertTrue(len(fs) == 1)
self.assertTrue(fs[0].GetNumAtoms() == 3)
mol = Chem.MolFromSmiles("CO")
em = Chem.EditableMol(mol)
em.RemoveBond(0, 1)
nm = em.GetMol()
fs = Chem.GetMolFrags(nm, asMols=True)
self.assertEqual([x.GetNumAtoms(onlyExplicit=False) for x in fs], [5, 3])
fs = Chem.GetMolFrags(nm, asMols=True, sanitizeFrags=False)
self.assertEqual([x.GetNumAtoms(onlyExplicit=False) for x in fs], [4, 2])
mol = Chem.MolFromSmiles("CC.CCC")
fs = Chem.GetMolFrags(mol, asMols=True)
self.assertEqual([x.GetNumAtoms() for x in fs], [2, 3])
frags = []
fragsMolAtomMapping = []
fs = Chem.GetMolFrags(mol, asMols=True, frags=frags, fragsMolAtomMapping=fragsMolAtomMapping)
self.assertEqual(mol.GetNumAtoms(onlyExplicit=True), len(frags))
fragsCheck = []
for i, f in enumerate(fs):
fragsCheck.extend([i] * f.GetNumAtoms(onlyExplicit=True))
self.assertEqual(frags, fragsCheck)
fragsMolAtomMappingCheck = []
i = 0
for f in fs:
n = f.GetNumAtoms(onlyExplicit=True)
fragsMolAtomMappingCheck.append(tuple(range(i, i + n)))
i += n
self.assertEqual(fragsMolAtomMapping, fragsMolAtomMappingCheck)
def test53Matrices(self):
""" test adjacency and distance matrices
"""
m = Chem.MolFromSmiles('CC=C')
d = Chem.GetDistanceMatrix(m, 0)
self.assertTrue(feq(d[0, 1], 1.0))
self.assertTrue(feq(d[0, 2], 2.0))
self.assertTrue(feq(d[1, 0], 1.0))
self.assertTrue(feq(d[2, 0], 2.0))
a = Chem.GetAdjacencyMatrix(m, 0)
self.assertTrue(a[0, 1] == 1)
self.assertTrue(a[0, 2] == 0)
self.assertTrue(a[1, 2] == 1)
self.assertTrue(a[1, 0] == 1)
self.assertTrue(a[2, 0] == 0)
m = Chem.MolFromSmiles('C1CC1')
d = Chem.GetDistanceMatrix(m, 0)
self.assertTrue(feq(d[0, 1], 1.0))
self.assertTrue(feq(d[0, 2], 1.0))
a = Chem.GetAdjacencyMatrix(m, 0)
self.assertTrue(a[0, 1] == 1)
self.assertTrue(a[0, 2] == 1)
self.assertTrue(a[1, 2] == 1)
m = Chem.MolFromSmiles('CC.C')
d = Chem.GetDistanceMatrix(m, 0)
self.assertTrue(feq(d[0, 1], 1.0))
self.assertTrue(d[0, 2] > 1000)
self.assertTrue(d[1, 2] > 1000)
a = Chem.GetAdjacencyMatrix(m, 0)
self.assertTrue(a[0, 1] == 1)
self.assertTrue(a[0, 2] == 0)
self.assertTrue(a[1, 2] == 0)
def test54Mol2Parser(self):
""" test the mol2 parser
"""
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'pyrazole_pyridine.mol2')
m = Chem.MolFromMol2File(fileN)
self.assertTrue(m.GetNumAtoms() == 5)
self.assertTrue(Chem.MolToSmiles(m) == 'c1cn[nH]c1', Chem.MolToSmiles(m))
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'3505.mol2')
m = Chem.MolFromMol2File(fileN)
self.assertTrue(m.GetBondBetweenAtoms(3, 12) is not None)
self.assertEqual(m.GetBondBetweenAtoms(3, 12).GetBondType(), Chem.BondType.SINGLE)
self.assertEqual(m.GetAtomWithIdx(12).GetFormalCharge(), 0)
m = Chem.MolFromMol2File(fileN, cleanupSubstructures=False)
self.assertTrue(m.GetBondBetweenAtoms(3, 12) is not None)
self.assertEqual(m.GetBondBetweenAtoms(3, 12).GetBondType(), Chem.BondType.DOUBLE)
self.assertEqual(m.GetAtomWithIdx(12).GetFormalCharge(), 1)
def test55LayeredFingerprint(self):
m1 = Chem.MolFromSmiles('CC(C)C')
fp1 = Chem.LayeredFingerprint(m1)
self.assertEqual(len(fp1), 2048)
atomCounts = [0] * m1.GetNumAtoms()
fp2 = Chem.LayeredFingerprint(m1, atomCounts=atomCounts)
self.assertEqual(fp1, fp2)
self.assertEqual(atomCounts, [4, 7, 4, 4])
fp2 = Chem.LayeredFingerprint(m1, atomCounts=atomCounts)
self.assertEqual(fp1, fp2)
self.assertEqual(atomCounts, [8, 14, 8, 8])
pbv = DataStructs.ExplicitBitVect(2048)
fp3 = Chem.LayeredFingerprint(m1, setOnlyBits=pbv)
self.assertEqual(fp3.GetNumOnBits(), 0)
fp3 = Chem.LayeredFingerprint(m1, setOnlyBits=fp2)
self.assertEqual(fp3, fp2)
m2 = Chem.MolFromSmiles('CC')
fp4 = Chem.LayeredFingerprint(m2)
atomCounts = [0] * m1.GetNumAtoms()
fp3 = Chem.LayeredFingerprint(m1, setOnlyBits=fp4, atomCounts=atomCounts)
self.assertEqual(atomCounts, [1, 3, 1, 1])
m2 = Chem.MolFromSmiles('CCC')
fp4 = Chem.LayeredFingerprint(m2)
atomCounts = [0] * m1.GetNumAtoms()
fp3 = Chem.LayeredFingerprint(m1, setOnlyBits=fp4, atomCounts=atomCounts)
self.assertEqual(atomCounts, [3, 6, 3, 3])
def test56LazySDMolSupplier(self):
if not hasattr(Chem, 'CompressedSDMolSupplier'):
return
self.assertRaises(ValueError, lambda: Chem.CompressedSDMolSupplier('nosuchfile.sdf.gz'))
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'NCI_aids_few.sdf.gz')
sdSup = Chem.CompressedSDMolSupplier(fileN)
molNames = [
"48", "78", "128", "163", "164", "170", "180", "186", "192", "203", "210", "211", "213",
"220", "229", "256"
]
chgs192 = {8: 1, 11: 1, 15: -1, 18: -1, 20: 1, 21: 1, 23: -1, 25: -1}
i = 0
for mol in sdSup:
self.assertTrue(mol)
self.assertTrue(mol.GetProp("_Name") == molNames[i])
i += 1
if (mol.GetProp("_Name") == "192"):
# test parsed charges on one of the molecules
for id in chgs192.keys():
self.assertTrue(mol.GetAtomWithIdx(id).GetFormalCharge() == chgs192[id])
self.assertEqual(i, 16)
sdSup = Chem.CompressedSDMolSupplier(fileN)
ns = [mol.GetProp("_Name") for mol in sdSup]
self.assertTrue(ns == molNames)
sdSup = Chem.CompressedSDMolSupplier(fileN, 0)
for mol in sdSup:
self.assertTrue(not mol.HasProp("numArom"))
def test57AddRecursiveQuery(self):
q1 = Chem.MolFromSmiles('CC')
q2 = Chem.MolFromSmiles('CO')
Chem.AddRecursiveQuery(q1, q2, 1)
m1 = Chem.MolFromSmiles('OCC')
self.assertTrue(m1.HasSubstructMatch(q2))
self.assertTrue(m1.HasSubstructMatch(q1))
self.assertTrue(m1.HasSubstructMatch(q1))
self.assertTrue(m1.GetSubstructMatch(q1) == (2, 1))
q3 = Chem.MolFromSmiles('CS')
Chem.AddRecursiveQuery(q1, q3, 1)
self.assertFalse(m1.HasSubstructMatch(q3))
self.assertFalse(m1.HasSubstructMatch(q1))
m2 = Chem.MolFromSmiles('OC(S)C')
self.assertTrue(m2.HasSubstructMatch(q1))
self.assertTrue(m2.GetSubstructMatch(q1) == (3, 1))
m3 = Chem.MolFromSmiles('SCC')
self.assertTrue(m3.HasSubstructMatch(q3))
self.assertFalse(m3.HasSubstructMatch(q1))
q1 = Chem.MolFromSmiles('CC')
Chem.AddRecursiveQuery(q1, q2, 1)
Chem.AddRecursiveQuery(q1, q3, 1, False)
self.assertTrue(m3.HasSubstructMatch(q1))
self.assertTrue(m3.GetSubstructMatch(q1) == (2, 1))
def test58Issue2983794(self):
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'Wrap', 'test_data',
'issue2983794.sdf')
m1 = Chem.MolFromMolFile(fileN)
self.assertTrue(m1)
em = Chem.EditableMol(m1)
em.RemoveAtom(0)
m2 = em.GetMol()
Chem.Kekulize(m2)
def test59Issue3007178(self):
m = Chem.MolFromSmiles('CCC')
a = m.GetAtomWithIdx(0)
m = None
self.assertEqual(Chem.MolToSmiles(a.GetOwningMol()), 'CCC')
a = None
m = Chem.MolFromSmiles('CCC')
b = m.GetBondWithIdx(0)
m = None
self.assertEqual(Chem.MolToSmiles(b.GetOwningMol()), 'CCC')
def test60SmilesWriterClose(self):
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'fewSmi.csv')
smiSup = Chem.SmilesMolSupplier(fileN, delimiter=",", smilesColumn=1, nameColumn=0, titleLine=0)
ms = [x for x in smiSup]
ofile = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'Wrap', 'test_data',
'outSmiles.txt')
writer = Chem.SmilesWriter(ofile)
for mol in ms:
writer.write(mol)
writer.close()
newsup = Chem.SmilesMolSupplier(ofile)
newms = [x for x in newsup]
self.assertEqual(len(ms), len(newms))
def test61PathToSubmol(self):
m = Chem.MolFromSmiles('CCCCCC1C(O)CC(O)N1C=CCO')
env = Chem.FindAtomEnvironmentOfRadiusN(m, 2, 11)
self.assertEqual(len(env), 8)
amap = {}
submol = Chem.PathToSubmol(m, env, atomMap=amap)
self.assertEqual(submol.GetNumAtoms(), len(amap.keys()))
self.assertEqual(submol.GetNumAtoms(), 9)
smi = Chem.MolToSmiles(submol, rootedAtAtom=amap[11])
self.assertEqual(smi[0], 'N')
refsmi = Chem.MolToSmiles(Chem.MolFromSmiles('N(C=C)(C(C)C)C(O)C'))
csmi = Chem.MolToSmiles(Chem.MolFromSmiles(smi))
self.assertEqual(refsmi, csmi)
def test62SmilesAndSmartsReplacements(self):
mol = Chem.MolFromSmiles('C{branch}C', replacements={'{branch}': 'C1(CC1)'})
self.assertEqual(mol.GetNumAtoms(), 5)
mol = Chem.MolFromSmarts('C{branch}C', replacements={'{branch}': 'C1(CC1)'})
self.assertEqual(mol.GetNumAtoms(), 5)
mol = Chem.MolFromSmiles('C{branch}C{acid}', replacements={
'{branch}': 'C1(CC1)',
'{acid}': "C(=O)O"
})
self.assertEqual(mol.GetNumAtoms(), 8)
def test63Issue3313539(self):
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'rgroups1.mol')
m = Chem.MolFromMolFile(fileN)
self.assertTrue(m is not None)
at = m.GetAtomWithIdx(3)
self.assertTrue(at is not None)
self.assertTrue(at.HasProp('_MolFileRLabel'))
p = at.GetProp('_MolFileRLabel')
self.assertEqual(p, '2')
self.assertEqual(Chem.GetAtomRLabel(at), 2)
at = m.GetAtomWithIdx(4)
self.assertTrue(at is not None)
self.assertTrue(at.HasProp('_MolFileRLabel'))
p = at.GetProp('_MolFileRLabel')
self.assertEqual(p, '1')
self.assertEqual(Chem.GetAtomRLabel(at), 1)
def test64MoleculeCleanup(self):
m = Chem.MolFromSmiles('CN(=O)=O', False)
self.assertTrue(m)
self.assertTrue(
m.GetAtomWithIdx(1).GetFormalCharge() == 0 and m.GetAtomWithIdx(2).GetFormalCharge() == 0
and m.GetAtomWithIdx(3).GetFormalCharge() == 0)
self.assertTrue(
m.GetBondBetweenAtoms(1, 3).GetBondType() == Chem.BondType.DOUBLE
and m.GetBondBetweenAtoms(1, 2).GetBondType() == Chem.BondType.DOUBLE)
Chem.Cleanup(m)
m.UpdatePropertyCache()
self.assertTrue(
m.GetAtomWithIdx(1).GetFormalCharge() == 1 and
(m.GetAtomWithIdx(2).GetFormalCharge() == -1 or m.GetAtomWithIdx(3).GetFormalCharge() == -1))
self.assertTrue(
m.GetBondBetweenAtoms(1, 3).GetBondType() == Chem.BondType.SINGLE
or m.GetBondBetweenAtoms(1, 2).GetBondType() == Chem.BondType.SINGLE)
def test65StreamSupplier(self):
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'NCI_aids_few.sdf.gz')
molNames = [
"48", "78", "128", "163", "164", "170", "180", "186", "192", "203", "210", "211", "213",
"220", "229", "256"
]
inf = gzip.open(fileN)
if 0:
sb = Chem.streambuf(inf)
suppl = Chem.ForwardSDMolSupplier(sb)
else:
suppl = Chem.ForwardSDMolSupplier(inf)
i = 0
while not suppl.atEnd():
mol = next(suppl)
self.assertTrue(mol)
self.assertTrue(mol.GetProp("_Name") == molNames[i])
i += 1
self.assertEqual(i, 16)
# make sure we have object ownership preserved
inf = gzip.open(fileN)
suppl = Chem.ForwardSDMolSupplier(inf)
inf = None
i = 0
while not suppl.atEnd():
mol = next(suppl)
self.assertTrue(mol)
self.assertTrue(mol.GetProp("_Name") == molNames[i])
i += 1
self.assertEqual(i, 16)
@unittest.skipIf(not hasattr(Chem, 'MaeMolSupplier'), "not build with MAEParser support")
def testMaeStreamSupplier(self):
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'NCI_aids_few.maegz')
molNames = [
"48", "78", "128", "163", "164", "170", "180", "186", "192", "203", "210", "211", "213",
"220", "229", "256"
]
inf = gzip.open(fileN)
suppl = Chem.MaeMolSupplier(inf)
i = 0
while not suppl.atEnd():
mol = next(suppl)
self.assertTrue(mol)
self.assertTrue(mol.GetProp("_Name") == molNames[i])
i += 1
self.assertEqual(i, 16)
# make sure we have object ownership preserved
inf = gzip.open(fileN)
suppl = Chem.MaeMolSupplier(inf)
inf = None
i = 0
while not suppl.atEnd():
mol = next(suppl)
self.assertTrue(mol)
self.assertTrue(mol.GetProp("_Name") == molNames[i])
i += 1
self.assertEqual(i, 16)
@unittest.skipIf(not hasattr(Chem, 'MaeMolSupplier'), "not build with MAEParser support")
def testMaeFileSupplier(self):
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'NCI_aids_few.mae')
molNames = [
"48", "78", "128", "163", "164", "170", "180", "186", "192", "203", "210", "211", "213",
"220", "229", "256"
]
suppl = Chem.MaeMolSupplier(fileN)
i = 0
while not suppl.atEnd():
mol = next(suppl)
self.assertTrue(mol)
self.assertTrue(mol.GetProp("_Name") == molNames[i])
i += 1
self.assertEqual(i, 16)
@unittest.skipIf(not hasattr(Chem, 'MaeMolSupplier'), "not build with MAEParser support")
def testMaeFileSupplierException(self):
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'bad_ppty.mae')
err_msg_substr = "Bad format for property"
ok = False
suppl = Chem.MaeMolSupplier(fileN)
for i in range(5):
try:
mol = next(suppl)
except RuntimeError as e:
self.assertEqual(i, 1)
self.assertTrue(err_msg_substr in str(e))
ok = True
break
else:
self.assertTrue(mol)
self.assertTrue(mol.HasProp("_Name"))
self.assertTrue(mol.GetNumAtoms() == 1)
self.assertFalse(suppl.atEnd())
self.assertTrue(ok)
def test66StreamSupplierIter(self):
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'NCI_aids_few.sdf.gz')
inf = gzip.open(fileN)
if 0:
sb = Chem.streambuf(inf)
suppl = Chem.ForwardSDMolSupplier(sb)
else:
suppl = Chem.ForwardSDMolSupplier(inf)
molNames = [
"48", "78", "128", "163", "164", "170", "180", "186", "192", "203", "210", "211", "213",
"220", "229", "256"
]
i = 0
for mol in suppl:
self.assertTrue(mol)
self.assertTrue(mol.GetProp("_Name") == molNames[i])
i += 1
self.assertEqual(i, 16)
def test67StreamSupplierStringIO(self):
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'NCI_aids_few.sdf.gz')
from io import BytesIO
sio = BytesIO(gzip.open(fileN).read())
suppl = Chem.ForwardSDMolSupplier(sio)
molNames = [
"48", "78", "128", "163", "164", "170", "180", "186", "192", "203", "210", "211", "213",
"220", "229", "256"
]
i = 0
for mol in suppl:
self.assertTrue(mol)
self.assertTrue(mol.GetProp("_Name") == molNames[i])
i += 1
self.assertEqual(i, 16)
def test68ForwardSupplierUsingFilename(self):
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'NCI_aids_few.sdf')
suppl = Chem.ForwardSDMolSupplier(fileN)
molNames = [
"48", "78", "128", "163", "164", "170", "180", "186", "192", "203", "210", "211", "213",
"220", "229", "256"
]
i = 0
for mol in suppl:
self.assertTrue(mol)
self.assertTrue(mol.GetProp("_Name") == molNames[i])
i += 1
self.assertEqual(i, 16)
self.assertRaises(IOError, lambda: Chem.ForwardSDMolSupplier('nosuchfile.sdf'))
def test69StreamSupplierStreambuf(self):
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'NCI_aids_few.sdf.gz')
sb = rdBase.streambuf(gzip.open(fileN))
suppl = Chem.ForwardSDMolSupplier(sb)
molNames = [
"48", "78", "128", "163", "164", "170", "180", "186", "192", "203", "210", "211", "213",
"220", "229", "256"
]
i = 0
for mol in suppl:
self.assertTrue(mol)
self.assertTrue(mol.GetProp("_Name") == molNames[i])
i += 1
self.assertEqual(i, 16)
def test70StreamSDWriter(self):
from io import BytesIO, StringIO
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'NCI_aids_few.sdf.gz')
inf = gzip.open(fileN)
suppl = Chem.ForwardSDMolSupplier(inf)
osio = StringIO()
w = Chem.SDWriter(osio)
molNames = [
"48", "78", "128", "163", "164", "170", "180", "186", "192", "203", "210", "211", "213",
"220", "229", "256"
]
i = 0
for mol in suppl:
self.assertTrue(mol)
self.assertTrue(mol.GetProp("_Name") == molNames[i])
w.write(mol)
i += 1
self.assertEqual(i, 16)
w.flush()
w = None
txt = osio.getvalue().encode()
isio = BytesIO(txt)
suppl = Chem.ForwardSDMolSupplier(isio)
i = 0
for mol in suppl:
self.assertTrue(mol)
self.assertTrue(mol.GetProp("_Name") == molNames[i])
i += 1
self.assertEqual(i, 16)
def test71StreamSmilesWriter(self):
from io import StringIO
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'esters.sdf')
suppl = Chem.ForwardSDMolSupplier(fileN)
osio = StringIO()
w = Chem.SmilesWriter(osio)
ms = [x for x in suppl]
w.SetProps(ms[0].GetPropNames())
i = 0
for mol in ms:
self.assertTrue(mol)
w.write(mol)
i += 1
self.assertEqual(i, 6)
w.flush()
w = None
txt = osio.getvalue()
self.assertEqual(txt.count('ID'), 1)
self.assertEqual(txt.count('\n'), 7)
def test72StreamTDTWriter(self):
from io import StringIO
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'esters.sdf')
suppl = Chem.ForwardSDMolSupplier(fileN)
osio = StringIO()
w = Chem.TDTWriter(osio)
ms = [x for x in suppl]
w.SetProps(ms[0].GetPropNames())
i = 0
for mol in ms:
self.assertTrue(mol)
w.write(mol)
i += 1
self.assertEqual(i, 6)
w.flush()
w = None
txt = osio.getvalue()
self.assertEqual(txt.count('ID'), 6)
self.assertEqual(txt.count('NAME'), 6)
def test73SanitizationOptions(self):
m = Chem.MolFromSmiles('c1ccccc1', sanitize=False)
res = Chem.SanitizeMol(m, catchErrors=True)
self.assertEqual(res, 0)
m = Chem.MolFromSmiles('c1cccc1', sanitize=False)
res = Chem.SanitizeMol(m, catchErrors=True)
self.assertEqual(res, Chem.SanitizeFlags.SANITIZE_KEKULIZE)
m = Chem.MolFromSmiles('CC(C)(C)(C)C', sanitize=False)
res = Chem.SanitizeMol(m, catchErrors=True)
self.assertEqual(res, Chem.SanitizeFlags.SANITIZE_PROPERTIES)
m = Chem.MolFromSmiles('c1cccc1', sanitize=False)
res = Chem.SanitizeMol(
m, sanitizeOps=Chem.SanitizeFlags.SANITIZE_ALL ^ Chem.SanitizeFlags.SANITIZE_KEKULIZE,
catchErrors=True)
self.assertEqual(res, Chem.SanitizeFlags.SANITIZE_NONE)
def test74Issue3510149(self):
mol = Chem.MolFromSmiles("CCC1CNCC1CC")
atoms = mol.GetAtoms()
mol = None
for atom in atoms:
idx = atom.GetIdx()
p = atom.GetOwningMol().GetNumAtoms()
mol = Chem.MolFromSmiles("CCC1CNCC1CC")
bonds = mol.GetBonds()
mol = None
for bond in bonds:
idx = bond.GetIdx()
p = atom.GetOwningMol().GetNumAtoms()
mol = Chem.MolFromSmiles("CCC1CNCC1CC")
bond = mol.GetBondBetweenAtoms(0, 1)
mol = None
idx = bond.GetBeginAtomIdx()
p = bond.GetOwningMol().GetNumAtoms()
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'NCI_aids_few.sdf')
sdSup = Chem.SDMolSupplier(fileN)
mol = next(sdSup)
nats = mol.GetNumAtoms()
conf = mol.GetConformer()
mol = None
self.assertEqual(nats, conf.GetNumAtoms())
conf.GetOwningMol().GetProp("_Name")
def test75AllBondsExplicit(self):
m = Chem.MolFromSmiles("CCC")
smi = Chem.MolToSmiles(m)
self.assertEqual(smi, "CCC")
smi = Chem.MolToSmiles(m, allBondsExplicit=True)
self.assertEqual(smi, "C-C-C")
m = Chem.MolFromSmiles("c1ccccc1")
smi = Chem.MolToSmiles(m)
self.assertEqual(smi, "c1ccccc1")
smi = Chem.MolToSmiles(m, allBondsExplicit=True)
self.assertEqual(smi, "c1:c:c:c:c:c:1")
def test76VeryLargeMolecule(self):
# this is sf.net issue 3524984
smi = '[C@H](F)(Cl)' + 'c1cc[nH]c1' * 500 + '[C@H](F)(Cl)'
m = Chem.MolFromSmiles(smi)
self.assertTrue(m)
self.assertEqual(m.GetNumAtoms(), 2506)
scs = Chem.FindMolChiralCenters(m)
self.assertEqual(len(scs), 2)
def test77MolFragmentToSmiles(self):
smi = "OC1CC1CC"
m = Chem.MolFromSmiles(smi)
fsmi = Chem.MolFragmentToSmiles(m, [1, 2, 3])
self.assertEqual(fsmi, "C1CC1")
fsmi = Chem.MolFragmentToSmiles(m, [1, 2, 3], bondsToUse=[1, 2, 5])
self.assertEqual(fsmi, "C1CC1")
fsmi = Chem.MolFragmentToSmiles(m, [1, 2, 3], bondsToUse=[1, 2])
self.assertEqual(fsmi, "CCC")
fsmi = Chem.MolFragmentToSmiles(m, [1, 2, 3], atomSymbols=["", "[A]", "[C]", "[B]", "", ""])
self.assertEqual(fsmi, "[A]1[B][C]1")
fsmi = Chem.MolFragmentToSmiles(m, [1, 2, 3], bondSymbols=["", "%", "%", "", "", "%"])
self.assertEqual(fsmi, "C1%C%C%1")
smi = "c1ccccc1C"
m = Chem.MolFromSmiles(smi)
fsmi = Chem.MolFragmentToSmiles(m, range(6))
self.assertEqual(fsmi, "c1ccccc1")
Chem.Kekulize(m)
fsmi = Chem.MolFragmentToSmiles(m, range(6), kekuleSmiles=True)
self.assertEqual(fsmi, "C1=CC=CC=C1")
fsmi = Chem.MolFragmentToSmiles(m, range(6), atomSymbols=["[C]"] * 7, kekuleSmiles=True)
self.assertEqual(fsmi, "[C]1=[C][C]=[C][C]=[C]1")
self.assertRaises(ValueError, lambda: Chem.MolFragmentToSmiles(m, []))
def test78AtomAndBondProps(self):
m = Chem.MolFromSmiles('c1ccccc1')
at = m.GetAtomWithIdx(0)
self.assertFalse(at.HasProp('foo'))
at.SetProp('foo', 'bar')
self.assertTrue(at.HasProp('foo'))
self.assertEqual(at.GetProp('foo'), 'bar')
bond = m.GetBondWithIdx(0)
self.assertFalse(bond.HasProp('foo'))
bond.SetProp('foo', 'bar')
self.assertTrue(bond.HasProp('foo'))
self.assertEqual(bond.GetProp('foo'), 'bar')
def test79AddRecursiveStructureQueries(self):
qs = {'carbonyl': Chem.MolFromSmiles('CO'), 'amine': Chem.MolFromSmiles('CN')}
q = Chem.MolFromSmiles('CCC')
q.GetAtomWithIdx(0).SetProp('query', 'carbonyl,amine')
Chem.MolAddRecursiveQueries(q, qs, 'query')
m = Chem.MolFromSmiles('CCCO')
self.assertTrue(m.HasSubstructMatch(q))
m = Chem.MolFromSmiles('CCCN')
self.assertTrue(m.HasSubstructMatch(q))
m = Chem.MolFromSmiles('CCCC')
self.assertFalse(m.HasSubstructMatch(q))
def test80ParseMolQueryDefFile(self):
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'ChemTransforms', 'testData',
'query_file1.txt')
d = Chem.ParseMolQueryDefFile(fileN, standardize=False)
self.assertTrue('CarboxylicAcid' in d)
m = Chem.MolFromSmiles('CC(=O)O')
self.assertTrue(m.HasSubstructMatch(d['CarboxylicAcid']))
self.assertFalse(m.HasSubstructMatch(d['CarboxylicAcid.Aromatic']))
d = Chem.ParseMolQueryDefFile(fileN)
self.assertTrue('carboxylicacid' in d)
self.assertFalse('CarboxylicAcid' in d)
def test81Issue275(self):
smi = Chem.MolToSmiles(Chem.MurckoDecompose(
Chem.MolFromSmiles('CCCCC[C@H]1CC[C@H](C(=O)O)CC1')))
self.assertEqual(smi, 'C1CCCCC1')
def test82Issue288(self):
m = Chem.MolFromSmiles('CC*')
m.GetAtomWithIdx(2).SetProp('molAtomMapNumber', '30')
smi = Chem.MolToSmiles(m)
self.assertEqual(smi, 'CC[*:30]')
# try newer api
m = Chem.MolFromSmiles('CC*')
m.GetAtomWithIdx(2).SetAtomMapNum(30)
smi = Chem.MolToSmiles(m)
self.assertEqual(smi, 'CC[*:30]')
def test83GitHubIssue19(self):
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'empty2.sdf')
with self.assertRaises(OSError):
sdSup = Chem.SDMolSupplier(fileN)
sdSup = Chem.SDMolSupplier()
sdSup.SetData('')
self.assertTrue(sdSup.atEnd())
self.assertRaises(IndexError, lambda: sdSup[0])
sdSup.SetData('')
self.assertRaises(IndexError, lambda: sdSup[0])
self.assertEqual(len(sdSup), 0)
def test84PDBBasics(self):
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'1CRN.pdb')
m = Chem.MolFromPDBFile(fileN, proximityBonding=False)
self.assertEqual(m.GetNumAtoms(), 327)
self.assertEqual(m.GetNumBonds(), 3)
m = Chem.MolFromPDBFile(fileN)
self.assertTrue(m is not None)
self.assertEqual(m.GetNumAtoms(), 327)
self.assertEqual(m.GetNumBonds(), 337)
self.assertTrue(m.GetAtomWithIdx(0).GetPDBResidueInfo())
self.assertEqual(m.GetAtomWithIdx(0).GetPDBResidueInfo().GetName(), " N ")
self.assertEqual(m.GetAtomWithIdx(0).GetPDBResidueInfo().GetResidueName(), "THR")
self.assertAlmostEqual(m.GetAtomWithIdx(0).GetPDBResidueInfo().GetTempFactor(), 13.79, 2)
m = Chem.MolFromPDBBlock(Chem.MolToPDBBlock(m))
self.assertEqual(m.GetNumAtoms(), 327)
self.assertEqual(m.GetNumBonds(), 337)
self.assertTrue(m.GetAtomWithIdx(0).GetPDBResidueInfo())
self.assertEqual(m.GetAtomWithIdx(0).GetPDBResidueInfo().GetName(), " N ")
self.assertEqual(m.GetAtomWithIdx(0).GetPDBResidueInfo().GetResidueName(), "THR")
self.assertAlmostEqual(m.GetAtomWithIdx(0).GetPDBResidueInfo().GetTempFactor(), 13.79, 2)
# test multivalent Hs
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'2c92_hypervalentH.pdb')
mol = Chem.MolFromPDBFile(fileN, sanitize=False, removeHs=False)
atom = mol.GetAtomWithIdx(84)
self.assertEqual(atom.GetAtomicNum(), 1) # is it H
self.assertEqual(atom.GetDegree(), 1) # H should have 1 bond
for n in atom.GetNeighbors(): # Check if neighbor is from the same residue
self.assertEqual(atom.GetPDBResidueInfo().GetResidueName(),
n.GetPDBResidueInfo().GetResidueName())
# test unbinding metals (ZN)
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'1ps3_zn.pdb')
mol = Chem.MolFromPDBFile(fileN, sanitize=False, removeHs=False)
atom = mol.GetAtomWithIdx(40)
self.assertEqual(atom.GetAtomicNum(), 30) # is it Zn
self.assertEqual(atom.GetDegree(), 4) # Zn should have 4 zero-order bonds
self.assertEqual(atom.GetExplicitValence(), 0)
bonds_order = [bond.GetBondType() for bond in atom.GetBonds()]
self.assertEqual(bonds_order, [Chem.BondType.ZERO] * atom.GetDegree())
# test metal bonds without proximity bonding
mol = Chem.MolFromPDBFile(fileN, sanitize=False, removeHs=False, proximityBonding=False)
atom = mol.GetAtomWithIdx(40)
self.assertEqual(atom.GetAtomicNum(), 30) # is it Zn
self.assertEqual(atom.GetDegree(), 4) # Zn should have 4 zero-order bonds
self.assertEqual(atom.GetExplicitValence(), 0)
bonds_order = [bond.GetBondType() for bond in atom.GetBonds()]
self.assertEqual(bonds_order, [Chem.BondType.ZERO] * atom.GetDegree())
# test unbinding HOHs
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'2vnf_bindedHOH.pdb')
mol = Chem.MolFromPDBFile(fileN, sanitize=False, removeHs=False)
atom = mol.GetAtomWithIdx(10)
self.assertEqual(atom.GetPDBResidueInfo().GetResidueName(), 'HOH')
self.assertEqual(atom.GetDegree(), 0) # HOH should have no bonds
# test metal bonding in ligand
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'2dej_APW.pdb')
mol = Chem.MolFromPDBFile(fileN, sanitize=False, removeHs=False)
atom = mol.GetAtomWithIdx(6)
self.assertEqual(atom.GetAtomicNum(), 12)
self.assertEqual(atom.GetDegree(), 2)
atom = mol.GetAtomWithIdx(35)
self.assertEqual(atom.GetPDBResidueInfo().GetResidueName(), 'HOH')
self.assertEqual(atom.GetDegree(), 0)
def test85AtomCopying(self):
"""Can a copied atom be added to a molecule?"""
import copy
m = Chem.MolFromSmiles('C1CC1')
a = m.GetAtomWithIdx(0)
a_copy1 = copy.copy(a)
a_copy2 = Chem.Atom(a)
m = None
a = None
def assert_is_valid_atom(a):
new_m = Chem.RWMol()
new_m.AddAtom(a)
# This will not match if the owning mol is unset for a_copy,
# or if there has been a clean up.
self.assertEqual(new_m.GetAtomWithIdx(0).GetIdx(), 0)
assert_is_valid_atom(a_copy1)
assert_is_valid_atom(a_copy2)
def test85MolCopying(self):
m = Chem.MolFromSmiles('C1CC1[C@H](F)Cl')
m.SetProp('foo', 'bar')
m2 = Chem.Mol(m)
self.assertEqual(Chem.MolToSmiles(m, True), Chem.MolToSmiles(m2, True))
self.assertTrue(m2.HasProp('foo'))
self.assertEqual(m2.GetProp('foo'), 'bar')
ri = m2.GetRingInfo()
self.assertTrue(ri)
self.assertEqual(ri.NumRings(), 1)
def test85MolCopying2(self):
import copy
m1 = Chem.MolFromSmiles('CC')
m1.SetProp('Foo', 'bar')
m1.foo = [1]
m2 = copy.copy(m1)
m3 = copy.copy(m2)
m4 = copy.deepcopy(m1)
m5 = copy.deepcopy(m2)
m6 = copy.deepcopy(m4)
self.assertEqual(m1.GetProp('Foo'), 'bar')
self.assertEqual(m2.GetProp('Foo'), 'bar')
self.assertEqual(m3.GetProp('Foo'), 'bar')
self.assertEqual(m4.GetProp('Foo'), 'bar')
self.assertEqual(m5.GetProp('Foo'), 'bar')
self.assertEqual(m6.GetProp('Foo'), 'bar')
m2.foo.append(4)
self.assertEqual(m1.foo, [1, 4])
self.assertEqual(m2.foo, [1, 4])
self.assertEqual(m3.foo, [1, 4])
self.assertEqual(m4.foo, [1])
self.assertEqual(m5.foo, [1])
self.assertEqual(m6.foo, [1])
m7 = Chem.RWMol(m1)
self.assertFalse(hasattr(m7, 'foo'))
m7.foo = [1]
m8 = copy.copy(m7)
m9 = copy.deepcopy(m7)
m8.foo.append(4)
self.assertEqual(m7.GetProp('Foo'), 'bar')
self.assertEqual(m8.GetProp('Foo'), 'bar')
self.assertEqual(m9.GetProp('Foo'), 'bar')
self.assertEqual(m8.foo, [1, 4])
self.assertEqual(m9.foo, [1])
def test86MolRenumbering(self):
import random
m = Chem.MolFromSmiles('C[C@H]1CC[C@H](C/C=C/[C@H](F)Cl)CC1')
cSmi = Chem.MolToSmiles(m, True)
for i in range(m.GetNumAtoms()):
ans = list(range(m.GetNumAtoms()))
random.shuffle(ans)
m2 = Chem.RenumberAtoms(m, ans)
nSmi = Chem.MolToSmiles(m2, True)
self.assertEqual(cSmi, nSmi)
def test87FragmentOnBonds(self):
m = Chem.MolFromSmiles('CC1CC(O)C1CCC1CC1')
bis = m.GetSubstructMatches(Chem.MolFromSmarts('[!R][R]'))
bs = []
labels = []
for bi in bis:
b = m.GetBondBetweenAtoms(bi[0], bi[1])
if b.GetBeginAtomIdx() == bi[0]:
labels.append((10, 1))
else:
labels.append((1, 10))
bs.append(b.GetIdx())
nm = Chem.FragmentOnBonds(m, bs)
frags = Chem.GetMolFrags(nm)
self.assertEqual(len(frags), 5)
self.assertEqual(frags,
((0, 12), (1, 2, 3, 5, 11, 14, 16), (4, 13), (6, 7, 15, 18), (8, 9, 10, 17)))
smi = Chem.MolToSmiles(nm, True)
self.assertEqual(smi, '*C1CC([4*])C1[6*].[1*]C.[3*]O.[5*]CC[8*].[7*]C1CC1')
nm = Chem.FragmentOnBonds(m, bs, dummyLabels=labels)
frags = Chem.GetMolFrags(nm)
self.assertEqual(len(frags), 5)
self.assertEqual(frags,
((0, 12), (1, 2, 3, 5, 11, 14, 16), (4, 13), (6, 7, 15, 18), (8, 9, 10, 17)))
smi = Chem.MolToSmiles(nm, True)
self.assertEqual(smi, '[1*]C.[1*]CC[1*].[1*]O.[10*]C1CC([10*])C1[10*].[10*]C1CC1')
m = Chem.MolFromSmiles('CCC(=O)CC(=O)C')
bis = m.GetSubstructMatches(Chem.MolFromSmarts('C=O'))
bs = []
for bi in bis:
b = m.GetBondBetweenAtoms(bi[0], bi[1])
bs.append(b.GetIdx())
bts = [Chem.BondType.DOUBLE] * len(bs)
nm = Chem.FragmentOnBonds(m, bs, bondTypes=bts)
frags = Chem.GetMolFrags(nm)
self.assertEqual(len(frags), 3)
smi = Chem.MolToSmiles(nm, True)
self.assertEqual(smi, '[2*]=O.[3*]=C(CC)CC(=[6*])C.[5*]=O')
# github issue 430:
m = Chem.MolFromSmiles('OCCCCN')
self.assertRaises(ValueError, lambda: Chem.FragmentOnBonds(m, ()))
def test88QueryAtoms(self):
from rdkit.Chem import rdqueries
m = Chem.MolFromSmiles('c1nc(C)n(CC)c1')
qa = rdqueries.ExplicitDegreeEqualsQueryAtom(3)
l = tuple([x.GetIdx() for x in m.GetAtomsMatchingQuery(qa)])
self.assertEqual(l, (2, 4))
qa.ExpandQuery(rdqueries.AtomNumEqualsQueryAtom(6, negate=True))
l = tuple([x.GetIdx() for x in m.GetAtomsMatchingQuery(qa)])
self.assertEqual(l, (4, ))
qa = rdqueries.ExplicitDegreeEqualsQueryAtom(3)
qa.ExpandQuery(rdqueries.AtomNumEqualsQueryAtom(6, negate=True),
how=Chem.CompositeQueryType.COMPOSITE_OR)
l = tuple([x.GetIdx() for x in m.GetAtomsMatchingQuery(qa)])
self.assertEqual(l, (1, 2, 4))
qa = rdqueries.ExplicitDegreeEqualsQueryAtom(3)
qa.ExpandQuery(rdqueries.AtomNumEqualsQueryAtom(6, negate=True),
how=Chem.CompositeQueryType.COMPOSITE_XOR)
l = tuple([x.GetIdx() for x in m.GetAtomsMatchingQuery(qa)])
self.assertEqual(l, (1, 2))
qa = rdqueries.ExplicitDegreeGreaterQueryAtom(2)
l = tuple([x.GetIdx() for x in m.GetAtomsMatchingQuery(qa)])
self.assertEqual(l, (2, 4))
qa = rdqueries.ExplicitDegreeLessQueryAtom(2)
l = tuple([x.GetIdx() for x in m.GetAtomsMatchingQuery(qa)])
self.assertEqual(l, (3, 6))
m = Chem.MolFromSmiles('N[CH][CH]')
qa = rdqueries.NumRadicalElectronsGreaterQueryAtom(0)
l = tuple([x.GetIdx() for x in m.GetAtomsMatchingQuery(qa)])
self.assertEqual(l, (1, 2))
qa = rdqueries.NumRadicalElectronsGreaterQueryAtom(1)
l = tuple([x.GetIdx() for x in m.GetAtomsMatchingQuery(qa)])
self.assertEqual(l, (2, ))
m = Chem.MolFromSmiles('F[C@H](Cl)C')
qa = rdqueries.HasChiralTagQueryAtom()
l = tuple([x.GetIdx() for x in m.GetAtomsMatchingQuery(qa)])
self.assertEqual(l, (1, ))
qa = rdqueries.MissingChiralTagQueryAtom()
l = tuple([x.GetIdx() for x in m.GetAtomsMatchingQuery(qa)])
self.assertEqual(l, ())
m = Chem.MolFromSmiles('F[CH](Cl)C')
qa = rdqueries.HasChiralTagQueryAtom()
l = tuple([x.GetIdx() for x in m.GetAtomsMatchingQuery(qa)])
self.assertEqual(l, ())
qa = rdqueries.MissingChiralTagQueryAtom()
l = tuple([x.GetIdx() for x in m.GetAtomsMatchingQuery(qa)])
self.assertEqual(l, (1, ))
m = Chem.MolFromSmiles('CNCON')
qa = rdqueries.NumHeteroatomNeighborsEqualsQueryAtom(2)
l = tuple([x.GetIdx() for x in m.GetAtomsMatchingQuery(qa)])
self.assertEqual(l, (2, ))
qa = rdqueries.NumHeteroatomNeighborsGreaterQueryAtom(0)
l = tuple([x.GetIdx() for x in m.GetAtomsMatchingQuery(qa)])
self.assertEqual(l, (0, 2, 3, 4))
def test89UnicodeInput(self):
m = Chem.MolFromSmiles(u'c1ccccc1')
self.assertTrue(m is not None)
self.assertEqual(m.GetNumAtoms(), 6)
m = Chem.MolFromSmarts(u'c1ccccc1')
self.assertTrue(m is not None)
self.assertEqual(m.GetNumAtoms(), 6)
def test90FragmentOnSomeBonds(self):
m = Chem.MolFromSmiles('OCCCCN')
pieces = Chem.FragmentOnSomeBonds(m, (0, 2, 4), 2)
self.assertEqual(len(pieces), 3)
frags = Chem.GetMolFrags(pieces[0])
self.assertEqual(len(frags), 3)
self.assertEqual(len(frags[0]), 2)
self.assertEqual(len(frags[1]), 4)
self.assertEqual(len(frags[2]), 4)
frags = Chem.GetMolFrags(pieces[1])
self.assertEqual(len(frags), 3)
self.assertEqual(len(frags[0]), 2)
self.assertEqual(len(frags[1]), 6)
self.assertEqual(len(frags[2]), 2)
frags = Chem.GetMolFrags(pieces[2])
self.assertEqual(len(frags), 3)
self.assertEqual(len(frags[0]), 4)
self.assertEqual(len(frags[1]), 4)
self.assertEqual(len(frags[2]), 2)
pieces, cpa = Chem.FragmentOnSomeBonds(m, (0, 2, 4), 2, returnCutsPerAtom=True)
self.assertEqual(len(pieces), 3)
self.assertEqual(len(cpa), 3)
self.assertEqual(len(cpa[0]), m.GetNumAtoms())
# github issue 430:
m = Chem.MolFromSmiles('OCCCCN')
self.assertRaises(ValueError, lambda: Chem.FragmentOnSomeBonds(m, ()))
pieces = Chem.FragmentOnSomeBonds(m, (0, 2, 4), 0)
self.assertEqual(len(pieces), 0)
def test91RankAtoms(self):
m = Chem.MolFromSmiles('ONCS.ONCS')
ranks = Chem.CanonicalRankAtoms(m, breakTies=False)
self.assertEqual(list(ranks[0:4]), list(ranks[4:]))
m = Chem.MolFromSmiles("c1ccccc1")
ranks = Chem.CanonicalRankAtoms(m, breakTies=False)
for x in ranks:
self.assertEqual(x, 0)
m = Chem.MolFromSmiles("C1NCN1")
ranks = Chem.CanonicalRankAtoms(m, breakTies=False)
self.assertEqual(ranks[0], ranks[2])
self.assertEqual(ranks[1], ranks[3])
def test92RankAtomsInFragment(self):
m = Chem.MolFromSmiles('ONCS.ONCS')
ranks = Chem.CanonicalRankAtomsInFragment(m, [0, 1, 2, 3], [0, 1, 2])
ranks2 = Chem.CanonicalRankAtomsInFragment(m, [4, 5, 6, 7], [3, 4, 5])
self.assertEqual(list(ranks[0:4]), list(ranks2[4:]))
self.assertEqual(list(ranks[4:]), [-1] * 4)
self.assertEqual(list(ranks2[0:4]), [-1] * 4)
# doc tests
mol = Chem.MolFromSmiles('C1NCN1.C1NCN1')
self.assertEqual(
list(Chem.CanonicalRankAtomsInFragment(mol, atomsToUse=range(0, 4), breakTies=False)),
[4, 6, 4, 6, -1, -1, -1, -1])
self.assertNotEqual(
list(Chem.CanonicalRankAtomsInFragment(mol, atomsToUse=range(0, 4), breakTies=True)),
[4, 6, 4, 6, -1, -1, -1, -1])
self.assertEqual(
list(Chem.CanonicalRankAtomsInFragment(mol, atomsToUse=range(4, 8), breakTies=False)),
[-1, -1, -1, -1, 4, 6, 4, 6])
self.assertNotEqual(
list(Chem.CanonicalRankAtomsInFragment(mol, atomsToUse=range(4, 8), breakTies=True)),
[-1, -1, -1, -1, 4, 6, 4, 6])
def test93RWMolsAsROMol(self):
""" test the RWMol class as a proper ROMol
"""
mol = Chem.MolFromSmiles('C1CCC1')
self.assertTrue(type(mol) == Chem.Mol)
rwmol = Chem.RWMol(mol)
self.assertEqual(Chem.MolToSmiles(rwmol, True), Chem.MolToSmiles(rwmol.GetMol()))
newAt = Chem.Atom(8)
rwmol.ReplaceAtom(0, newAt)
self.assertEqual(Chem.MolToSmiles(rwmol, True), Chem.MolToSmiles(rwmol.GetMol()))
def test94CopyWithConfs(self):
""" test copying Mols with some conformers
"""
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'cmpd2.tpl')
m1 = Chem.MolFromTPLFile(fileN)
self.assertTrue(m1 is not None)
self.assertEqual(m1.GetNumAtoms(), 12)
self.assertEqual(m1.GetNumConformers(), 2)
self.assertEqual(m1.GetConformer(0).GetNumAtoms(), 12)
self.assertEqual(m1.GetConformer(1).GetNumAtoms(), 12)
m2 = Chem.Mol(m1)
self.assertEqual(m2.GetNumAtoms(), 12)
self.assertEqual(m2.GetNumConformers(), 2)
self.assertEqual(m2.GetConformer(0).GetNumAtoms(), 12)
self.assertEqual(m2.GetConformer(1).GetNumAtoms(), 12)
m2 = Chem.Mol(m1, False, 0)
self.assertEqual(m2.GetNumAtoms(), 12)
self.assertEqual(m2.GetNumConformers(), 1)
self.assertEqual(m2.GetConformer(0).GetNumAtoms(), 12)
m2 = Chem.Mol(m1, False, 1)
self.assertEqual(m2.GetNumAtoms(), 12)
self.assertEqual(m2.GetNumConformers(), 1)
self.assertEqual(m2.GetConformer(1).GetNumAtoms(), 12)
m2 = Chem.Mol(m1, True)
self.assertTrue(m2.GetNumAtoms() == 12)
self.assertTrue(m2.GetNumConformers() == 0)
m2 = Chem.RWMol(m1)
self.assertEqual(m2.GetNumAtoms(), 12)
self.assertEqual(m2.GetNumConformers(), 2)
self.assertEqual(m2.GetConformer(0).GetNumAtoms(), 12)
self.assertEqual(m2.GetConformer(1).GetNumAtoms(), 12)
m2 = Chem.RWMol(m1, False, 0)
self.assertEqual(m2.GetNumAtoms(), 12)
self.assertEqual(m2.GetNumConformers(), 1)
self.assertEqual(m2.GetConformer(0).GetNumAtoms(), 12)
m2 = Chem.RWMol(m1, False, 1)
self.assertEqual(m2.GetNumAtoms(), 12)
self.assertEqual(m2.GetNumConformers(), 1)
self.assertEqual(m2.GetConformer(1).GetNumAtoms(), 12)
m2 = Chem.RWMol(m1, True)
self.assertTrue(m2.GetNumAtoms() == 12)
self.assertTrue(m2.GetNumConformers() == 0)
def testAtomPropQueries(self):
""" test the property queries
"""
from rdkit.Chem import rdqueries
m = Chem.MolFromSmiles("C" * 14)
atoms = m.GetAtoms()
atoms[0].SetProp("hah", "hah")
atoms[1].SetIntProp("bar", 1)
atoms[2].SetIntProp("bar", 2)
atoms[3].SetBoolProp("baz", True)
atoms[4].SetBoolProp("baz", False)
atoms[5].SetProp("boo", "hoo")
atoms[6].SetProp("boo", "-urns")
atoms[7].SetDoubleProp("boot", 1.0)
atoms[8].SetDoubleProp("boot", 4.0)
atoms[9].SetDoubleProp("number", 4.0)
atoms[10].SetIntProp("number", 4)
tests = ((rdqueries.HasIntPropWithValueQueryAtom, "bar", {
1: [1],
2: [2]
}), (rdqueries.HasBoolPropWithValueQueryAtom, "baz", {
True: [3],
False: [4]
}), (rdqueries.HasStringPropWithValueQueryAtom, "boo", {
"hoo": [5],
"-urns": [6]
}), (rdqueries.HasDoublePropWithValueQueryAtom, "boot", {
1.0: [7],
4.0: [8]
}))
for query, name, lookups in tests:
for t, v in lookups.items():
q = query(name, t)
self.assertEqual(v, [x.GetIdx() for x in m.GetAtomsMatchingQuery(q)])
q = query(name, t, negate=True)
self.assertEqual(sorted(set(range(14)) - set(v)),
[x.GetIdx() for x in m.GetAtomsMatchingQuery(q)])
# check tolerances
self.assertEqual([
x.GetIdx() for x in m.GetAtomsMatchingQuery(
rdqueries.HasDoublePropWithValueQueryAtom("boot", 1.0, tolerance=3.))
], [7, 8])
# numbers are numbers?, i.e. int!=double
self.assertEqual([
x.GetIdx()
for x in m.GetAtomsMatchingQuery(rdqueries.HasIntPropWithValueQueryAtom("number", 4))
], [10])
def testBondPropQueries(self):
""" test the property queries
"""
from rdkit.Chem import rdqueries
m = Chem.MolFromSmiles("C" * 14)
bonds = m.GetBonds()
bonds[0].SetProp("hah", "hah")
bonds[1].SetIntProp("bar", 1)
bonds[2].SetIntProp("bar", 2)
bonds[3].SetBoolProp("baz", True)
bonds[4].SetBoolProp("baz", False)
bonds[5].SetProp("boo", "hoo")
bonds[6].SetProp("boo", "-urns")
bonds[7].SetDoubleProp("boot", 1.0)
bonds[8].SetDoubleProp("boot", 4.0)
bonds[9].SetDoubleProp("number", 4.0)
bonds[10].SetIntProp("number", 4)
tests = ((rdqueries.HasIntPropWithValueQueryBond, "bar", {
1: [1],
2: [2]
}), (rdqueries.HasBoolPropWithValueQueryBond, "baz", {
True: [3],
False: [4]
}), (rdqueries.HasStringPropWithValueQueryBond, "boo", {
"hoo": [5],
"-urns": [6]
}), (rdqueries.HasDoublePropWithValueQueryBond, "boot", {
1.0: [7],
4.0: [8]
}))
for query, name, lookups in tests:
for t, v in lookups.items():
q = query(name, t)
self.assertEqual(v, [x.GetIdx() for x in m.GetBonds() if q.Match(x)])
q = query(name, t, negate=True)
self.assertEqual(sorted(set(range(13)) - set(v)),
[x.GetIdx() for x in m.GetBonds() if q.Match(x)])
# check tolerances
q = rdqueries.HasDoublePropWithValueQueryBond("boot", 1.0, tolerance=3.)
self.assertEqual([x.GetIdx() for x in m.GetBonds() if q.Match(x)], [7, 8])
# numbers are numbers?, i.e. int!=double
q = rdqueries.HasIntPropWithValueQueryBond("number", 4)
self.assertEqual([x.GetIdx() for x in m.GetBonds() if q.Match(x)], [10])
def testGetShortestPath(self):
""" test the GetShortestPath() wrapper
"""
smi = "CC(OC1C(CCCC3)C3C(CCCC2)C2C1OC(C)=O)=O"
m = Chem.MolFromSmiles(smi)
path = Chem.GetShortestPath(m, 1, 20)
self.assertEqual(path, (1, 2, 3, 16, 17, 18, 20))
def testGithub497(self):
with tempfile.TemporaryFile() as tmp, gzip.open(tmp) as outf:
with self.assertRaises(ValueError):
w = Chem.SDWriter(outf)
def testGithub498(self):
if (sys.version_info < (3, 0)):
mode = 'w+'
else:
mode = 'wt+'
m = Chem.MolFromSmiles('C')
with tempfile.NamedTemporaryFile() as tmp, gzip.open(tmp, mode) as outf:
w = Chem.SDWriter(outf)
w.write(m)
w.close()
def testReplaceBond(self):
origmol = Chem.RWMol(Chem.MolFromSmiles("CC"))
bonds = list(origmol.GetBonds())
self.assertEqual(len(bonds), 1)
singlebond = bonds[0]
self.assertEqual(singlebond.GetBondType(), Chem.BondType.SINGLE)
# this is the only way we create a bond, is take it from another molecule
doublebonded = Chem.MolFromSmiles("C=C")
doublebond = list(doublebonded.GetBonds())[0]
# make sure replacing the bond changes the smiles
self.assertEqual(Chem.MolToSmiles(origmol), "CC")
origmol.ReplaceBond(singlebond.GetIdx(), doublebond)
Chem.SanitizeMol(origmol)
self.assertEqual(Chem.MolToSmiles(origmol), "C=C")
def testAdjustQueryProperties(self):
m = Chem.MolFromSmarts('C1CCC1*')
am = Chem.AdjustQueryProperties(m)
self.assertTrue(Chem.MolFromSmiles('C1CCC1C').HasSubstructMatch(m))
self.assertTrue(Chem.MolFromSmiles('C1CCC1C').HasSubstructMatch(am))
self.assertTrue(Chem.MolFromSmiles('C1CC(C)C1C').HasSubstructMatch(m))
self.assertFalse(Chem.MolFromSmiles('C1CC(C)C1C').HasSubstructMatch(am))
m = Chem.MolFromSmiles('C1CCC1*')
am = Chem.AdjustQueryProperties(m)
self.assertFalse(Chem.MolFromSmiles('C1CCC1C').HasSubstructMatch(m))
self.assertTrue(Chem.MolFromSmiles('C1CCC1C').HasSubstructMatch(am))
qps = Chem.AdjustQueryParameters()
qps.makeDummiesQueries = False
am = Chem.AdjustQueryProperties(m, qps)
self.assertFalse(Chem.MolFromSmiles('C1CCC1C').HasSubstructMatch(am))
m = Chem.MolFromSmiles('C1=CC=CC=C1', sanitize=False)
am = Chem.AdjustQueryProperties(m)
self.assertTrue(Chem.MolFromSmiles('c1ccccc1').HasSubstructMatch(am))
qp = Chem.AdjustQueryParameters()
qp.aromatizeIfPossible = False
am = Chem.AdjustQueryProperties(m, qp)
self.assertFalse(Chem.MolFromSmiles('c1ccccc1').HasSubstructMatch(am))
m = Chem.MolFromSmiles('C1CCC1OC')
qps = Chem.AdjustQueryParameters()
qps.makeAtomsGeneric = True
am = Chem.AdjustQueryProperties(m, qps)
self.assertEqual(Chem.MolToSmarts(am), '*1-*-*-*-1-*-*')
qps.makeAtomsGenericFlags = Chem.ADJUST_IGNORERINGS
am = Chem.AdjustQueryProperties(m, qps)
self.assertEqual(Chem.MolToSmarts(am), '[#6&D2]1-[#6&D2]-[#6&D2]-[#6&D3]-1-*-*')
qps = Chem.AdjustQueryParameters()
qps.makeBondsGeneric = True
am = Chem.AdjustQueryProperties(m, qps)
self.assertEqual(Chem.MolToSmarts(am), '[#6&D2]1~[#6&D2]~[#6&D2]~[#6&D3]~1~[#8]~[#6]')
qps.makeBondsGenericFlags = Chem.ADJUST_IGNORERINGS
am = Chem.AdjustQueryProperties(m, qps)
self.assertEqual(Chem.MolToSmarts(am), '[#6&D2]1-[#6&D2]-[#6&D2]-[#6&D3]-1~[#8]~[#6]')
def testMolFragmentSmarts(self):
m = Chem.MolFromSmiles('C1CCC1OC')
self.assertEqual(Chem.MolFragmentToSmarts(m, [0, 1, 2]), '[#6]-[#6]-[#6]')
# if bondsToUse is honored, the ring won't show up
self.assertEqual(Chem.MolFragmentToSmarts(m, [0, 1, 2, 3], bondsToUse=[0, 1, 2, 3]),
'[#6]-[#6]-[#6]-[#6]')
# Does MolFragmentToSmarts accept output of AdjustQueryProperties?
qps = Chem.AdjustQueryParameters()
qps.makeAtomsGeneric = True
am = Chem.AdjustQueryProperties(m, qps)
self.assertEqual(Chem.MolFragmentToSmarts(am, [0, 1, 2]), '*-*-*')
def testAdjustQueryPropertiesgithubIssue1474(self):
core = Chem.MolFromSmiles('[*:1]C1N([*:2])C([*:3])O1')
core.GetAtomWithIdx(0).SetProp('foo', 'bar')
core.GetAtomWithIdx(1).SetProp('foo', 'bar')
ap = Chem.AdjustQueryProperties(core)
self.assertEqual(ap.GetAtomWithIdx(0).GetPropsAsDict()["foo"], "bar")
self.assertEqual(ap.GetAtomWithIdx(1).GetPropsAsDict()["foo"], "bar")
def testGithubIssue579(self):
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'NCI_aids_few.sdf.gz')
inf = gzip.open(fileN)
suppl = Chem.ForwardSDMolSupplier(inf)
m0 = next(suppl)
self.assertIsNot(m0, None)
inf.close()
del suppl
def testSequenceBasics(self):
" very basic round-tripping of the sequence reader/writer support "
helm = 'PEPTIDE1{C.Y.I.Q.N.C.P.L.G}$$$$'
seq = 'CYIQNCPLG'
fasta = '>\nCYIQNCPLG\n'
smi = 'CC[C@H](C)[C@H](NC(=O)[C@H](Cc1ccc(O)cc1)NC(=O)[C@@H](N)CS)C(=O)N[C@@H](CCC(N)=O)C(=O)N[C@@H](CC(N)=O)C(=O)N[C@@H](CS)C(=O)N1CCC[C@H]1C(=O)N[C@@H](CC(C)C)C(=O)NCC(=O)O'
m = Chem.MolFromSequence(seq)
self.assertTrue(m is not None)
self.assertEqual(Chem.MolToSequence(m), seq)
self.assertEqual(Chem.MolToHELM(m), helm)
self.assertEqual(Chem.MolToFASTA(m), fasta)
self.assertEqual(Chem.MolToSmiles(m, isomericSmiles=True), smi)
m = Chem.MolFromHELM(helm)
self.assertTrue(m is not None)
self.assertEqual(Chem.MolToSequence(m), seq)
self.assertEqual(Chem.MolToHELM(m), helm)
self.assertEqual(Chem.MolToFASTA(m), fasta)
self.assertEqual(Chem.MolToSmiles(m, isomericSmiles=True), smi)
m = Chem.MolFromFASTA(fasta)
self.assertTrue(m is not None)
self.assertEqual(Chem.MolToSequence(m), seq)
self.assertEqual(Chem.MolToHELM(m), helm)
self.assertEqual(Chem.MolToFASTA(m), fasta)
self.assertEqual(Chem.MolToSmiles(m, isomericSmiles=True), smi)
seq = "CGCGAATTACCGCG"
m = Chem.MolFromSequence(seq, flavor=6) # DNA
self.assertEqual(Chem.MolToSequence(m), 'CGCGAATTACCGCG')
self.assertEqual(
Chem.MolToHELM(m),
'RNA1{[dR](C)P.[dR](G)P.[dR](C)P.[dR](G)P.[dR](A)P.[dR](A)P.[dR](T)P.[dR](T)P.[dR](A)P.[dR](C)P.[dR](C)P.[dR](G)P.[dR](C)P.[dR](G)}$$$$'
)
seq = "CGCGAAUUACCGCG"
m = Chem.MolFromSequence(seq, flavor=2) # RNA
self.assertEqual(Chem.MolToSequence(m), 'CGCGAAUUACCGCG')
self.assertEqual(
Chem.MolToHELM(m),
'RNA1{R(C)P.R(G)P.R(C)P.R(G)P.R(A)P.R(A)P.R(U)P.R(U)P.R(A)P.R(C)P.R(C)P.R(G)P.R(C)P.R(G)}$$$$'
)
m = Chem.MolFromSequence(seq, flavor=3) # RNA - 5' cap
self.assertEqual(Chem.MolToSequence(m), 'CGCGAAUUACCGCG')
self.assertEqual(
Chem.MolToHELM(m),
'RNA1{P.R(C)P.R(G)P.R(C)P.R(G)P.R(A)P.R(A)P.R(U)P.R(U)P.R(A)P.R(C)P.R(C)P.R(G)P.R(C)P.R(G)}$$$$'
)
def testResMolSupplier(self):
mol = Chem.MolFromSmiles('CC')
resMolSuppl = Chem.ResonanceMolSupplier(mol)
del resMolSuppl
resMolSuppl = Chem.ResonanceMolSupplier(mol)
self.assertEqual(resMolSuppl.GetNumConjGrps(), 0)
self.assertEqual(len(resMolSuppl), 1)
self.assertEqual(resMolSuppl.GetNumConjGrps(), 0)
mol = Chem.MolFromSmiles('NC(=[NH2+])c1ccc(cc1)C(=O)[O-]')
totalFormalCharge = getTotalFormalCharge(mol)
resMolSuppl = Chem.ResonanceMolSupplier(mol)
self.assertFalse(resMolSuppl.GetIsEnumerated())
self.assertEqual(len(resMolSuppl), 4)
self.assertTrue(resMolSuppl.GetIsEnumerated())
resMolSuppl = Chem.ResonanceMolSupplier(mol)
self.assertFalse(resMolSuppl.GetIsEnumerated())
resMolSuppl.Enumerate()
self.assertTrue(resMolSuppl.GetIsEnumerated())
self.assertTrue(
(resMolSuppl[0].GetBondBetweenAtoms(0, 1).GetBondType() != resMolSuppl[1].GetBondBetweenAtoms(
0, 1).GetBondType()) or (resMolSuppl[0].GetBondBetweenAtoms(9, 10).GetBondType() !=
resMolSuppl[1].GetBondBetweenAtoms(9, 10).GetBondType()))
resMolSuppl = Chem.ResonanceMolSupplier(mol, Chem.KEKULE_ALL)
self.assertEqual(len(resMolSuppl), 8)
bondTypeSet = set()
# check that we actually have two alternate Kekule structures
bondTypeSet.add(resMolSuppl[0].GetBondBetweenAtoms(3, 4).GetBondType())
bondTypeSet.add(resMolSuppl[1].GetBondBetweenAtoms(3, 4).GetBondType())
self.assertEqual(len(bondTypeSet), 2)
bondTypeDict = {}
resMolSuppl = Chem.ResonanceMolSupplier(
mol, Chem.ALLOW_INCOMPLETE_OCTETS
| Chem.UNCONSTRAINED_CATIONS
| Chem.UNCONSTRAINED_ANIONS)
self.assertEqual(len(resMolSuppl), 32)
for i in range(len(resMolSuppl)):
resMol = resMolSuppl[i]
self.assertEqual(getTotalFormalCharge(resMol), totalFormalCharge)
while (not resMolSuppl.atEnd()):
resMol = next(resMolSuppl)
self.assertEqual(getTotalFormalCharge(resMol), totalFormalCharge)
resMolSuppl.reset()
cmpFormalChargeBondOrder(self, resMolSuppl[0], next(resMolSuppl))
resMolSuppl = Chem.ResonanceMolSupplier(
mol, Chem.ALLOW_INCOMPLETE_OCTETS
| Chem.UNCONSTRAINED_CATIONS
| Chem.UNCONSTRAINED_ANIONS, 10)
self.assertEqual(len(resMolSuppl), 10)
crambinPdb = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'1CRN.pdb')
mol = Chem.MolFromPDBFile(crambinPdb)
resMolSuppl = Chem.ResonanceMolSupplier(mol)
self.assertEqual(len(resMolSuppl), 1)
resMolSuppl = Chem.ResonanceMolSupplier(mol, Chem.KEKULE_ALL)
self.assertEqual(len(resMolSuppl), 8)
def testSubstructMatchAcetate(self):
mol = Chem.MolFromSmiles('CC(=O)[O-]')
query = Chem.MolFromSmarts('C(=O)[O-]')
resMolSuppl = Chem.ResonanceMolSupplier(mol)
matches = mol.GetSubstructMatches(query)
self.assertEqual(len(matches), 1)
self.assertEqual(matches, ((1, 2, 3), ))
matches = mol.GetSubstructMatches(query, uniquify=True)
self.assertEqual(len(matches), 1)
self.assertEqual(matches, ((1, 2, 3), ))
matches = mol.GetSubstructMatches(query, uniquify=False)
self.assertEqual(len(matches), 1)
self.assertEqual(matches, ((1, 2, 3), ))
matches = resMolSuppl.GetSubstructMatches(query)
self.assertEqual(len(matches), 2)
self.assertEqual(matches, ((1, 2, 3), (1, 3, 2)))
matches = resMolSuppl.GetSubstructMatches(query, uniquify=True)
self.assertEqual(len(matches), 1)
self.assertEqual(matches, ((1, 2, 3), ))
matches = resMolSuppl.GetSubstructMatches(query, uniquify=False)
self.assertEqual(len(matches), 2)
self.assertEqual(matches, ((1, 2, 3), (1, 3, 2)))
query = Chem.MolFromSmarts('C(~O)~O')
matches = mol.GetSubstructMatches(query, uniquify=False)
self.assertEqual(len(matches), 2)
self.assertEqual(matches, ((1, 2, 3), (1, 3, 2)))
matches = mol.GetSubstructMatches(query, uniquify=True)
self.assertEqual(len(matches), 1)
self.assertEqual(matches, ((1, 2, 3), ))
matches = resMolSuppl.GetSubstructMatches(query, uniquify=False)
self.assertEqual(len(matches), 2)
self.assertEqual(matches, ((1, 2, 3), (1, 3, 2)))
matches = resMolSuppl.GetSubstructMatches(query, uniquify=True)
self.assertEqual(len(matches), 1)
self.assertEqual(matches, ((1, 2, 3), ))
def testSubstructMatchDMAP(self):
mol = Chem.MolFromSmiles('C(C)Nc1cc[nH+]cc1')
query = Chem.MolFromSmarts('[#7+]')
resMolSuppl = Chem.ResonanceMolSupplier(mol)
matches = mol.GetSubstructMatches(query, False, False, False)
self.assertEqual(len(matches), 1)
p = matches[0]
self.assertEqual(p[0], 6)
matches = resMolSuppl.GetSubstructMatches(query, False, False, False)
self.assertEqual(len(matches), 2)
v = []
p = matches[0]
v.append(p[0])
p = matches[1]
v.append(p[0])
v.sort()
self.assertEqual(v[0], 2)
self.assertEqual(v[1], 6)
def testCrambin(self):
crambinPdb = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'1CRN.pdb')
crambin = Chem.MolFromPDBFile(crambinPdb)
res = []
# protonate NH2
res.append(Chem.MolFromSmarts('[Nh2][Ch;Ch2]'))
# protonate Arg
res.append(Chem.MolFromSmarts('[Nh][C]([Nh2])=[Nh]'))
setResidueFormalCharge(crambin, res, 1)
res = []
# deprotonate COOH
res.append(Chem.MolFromSmarts('C(=O)[Oh]'))
setResidueFormalCharge(crambin, res, -1)
res = []
resMolSupplST = Chem.ResonanceMolSupplier(crambin)
# crambin has 2 Arg (3 resonance structures each); 1 Asp, 1 Glu
# and 1 terminal COO- (2 resonance structures each)
# so possible resonance structures are 3^2 * 2^3 = 72
self.assertEqual(len(resMolSupplST), 72)
self.assertEqual(resMolSupplST.GetNumConjGrps(), 56)
carboxylateQuery = Chem.MolFromSmarts('C(=O)[O-]')
guanidiniumQuery = Chem.MolFromSmarts('NC(=[NH2+])N')
matches = crambin.GetSubstructMatches(carboxylateQuery)
self.assertEqual(len(matches), 3)
matches = crambin.GetSubstructMatches(carboxylateQuery, uniquify=False)
self.assertEqual(len(matches), 3)
matches = crambin.GetSubstructMatches(guanidiniumQuery)
self.assertEqual(len(matches), 0)
matches = crambin.GetSubstructMatches(guanidiniumQuery, uniquify=False)
self.assertEqual(len(matches), 0)
matches = resMolSupplST.GetSubstructMatches(carboxylateQuery)
self.assertEqual(len(matches), 6)
self.assertEqual(matches, ((166, 167, 168), (166, 168, 167), (298, 299, 300), (298, 300, 299),
(320, 321, 326), (320, 326, 321)))
matches = resMolSupplST.GetSubstructMatches(carboxylateQuery, uniquify=True)
self.assertEqual(len(matches), 3)
self.assertEqual(matches, ((166, 167, 168), (298, 299, 300), (320, 321, 326)))
matches = resMolSupplST.GetSubstructMatches(guanidiniumQuery)
self.assertEqual(len(matches), 8)
self.assertEqual(matches, ((66, 67, 68, 69), (66, 67, 69, 68), (68, 67, 69, 66),
(69, 67, 68, 66), (123, 124, 125, 126), (123, 124, 126, 125),
(125, 124, 126, 123), (126, 124, 125, 123)))
matches = resMolSupplST.GetSubstructMatches(guanidiniumQuery, uniquify=True)
self.assertEqual(len(matches), 2)
self.assertEqual(matches, ((66, 67, 68, 69), (123, 124, 125, 126)))
btList2ST = getBtList2(resMolSupplST)
self.assertTrue(btList2ST)
resMolSupplMT = Chem.ResonanceMolSupplier(crambin)
resMolSupplMT.SetNumThreads(0)
self.assertEqual(len(resMolSupplST), len(resMolSupplMT))
btList2MT = getBtList2(resMolSupplMT)
self.assertTrue(btList2MT)
self.assertEqual(len(btList2ST), len(btList2MT))
for i in range(len(btList2ST)):
for j in range(len(btList2ST)):
self.assertEqual(btList2ST[i][j], btList2MT[i][j])
for suppl in [resMolSupplST, resMolSupplMT]:
matches = suppl.GetSubstructMatches(carboxylateQuery, numThreads=0)
self.assertEqual(len(matches), 6)
self.assertEqual(matches, ((166, 167, 168), (166, 168, 167), (298, 299, 300), (298, 300, 299),
(320, 321, 326), (320, 326, 321)))
matches = suppl.GetSubstructMatches(carboxylateQuery, uniquify=True, numThreads=0)
self.assertEqual(len(matches), 3)
self.assertEqual(matches, ((166, 167, 168), (298, 299, 300), (320, 321, 326)))
matches = suppl.GetSubstructMatches(guanidiniumQuery, numThreads=0)
self.assertEqual(len(matches), 8)
self.assertEqual(matches, ((66, 67, 68, 69), (66, 67, 69, 68), (68, 67, 69, 66),
(69, 67, 68, 66), (123, 124, 125, 126), (123, 124, 126, 125),
(125, 124, 126, 123), (126, 124, 125, 123)))
matches = suppl.GetSubstructMatches(guanidiniumQuery, uniquify=True, numThreads=0)
self.assertEqual(len(matches), 2)
self.assertEqual(matches, ((66, 67, 68, 69), (123, 124, 125, 126)))
def testGitHub1166(self):
mol = Chem.MolFromSmiles('NC(=[NH2+])c1ccc(cc1)C(=O)[O-]')
resMolSuppl = Chem.ResonanceMolSupplier(mol, Chem.KEKULE_ALL)
self.assertEqual(len(resMolSuppl), 8)
# check that formal charges on odd indices are in the same position
# as on even indices
for i in range(0, len(resMolSuppl), 2):
self.assertEqual(resMolSuppl[i].GetNumAtoms(), resMolSuppl[i + 1].GetNumAtoms())
for atomIdx in range(resMolSuppl[i].GetNumAtoms()):
self.assertEqual(resMolSuppl[i].GetAtomWithIdx(atomIdx).GetFormalCharge(),
resMolSuppl[i + 1].GetAtomWithIdx(atomIdx).GetFormalCharge())
# check that bond orders are alternate on aromatic bonds between
# structures on odd indices and structures on even indices
self.assertEqual(resMolSuppl[i].GetNumBonds(), resMolSuppl[i + 1].GetNumBonds())
for bondIdx in range(resMolSuppl[i].GetNumBonds()):
self.assertTrue(
((not resMolSuppl[i].GetBondWithIdx(bondIdx).GetIsAromatic()) and
(not resMolSuppl[i + 1].GetBondWithIdx(bondIdx).GetIsAromatic()) and
(resMolSuppl[i].GetBondWithIdx(bondIdx).GetBondType()
== resMolSuppl[i + 1].GetBondWithIdx(bondIdx).GetBondType()))
or (resMolSuppl[i].GetBondWithIdx(bondIdx).GetIsAromatic()
and resMolSuppl[i + 1].GetBondWithIdx(bondIdx).GetIsAromatic() and (int(
round(resMolSuppl[i].GetBondWithIdx(bondIdx).GetBondTypeAsDouble() +
resMolSuppl[i + 1].GetBondWithIdx(bondIdx).GetBondTypeAsDouble())) == 3)))
def testConjGrpPerception(self):
mol1 = Chem.MolFromMolBlock("""\
RDKit 2D
14 15 0 0 0 0 0 0 0 0999 V2000
3.7539 -1.2744 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.4317 -0.5660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.1571 -1.3568 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.1651 -0.6484 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.4397 -1.4393 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.3921 -2.9385 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
-2.7619 -0.7309 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.8095 0.7684 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.1316 1.4768 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
-1.5349 1.5592 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.2127 0.8508 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.0619 1.6417 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
2.3841 0.9333 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.6587 1.7241 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 4 0
3 4 4 0
4 5 4 0
5 6 1 0
5 7 4 0
7 8 4 0
8 9 1 0
8 10 4 0
10 11 4 0
11 12 4 0
12 13 4 0
13 14 1 0
13 2 4 0
11 4 4 0
M END
$$$$
""")
mol2 = Chem.MolFromMolBlock("""\
RDKit 2D
14 15 0 0 0 0 0 0 0 0999 V2000
1.0619 -1.6417 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-0.2127 -0.8508 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.5349 -1.5592 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.8095 -0.7684 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.7619 0.7309 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.4397 1.4393 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.1651 0.6484 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.1571 1.3568 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.4317 0.5660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.7539 1.2744 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.3841 -0.9333 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.6587 -1.7241 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.1316 -1.4768 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
-1.3921 2.9385 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
1 2 4 0
3 4 4 0
4 5 4 0
5 6 4 0
2 3 4 0
2 7 4 0
7 8 4 0
8 9 4 0
9 10 1 0
9 11 4 0
11 12 1 0
11 1 4 0
6 7 4 0
4 13 1 0
6 14 1 0
M END
$$$$
""")
resMolSuppl1 = Chem.ResonanceMolSupplier(mol1, Chem.KEKULE_ALL)
self.assertEqual(len(resMolSuppl1), 3)
resMolSuppl2 = Chem.ResonanceMolSupplier(mol2, Chem.KEKULE_ALL)
self.assertEqual(len(resMolSuppl2), 3)
def testGitHub2597(self):
class MyBrokenCallBack(Chem.ResonanceMolSupplier):
def __call__(self):
return True
class MyBrokenCallBack2(Chem.ResonanceMolSupplierCallback):
pass
class ExceedNumStructures(Chem.ResonanceMolSupplierCallback):
def __init__(self, parent):
super().__init__()
self._parent = parent
def __call__(self):
self._parent.assertEqual(self.GetNumConjGrps(), 1)
return (self.GetNumStructures(0) < 12)
class ExceedNumDiverseStructures(Chem.ResonanceMolSupplierCallback):
def __init__(self, parent):
super().__init__()
self._parent = parent
def __call__(self):
self._parent.assertEqual(self.GetNumConjGrps(), 1)
return (self.GetNumDiverseStructures(0) < 8)
class ExceedTimeout(Chem.ResonanceMolSupplierCallback):
def __init__(self, parent):
super().__init__()
self.start_time = None
self.timeout = timedelta(seconds=3)
self._parent = parent
def __call__(self):
if (self.start_time is None):
self.start_time = datetime.now()
return (datetime.now() - self.start_time < self.timeout)
mol = Chem.MolFromSmiles(
"ClC1=NC(NC2=CC=CC3=C2C(=O)C2=CC=CC=C2C3=O)=NC(NC2=CC=CC3=C2C(=O)C2=CC=CC=C2C3=O)=N1")
resMolSuppl = Chem.ResonanceMolSupplier(mol)
self.assertEqual(len(resMolSuppl), 1)
resMolSuppl = Chem.ResonanceMolSupplier(mol, Chem.KEKULE_ALL)
self.assertEqual(len(resMolSuppl), 32)
resMolSuppl = Chem.ResonanceMolSupplier(mol, Chem.ALLOW_CHARGE_SEPARATION, 10)
self.assertEqual(len(resMolSuppl), 10)
self.assertFalse(resMolSuppl.WasCanceled())
resMolSuppl = Chem.ResonanceMolSupplier(mol, Chem.ALLOW_CHARGE_SEPARATION)
callback = resMolSuppl.GetProgressCallback()
self.assertIsNone(callback)
resMolSuppl.SetProgressCallback(ExceedNumStructures(self))
callback = resMolSuppl.GetProgressCallback()
self.assertTrue(isinstance(callback, ExceedNumStructures))
resMolSuppl.SetProgressCallback(None)
callback = resMolSuppl.GetProgressCallback()
self.assertIsNone(callback)
resMolSuppl.SetProgressCallback(ExceedNumStructures(self))
self.assertEqual(len(resMolSuppl), 12)
self.assertTrue(resMolSuppl.WasCanceled())
resMolSuppl = Chem.ResonanceMolSupplier(mol, Chem.ALLOW_CHARGE_SEPARATION)
with self.assertRaises(TypeError):
resMolSuppl.SetProgressCallback(MyBrokenCallBack())
with self.assertRaises(AttributeError):
resMolSuppl.SetProgressCallback(MyBrokenCallBack2())
resMolSuppl.SetProgressCallback(ExceedNumDiverseStructures(self))
self.assertEqual(len(resMolSuppl), 9)
self.assertTrue(resMolSuppl.WasCanceled())
resMolSuppl = Chem.ResonanceMolSupplier(
mol, Chem.UNCONSTRAINED_CATIONS | Chem.UNCONSTRAINED_ANIONS | Chem.KEKULE_ALL)
resMolSuppl.SetProgressCallback(ExceedTimeout(self))
resMolSuppl.Enumerate()
print(len(resMolSuppl))
self.assertTrue(resMolSuppl.WasCanceled())
def testAtomBondProps(self):
m = Chem.MolFromSmiles('c1ccccc1')
for atom in m.GetAtoms():
d = atom.GetPropsAsDict()
self.assertEqual(set(d.keys()), set(['_CIPRank', '__computedProps']))
self.assertEqual(d['_CIPRank'], 0)
self.assertEqual(list(d['__computedProps']), ['_CIPRank'])
for bond in m.GetBonds():
self.assertEqual(bond.GetPropsAsDict(), {})
def testSDProps(self):
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'NCI_aids_few.sdf')
#fileN = "../FileParsers/test_data/NCI_aids_few.sdf"
sddata = [
{
'_MolFileInfo': 'BBtclserve11129916382D 0 0.00000 0.00000 48',
'NSC': 48,
'NCI_AIDS_Antiviral_Screen_IC50': '2.00E-04\tM\t=\t2.46E-05\t3',
'_Name': 48,
'CAS_RN': '15716-70-8',
'_MolFileComments': '15716-70-8',
'NCI_AIDS_Antiviral_Screen_EC50': '2.00E-04\tM\t>\t2.00E-04\t3',
'NCI_AIDS_Antiviral_Screen_Conclusion': 'CI'
},
{
'_MolFileInfo': 'BBtclserve11129916382D 0 0.00000 0.00000 78',
'NSC': 78,
'NCI_AIDS_Antiviral_Screen_IC50': '2.00E-04\tM\t=\t9.80E-05\t3',
'_Name': 78,
'CAS_RN': '6290-84-2',
'_MolFileComments': '6290-84-2',
'NCI_AIDS_Antiviral_Screen_EC50': '2.00E-04\tM\t>\t2.00E-04\t3',
'NCI_AIDS_Antiviral_Screen_Conclusion': 'CI'
},
{
'_MolFileInfo': 'BBtclserve11129916382D 0 0.00000 0.00000 128',
'NSC': 128,
'NCI_AIDS_Antiviral_Screen_IC50': '2.00E-04\tM\t=\t4.60E-05\t4',
'_Name': 128,
'CAS_RN': '5395-10-8',
'_MolFileComments': '5395-10-8',
'NCI_AIDS_Antiviral_Screen_EC50': '2.00E-04\tM\t>\t2.00E-04\t4',
'NCI_AIDS_Antiviral_Screen_Conclusion': 'CI'
},
{
'_MolFileInfo': 'BBtclserve11129916382D 0 0.00000 0.00000 163',
'NSC': 163,
'NCI_AIDS_Antiviral_Screen_IC50': '6.75E-04\tM\t>\t6.75E-04\t2',
'_Name': 163,
'CAS_RN': '81-11-8',
'_MolFileComments': '81-11-8',
'NCI_AIDS_Antiviral_Screen_EC50': '6.75E-04\tM\t>\t6.75E-04\t2',
'NCI_AIDS_Antiviral_Screen_Conclusion': 'CI'
},
{
'_MolFileInfo': 'BBtclserve11129916382D 0 0.00000 0.00000 164',
'NSC': 164,
'NCI_AIDS_Antiviral_Screen_IC50': '2.00E-04\tM\t>\t2.00E-04\t2',
'_Name': 164,
'CAS_RN': '5325-43-9',
'_MolFileComments': '5325-43-9',
'NCI_AIDS_Antiviral_Screen_EC50': '2.00E-04\tM\t>\t2.00E-04\t2',
'NCI_AIDS_Antiviral_Screen_Conclusion': 'CI'
},
{
'_MolFileInfo': 'BBtclserve11129916382D 0 0.00000 0.00000 170',
'NSC': 170,
'_Name': 170,
'CAS_RN': '999-99-9',
'_MolFileComments': '999-99-9',
'NCI_AIDS_Antiviral_Screen_EC50': '9.47E-04\tM\t>\t9.47E-04\t1',
'NCI_AIDS_Antiviral_Screen_Conclusion': 'CI'
},
{
'_MolFileInfo': 'BBtclserve11129916382D 0 0.00000 0.00000 180',
'NSC': 180,
'NCI_AIDS_Antiviral_Screen_IC50':
'6.46E-04\tM\t=\t5.80E-04\t2\n1.81E-03\tM\t=\t6.90E-04\t2',
'_Name': 180,
'CAS_RN': '69-72-7',
'_MolFileComments': '69-72-7',
'NCI_AIDS_Antiviral_Screen_EC50':
'6.46E-04\tM\t>\t6.46E-04\t2\n1.81E-03\tM\t>\t1.81E-03\t2',
'NCI_AIDS_Antiviral_Screen_Conclusion': 'CI'
},
{
'_MolFileInfo': 'BBtclserve11129916382D 0 0.00000 0.00000 186',
'NSC': 186,
'NCI_AIDS_Antiviral_Screen_IC50': '1.44E-04\tM\t=\t2.49E-05\t2',
'_Name': 186,
'CAS_RN': '518-75-2',
'_MolFileComments': '518-75-2',
'NCI_AIDS_Antiviral_Screen_EC50': '1.44E-04\tM\t>\t1.44E-04\t2',
'NCI_AIDS_Antiviral_Screen_Conclusion': 'CI'
},
{
'_MolFileInfo': 'BBtclserve11129916382D 0 0.00000 0.00000 192',
'NSC': 192,
'NCI_AIDS_Antiviral_Screen_IC50': '2.00E-04\tM\t=\t3.38E-06\t2',
'_Name': 192,
'CAS_RN': '2217-55-2',
'_MolFileComments': '2217-55-2',
'NCI_AIDS_Antiviral_Screen_EC50': '2.00E-04\tM\t>\t2.00E-04\t2',
'NCI_AIDS_Antiviral_Screen_Conclusion': 'CI'
},
{
'_MolFileInfo': 'BBtclserve11129916382D 0 0.00000 0.00000 203',
'NSC': 203,
'_Name': 203,
'CAS_RN': '1155-00-6',
'_MolFileComments': '1155-00-6',
'NCI_AIDS_Antiviral_Screen_Conclusion': 'CI'
},
{
'_MolFileInfo': 'BBtclserve11129916382D 0 0.00000 0.00000 210',
'NSC': 210,
'NCI_AIDS_Antiviral_Screen_IC50': '1.33E-03\tM\t>\t1.33E-03\t2',
'_Name': 210,
'CAS_RN': '5325-75-7',
'_MolFileComments': '5325-75-7',
'NCI_AIDS_Antiviral_Screen_EC50': '1.33E-03\tM\t>\t1.33E-03\t2',
'NCI_AIDS_Antiviral_Screen_Conclusion': 'CI'
},
{
'_MolFileInfo': 'BBtclserve11129916382D 0 0.00000 0.00000 211',
'NSC': 211,
'NCI_AIDS_Antiviral_Screen_IC50':
'2.00E-04\tM\t>\t2.00E-04\t8\n2.00E-03\tM\t=\t1.12E-03\t2',
'_Name': 211,
'CAS_RN': '5325-76-8',
'_MolFileComments': '5325-76-8',
'NCI_AIDS_Antiviral_Screen_EC50':
'2.00E-04\tM\t>\t7.42E-05\t8\n2.00E-03\tM\t=\t6.35E-05\t2',
'NCI_AIDS_Antiviral_Screen_Conclusion': 'CM'
},
{
'_MolFileInfo': 'BBtclserve11129916382D 0 0.00000 0.00000 213',
'NSC': 213,
'NCI_AIDS_Antiviral_Screen_IC50': '2.00E-04\tM\t>\t2.00E-04\t4',
'_Name': 213,
'CAS_RN': '119-80-2',
'_MolFileComments': '119-80-2',
'NCI_AIDS_Antiviral_Screen_EC50': '2.00E-04\tM\t>\t2.00E-04\t4',
'NCI_AIDS_Antiviral_Screen_Conclusion': 'CI'
},
{
'_MolFileInfo': 'BBtclserve11129916382D 0 0.00000 0.00000 220',
'NSC': 220,
'NCI_AIDS_Antiviral_Screen_IC50': '2.00E-04\tM\t>\t2.00E-04\t4',
'_Name': 220,
'CAS_RN': '5325-83-7',
'_MolFileComments': '5325-83-7',
'NCI_AIDS_Antiviral_Screen_EC50': '2.00E-04\tM\t>\t2.00E-04\t4',
'NCI_AIDS_Antiviral_Screen_Conclusion': 'CI'
},
{
'_MolFileInfo': 'BBtclserve11129916382D 0 0.00000 0.00000 229',
'NSC': 229,
'NCI_AIDS_Antiviral_Screen_IC50': '2.00E-04\tM\t>\t2.00E-04\t2',
'_Name': 229,
'CAS_RN': '5325-88-2',
'_MolFileComments': '5325-88-2',
'NCI_AIDS_Antiviral_Screen_EC50': '2.00E-04\tM\t>\t2.00E-04\t2',
'NCI_AIDS_Antiviral_Screen_Conclusion': 'CI'
},
{
'_MolFileInfo': 'BBtclserve11129916382D 0 0.00000 0.00000 256',
'NSC': 256,
'NCI_AIDS_Antiviral_Screen_IC50': '2.00E-04\tM\t>\t2.00E-04\t4',
'_Name': 256,
'CAS_RN': '5326-06-7',
'_MolFileComments': '5326-06-7',
'NCI_AIDS_Antiviral_Screen_EC50': '2.00E-04\tM\t>\t2.00E-04\t4',
'NCI_AIDS_Antiviral_Screen_Conclusion': 'CI'
},
]
sdSup = Chem.SDMolSupplier(fileN)
for i, mol in enumerate(sdSup):
self.assertEqual(mol.GetPropsAsDict(includePrivate=True), sddata[i])
def testGetSetProps(self):
m = Chem.MolFromSmiles("CC")
errors = {
"int":
"key `foo` exists but does not result in an integer value reason: boost::bad_any_cast: failed conversion using boost::any_cast",
"uint overflow":
"key `foo` exists but does not result in an unsigned integer value reason: bad numeric conversion: negative overflow",
"int overflow":
"key `foo` exists but does not result in an integer value reason: bad numeric conversion: positive overflow",
"double":
"key `foo` exists but does not result in a double value reason: boost::bad_any_cast: failed conversion using boost::any_cast",
"bool":
"key `foo` exists but does not result in a True or False value reason: boost::bad_any_cast: failed conversion using boost::any_cast"
}
for ob in [m, list(m.GetAtoms())[0], list(m.GetBonds())[0]]:
ob.SetDoubleProp("foo", 2.0)
with self.assertRaises(ValueError) as e:
ob.GetBoolProp("foo")
self.assertEqual(str(e.exception), errors["bool"])
with self.assertRaises(ValueError) as e:
ob.GetIntProp("foo")
self.assertEqual(str(e.exception), errors["int"])
ob.SetBoolProp("foo", True)
with self.assertRaises(ValueError) as e:
ob.GetDoubleProp("foo")
self.assertEqual(str(e.exception), errors["double"])
with self.assertRaises(ValueError) as e:
ob.GetIntProp("foo")
self.assertEqual(str(e.exception), errors["int"])
ob.SetIntProp("foo", -1)
with self.assertRaises(ValueError) as e:
ob.GetUnsignedProp("foo")
self.assertEqual(str(e.exception), errors["uint overflow"])
ob.SetUnsignedProp("foo", 4294967295)
self.assertEqual(ob.GetUnsignedProp("foo"), 4294967295)
with self.assertRaises(ValueError) as e:
ob.GetIntProp("foo")
self.assertEqual(str(e.exception), errors["int overflow"])
def testInvariantException(self):
m = Chem.MolFromSmiles("C")
try:
m.GetAtomWithIdx(3)
except RuntimeError as e:
import platform
details = str(e)
if platform.system() == 'Windows':
details = details.replace('\\', '/')
self.assertTrue("Code/GraphMol/ROMol.cpp".lower() in details.lower())
self.assertTrue("Failed Expression: 3 < 1" in details)
self.assertTrue("RDKIT:" in details)
self.assertTrue(__version__ in details)
def testGetSDText(self):
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'NCI_aids_few.sdf')
#fileN = "../FileParsers/test_data/NCI_aids_few.sdf"
sdSup = Chem.SDMolSupplier(fileN)
for m in sdSup:
sdt = Chem.SDWriter.GetText(m)
ts = Chem.SDMolSupplier()
ts.SetData(sdt)
nm = next(ts)
self.assertEqual(Chem.MolToSmiles(m, True), Chem.MolToSmiles(nm, True))
for pn in m.GetPropNames():
self.assertTrue(nm.HasProp(pn))
self.assertEqual(m.GetProp(pn), nm.GetProp(pn))
def testUnfoldedRDKFingerprint(self):
from rdkit.Chem import AllChem
m = Chem.MolFromSmiles('c1ccccc1N')
fp = AllChem.UnfoldedRDKFingerprintCountBased(m)
fpDict = fp.GetNonzeroElements()
self.assertEqual(len(fpDict.items()), 19)
self.assertTrue(374073638 in fpDict)
self.assertEqual(fpDict[374073638], 6)
self.assertTrue(464351883 in fpDict)
self.assertEqual(fpDict[464351883], 2)
self.assertTrue(1949583554 in fpDict)
self.assertEqual(fpDict[1949583554], 6)
self.assertTrue(4105342207 in fpDict)
self.assertEqual(fpDict[4105342207], 1)
self.assertTrue(794080973 in fpDict)
self.assertEqual(fpDict[794080973], 1)
self.assertTrue(3826517238 in fpDict)
self.assertEqual(fpDict[3826517238], 2)
m = Chem.MolFromSmiles('Cl')
fp = AllChem.UnfoldedRDKFingerprintCountBased(m)
fpDict = fp.GetNonzeroElements()
self.assertEqual(len(fpDict.items()), 0)
m = Chem.MolFromSmiles('CCCO')
aBits = {}
fp = AllChem.UnfoldedRDKFingerprintCountBased(m, bitInfo=aBits)
fpDict = fp.GetNonzeroElements()
self.assertEqual(len(fpDict.items()), 5)
self.assertTrue(1524090560 in fpDict)
self.assertEqual(fpDict[1524090560], 1)
self.assertTrue(1940446997 in fpDict)
self.assertEqual(fpDict[1940446997], 1)
self.assertTrue(3977409745 in fpDict)
self.assertEqual(fpDict[3977409745], 1)
self.assertTrue(4274652475 in fpDict)
self.assertEqual(fpDict[4274652475], 1)
self.assertTrue(4275705116 in fpDict)
self.assertEqual(fpDict[4275705116], 2)
self.assertTrue(1524090560 in aBits)
self.assertEqual(aBits[1524090560], [[1, 2]])
self.assertTrue(1940446997 in aBits)
self.assertEqual(aBits[1940446997], [[0, 1]])
self.assertTrue(3977409745 in aBits)
self.assertEqual(aBits[3977409745], [[0, 1, 2]])
self.assertTrue(4274652475 in aBits)
self.assertEqual(aBits[4274652475], [[2]])
self.assertTrue(4275705116 in aBits)
self.assertEqual(aBits[4275705116], [[0], [1]])
def testRDKFingerprintBitInfo(self):
m = Chem.MolFromSmiles('CCCO')
aBits = {}
fp1 = Chem.RDKFingerprint(m, bitInfo=aBits)
self.assertTrue(1183 in aBits)
self.assertEqual(aBits[1183], [[1, 2]])
self.assertTrue(709 in aBits)
self.assertEqual(aBits[709], [[0, 1]])
self.assertTrue(1118 in aBits)
self.assertEqual(aBits[1118], [[0, 1, 2]])
self.assertTrue(562 in aBits)
self.assertEqual(aBits[562], [[2]])
self.assertTrue(1772 in aBits)
self.assertEqual(aBits[1772], [[0], [1]])
def testSimpleAromaticity(self):
m = Chem.MolFromSmiles('c1ccccc1')
self.assertTrue(m.GetBondWithIdx(0).GetIsAromatic())
self.assertTrue(m.GetAtomWithIdx(0).GetIsAromatic())
Chem.Kekulize(m, True)
self.assertFalse(m.GetBondWithIdx(0).GetIsAromatic())
self.assertFalse(m.GetAtomWithIdx(0).GetIsAromatic())
Chem.SetAromaticity(m, Chem.AROMATICITY_SIMPLE)
self.assertTrue(m.GetBondWithIdx(0).GetIsAromatic())
self.assertTrue(m.GetAtomWithIdx(0).GetIsAromatic())
m = Chem.MolFromSmiles('c1c[nH]cc1')
self.assertTrue(m.GetBondWithIdx(0).GetIsAromatic())
self.assertTrue(m.GetAtomWithIdx(0).GetIsAromatic())
Chem.Kekulize(m, True)
self.assertFalse(m.GetBondWithIdx(0).GetIsAromatic())
self.assertFalse(m.GetAtomWithIdx(0).GetIsAromatic())
Chem.SetAromaticity(m, Chem.AROMATICITY_SIMPLE)
self.assertTrue(m.GetBondWithIdx(0).GetIsAromatic())
self.assertTrue(m.GetAtomWithIdx(0).GetIsAromatic())
m = Chem.MolFromSmiles('c1cccoocc1')
self.assertTrue(m.GetBondWithIdx(0).GetIsAromatic())
self.assertTrue(m.GetAtomWithIdx(0).GetIsAromatic())
Chem.Kekulize(m, True)
self.assertFalse(m.GetBondWithIdx(0).GetIsAromatic())
self.assertFalse(m.GetAtomWithIdx(0).GetIsAromatic())
Chem.SetAromaticity(m, Chem.AROMATICITY_SIMPLE)
self.assertFalse(m.GetBondWithIdx(0).GetIsAromatic())
self.assertFalse(m.GetAtomWithIdx(0).GetIsAromatic())
m = Chem.MolFromSmiles('c1ooc1')
self.assertTrue(m.GetBondWithIdx(0).GetIsAromatic())
self.assertTrue(m.GetAtomWithIdx(0).GetIsAromatic())
Chem.Kekulize(m, True)
self.assertFalse(m.GetBondWithIdx(0).GetIsAromatic())
self.assertFalse(m.GetAtomWithIdx(0).GetIsAromatic())
Chem.SetAromaticity(m, Chem.AROMATICITY_SIMPLE)
self.assertFalse(m.GetBondWithIdx(0).GetIsAromatic())
self.assertFalse(m.GetAtomWithIdx(0).GetIsAromatic())
m = Chem.MolFromSmiles('C1=CC2=CC=CC=CC2=C1')
self.assertTrue(m.GetBondWithIdx(0).GetIsAromatic())
self.assertTrue(m.GetAtomWithIdx(0).GetIsAromatic())
Chem.Kekulize(m, True)
self.assertFalse(m.GetBondWithIdx(0).GetIsAromatic())
self.assertFalse(m.GetAtomWithIdx(0).GetIsAromatic())
Chem.SetAromaticity(m, Chem.AROMATICITY_SIMPLE)
self.assertFalse(m.GetBondWithIdx(0).GetIsAromatic())
self.assertFalse(m.GetAtomWithIdx(0).GetIsAromatic())
def testGithub955(self):
m = Chem.MolFromSmiles("CCC")
m.GetAtomWithIdx(0).SetProp("foo", "1")
self.assertEqual(list(m.GetAtomWithIdx(0).GetPropNames()), ["foo"])
m.GetBondWithIdx(0).SetProp("foo", "1")
self.assertEqual(list(m.GetBondWithIdx(0).GetPropNames()), ["foo"])
def testMDLProps(self):
m = Chem.MolFromSmiles("CCC")
m.GetAtomWithIdx(0).SetAtomMapNum(1)
Chem.SetAtomAlias(m.GetAtomWithIdx(1), "foo")
Chem.SetAtomValue(m.GetAtomWithIdx(1), "bar")
m = Chem.MolFromMolBlock(Chem.MolToMolBlock(m))
self.assertEqual(m.GetAtomWithIdx(0).GetAtomMapNum(), 1)
self.assertEqual(Chem.GetAtomAlias(m.GetAtomWithIdx(1)), "foo")
self.assertEqual(Chem.GetAtomValue(m.GetAtomWithIdx(1)), "bar")
def testSmilesProps(self):
m = Chem.MolFromSmiles("C")
Chem.SetSupplementalSmilesLabel(m.GetAtomWithIdx(0), 'xxx')
self.assertEqual(Chem.MolToSmiles(m), "Cxxx")
def testGithub1051(self):
# just need to test that this exists:
self.assertTrue(Chem.BondDir.EITHERDOUBLE)
def testGithub1041(self):
a = Chem.Atom(6)
self.assertRaises(RuntimeError, lambda: a.GetOwningMol())
self.assertRaises(RuntimeError, lambda: a.GetNeighbors())
self.assertRaises(RuntimeError, lambda: a.GetBonds())
self.assertRaises(RuntimeError, lambda: a.IsInRing())
self.assertRaises(RuntimeError, lambda: a.IsInRingSize(4))
def testSmilesParseParams(self):
smi = "CCC |$foo;;bar$| ourname"
m = Chem.MolFromSmiles(smi)
self.assertTrue(m is not None)
ps = Chem.SmilesParserParams()
ps.allowCXSMILES = False
ps.parseName = False
m = Chem.MolFromSmiles(smi, ps)
self.assertTrue(m is None)
ps.allowCXSMILES = True
ps.parseName = True
m = Chem.MolFromSmiles(smi, ps)
self.assertTrue(m is not None)
self.assertTrue(m.GetAtomWithIdx(0).HasProp('atomLabel'))
self.assertEqual(m.GetAtomWithIdx(0).GetProp('atomLabel'), "foo")
self.assertTrue(m.HasProp('_Name'))
self.assertEqual(m.GetProp('_Name'), "ourname")
self.assertEqual(m.GetProp("_CXSMILES_Data"), "|$foo;;bar$|")
def testWriteCXSmiles(self):
smi = "CCC |$foo;;bar$|"
ps = Chem.SmilesParserParams()
ps.allowCXSMILES = True
m = Chem.MolFromSmiles(smi, ps)
self.assertTrue(m is not None)
self.assertTrue(m.GetAtomWithIdx(0).HasProp('atomLabel'))
self.assertEqual(m.GetAtomWithIdx(0).GetProp('atomLabel'), "foo")
self.assertEqual(Chem.MolToCXSmiles(m), 'CCC |$foo;;bar$|')
smi = "Cl.CCC |$;foo;;bar$|"
m = Chem.MolFromSmiles(smi, ps)
self.assertTrue(m is not None)
self.assertTrue(m.GetAtomWithIdx(1).HasProp('atomLabel'))
self.assertEqual(m.GetAtomWithIdx(1).GetProp('atomLabel'), "foo")
self.assertEqual(Chem.MolFragmentToCXSmiles(m, atomsToUse=(1, 2, 3)), 'CCC |$foo;;bar$|')
def testPickleProps(self):
import pickle
m = Chem.MolFromSmiles('C1=CN=CC=C1')
m.SetProp("_Name", "Name")
for atom in m.GetAtoms():
atom.SetProp("_foo", "bar" + str(atom.GetIdx()))
atom.SetProp("foo", "baz" + str(atom.GetIdx()))
Chem.SetDefaultPickleProperties(Chem.PropertyPickleOptions.AllProps)
pkl = pickle.dumps(m)
m2 = pickle.loads(pkl)
smi1 = Chem.MolToSmiles(m)
smi2 = Chem.MolToSmiles(m2)
self.assertTrue(smi1 == smi2)
self.assertEqual(m2.GetProp("_Name"), "Name")
for atom in m2.GetAtoms():
self.assertEqual(atom.GetProp("_foo"), "bar" + str(atom.GetIdx()))
self.assertEqual(atom.GetProp("foo"), "baz" + str(atom.GetIdx()))
Chem.SetDefaultPickleProperties(Chem.PropertyPickleOptions.AtomProps)
pkl = pickle.dumps(m)
m2 = pickle.loads(pkl)
smi1 = Chem.MolToSmiles(m)
smi2 = Chem.MolToSmiles(m2)
self.assertTrue(smi1 == smi2)
self.assertFalse(m2.HasProp("_Name"))
for atom in m2.GetAtoms():
self.assertFalse(atom.HasProp("_foo"))
self.assertEqual(atom.GetProp("foo"), "baz" + str(atom.GetIdx()))
Chem.SetDefaultPickleProperties(Chem.PropertyPickleOptions.NoProps)
pkl = pickle.dumps(m)
m2 = pickle.loads(pkl)
smi1 = Chem.MolToSmiles(m)
smi2 = Chem.MolToSmiles(m2)
self.assertTrue(smi1 == smi2)
self.assertFalse(m2.HasProp("_Name"))
for atom in m2.GetAtoms():
self.assertFalse(atom.HasProp("_foo"))
self.assertFalse(atom.HasProp("foo"))
Chem.SetDefaultPickleProperties(Chem.PropertyPickleOptions.MolProps
| Chem.PropertyPickleOptions.PrivateProps)
pkl = pickle.dumps(m)
m2 = pickle.loads(pkl)
smi1 = Chem.MolToSmiles(m)
smi2 = Chem.MolToSmiles(m2)
self.assertTrue(smi1 == smi2)
self.assertEqual(m2.GetProp("_Name"), "Name")
for atom in m2.GetAtoms():
self.assertFalse(atom.HasProp("_foo"))
self.assertFalse(atom.HasProp("foo"))
def testGithub1352(self):
self.assertTrue('SP' in Chem.HybridizationType.names)
self.assertTrue('S' in Chem.HybridizationType.names)
m = Chem.MolFromSmiles('CC(=O)O.[Na]')
self.assertEqual(m.GetAtomWithIdx(0).GetHybridization().name, 'SP3')
self.assertEqual(m.GetAtomWithIdx(4).GetHybridization().name, 'S')
def testGithub1366(self):
mol = Chem.MolFromSmiles('*C*')
mol = Chem.RWMol(mol)
ats = iter(mol.GetAtoms())
atom = next(ats)
mol.RemoveAtom(atom.GetIdx())
self.assertRaises(RuntimeError, next, ats)
mol = Chem.MolFromSmiles('*C*')
mol = Chem.RWMol(mol)
bonds = iter(mol.GetBonds())
bond = next(bonds)
mol.RemoveBond(bond.GetBeginAtomIdx(), bond.GetEndAtomIdx())
self.assertRaises(RuntimeError, next, bonds)
def testGithub1478(self):
data = """
MJ150720
8 8 0 0 0 0 0 0 0 0999 V2000
-0.4242 -1.4883 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
0.2901 -1.0758 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.0046 0.9865 0.0000 A 0 0 0 0 0 0 0 0 0 0 0 0
1.0046 0.1614 0.0000 A 0 0 0 0 0 0 0 0 0 0 0 0
0.2901 -0.2508 0.0000 A 0 0 0 0 0 0 0 0 0 0 0 0
-0.4243 0.1614 0.0000 A 0 0 0 0 0 0 0 0 0 0 0 0
-0.4243 0.9865 0.0000 A 0 0 0 0 0 0 0 0 0 0 0 0
0.2901 1.3990 0.0000 A 0 0 0 0 0 0 0 0 0 0 0 0
7 6 4 0 0 0 0
8 7 4 0 0 0 0
6 5 4 0 0 0 0
5 4 4 0 0 0 0
5 2 1 0 0 0 0
4 3 4 0 0 0 0
8 3 4 0 0 0 0
2 1 2 0 0 0 0
M END
"""
pattern = Chem.MolFromMolBlock(data)
m = Chem.MolFromSmiles("c1ccccc1C=O")
self.assertTrue(m.HasSubstructMatch(pattern))
def testGithub1320(self):
import pickle
mol = Chem.MolFromSmiles('N[C@@H](C)O')
mol2 = pickle.loads(pickle.dumps(mol))
self.assertEqual(Chem.MolToSmiles(mol, isomericSmiles=True),
Chem.MolToSmiles(mol2, isomericSmiles=True))
Chem.SetDefaultPickleProperties(Chem.PropertyPickleOptions.AtomProps
| Chem.PropertyPickleOptions.BondProps
| Chem.PropertyPickleOptions.MolProps
| Chem.PropertyPickleOptions.PrivateProps
| Chem.PropertyPickleOptions.ComputedProps)
mol3 = pickle.loads(pickle.dumps(mol))
for a1, a2 in zip(mol.GetAtoms(), mol3.GetAtoms()):
d1 = a1.GetPropsAsDict()
d2 = a2.GetPropsAsDict()
if "__computedProps" in d1:
c1 = list(d1["__computedProps"])
c2 = list(d2["__computedProps"])
del d1["__computedProps"]
del d2["__computedProps"]
self.assertEqual(c1, c2)
assert d1 == d2
for a1, a2 in zip(mol.GetBonds(), mol3.GetBonds()):
d1 = a1.GetPropsAsDict()
d2 = a2.GetPropsAsDict()
if "__computedProps" in d1:
c1 = list(d1["__computedProps"])
c2 = list(d2["__computedProps"])
del d1["__computedProps"]
del d2["__computedProps"]
self.assertEqual(c1, c2)
assert d1 == d2
self.assertEqual(Chem.MolToSmiles(mol, isomericSmiles=True),
Chem.MolToSmiles(mol3, isomericSmiles=True))
def testOldPropPickles(self):
data = 'crdkit.Chem.rdchem\nMol\np0\n(S\'\\xef\\xbe\\xad\\xde\\x00\\x00\\x00\\x00\\x08\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00)\\x00\\x00\\x00-\\x00\\x00\\x00\\x80\\x01\\x06\\x00`\\x00\\x00\\x00\\x01\\x03\\x07\\x00`\\x00\\x00\\x00\\x02\\x01\\x06 4\\x00\\x00\\x00\\x01\\x01\\x04\\x06\\x00`\\x00\\x00\\x00\\x01\\x03\\x06\\x00(\\x00\\x00\\x00\\x03\\x04\\x08\\x00(\\x00\\x00\\x00\\x03\\x02\\x07\\x00h\\x00\\x00\\x00\\x03\\x02\\x01\\x06 4\\x00\\x00\\x00\\x02\\x01\\x04\\x06\\x00(\\x00\\x00\\x00\\x03\\x04\\x08\\x00(\\x00\\x00\\x00\\x03\\x02\\x07\\x00(\\x00\\x00\\x00\\x03\\x03\\x06\\x00`\\x00\\x00\\x00\\x02\\x02\\x06 4\\x00\\x00\\x00\\x01\\x01\\x04\\x08\\x00(\\x00\\x00\\x00\\x03\\x02\\x06@(\\x00\\x00\\x00\\x03\\x04\\x06@h\\x00\\x00\\x00\\x03\\x03\\x01\\x06@h\\x00\\x00\\x00\\x03\\x03\\x01\\x06@h\\x00\\x00\\x00\\x03\\x03\\x01\\x06@h\\x00\\x00\\x00\\x03\\x03\\x01\\x06@h\\x00\\x00\\x00\\x03\\x03\\x01\\x06\\x00`\\x00\\x00\\x00\\x02\\x02\\x06 4\\x00\\x00\\x00\\x01\\x01\\x04\\x06\\x00(\\x00\\x00\\x00\\x03\\x04\\x08\\x00(\\x00\\x00\\x00\\x03\\x02\\x07\\x00h\\x00\\x00\\x00\\x03\\x02\\x01\\x06 4\\x00\\x00\\x00\\x02\\x01\\x04\\x06\\x00`\\x00\\x00\\x00\\x02\\x02\\x06\\x00`\\x00\\x00\\x00\\x02\\x02\\x06\\x00`\\x00\\x00\\x00\\x02\\x02\\x06@(\\x00\\x00\\x00\\x03\\x04\\x06@h\\x00\\x00\\x00\\x03\\x03\\x01\\x06@h\\x00\\x00\\x00\\x03\\x03\\x01\\x06@h\\x00\\x00\\x00\\x03\\x03\\x01\\x06@h\\x00\\x00\\x00\\x03\\x03\\x01\\x06@(\\x00\\x00\\x00\\x03\\x04\\x06\\x00`\\x00\\x00\\x00\\x03\\x01\\x06\\x00`\\x00\\x00\\x00\\x02\\x02\\x06\\x00`\\x00\\x00\\x00\\x02\\x02\\x06\\x00`\\x00\\x00\\x00\\x02\\x02\\x06\\x00`\\x00\\x00\\x00\\x02\\x02\\x06\\x00`\\x00\\x00\\x00\\x02\\x02\\x0b\\x00\\x01\\x00\\x01\\x02\\x00\\x02\\x03\\x00\\x02\\x04\\x00\\x04\\x05(\\x02\\x04\\x06 \\x06\\x07\\x00\\x07\\x08\\x00\\x08\\t(\\x02\\x08\\n \\n\\x0b\\x00\\x0b\\x0c\\x00\\x0c\\r\\x00\\r\\x0e \\x0e\\x0fh\\x0c\\x0f\\x10h\\x0c\\x10\\x11h\\x0c\\x11\\x12h\\x0c\\x12\\x13h\\x0c\\x0c\\x14\\x00\\x14\\x15\\x00\\x15\\x16\\x00\\x16\\x17(\\x02\\x16\\x18 \\x18\\x19\\x00\\x19\\x1a\\x00\\x1a\\x1b\\x00\\x1b\\x1c\\x00\\x1c\\x1d\\x00\\x1d\\x1eh\\x0c\\x1e\\x1fh\\x0c\\x1f h\\x0c !h\\x0c!"h\\x0c\\x07#\\x00#$\\x00$%\\x00%&\\x00&\\\'\\x00\\\'(\\x00\\x15\\n\\x00"\\x19\\x00(#\\x00\\x13\\x0eh\\x0c"\\x1dh\\x0c\\x14\\x05\\x05\\x0b\\n\\x15\\x14\\x0c\\x06\\x0f\\x10\\x11\\x12\\x13\\x0e\\x06\\x1a\\x1b\\x1c\\x1d"\\x19\\x06\\x1e\\x1f !"\\x1d\\x06$%&\\\'(#\\x17\\x00\\x00\\x00\\x00\\x12\\x03\\x00\\x00\\x00\\x07\\x00\\x00\\x00numArom\\x01\\x02\\x00\\x00\\x00\\x0f\\x00\\x00\\x00_StereochemDone\\x01\\x01\\x00\\x00\\x00\\x03\\x00\\x00\\x00foo\\x00\\x03\\x00\\x00\\x00bar\\x13:\\x02\\x00\\x00\\x00\\x08\\x00\\x00\\x00_CIPRank\\x02\\x12\\x00\\x00\\x00\\x05\\x00\\x00\\x00myidx\\x00\\x01\\x00\\x00\\x000\\x02\\x00\\x00\\x00\\x08\\x00\\x00\\x00_CIPRank\\x02\\x1d\\x00\\x00\\x00\\x05\\x00\\x00\\x00myidx\\x00\\x01\\x00\\x00\\x001\\x04\\x00\\x00\\x00\\x08\\x00\\x00\\x00_CIPRank\\x02\\x15\\x00\\x00\\x00\\x12\\x00\\x00\\x00_ChiralityPossible\\x01\\x01\\x00\\x00\\x00\\x08\\x00\\x00\\x00_CIPCode\\x00\\x01\\x00\\x00\\x00S\\x05\\x00\\x00\\x00myidx\\x00\\x01\\x00\\x00\\x002\\x02\\x00\\x00\\x00\\x08\\x00\\x00\\x00_CIPRank\\x02\\x00\\x00\\x00\\x00\\x05\\x00\\x00\\x00myidx\\x00\\x01\\x00\\x00\\x003\\x02\\x00\\x00\\x00\\x08\\x00\\x00\\x00_CIPRank\\x02\\x1a\\x00\\x00\\x00\\x05\\x00\\x00\\x00myidx\\x00\\x01\\x00\\x00\\x004\\x02\\x00\\x00\\x00\\x08\\x00\\x00\\x00_CIPRank\\x02"\\x00\\x00\\x00\\x05\\x00\\x00\\x00myidx\\x00\\x01\\x00\\x00\\x005\\x02\\x00\\x00\\x00\\x08\\x00\\x00\\x00_CIPRank\\x02\\x1f\\x00\\x00\\x00\\x05\\x00\\x00\\x00myidx\\x00\\x01\\x00\\x00\\x006\\x04\\x00\\x00\\x00\\x08\\x00\\x00\\x00_CIPRank\\x02\\x16\\x00\\x00\\x00\\x12\\x00\\x00\\x00_ChiralityPossible\\x01\\x01\\x00\\x00\\x00\\x08\\x00\\x00\\x00_CIPCode\\x00\\x01\\x00\\x00\\x00S\\x05\\x00\\x00\\x00myidx\\x00\\x01\\x00\\x00\\x007\\x02\\x00\\x00\\x00\\x08\\x00\\x00\\x00_CIPRank\\x02\\x1c\\x00\\x00\\x00\\x05\\x00\\x00\\x00myidx\\x00\\x01\\x00\\x00\\x008\\x02\\x00\\x00\\x00\\x08\\x00\\x00\\x00_CIPRank\\x02$\\x00\\x00\\x00\\x05\\x00\\x00\\x00myidx\\x00\\x01\\x00\\x00\\x009\\x02\\x00\\x00\\x00\\x08\\x00\\x00\\x00_CIPRank\\x02 \\x00\\x00\\x00\\x05\\x00\\x00\\x00myidx\\x00\\x02\\x00\\x00\\x0010\\x02\\x00\\x00\\x00\\x08\\x00\\x00\\x00_CIPRank\\x02\\x13\\x00\\x00\\x00\\x05\\x00\\x00\\x00myidx\\x00\\x02\\x00\\x00\\x0011\\x04\\x00\\x00\\x00\\x08\\x00\\x00\\x00_CIPRank\\x02\\x18\\x00\\x00\\x00\\x12\\x00\\x00\\x00_ChiralityPossible\\x01\\x01\\x00\\x00\\x00\\x08\\x00\\x00\\x00_CIPCode\\x00\\x01\\x00\\x00\\x00S\\x05\\x00\\x00\\x00myidx\\x00\\x02\\x00\\x00\\x0012\\x02\\x00\\x00\\x00\\x08\\x00\\x00\\x00_CIPRank\\x02!\\x00\\x00\\x00\\x05\\x00\\x00\\x00myidx\\x00\\x02\\x00\\x00\\x0013\\x02\\x00\\x00\\x00\\x08\\x00\\x00\\x00_CIPRank\\x02\\x19\\x00\\x00\\x00\\x05\\x00\\x00\\x00myidx\\x00\\x02\\x00\\x00\\x0014\\x02\\x00\\x00\\x00\\x08\\x00\\x00\\x00_CIPRank\\x02\\x0f\\x00\\x00\\x00\\x05\\x00\\x00\\x00myidx\\x00\\x02\\x00\\x00\\x0015\\x02\\x00\\x00\\x00\\x08\\x00\\x00\\x00_CIPRank\\x02\\x0b\\x00\\x00\\x00\\x05\\x00\\x00\\x00myidx\\x00\\x02\\x00\\x00\\x0016\\x02\\x00\\x00\\x00\\x08\\x00\\x00\\x00_CIPRank\\x02\\x08\\x00\\x00\\x00\\x05\\x00\\x00\\x00myidx\\x00\\x02\\x00\\x00\\x0017\\x02\\x00\\x00\\x00\\x08\\x00\\x00\\x00_CIPRank\\x02\\x0b\\x00\\x00\\x00\\x05\\x00\\x00\\x00myidx\\x00\\x02\\x00\\x00\\x0018\\x02\\x00\\x00\\x00\\x08\\x00\\x00\\x00_CIPRank\\x02\\x0f\\x00\\x00\\x00\\x05\\x00\\x00\\x00myidx\\x00\\x02\\x00\\x00\\x0019\\x02\\x00\\x00\\x00\\x08\\x00\\x00\\x00_CIPRank\\x02\\x07\\x00\\x00\\x00\\x05\\x00\\x00\\x00myidx\\x00\\x02\\x00\\x00\\x0020\\x04\\x00\\x00\\x00\\x08\\x00\\x00\\x00_CIPRank\\x02\\x17\\x00\\x00\\x00\\x12\\x00\\x00\\x00_ChiralityPossible\\x01\\x01\\x00\\x00\\x00\\x08\\x00\\x00\\x00_CIPCode\\x00\\x01\\x00\\x00\\x00S\\x05\\x00\\x00\\x00myidx\\x00\\x02\\x00\\x00\\x0021\\x02\\x00\\x00\\x00\\x08\\x00\\x00\\x00_CIPRank\\x02\\x1b\\x00\\x00\\x00\\x05\\x00\\x00\\x00myidx\\x00\\x02\\x00\\x00\\x0022\\x02\\x00\\x00\\x00\\x08\\x00\\x00\\x00_CIPRank\\x02#\\x00\\x00\\x00\\x05\\x00\\x00\\x00myidx\\x00\\x02\\x00\\x00\\x0023\\x02\\x00\\x00\\x00\\x08\\x00\\x00\\x00_CIPRank\\x02\\x1e\\x00\\x00\\x00\\x05\\x00\\x00\\x00myidx\\x00\\x02\\x00\\x00\\x0024\\x04\\x00\\x00\\x00\\x08\\x00\\x00\\x00_CIPRank\\x02\\x14\\x00\\x00\\x00\\x12\\x00\\x00\\x00_ChiralityPossible\\x01\\x01\\x00\\x00\\x00\\x08\\x00\\x00\\x00_CIPCode\\x00\\x01\\x00\\x00\\x00R\\x05\\x00\\x00\\x00myidx\\x00\\x02\\x00\\x00\\x0025\\x02\\x00\\x00\\x00\\x08\\x00\\x00\\x00_CIPRank\\x02\\x06\\x00\\x00\\x00\\x05\\x00\\x00\\x00myidx\\x00\\x02\\x00\\x00\\x0026\\x02\\x00\\x00\\x00\\x08\\x00\\x00\\x00_CIPRank\\x02\\x03\\x00\\x00\\x00\\x05\\x00\\x00\\x00myidx\\x00\\x02\\x00\\x00\\x0027\\x02\\x00\\x00\\x00\\x08\\x00\\x00\\x00_CIPRank\\x02\\x05\\x00\\x00\\x00\\x05\\x00\\x00\\x00myidx\\x00\\x02\\x00\\x00\\x0028\\x02\\x00\\x00\\x00\\x08\\x00\\x00\\x00_CIPRank\\x02\\x10\\x00\\x00\\x00\\x05\\x00\\x00\\x00myidx\\x00\\x02\\x00\\x00\\x0029\\x02\\x00\\x00\\x00\\x08\\x00\\x00\\x00_CIPRank\\x02\\x0c\\x00\\x00\\x00\\x05\\x00\\x00\\x00myidx\\x00\\x02\\x00\\x00\\x0030\\x02\\x00\\x00\\x00\\x08\\x00\\x00\\x00_CIPRank\\x02\\t\\x00\\x00\\x00\\x05\\x00\\x00\\x00myidx\\x00\\x02\\x00\\x00\\x0031\\x02\\x00\\x00\\x00\\x08\\x00\\x00\\x00_CIPRank\\x02\\n\\x00\\x00\\x00\\x05\\x00\\x00\\x00myidx\\x00\\x02\\x00\\x00\\x0032\\x02\\x00\\x00\\x00\\x08\\x00\\x00\\x00_CIPRank\\x02\\r\\x00\\x00\\x00\\x05\\x00\\x00\\x00myidx\\x00\\x02\\x00\\x00\\x0033\\x02\\x00\\x00\\x00\\x08\\x00\\x00\\x00_CIPRank\\x02\\x11\\x00\\x00\\x00\\x05\\x00\\x00\\x00myidx\\x00\\x02\\x00\\x00\\x0034\\x02\\x00\\x00\\x00\\x08\\x00\\x00\\x00_CIPRank\\x02\\x0e\\x00\\x00\\x00\\x05\\x00\\x00\\x00myidx\\x00\\x02\\x00\\x00\\x0035\\x02\\x00\\x00\\x00\\x08\\x00\\x00\\x00_CIPRank\\x02\\x04\\x00\\x00\\x00\\x05\\x00\\x00\\x00myidx\\x00\\x02\\x00\\x00\\x0036\\x02\\x00\\x00\\x00\\x08\\x00\\x00\\x00_CIPRank\\x02\\x02\\x00\\x00\\x00\\x05\\x00\\x00\\x00myidx\\x00\\x02\\x00\\x00\\x0037\\x02\\x00\\x00\\x00\\x08\\x00\\x00\\x00_CIPRank\\x02\\x01\\x00\\x00\\x00\\x05\\x00\\x00\\x00myidx\\x00\\x02\\x00\\x00\\x0038\\x02\\x00\\x00\\x00\\x08\\x00\\x00\\x00_CIPRank\\x02\\x02\\x00\\x00\\x00\\x05\\x00\\x00\\x00myidx\\x00\\x02\\x00\\x00\\x0039\\x02\\x00\\x00\\x00\\x08\\x00\\x00\\x00_CIPRank\\x02\\x04\\x00\\x00\\x00\\x05\\x00\\x00\\x00myidx\\x00\\x02\\x00\\x00\\x0040\\x13\\x16\'\np1\ntp2\nRp3\n.'
import pickle
# bonds were broken in v1
m2 = pickle.loads(data.encode("utf-8"), encoding='bytes')
self.assertEqual(m2.GetProp("foo"), "bar")
for atom in m2.GetAtoms():
self.assertEqual(atom.GetProp("myidx"), str(atom.GetIdx()))
self.assertEqual(
Chem.MolToSmiles(m2, True),
Chem.MolToSmiles(
Chem.MolFromSmiles(
"CN[C@@H](C)C(=O)N[C@H](C(=O)N1C[C@@H](Oc2ccccc2)C[C@H]1C(=O)N[C@@H]1CCCc2ccccc21)C1CCCCC1"
), True))
def testGithub1461(self):
# this is simple, it should throw a precondition and not seg fault
m = Chem.RWMol()
try:
m.AddBond(0, 1, Chem.BondType.SINGLE)
self.assertFalse(True) # shouldn't get here
except RuntimeError:
pass
def testMolBundles1(self):
b = Chem.MolBundle()
smis = ('CC(Cl)(F)CC(F)(Br)', 'C[C@](Cl)(F)C[C@H](F)(Br)', 'C[C@](Cl)(F)C[C@@H](F)(Br)')
for smi in smis:
b.AddMol(Chem.MolFromSmiles(smi))
self.assertEqual(len(b), 3)
self.assertEqual(b.Size(), 3)
self.assertRaises(IndexError, lambda: b[4])
self.assertEqual(Chem.MolToSmiles(b[1], isomericSmiles=True),
Chem.MolToSmiles(Chem.MolFromSmiles(smis[1]), isomericSmiles=True))
self.assertTrue(b.HasSubstructMatch(Chem.MolFromSmiles('CC(Cl)(F)CC(F)(Br)'),
useChirality=True))
self.assertTrue(
b.HasSubstructMatch(Chem.MolFromSmiles('C[C@](Cl)(F)C[C@@H](F)(Br)'), useChirality=True))
self.assertTrue(
b.HasSubstructMatch(Chem.MolFromSmiles('C[C@@](Cl)(F)C[C@@H](F)(Br)'), useChirality=False))
self.assertFalse(
b.HasSubstructMatch(Chem.MolFromSmiles('C[C@@](Cl)(F)C[C@@H](F)(Br)'), useChirality=True))
self.assertEqual(
len(b.GetSubstructMatch(Chem.MolFromSmiles('CC(Cl)(F)CC(F)(Br)'), useChirality=True)), 8)
self.assertEqual(
len(b.GetSubstructMatch(Chem.MolFromSmiles('C[C@](Cl)(F)C[C@@H](F)(Br)'), useChirality=True)),
8)
self.assertEqual(
len(b.GetSubstructMatch(Chem.MolFromSmiles('C[C@@](Cl)(F)C[C@@H](F)(Br)'),
useChirality=False)), 8)
self.assertEqual(
len(b.GetSubstructMatch(Chem.MolFromSmiles('C[C@@](Cl)(F)C[C@@H](F)(Br)'),
useChirality=True)), 0)
self.assertEqual(
len(b.GetSubstructMatches(Chem.MolFromSmiles('CC(Cl)(F)CC(F)(Br)'), useChirality=True)), 1)
self.assertEqual(
len(b.GetSubstructMatches(Chem.MolFromSmiles('C[C@](Cl)(F)C[C@@H](F)(Br)'),
useChirality=True)), 1)
self.assertEqual(
len(
b.GetSubstructMatches(Chem.MolFromSmiles('C[C@@](Cl)(F)C[C@@H](F)(Br)'),
useChirality=False)), 1)
self.assertEqual(
len(
b.GetSubstructMatches(Chem.MolFromSmiles('C[C@@](Cl)(F)C[C@@H](F)(Br)'),
useChirality=True)), 0)
self.assertEqual(
len(b.GetSubstructMatches(Chem.MolFromSmiles('CC(Cl)(F)CC(F)(Br)'), useChirality=True)[0]), 8)
self.assertEqual(
len(
b.GetSubstructMatches(Chem.MolFromSmiles('C[C@](Cl)(F)C[C@@H](F)(Br)'),
useChirality=True)[0]), 8)
self.assertEqual(
len(
b.GetSubstructMatches(Chem.MolFromSmiles('C[C@@](Cl)(F)C[C@@H](F)(Br)'),
useChirality=False)[0]), 8)
def testMolBundles2(self):
b = Chem.MolBundle()
smis = ('Fc1c(Cl)cccc1', 'Fc1cc(Cl)ccc1', 'Fc1ccc(Cl)cc1')
for smi in smis:
b.AddMol(Chem.MolFromSmiles(smi))
self.assertEqual(len(b), 3)
self.assertEqual(b.Size(), 3)
self.assertTrue(Chem.MolFromSmiles('Fc1c(Cl)cccc1').HasSubstructMatch(b))
self.assertTrue(Chem.MolFromSmiles('Fc1cc(Cl)ccc1').HasSubstructMatch(b))
self.assertTrue(Chem.MolFromSmiles('Fc1c(Cl)cccc1C').HasSubstructMatch(b))
self.assertTrue(Chem.MolFromSmiles('Fc1cc(Cl)ccc1C').HasSubstructMatch(b))
self.assertFalse(Chem.MolFromSmiles('Fc1c(Br)cccc1').HasSubstructMatch(b))
self.assertEqual(len(Chem.MolFromSmiles('Fc1c(Cl)cccc1').GetSubstructMatch(b)), 8)
self.assertEqual(len(Chem.MolFromSmiles('Fc1c(Cl)cccc1').GetSubstructMatches(b)), 1)
self.assertEqual(len(Chem.MolFromSmiles('Fc1c(Cl)cccc1').GetSubstructMatches(b)[0]), 8)
self.assertEqual(len(Chem.MolFromSmiles('Fc1ccc(Cl)cc1').GetSubstructMatches(b)), 1)
self.assertEqual(
len(Chem.MolFromSmiles('Fc1ccc(Cl)cc1').GetSubstructMatches(b, uniquify=False)), 2)
self.assertEqual(len(Chem.MolFromSmiles('Fc1c(C)cccc1').GetSubstructMatch(b)), 0)
self.assertEqual(len(Chem.MolFromSmiles('Fc1c(C)cccc1').GetSubstructMatches(b)), 0)
def testMolBundles3(self):
smis = ('CCC', 'CCO', 'CCN')
b = Chem.FixedMolSizeMolBundle()
for smi in smis:
b.AddMol(Chem.MolFromSmiles(smi))
self.assertEqual(len(b), 3)
self.assertEqual(b.Size(), 3)
with self.assertRaises(ValueError):
b.AddMol(Chem.MolFromSmiles('CCCC'))
b = Chem.MolBundle()
for smi in smis:
b.AddMol(Chem.MolFromSmiles(smi))
self.assertEqual(len(b), 3)
self.assertEqual(b.Size(), 3)
b.AddMol(Chem.MolFromSmiles('CCCC'))
self.assertEqual(b.Size(), 4)
def testGithub1622(self):
nonaromatics = (
"C1=C[N]C=C1", # radicals are not two electron donors
"O=C1C=CNC=C1", # exocyclic double bonds don't steal electrons
"C1=CS(=O)C=C1", # not sure how to classify this example from the
# OEChem docs
"C1#CC=CC=C1" # benzyne
# 5-membered heterocycles
"C1=COC=C1", # furan
"C1=CSC=C1", # thiophene
"C1=CNC=C1", #pyrrole
"C1=COC=N1", # oxazole
"C1=CSC=N1", # thiazole
"C1=CNC=N1", # imidazole
"C1=CNN=C1", # pyrazole
"C1=CON=C1", # isoxazole
"C1=CSN=C1", # isothiazole
"C1=CON=N1", # 1,2,3-oxadiazole
"C1=CNN=N1", # 1,2,3-triazole
"N1=CSC=N1", # 1,3,4-thiadiazole
# not outside the second rows
"C1=CC=C[Si]=C1",
"C1=CC=CC=P1",
# 5-membered heterocycles outside the second row
"C1=C[Se]C=C1",
'C1=C[Te]C=C1')
for smi in nonaromatics:
m = Chem.MolFromSmiles(smi, sanitize=False)
Chem.SanitizeMol(m, Chem.SANITIZE_ALL ^ Chem.SANITIZE_SETAROMATICITY)
Chem.SetAromaticity(m, Chem.AROMATICITY_MDL)
self.assertFalse(m.GetAtomWithIdx(0).GetIsAromatic())
aromatics = (
"C1=CC=CC=C1", # benzene, of course
# hetrocyclics
"N1=CC=CC=C1", # pyridine
"N1=CC=CC=N1", # pyridazine
"N1=CC=CN=C1", # pyrimidine
"N1=CC=NC=C1", # pyrazine
"N1=CN=CN=C1", # 1,3,5-triazine
# polycyclic aromatics
"C1=CC2=CC=CC=CC2=C1", # azulene
"C1=CC=CC2=CC=CC=C12",
"C1=CC2=CC=CC=CC=C12",
"C1=CC=C2C(=C1)N=CC=N2",
"C1=CN=CC2C=CC=CC1=2",
"C1=CC=C2C(=C1)N=C3C=CC=CC3=N2",
"C1=CN=NC2C=CC=CC1=2",
# macrocycle aromatics
"C1=CC=CC=CC=CC=C1",
"C1=CC=CC=CC=CC=CC=CC=CC=CC=C1",
"N1=CN=NC=CC=CC=CC=CC=CC=CC=CC=CC=CC=CC=CC=CC=C1")
for smi in aromatics:
m = Chem.MolFromSmiles(smi, sanitize=False)
Chem.SanitizeMol(m, Chem.SANITIZE_ALL ^ Chem.SANITIZE_SETAROMATICITY)
Chem.SetAromaticity(m, Chem.AROMATICITY_MDL)
self.assertTrue(m.GetAtomWithIdx(0).GetIsAromatic())
def testMolBlockChirality(self):
m = Chem.MolFromSmiles('C[C@H](Cl)Br')
mb = Chem.MolToMolBlock(m)
m2 = Chem.MolFromMolBlock(mb)
csmi1 = Chem.MolToSmiles(m, isomericSmiles=True)
csmi2 = Chem.MolToSmiles(m2, isomericSmiles=True)
self.assertEqual(csmi1, csmi2)
def testIssue1735(self):
# this shouldn't seg fault...
m = Chem.RWMol()
ranks = Chem.CanonicalRankAtoms(m, breakTies=False)
ranks = Chem.CanonicalRankAtoms(m, breakTies=True)
def testGithub1615(self):
mb = """Issue399a.mol
ChemDraw04050615582D
4 4 0 0 0 0 0 0 0 0999 V2000
-0.7697 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0553 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7697 0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7697 -0.4125 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
2 1 1 0
2 3 1 0
3 4 1 0
2 4 1 0
M END"""
m = Chem.MolFromMolBlock(mb)
self.assertFalse(m.GetAtomWithIdx(1).HasProp("_CIPCode"))
self.assertEqual(m.GetBondWithIdx(0).GetBondDir(), Chem.BondDir.NONE)
self.assertEqual(m.GetAtomWithIdx(1).GetChiralTag(), Chem.ChiralType.CHI_UNSPECIFIED)
m.GetAtomWithIdx(1).SetChiralTag(Chem.ChiralType.CHI_TETRAHEDRAL_CW)
Chem.AssignStereochemistry(m, force=True)
self.assertTrue(m.GetAtomWithIdx(1).HasProp("_CIPCode"))
self.assertEqual(m.GetAtomWithIdx(1).GetProp("_CIPCode"), "S")
self.assertEqual(m.GetBondWithIdx(0).GetBondDir(), Chem.BondDir.NONE)
Chem.WedgeBond(m.GetBondWithIdx(0), 1, m.GetConformer())
self.assertEqual(m.GetBondWithIdx(0).GetBondDir(), Chem.BondDir.BEGINWEDGE)
def testSmilesToAtom(self):
a = Chem.AtomFromSmiles("C")
self.assertEqual(a.GetAtomicNum(), 6)
b = Chem.BondFromSmiles("=")
self.assertEqual(b.GetBondType(), Chem.BondType.DOUBLE)
a = Chem.AtomFromSmiles("error")
self.assertIs(a, None)
b = Chem.BondFromSmiles("d")
self.assertIs(b, None)
a = Chem.AtomFromSmarts("C")
self.assertEqual(a.GetAtomicNum(), 6)
b = Chem.BondFromSmarts("=")
self.assertEqual(b.GetBondType(), Chem.BondType.DOUBLE)
a = Chem.AtomFromSmarts("error")
self.assertIs(a, None)
b = Chem.BondFromSmarts("d")
self.assertIs(b, None)
def testSVGParsing(self):
svg = """<?xml version='1.0' encoding='iso-8859-1'?>
<svg version='1.1' baseProfile='full'
xmlns='http://www.w3.org/2000/svg'
xmlns:rdkit='http://www.rdkit.org/xml'
xmlns:xlink='http://www.w3.org/1999/xlink'
xml:space='preserve'
width='200px' height='200px' >
<rect style='opacity:1.0;fill:#FFFFFF;stroke:none' width='200' height='200' x='0' y='0'> </rect>
<path d='M 9.09091,89.4974 24.2916,84.7462' style='fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />
<path d='M 24.2916,84.7462 39.4923,79.9949' style='fill:none;fill-rule:evenodd;stroke:#0000FF;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />
<path d='M 86.2908,106.814 75.1709,93.4683 72.0765,96.8285 86.2908,106.814' style='fill:#000000;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />
<path d='M 75.1709,93.4683 57.8622,86.8431 64.051,80.1229 75.1709,93.4683' style='fill:#0000FF;fill-rule:evenodd;stroke:#0000FF;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />
<path d='M 75.1709,93.4683 72.0765,96.8285 57.8622,86.8431 75.1709,93.4683' style='fill:#0000FF;fill-rule:evenodd;stroke:#0000FF;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />
<path d='M 86.2908,106.814 82.1459,125.293' style='fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />
<path d='M 82.1459,125.293 78.0009,143.772' style='fill:none;fill-rule:evenodd;stroke:#00CC00;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />
<path d='M 86.2908,106.814 129.89,93.1862' style='fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />
<path d='M 134.347,94.186 138.492,75.7069' style='fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />
<path d='M 138.492,75.7069 142.637,57.2277' style='fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />
<path d='M 125.432,92.1865 129.577,73.7074' style='fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />
<path d='M 129.577,73.7074 133.722,55.2282' style='fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />
<path d='M 129.89,93.1862 142.557,104.852' style='fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />
<path d='M 142.557,104.852 155.224,116.517' style='fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />
<text x='39.4923' y='83.483' style='font-size:15px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#0000FF' ><tspan>NH</tspan></text>
<text x='67.6656' y='158.998' style='font-size:15px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#00CC00' ><tspan>Cl</tspan></text>
<text x='132.777' y='56.228' style='font-size:15px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#FF0000' ><tspan>O</tspan></text>
<text x='149.782' y='131.743' style='font-size:15px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#FF0000' ><tspan>OH</tspan></text>
<text x='89.9952' y='194' style='font-size:12px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#000000' ><tspan>m1</tspan></text>
<metadata>
<rdkit:mol xmlns:rdkit = "http://www.rdkit.org/xml" version="0.9">
<rdkit:atom idx="1" atom-smiles="[CH3]" drawing-x="9.09091" drawing-y="89.4974" x="-2.78651" y="0.295614" z="0" />
<rdkit:atom idx="2" atom-smiles="[NH]" drawing-x="52.6897" drawing-y="75.8699" x="-1.35482" y="0.743114" z="0" />
<rdkit:atom idx="3" atom-smiles="[C@H]" drawing-x="86.2908" drawing-y="106.814" x="-0.251428" y="-0.273019" z="0" />
<rdkit:atom idx="4" atom-smiles="[Cl]" drawing-x="76.2932" drawing-y="151.385" x="-0.579728" y="-1.73665" z="0" />
<rdkit:atom idx="5" atom-smiles="[C]" drawing-x="129.89" drawing-y="93.1862" x="1.18027" y="0.174481" z="0" />
<rdkit:atom idx="6" atom-smiles="[O]" drawing-x="139.887" drawing-y="48.6148" x="1.50857" y="1.63811" z="0" />
<rdkit:atom idx="7" atom-smiles="[OH]" drawing-x="163.491" drawing-y="124.13" x="2.28366" y="-0.841652" z="0" />
<rdkit:bond idx="1" begin-atom-idx="1" end-atom-idx="2" bond-smiles="-" />
<rdkit:bond idx="2" begin-atom-idx="2" end-atom-idx="3" bond-smiles="-" />
<rdkit:bond idx="3" begin-atom-idx="3" end-atom-idx="4" bond-smiles="-" />
<rdkit:bond idx="4" begin-atom-idx="3" end-atom-idx="5" bond-smiles="-" />
<rdkit:bond idx="5" begin-atom-idx="5" end-atom-idx="6" bond-smiles="=" />
<rdkit:bond idx="6" begin-atom-idx="5" end-atom-idx="7" bond-smiles="-" />
</rdkit:mol></metadata>
</svg>"""
mol = Chem.MolFromRDKitSVG(svg)
self.assertEqual(mol.GetNumAtoms(), 7)
self.assertEqual(Chem.MolToSmiles(mol), 'CN[C@H](Cl)C(=O)O')
svg2 = """<?xml version='1.0' encoding='iso-8859-1'?>
<svg version='1.1' baseProfile='full'
xmlns='http://www.w3.org/2000/svg'
xmlns:rdkit='http://www.rdkit.org/xml'
xmlns:xlink='http://www.w3.org/1999/xlink'
xml:space='preserve'
width='200px' height='200px' >
<rect style='opacity:1.0;fill:#FFFFFF;stroke:none' width='200' height='200' x='0' y='0'> </rect>
<path d='M 9.09091,89.4974 24.2916,84.7462' style='fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />
<path d='M 24.2916,84.7462 39.4923,79.9949' style='fill:none;fill-rule:evenodd;stroke:#0000FF;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />
<path d='M 86.2908,106.814 75.1709,93.4683 72.0765,96.8285 86.2908,106.814' style='fill:#000000;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />
<path d='M 75.1709,93.4683 57.8622,86.8431 64.051,80.1229 75.1709,93.4683' style='fill:#0000FF;fill-rule:evenodd;stroke:#0000FF;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />
<path d='M 75.1709,93.4683 72.0765,96.8285 57.8622,86.8431 75.1709,93.4683' style='fill:#0000FF;fill-rule:evenodd;stroke:#0000FF;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />
<path d='M 86.2908,106.814 82.1459,125.293' style='fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />
<path d='M 82.1459,125.293 78.0009,143.772' style='fill:none;fill-rule:evenodd;stroke:#00CC00;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />
<path d='M 86.2908,106.814 129.89,93.1862' style='fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />
<path d='M 134.347,94.186 138.492,75.7069' style='fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />
<path d='M 138.492,75.7069 142.637,57.2277' style='fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />
<path d='M 125.432,92.1865 129.577,73.7074' style='fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />
<path d='M 129.577,73.7074 133.722,55.2282' style='fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />
<path d='M 129.89,93.1862 142.557,104.852' style='fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />
<path d='M 142.557,104.852 155.224,116.517' style='fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />
<text x='39.4923' y='83.483' style='font-size:15px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#0000FF' ><tspan>NH</tspan></text>
<text x='67.6656' y='158.998' style='font-size:15px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#00CC00' ><tspan>Cl</tspan></text>
<text x='132.777' y='56.228' style='font-size:15px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#FF0000' ><tspan>O</tspan></text>
<text x='149.782' y='131.743' style='font-size:15px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#FF0000' ><tspan>OH</tspan></text>
<text x='89.9952' y='194' style='font-size:12px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#000000' ><tspan>m1</tspan></text>
</svg>"""
mol = Chem.MolFromRDKitSVG(svg2)
self.assertTrue(mol is None)
with self.assertRaises(RuntimeError):
mol = Chem.MolFromRDKitSVG("bad svg")
def testAssignChiralTypesFromBondDirs(self):
"""
Just check to see that AssignChiralTypesFromBondDirs is wrapped.
Critical tests of the underlying C++ function already exist
in SD file reader tests.
"""
mol = Chem.MolFromSmiles('C(F)(Cl)Br')
rdkit.Chem.rdDepictor.Compute2DCoords(mol)
atom0 = mol.GetAtomWithIdx(0)
self.assertEqual(atom0.GetChiralTag(), Chem.rdchem.ChiralType.CHI_UNSPECIFIED)
bond = mol.GetBondBetweenAtoms(0, 1)
bond.SetBondDir(Chem.rdchem.BondDir.BEGINWEDGE)
Chem.AssignChiralTypesFromBondDirs(mol)
self.assertEqual(atom0.GetChiralTag(), Chem.rdchem.ChiralType.CHI_TETRAHEDRAL_CCW)
def testAssignStereochemistryFrom3D(self):
def _stereoTester(mol, expectedCIP, expectedStereo):
mol.UpdatePropertyCache()
self.assertEqual(mol.GetNumAtoms(), 9)
self.assertFalse(mol.GetAtomWithIdx(1).HasProp("_CIPCode"))
self.assertEqual(mol.GetBondWithIdx(3).GetStereo(), Chem.BondStereo.STEREONONE)
for bond in mol.GetBonds():
bond.SetBondDir(Chem.BondDir.NONE)
Chem.AssignStereochemistryFrom3D(mol)
self.assertTrue(mol.GetAtomWithIdx(1).HasProp("_CIPCode"))
self.assertEqual(mol.GetAtomWithIdx(1).GetProp("_CIPCode"), expectedCIP)
self.assertEqual(mol.GetBondWithIdx(3).GetStereo(), expectedStereo)
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'test_data', 'stereochem.sdf')
suppl = Chem.SDMolSupplier(fileN, sanitize=False)
expected = (
("R", Chem.BondStereo.STEREOZ),
("R", Chem.BondStereo.STEREOE),
("S", Chem.BondStereo.STEREOZ),
("S", Chem.BondStereo.STEREOE),
)
for i, mol in enumerate(suppl):
cip, stereo = expected[i]
_stereoTester(mol, cip, stereo)
def testGitHub2082(self):
ctab = """
MJ150720
9 9 0 0 0 0 0 0 0 0999 V2000
2.5687 -0.7144 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.1562 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.5687 0.7144 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1.3312 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.9187 -0.7144 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0937 -0.7144 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3187 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0937 0.7144 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.9187 0.7144 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2 1 1 6
2 3 1 0
2 4 1 0
4 5 2 0
5 6 1 0
6 7 2 0
7 8 1 0
8 9 2 0
9 4 1 0
M END
"""
mol = Chem.MolFromMolBlock(ctab)
self.assertFalse(mol.GetConformer().Is3D())
self.assertTrue("@" in Chem.MolToSmiles(mol, True))
def testGitHub2082_2(self):
# test a mol block that lies is 3D but labelled 2D
ofile = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'Wrap', 'test_data',
'issue2082.mol')
with open(ofile) as inf:
ctab = inf.read()
m = Chem.MolFromMolBlock(ctab)
self.assertTrue(m.GetConformer().Is3D())
def testSetQuery(self):
from rdkit.Chem import rdqueries
pat = Chem.MolFromSmarts("[C]")
self.assertFalse(Chem.MolFromSmiles("c1ccccc1").HasSubstructMatch(pat))
q = rdqueries.AtomNumEqualsQueryAtom(6)
for atom in pat.GetAtoms():
atom.SetQuery(q)
self.assertTrue(Chem.MolFromSmiles("c1ccccc1").HasSubstructMatch(pat))
def testGetQueryType(self):
query_a = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'query_A.mol')
m = next(Chem.SDMolSupplier(query_a))
self.assertTrue(m.GetAtomWithIdx(6).HasQuery())
self.assertTrue(m.GetAtomWithIdx(6).GetQueryType() == "A")
query_a_v3k = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'query_A.v3k.mol')
m = next(Chem.SDMolSupplier(query_a_v3k))
self.assertTrue(m.GetAtomWithIdx(6).HasQuery())
self.assertTrue(m.GetAtomWithIdx(6).GetQueryType() == "A")
query_q = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'query_Q.mol')
m = next(Chem.SDMolSupplier(query_q))
self.assertTrue(m.GetAtomWithIdx(6).HasQuery())
self.assertTrue(m.GetAtomWithIdx(6).GetQueryType() == "Q")
query_q_v3k = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'query_Q.v3k.mol')
m = next(Chem.SDMolSupplier(query_q_v3k))
self.assertTrue(m.GetAtomWithIdx(6).HasQuery())
self.assertTrue(m.GetAtomWithIdx(6).GetQueryType() == "Q")
m = Chem.MolFromSmiles("*CC")
params = Chem.rdmolops.AdjustQueryParameters.NoAdjustments()
params.makeDummiesQueries = True
m = Chem.rdmolops.AdjustQueryProperties(m, params)
self.assertTrue(m.GetAtomWithIdx(0).HasQuery())
self.assertTrue(m.GetAtomWithIdx(0).GetQueryType() == "")
def testBondSetQuery(self):
pat = Chem.MolFromSmarts('[#6]=[#6]')
mol = Chem.MolFromSmiles("c1ccccc1")
self.assertFalse(mol.HasSubstructMatch(pat))
pat2 = Chem.MolFromSmarts('C:C')
for bond in pat.GetBonds():
bond.SetQuery(pat2.GetBondWithIdx(0))
self.assertTrue(mol.HasSubstructMatch(pat))
def testBondExpandQuery(self):
pat = Chem.MolFromSmarts('C-C')
mol = Chem.MolFromSmiles("C=C-C")
self.assertEqual(len(mol.GetSubstructMatches(pat)), 1)
pat2 = Chem.MolFromSmarts('C=C')
for bond in pat.GetBonds():
bond.ExpandQuery(pat2.GetBondWithIdx(0), Chem.CompositeQueryType.COMPOSITE_OR)
self.assertEqual(len(mol.GetSubstructMatches(pat)), 2)
def testGitHub1985(self):
# simple check, this used to throw an exception
try:
Chem.MolToSmarts(Chem.MolFromSmarts("[C@]"))
except Exception:
self.fail("[C@] caused an exception when roundtripping smarts")
def testGetEnhancedStereo(self):
rdbase = os.environ['RDBASE']
filename = os.path.join(rdbase, 'Code/GraphMol/FileParsers/test_data/two_centers_or.mol')
m = Chem.MolFromMolFile(filename)
sg = m.GetStereoGroups()
self.assertEqual(len(sg), 2)
group1 = sg[1]
self.assertEqual(group1.GetGroupType(), Chem.StereoGroupType.STEREO_OR)
stereo_atoms = group1.GetAtoms()
self.assertEqual(len(stereo_atoms), 2)
# file is 1 indexed and says 5
self.assertEqual(stereo_atoms[1].GetIdx(), 4)
# make sure the atoms are connected to the parent molecule
stereo_atoms[1].SetProp("foo", "bar")
self.assertTrue(m.GetAtomWithIdx(4).HasProp("foo"))
# make sure that we can iterate over the atoms:
for at in stereo_atoms:
at.SetProp("foo2", "bar2")
self.assertTrue(m.GetAtomWithIdx(at.GetIdx()).HasProp("foo2"))
def testEnhancedStereoPreservesMol(self):
"""
Check that the stereo group (and the atoms therein) preserve the lifetime
of the associated mol.
"""
rdbase = os.environ['RDBASE']
filename = os.path.join(rdbase, 'Code/GraphMol/FileParsers/test_data/two_centers_or.mol')
m = Chem.MolFromMolFile(filename)
sg = m.GetStereoGroups()
m = None
gc.collect()
self.assertEqual(len(sg), 2)
group1 = sg[1]
stereo_atoms = group1.GetAtoms()
sg = None
gc.collect()
self.assertEqual(stereo_atoms[1].GetIdx(), 4)
self.assertEqual(stereo_atoms[1].GetOwningMol().GetNumAtoms(), 8)
def testSetEnhancedStereoGroup(self):
m = Chem.MolFromSmiles('F[C@@H](Br)[C@H](F)Cl |o1:1|')
m2 = Chem.RWMol(m)
groups = m2.GetStereoGroups()
self.assertEqual(len(groups), 1)
# Can clear the StereoGroups by setting to an empty list
m2.SetStereoGroups([])
self.assertEqual(len(m2.GetStereoGroups()), 0)
# Can add new StereoGroups
group1 = Chem.rdchem.CreateStereoGroup(Chem.rdchem.StereoGroupType.STEREO_OR, m2, [1])
m2.SetStereoGroups([group1])
self.assertEqual(len(m2.GetStereoGroups()), 1)
def testSetEnhancedStereoGroupOwnershipCheck(self):
# make sure that the object returned by CreateStereoGroup()
# preserves the owning molecule:
m = Chem.RWMol(Chem.MolFromSmiles('F[C@@H](Br)[C@H](F)Cl'))
group1 = Chem.rdchem.CreateStereoGroup(Chem.rdchem.StereoGroupType.STEREO_OR, m, [1])
m.SetStereoGroups([group1])
self.assertEqual(len(m.GetStereoGroups()), 1)
m = None
gc.collect()
stereo_atoms = group1.GetAtoms()
self.assertEqual(stereo_atoms[0].GetIdx(), 1)
return
self.assertEqual(stereo_atoms[0].GetOwningMol().GetNumAtoms(), 6)
# make sure we can't add StereoGroups constructed from one molecule
# to a different one:
m2 = Chem.RWMol(Chem.MolFromSmiles('F[C@@H](Br)[C@H](F)Cl'))
with self.assertRaises(ValueError):
m2.SetStereoGroups([group1])
def testSetEnhancedStereoTypeChecking(self):
m = Chem.RWMol(Chem.MolFromSmiles('F[C@@H](Br)[C@H](F)Cl'))
# List or tuple should be allowed:
group = Chem.rdchem.CreateStereoGroup(Chem.rdchem.StereoGroupType.STEREO_OR, m, [1, 3])
group = Chem.rdchem.CreateStereoGroup(Chem.rdchem.StereoGroupType.STEREO_OR, m, (1, 3))
# Python ValueError (range error) with index past the end
with self.assertRaises(ValueError):
group = Chem.rdchem.CreateStereoGroup(Chem.rdchem.StereoGroupType.STEREO_OR, m, [100])
# Mol is None
with self.assertRaises(TypeError):
group = Chem.rdchem.CreateStereoGroup(Chem.rdchem.StereoGroupType.STEREO_OR, None, [1])
# Atom indices must be numbers
with self.assertRaises(TypeError):
group = Chem.rdchem.CreateStereoGroup(Chem.rdchem.StereoGroupType.STEREO_OR, m, [1, 'text'])
def testSubstructParameters(self):
m = Chem.MolFromSmiles('C[C@](F)(Cl)OCC')
p1 = Chem.MolFromSmiles('C[C@](F)(Cl)O')
p2 = Chem.MolFromSmiles('C[C@@](F)(Cl)O')
p3 = Chem.MolFromSmiles('CC(F)(Cl)O')
ps = Chem.SubstructMatchParameters()
self.assertTrue(m.HasSubstructMatch(p1, ps))
self.assertTrue(m.HasSubstructMatch(p2, ps))
self.assertTrue(m.HasSubstructMatch(p3, ps))
self.assertEqual(m.GetSubstructMatch(p1, ps), (0, 1, 2, 3, 4))
self.assertEqual(m.GetSubstructMatch(p2, ps), (0, 1, 2, 3, 4))
self.assertEqual(m.GetSubstructMatch(p3, ps), (0, 1, 2, 3, 4))
self.assertEqual(m.GetSubstructMatches(p1, ps), ((0, 1, 2, 3, 4), ))
self.assertEqual(m.GetSubstructMatches(p2, ps), ((0, 1, 2, 3, 4), ))
self.assertEqual(m.GetSubstructMatches(p3, ps), ((0, 1, 2, 3, 4), ))
ps.useChirality = True
self.assertTrue(m.HasSubstructMatch(p1, ps))
self.assertFalse(m.HasSubstructMatch(p2, ps))
self.assertTrue(m.HasSubstructMatch(p3, ps))
self.assertEqual(m.GetSubstructMatch(p1, ps), (0, 1, 2, 3, 4))
self.assertEqual(m.GetSubstructMatch(p2, ps), ())
self.assertEqual(m.GetSubstructMatch(p3, ps), (0, 1, 2, 3, 4))
self.assertEqual(m.GetSubstructMatches(p1, ps), ((0, 1, 2, 3, 4), ))
self.assertEqual(m.GetSubstructMatches(p2, ps), ())
self.assertEqual(m.GetSubstructMatches(p3, ps), ((0, 1, 2, 3, 4), ))
def testSubstructParametersBundles(self):
b = Chem.MolBundle()
smis = ('C[C@](F)(Cl)O', 'C[C@](Br)(Cl)O', 'C[C@](I)(Cl)O')
for smi in smis:
b.AddMol(Chem.MolFromSmiles(smi))
self.assertEqual(len(b), 3)
self.assertEqual(b.Size(), 3)
ps = Chem.SubstructMatchParameters()
ps.useChirality = True
self.assertTrue(Chem.MolFromSmiles('C[C@](F)(Cl)OCC').HasSubstructMatch(b, ps))
self.assertFalse(Chem.MolFromSmiles('C[C@@](F)(Cl)OCC').HasSubstructMatch(b, ps))
self.assertTrue(Chem.MolFromSmiles('C[C@](I)(Cl)OCC').HasSubstructMatch(b, ps))
self.assertFalse(Chem.MolFromSmiles('C[C@@](I)(Cl)OCC').HasSubstructMatch(b, ps))
self.assertEqual(
Chem.MolFromSmiles('C[C@](F)(Cl)OCC').GetSubstructMatch(b, ps), (0, 1, 2, 3, 4))
self.assertEqual(Chem.MolFromSmiles('C[C@@](F)(Cl)OCC').GetSubstructMatch(b, ps), ())
self.assertEqual(
Chem.MolFromSmiles('C[C@](I)(Cl)OCC').GetSubstructMatch(b, ps), (0, 1, 2, 3, 4))
self.assertEqual(Chem.MolFromSmiles('C[C@@](I)(Cl)OCC').GetSubstructMatch(b, ps), ())
self.assertEqual(
Chem.MolFromSmiles('C[C@](F)(Cl)OCC').GetSubstructMatches(b, ps), ((0, 1, 2, 3, 4), ))
self.assertEqual(Chem.MolFromSmiles('C[C@@](F)(Cl)OCC').GetSubstructMatches(b, ps), ())
self.assertEqual(
Chem.MolFromSmiles('C[C@](I)(Cl)OCC').GetSubstructMatches(b, ps), ((0, 1, 2, 3, 4), ))
self.assertEqual(Chem.MolFromSmiles('C[C@@](I)(Cl)OCC').GetSubstructMatches(b, ps), ())
def testSubstructParametersBundles2(self):
b = Chem.MolBundle()
smis = ('C[C@](F)(Cl)O', 'C[C@](Br)(Cl)O', 'C[C@](I)(Cl)O')
for smi in smis:
b.AddMol(Chem.MolFromSmiles(smi))
self.assertEqual(len(b), 3)
b2 = Chem.MolBundle()
smis = ('C[C@@](F)(Cl)O', 'C[C@@](Br)(Cl)O', 'C[C@@](I)(Cl)O')
for smi in smis:
b2.AddMol(Chem.MolFromSmiles(smi))
self.assertEqual(len(b2), 3)
ps = Chem.SubstructMatchParameters()
ps.useChirality = True
self.assertTrue(b.HasSubstructMatch(b, ps))
self.assertFalse(b.HasSubstructMatch(b2, ps))
self.assertFalse(b2.HasSubstructMatch(b, ps))
self.assertEqual(b.GetSubstructMatch(b, ps), (0, 1, 2, 3, 4))
self.assertEqual(b.GetSubstructMatch(b2, ps), ())
self.assertEqual(b2.GetSubstructMatch(b, ps), ())
self.assertEqual(b.GetSubstructMatches(b, ps), ((0, 1, 2, 3, 4), ))
self.assertEqual(b.GetSubstructMatches(b2, ps), ())
self.assertEqual(b2.GetSubstructMatches(b, ps), ())
def testGithub2285(self):
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'github2285.sdf')
supp = Chem.ForwardSDMolSupplier(fileN, removeHs=False)
if hasattr(supp, "__next__"):
self.assertTrue(supp.__next__() is not None)
else:
self.assertTrue(supp.next() is not None)
def testBitVectProp(self):
bv = DataStructs.ExplicitBitVect(100)
m = Chem.MolFromSmiles("CC")
for atom in m.GetAtoms():
bv.SetBit(atom.GetIdx())
atom.SetExplicitBitVectProp("prop", bv)
for atom in m.GetAtoms():
bv = atom.GetExplicitBitVectProp("prop")
self.assertTrue(bv.GetBit(atom.GetIdx()))
def testBitVectQuery(self):
bv = DataStructs.ExplicitBitVect(4)
bv.SetBit(0)
bv.SetBit(2)
# wow, what a mouthfull..
qa = rdqueries.HasBitVectPropWithValueQueryAtom("prop", bv, tolerance=0.0)
m = Chem.MolFromSmiles("CC")
for atom in m.GetAtoms():
if atom.GetIdx() == 0:
atom.SetExplicitBitVectProp("prop", bv)
l = tuple([x.GetIdx() for x in m.GetAtomsMatchingQuery(qa)])
self.assertEqual(l, (0, ))
m = Chem.MolFromSmiles("CC")
for atom in m.GetAtoms():
bv = DataStructs.ExplicitBitVect(4)
bv.SetBit(atom.GetIdx())
atom.SetExplicitBitVectProp("prop", bv)
sma = Chem.MolFromSmarts("C")
for atom in sma.GetAtoms():
bv = DataStructs.ExplicitBitVect(4)
bv.SetBit(1)
qa = rdqueries.HasBitVectPropWithValueQueryAtom("prop", bv, tolerance=0.0)
atom.ExpandQuery(qa)
res = m.GetSubstructMatches(sma)
self.assertEqual(res, ((1, ), ))
sma = Chem.MolFromSmarts("C")
for atom in sma.GetAtoms():
bv = DataStructs.ExplicitBitVect(4)
bv.SetBit(0)
qa = rdqueries.HasBitVectPropWithValueQueryAtom("prop", bv, tolerance=0.0)
atom.ExpandQuery(qa)
res = m.GetSubstructMatches(sma)
self.assertEqual(res, ((0, ), ))
sma = Chem.MolFromSmarts("C")
for atom in sma.GetAtoms():
bv = DataStructs.ExplicitBitVect(4)
bv.SetBit(0)
qa = rdqueries.HasBitVectPropWithValueQueryAtom("prop", bv, tolerance=1.0)
atom.ExpandQuery(qa)
res = m.GetSubstructMatches(sma)
self.assertEqual(res, ((0, ), (1, )))
def testGithub2441(self):
m = Chem.MolFromSmiles("CC")
conf = Chem.Conformer(2)
m.AddConformer(conf, assignId=False)
m.GetConformer().SetIntProp("foo", 1)
m.GetConformer().SetProp("bar", "foo")
self.assertTrue(m.GetConformer().HasProp("foo"))
self.assertFalse(m.GetConformer().HasProp("food"))
d = m.GetConformer().GetPropsAsDict()
self.assertTrue('foo' in d)
self.assertTrue('bar' in d)
self.assertEqual(d['bar'], 'foo')
self.assertEqual(m.GetConformer().GetProp("bar"), "foo")
self.assertEqual(m.GetConformer().GetIntProp("foo"), 1)
def testGithub2479(self):
# Chemistry failure in last entry
smi2 = '''c1ccccc duff
c1ccccc1 ok
c1ccncc1 pyridine
C(C garbage
C1CC1 ok2
C1C(Cl)C1 ok3
CC(C)(C)(C)C duff2
'''
suppl2 = Chem.SmilesMolSupplier()
suppl2.SetData(smi2, titleLine=False, nameColumn=1)
l = [x for x in suppl2]
self.assertEqual(len(l), 7)
self.assertTrue(l[6] is None)
# SMILES failure in last entry
smi2 = '''c1ccccc duff
c1ccccc1 ok
c1ccncc1 pyridine
C(C garbage
C1CC1 ok2
C1C(Cl)C1 ok3
C1C(Cl)CCCC duff2
'''
suppl2 = Chem.SmilesMolSupplier()
suppl2.SetData(smi2, titleLine=False, nameColumn=1)
l = [x for x in suppl2]
self.assertEqual(len(l), 7)
self.assertTrue(l[6] is None)
sdf = b"""
Mrv1810 06051911332D
3 2 0 0 0 0 999 V2000
-13.3985 4.9850 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-12.7066 5.4343 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-12.0654 4.9151 0.0000 C 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
M END
$$$$
Mrv1810 06051911332D
3 2 0 0 0 0 999 V2000
-10.3083 4.8496 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-9.6408 5.3345 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
-9.0277 4.7825 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
M END
$$$$
Mrv1810 06051911332D
3 2 0 0 0 0 999 V2000
-10.3083 4.8496 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-9.6"""
suppl3 = Chem.SDMolSupplier()
suppl3.SetData(sdf)
l = [x for x in suppl3]
self.assertEqual(len(l), 3)
self.assertTrue(l[1] is None)
self.assertTrue(l[2] is None)
from io import BytesIO
sio = BytesIO(sdf)
suppl3 = Chem.ForwardSDMolSupplier(sio)
l = [x for x in suppl3]
self.assertEqual(len(l), 3)
self.assertTrue(l[1] is None)
self.assertTrue(l[2] is None)
sdf = b"""
Mrv1810 06051911332D
3 2 0 0 0 0 999 V2000
-13.3985 4.9850 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-12.7066 5.4343 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-12.0654 4.9151 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
M END
> <pval> (1)
[1,2,]
$$$$
Mrv1810 06051911332D
3 2 0 0 0 0 999 V2000
-10.3083 4.8496 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-9.6408 5.3345 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-9.0277 4.7825 0.0000 C 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
M END
> <pval> (1)
[1,2,]
"""
suppl3 = Chem.SDMolSupplier()
suppl3.SetData(sdf)
l = [x for x in suppl3]
self.assertEqual(len(l), 2)
self.assertTrue(l[0] is not None)
self.assertTrue(l[1] is not None)
from io import BytesIO
sio = BytesIO(sdf)
suppl3 = Chem.ForwardSDMolSupplier(sio)
l = [x for x in suppl3]
self.assertEqual(len(l), 2)
self.assertTrue(l[0] is not None)
self.assertTrue(l[1] is not None)
def testCMLWriter(self):
self.maxDiff = None # XXX
conf = Chem.Conformer(11)
conf.SetAtomPosition(0, [-0.95330, 0.60416, 1.01609])
conf.SetAtomPosition(1, [-1.00832, 1.68746, 0.83520])
conf.SetAtomPosition(2, [-1.96274, 0.16103, 0.94471])
conf.SetAtomPosition(3, [-0.57701, 0.44737, 2.04167])
conf.SetAtomPosition(4, [0.00000, 0.00000, 0.00000])
conf.SetAtomPosition(5, [-0.43038, 0.18596, -1.01377])
conf.SetAtomPosition(6, [0.22538, -1.36531, 0.19373])
conf.SetAtomPosition(7, [1.21993, -1.33937, 0.14580])
conf.SetAtomPosition(8, [1.38490, 0.73003, 0.00000])
conf.SetAtomPosition(9, [1.38490, 1.96795, 0.00000])
conf.SetAtomPosition(10, [2.35253, -0.07700, 0.00000])
emol = Chem.EditableMol(Chem.Mol())
for z in [6, 1, 1, 1, 6, 1, 8, 1, 6, 8, 8]:
emol.AddAtom(Chem.Atom(z))
emol.AddBond(0, 1, Chem.BondType.SINGLE)
emol.AddBond(0, 2, Chem.BondType.SINGLE)
emol.AddBond(0, 3, Chem.BondType.SINGLE)
emol.AddBond(0, 4, Chem.BondType.SINGLE)
emol.AddBond(4, 5, Chem.BondType.SINGLE)
emol.AddBond(4, 6, Chem.BondType.SINGLE)
emol.AddBond(4, 8, Chem.BondType.SINGLE)
emol.AddBond(6, 7, Chem.BondType.SINGLE)
emol.AddBond(8, 9, Chem.BondType.DOUBLE)
emol.AddBond(8, 10, Chem.BondType.SINGLE)
mol = emol.GetMol()
mol.SetProp('_Name', 'S-lactic acid')
mol.AddConformer(conf)
mol.GetAtomWithIdx(7).SetIsotope(2)
mol.GetAtomWithIdx(10).SetFormalCharge(-1)
mol.GetAtomWithIdx(4).SetChiralTag(Chem.ChiralType.CHI_TETRAHEDRAL_CCW)
cmlblock_expected = """<?xml version="1.0" encoding="utf-8"?>
<cml xmlns="http://www.xml-cml.org/schema" xmlns:convention="http://www.xml-cml.org/convention/" convention="convention:molecular">
<molecule id="m-1" formalCharge="-1" spinMultiplicity="1">
<name>S-lactic acid</name>
<atomArray>
<atom id="a0" elementType="C" formalCharge="0" hydrogenCount="3" x3="-0.953300" y3="0.604160" z3="1.016090"/>
<atom id="a1" elementType="H" formalCharge="0" hydrogenCount="0" x3="-1.008320" y3="1.687460" z3="0.835200"/>
<atom id="a2" elementType="H" formalCharge="0" hydrogenCount="0" x3="-1.962740" y3="0.161030" z3="0.944710"/>
<atom id="a3" elementType="H" formalCharge="0" hydrogenCount="0" x3="-0.577010" y3="0.447370" z3="2.041670"/>
<atom id="a4" elementType="C" formalCharge="0" hydrogenCount="1" x3="0.000000" y3="0.000000" z3="0.000000">
<atomParity atomRefs4="a0 a5 a6 a8">1</atomParity>
</atom>
<atom id="a5" elementType="H" formalCharge="0" hydrogenCount="0" x3="-0.430380" y3="0.185960" z3="-1.013770"/>
<atom id="a6" elementType="O" formalCharge="0" hydrogenCount="1" x3="0.225380" y3="-1.365310" z3="0.193730"/>
<atom id="a7" elementType="H" formalCharge="0" hydrogenCount="0" isotopeNumber="2" x3="1.219930" y3="-1.339370" z3="0.145800"/>
<atom id="a8" elementType="C" formalCharge="0" hydrogenCount="0" x3="1.384900" y3="0.730030" z3="0.000000"/>
<atom id="a9" elementType="O" formalCharge="0" hydrogenCount="0" x3="1.384900" y3="1.967950" z3="0.000000"/>
<atom id="a10" elementType="O" formalCharge="-1" hydrogenCount="0" x3="2.352530" y3="-0.077000" z3="0.000000"/>
</atomArray>
<bondArray>
<bond atomRefs2="a0 a1" id="b0" order="S"/>
<bond atomRefs2="a0 a2" id="b1" order="S"/>
<bond atomRefs2="a0 a3" id="b2" order="S"/>
<bond atomRefs2="a0 a4" id="b3" order="S"/>
<bond atomRefs2="a4 a5" id="b4" order="S" bondStereo="H"/>
<bond atomRefs2="a4 a6" id="b5" order="S"/>
<bond atomRefs2="a4 a8" id="b6" order="S"/>
<bond atomRefs2="a6 a7" id="b7" order="S"/>
<bond atomRefs2="a8 a9" id="b8" order="D"/>
<bond atomRefs2="a8 a10" id="b9" order="S"/>
</bondArray>
</molecule>
</cml>
"""
self.assertEqual(Chem.MolToCMLBlock(mol), cmlblock_expected)
def testXYZ(self):
conf = Chem.Conformer(5)
conf.SetAtomPosition(0, [0.000, 0.000, 0.000])
conf.SetAtomPosition(1, [-0.635, -0.635, 0.635])
conf.SetAtomPosition(2, [-0.635, 0.635, -0.635])
conf.SetAtomPosition(3, [0.635, -0.635, -0.635])
conf.SetAtomPosition(4, [0.635, 0.635, 0.635])
emol = Chem.EditableMol(Chem.Mol())
for z in [6, 1, 1, 1, 1]:
emol.AddAtom(Chem.Atom(z))
mol = emol.GetMol()
mol.SetProp('_Name', 'methane\nthis part should not be output')
mol.AddConformer(conf)
xyzblock_expected = """5
methane
C 0.000000 0.000000 0.000000
H -0.635000 -0.635000 0.635000
H -0.635000 0.635000 -0.635000
H 0.635000 -0.635000 -0.635000
H 0.635000 0.635000 0.635000
"""
self.assertEqual(Chem.MolToXYZBlock(mol), xyzblock_expected)
def testSanitizationExceptionBasics(self):
try:
Chem.SanitizeMol(Chem.MolFromSmiles('CFC', sanitize=False))
except Chem.AtomValenceException as exc:
self.assertEqual(exc.cause.GetAtomIdx(), 1)
else:
self.assertFalse(True)
try:
Chem.SanitizeMol(Chem.MolFromSmiles('c1cc1', sanitize=False))
except Chem.KekulizeException as exc:
self.assertEqual(exc.cause.GetAtomIndices(), (0, 1, 2))
else:
self.assertFalse(True)
def testSanitizationExceptionHierarchy(self):
with self.assertRaises(Chem.AtomValenceException):
Chem.SanitizeMol(Chem.MolFromSmiles('CFC', sanitize=False))
with self.assertRaises(Chem.AtomSanitizeException):
Chem.SanitizeMol(Chem.MolFromSmiles('CFC', sanitize=False))
with self.assertRaises(Chem.MolSanitizeException):
Chem.SanitizeMol(Chem.MolFromSmiles('CFC', sanitize=False))
with self.assertRaises(ValueError):
Chem.SanitizeMol(Chem.MolFromSmiles('CFC', sanitize=False))
with self.assertRaises(Chem.KekulizeException):
Chem.SanitizeMol(Chem.MolFromSmiles('c1cc1', sanitize=False))
with self.assertRaises(Chem.MolSanitizeException):
Chem.SanitizeMol(Chem.MolFromSmiles('c1cc1', sanitize=False))
with self.assertRaises(ValueError):
Chem.SanitizeMol(Chem.MolFromSmiles('c1cc1', sanitize=False))
def testNoExceptionSmilesParserParams(self):
"""
MolFromSmiles should catch exceptions even when SmilesParserParams
is provided.
"""
smiles_params = Chem.SmilesParserParams()
mol = Chem.MolFromSmiles("C1CC", smiles_params)
self.assertIsNone(mol)
def testDetectChemistryProblems(self):
m = Chem.MolFromSmiles('CFCc1cc1FC', sanitize=False)
ps = Chem.DetectChemistryProblems(m)
self.assertEqual(len(ps), 3)
self.assertEqual([x.GetType() for x in ps],
['AtomValenceException', 'AtomValenceException', 'KekulizeException'])
self.assertEqual(ps[0].GetAtomIdx(), 1)
self.assertEqual(ps[1].GetAtomIdx(), 6)
self.assertEqual(ps[2].GetAtomIndices(), (3, 4, 5))
def testGithub2611(self):
mol = Chem.MolFromSmiles('ONCS.ONCS')
for atom in mol.GetAtoms():
atom.SetIsotope(atom.GetIdx())
order1 = list(
Chem.CanonicalRankAtomsInFragment(mol, atomsToUse=range(0, 4), breakTies=False,
includeIsotopes=True))
order2 = list(
Chem.CanonicalRankAtomsInFragment(mol, atomsToUse=range(0, 8), breakTies=False,
includeIsotopes=False))
self.assertNotEqual(order1[:4], order2[4:])
# ensure that the orders are ignored in the second batch
self.assertEqual(order2[:4], order2[4:])
for smi in ['ONCS.ONCS', 'F[C@@H](Br)[C@H](F)Cl']:
mol = Chem.MolFromSmiles(smi)
for atom in mol.GetAtoms():
atom.SetIsotope(atom.GetIdx())
for iso, chiral in [(True, True), (True, False), (False, True), (False, False)]:
order1 = list(
Chem.CanonicalRankAtomsInFragment(mol, atomsToUse=range(0, mol.GetNumAtoms()),
bondsToUse=range(0,
mol.GetNumBonds()), breakTies=False,
includeIsotopes=iso, includeChirality=chiral))
order2 = list(
Chem.CanonicalRankAtomsInFragment(mol, atomsToUse=range(0, mol.GetNumAtoms()),
bondsToUse=range(0,
mol.GetNumBonds()), breakTies=True,
includeIsotopes=iso, includeChirality=chiral))
order3 = list(
Chem.CanonicalRankAtoms(mol, breakTies=False, includeIsotopes=iso,
includeChirality=chiral))
order4 = list(
Chem.CanonicalRankAtoms(mol, breakTies=True, includeIsotopes=iso,
includeChirality=chiral))
self.assertEqual(order1, order3)
self.assertEqual(order2, order4)
def testSetBondStereoFromDirections(self):
m1 = Chem.MolFromMolBlock(
'''
Mrv1810 10141909482D
4 3 0 0 0 0 999 V2000
3.3412 -2.9968 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.5162 -2.9968 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.1037 -3.7112 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.7537 -2.2823 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0 0 0 0
2 3 1 0 0 0 0
1 4 1 0 0 0 0
M END
''', sanitize=False)
self.assertEqual(m1.GetBondBetweenAtoms(0, 1).GetBondType(), Chem.BondType.DOUBLE)
self.assertEqual(m1.GetBondBetweenAtoms(0, 1).GetStereo(), Chem.BondStereo.STEREONONE)
Chem.SetBondStereoFromDirections(m1)
self.assertEqual(m1.GetBondBetweenAtoms(0, 1).GetStereo(), Chem.BondStereo.STEREOTRANS)
m2 = Chem.MolFromMolBlock(
'''
Mrv1810 10141909542D
4 3 0 0 0 0 999 V2000
3.4745 -5.2424 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.6495 -5.2424 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.2370 -5.9569 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.8870 -5.9569 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0 0 0 0
2 3 1 0 0 0 0
1 4 1 0 0 0 0
M END
''', sanitize=False)
self.assertEqual(m2.GetBondBetweenAtoms(0, 1).GetBondType(), Chem.BondType.DOUBLE)
self.assertEqual(m2.GetBondBetweenAtoms(0, 1).GetStereo(), Chem.BondStereo.STEREONONE)
Chem.SetBondStereoFromDirections(m2)
self.assertEqual(m2.GetBondBetweenAtoms(0, 1).GetStereo(), Chem.BondStereo.STEREOCIS)
def testSetBondDirFromStereo(self):
m1 = Chem.MolFromSmiles('CC=CC')
m1.GetBondWithIdx(1).SetStereoAtoms(0, 3)
m1.GetBondWithIdx(1).SetStereo(Chem.BondStereo.STEREOCIS)
Chem.SetDoubleBondNeighborDirections(m1)
self.assertEqual(Chem.MolToSmiles(m1), r"C/C=C\C")
self.assertEqual(m1.GetBondWithIdx(0).GetBondDir(), Chem.BondDir.ENDUPRIGHT)
self.assertEqual(m1.GetBondWithIdx(2).GetBondDir(), Chem.BondDir.ENDDOWNRIGHT)
def testAssignChiralTypesFromMolParity(self):
class TestAssignChiralTypesFromMolParity:
class BondDef:
def __init__(self, bi, ei, t):
self.beginIdx = bi
self.endIdx = ei
self.type = t
def __init__(self, mol, parent):
self.parent = parent
self.parityMap = {
Chem.ChiralType.CHI_TETRAHEDRAL_CW: 1,
Chem.ChiralType.CHI_TETRAHEDRAL_CCW: 2,
Chem.ChiralType.CHI_UNSPECIFIED: 0,
Chem.ChiralType.CHI_OTHER: 0
}
self.d_rwMol = Chem.RWMol(mol)
self.assignMolParity()
self.fillBondDefVect()
Chem.AssignAtomChiralTagsFromMolParity(self.d_rwMol)
self.d_refSmiles = Chem.MolToSmiles(self.d_rwMol)
self.heapPermutation()
def assignMolParity(self):
Chem.AssignAtomChiralTagsFromStructure(self.d_rwMol)
for a in self.d_rwMol.GetAtoms():
parity = self.parityMap[a.GetChiralTag()]
a.SetIntProp("molParity", parity)
a.SetChiralTag(Chem.ChiralType.CHI_UNSPECIFIED)
def fillBondDefVect(self):
self.d_bondDefVect = [
self.BondDef(b.GetBeginAtomIdx(), b.GetEndAtomIdx(), b.GetBondType())
for b in self.d_rwMol.GetBonds()
]
def stripBonds(self):
for i in reversed(range(self.d_rwMol.GetNumBonds())):
b = self.d_rwMol.GetBondWithIdx(i)
self.d_rwMol.RemoveBond(b.GetBeginAtomIdx(), b.GetEndAtomIdx())
def addBonds(self):
[
self.d_rwMol.AddBond(bondDef.beginIdx, bondDef.endIdx, bondDef.type)
for bondDef in self.d_bondDefVect
]
def checkBondPermutation(self):
self.stripBonds()
self.addBonds()
Chem.SanitizeMol(self.d_rwMol)
Chem.AssignAtomChiralTagsFromMolParity(self.d_rwMol)
self.parent.assertEqual(Chem.MolToSmiles(self.d_rwMol), self.d_refSmiles)
def heapPermutation(self, s=0):
# if size becomes 1 the permutation is ready to use
if (s == 0):
s = len(self.d_bondDefVect)
if (s == 1):
self.checkBondPermutation()
return
for i in range(s):
self.heapPermutation(s - 1)
# if size is odd, swap first and last element
j = 0 if (s % 2 == 1) else i
self.d_bondDefVect[j], self.d_bondDefVect[s - 1] = \
self.d_bondDefVect[s - 1], self.d_bondDefVect[j]
molb = """
RDKit 3D
6 5 0 0 1 0 0 0 0 0999 V2000
-2.9747 1.7234 0.0753 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.4586 1.4435 0.1253 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.5885 2.6215 1.4893 Cl 0 0 0 0 0 0 0 0 0 0 0 0
-3.7306 0.3885 -0.0148 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3395 3.0471 0.1580 Br 0 0 0 0 0 0 0 0 0 0 0 0
-1.1574 0.7125 1.2684 F 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
1 3 1 0
1 4 1 0
2 5 1 0
2 6 1 0
M END
"""
m = Chem.RWMol(Chem.MolFromMolBlock(molb, sanitize=True, removeHs=False))
self.assertIsNotNone(m)
TestAssignChiralTypesFromMolParity(m, self)
def testCXSMILESErrors(self):
smi = "CCC |FAILURE|"
ps = Chem.SmilesParserParams()
ps.strictCXSMILES = False
m = Chem.MolFromSmiles(smi, ps)
self.assertTrue(m is not None)
self.assertEqual(m.GetNumAtoms(), 3)
def testRemoveHsParams(self):
smips = Chem.SmilesParserParams()
smips.removeHs = False
m = Chem.MolFromSmiles('F.[H]', smips)
ps = Chem.RemoveHsParameters()
m = Chem.RemoveHs(m, ps)
self.assertEqual(m.GetNumAtoms(), 2)
ps.removeDegreeZero = True
m = Chem.RemoveHs(m, ps)
self.assertEqual(m.GetNumAtoms(), 1)
m = Chem.MolFromSmiles('F[H-]F', smips)
ps = Chem.RemoveHsParameters()
m = Chem.RemoveHs(m, ps)
self.assertEqual(m.GetNumAtoms(), 3)
m = Chem.MolFromSmiles('F[H-]F', smips)
ps.removeHigherDegrees = True
m = Chem.RemoveHs(m, ps)
self.assertEqual(m.GetNumAtoms(), 2)
m = Chem.MolFromSmiles('[H][H]', smips)
ps = Chem.RemoveHsParameters()
m = Chem.RemoveHs(m, ps)
self.assertEqual(m.GetNumAtoms(), 2)
m = Chem.MolFromSmiles('[H][H]', smips)
ps.removeOnlyHNeighbors = True
m = Chem.RemoveHs(m, ps)
self.assertEqual(m.GetNumAtoms(), 0)
m = Chem.MolFromSmiles('F[2H]', smips)
ps = Chem.RemoveHsParameters()
m = Chem.RemoveHs(m, ps)
self.assertEqual(m.GetNumAtoms(), 2)
m = Chem.MolFromSmiles('F[2H]', smips)
ps.removeIsotopes = True
m = Chem.RemoveHs(m, ps)
self.assertEqual(m.GetNumAtoms(), 1)
m = Chem.MolFromSmiles('c1c(C([2H])([2H])F)cccc1', smips)
ps = Chem.RemoveHsParameters()
m_noh = Chem.RemoveHs(m, ps)
self.assertEqual(m_noh.GetNumAtoms(), m.GetNumAtoms())
ps.removeAndTrackIsotopes = True
m_noh = Chem.RemoveHs(m, ps)
self.assertEqual(m_noh.GetNumAtoms(), m.GetNumAtoms() - 2)
self.assertTrue(m_noh.GetAtomWithIdx(2).HasProp("_isotopicHs"))
self.assertEqual(tuple(m_noh.GetAtomWithIdx(2).GetPropsAsDict().get("_isotopicHs")), (2, 2))
m_h = Chem.AddHs(m_noh)
self.assertFalse(m_h.GetAtomWithIdx(2).HasProp("_isotopicHs"))
self.assertEqual(
sum([
1 for nbr in m_h.GetAtomWithIdx(2).GetNeighbors()
if (nbr.GetAtomicNum() == 1 and nbr.GetIsotope())
]), 2)
m = Chem.MolFromSmiles('*[H]', smips)
ps = Chem.RemoveHsParameters()
m = Chem.RemoveHs(m, ps)
self.assertEqual(m.GetNumAtoms(), 2)
m = Chem.MolFromSmiles('*[H]', smips)
ps.removeDummyNeighbors = True
m = Chem.RemoveHs(m, ps)
self.assertEqual(m.GetNumAtoms(), 1)
m = Chem.MolFromSmiles('F/C=N/[H]', smips)
ps = Chem.RemoveHsParameters()
m = Chem.RemoveHs(m, ps)
self.assertEqual(m.GetNumAtoms(), 4)
m = Chem.MolFromSmiles('F/C=N/[H]', smips)
ps.removeDefiningBondStereo = True
m = Chem.RemoveHs(m, ps)
self.assertEqual(m.GetNumAtoms(), 3)
m = Chem.MolFromSmiles('FC([H])(O)Cl', smips)
m.GetBondBetweenAtoms(1, 2).SetBondDir(Chem.BondDir.BEGINWEDGE)
ps = Chem.RemoveHsParameters()
m = Chem.RemoveHs(m, ps)
self.assertEqual(m.GetNumAtoms(), 4)
m = Chem.MolFromSmiles('FC([H])(O)Cl', smips)
m.GetBondBetweenAtoms(1, 2).SetBondDir(Chem.BondDir.BEGINWEDGE)
ps.removeWithWedgedBond = False
m = Chem.RemoveHs(m, ps)
self.assertEqual(m.GetNumAtoms(), 5)
m = Chem.MolFromSmarts('F[#1]')
ps = Chem.RemoveHsParameters()
m = Chem.RemoveHs(m, ps)
self.assertEqual(m.GetNumAtoms(), 2)
m = Chem.MolFromSmarts('F[#1]')
ps.removeWithQuery = True
m = Chem.RemoveHs(m, ps)
self.assertEqual(m.GetNumAtoms(), 1)
m = Chem.MolFromSmiles('[C@]12([H])CCC1CO2.[H+].F[H-]F.[H][H].[H]*.F/C=C/[H]')
m = Chem.RemoveAllHs(m)
for at in m.GetAtoms():
self.assertNotEqual(at.GetAtomicNum(), 1)
def testPickleCoordsAsDouble(self):
import pickle
m = Chem.MolFromSmiles('C')
test_num = 1e50
conf = Chem.Conformer(1)
conf.SetAtomPosition(0, (test_num, 0.0, 0.0))
m.AddConformer(conf)
opts = Chem.GetDefaultPickleProperties()
Chem.SetDefaultPickleProperties(Chem.PropertyPickleOptions.NoProps)
self.assertNotEqual(pickle.loads(pickle.dumps(m)).GetConformer().GetAtomPosition(0).x, test_num)
try:
Chem.SetDefaultPickleProperties(Chem.PropertyPickleOptions.CoordsAsDouble)
self.assertEqual(pickle.loads(pickle.dumps(m)).GetConformer().GetAtomPosition(0).x, test_num)
finally:
Chem.SetDefaultPickleProperties(opts)
def testCustomSubstructMatchCheck(self):
def accept_none(mol, vect):
return False
def accept_all(mol, vect):
return True
def accept_large(mol, vect):
return sum(vect) > 5
m = Chem.MolFromSmiles('CCOCC')
p = Chem.MolFromSmiles('CCO')
ps = Chem.SubstructMatchParameters()
self.assertEqual(len(m.GetSubstructMatches(p, ps)), 2)
ps.setExtraFinalCheck(accept_none)
self.assertEqual(len(m.GetSubstructMatches(p, ps)), 0)
self.assertEqual(len(m.GetSubstructMatch(p, ps)), 0)
self.assertFalse(m.HasSubstructMatch(p, ps))
ps.setExtraFinalCheck(accept_all)
self.assertEqual(len(m.GetSubstructMatches(p, ps)), 2)
self.assertEqual(len(m.GetSubstructMatch(p, ps)), 3)
self.assertTrue(m.HasSubstructMatch(p, ps))
ps.setExtraFinalCheck(accept_large)
self.assertEqual(len(m.GetSubstructMatches(p, ps)), 1)
self.assertEqual(len(m.GetSubstructMatch(p, ps)), 3)
self.assertTrue(m.HasSubstructMatch(p, ps))
def testMostSubstitutedCoreMatch(self):
core = Chem.MolFromSmarts("[*:1]c1cc([*:2])ccc1[*:3]")
orthoMeta = Chem.MolFromSmiles("c1ccc(-c2ccc(-c3ccccc3)c(-c3ccccc3)c2)cc1")
ortho = Chem.MolFromSmiles("c1ccc(-c2ccccc2-c2ccccc2)cc1")
meta = Chem.MolFromSmiles("c1ccc(-c2cccc(-c3ccccc3)c2)cc1")
biphenyl = Chem.MolFromSmiles("c1ccccc1-c1ccccc1")
phenyl = Chem.MolFromSmiles("c1ccccc1")
def numHsMatchingDummies(mol, core, match):
return sum([
1 for qi, ai in enumerate(match) if core.GetAtomWithIdx(qi).GetAtomicNum() == 0
and mol.GetAtomWithIdx(ai).GetAtomicNum() == 1
])
for mol, res in ((orthoMeta, 0), (ortho, 1), (meta, 1), (biphenyl, 2), (phenyl, 3)):
mol = Chem.AddHs(mol)
matches = mol.GetSubstructMatches(core)
bestMatch = Chem.GetMostSubstitutedCoreMatch(mol, core, matches)
self.assertEqual(numHsMatchingDummies(mol, core, bestMatch), res)
ctrlCounts = sorted([numHsMatchingDummies(mol, core, match) for match in matches])
sortedCounts = [
numHsMatchingDummies(mol, core, match)
for match in Chem.SortMatchesByDegreeOfCoreSubstitution(mol, core, matches)
]
self.assertEqual(len(ctrlCounts), len(sortedCounts))
self.assertTrue(all(ctrl == sortedCounts[i] for i, ctrl in enumerate(ctrlCounts)))
with self.assertRaises(ValueError):
Chem.GetMostSubstitutedCoreMatch(orthoMeta, core, [])
with self.assertRaises(ValueError):
Chem.SortMatchesByDegreeOfCoreSubstitution(orthoMeta, core, [])
def testSetCoordsTerminalAtom(self):
mol = Chem.MolFromMolBlock("""
RDKit 2D
6 6 0 0 0 0 0 0 0 0999 V2000
1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7500 1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7500 1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0
2 3 1 0
3 4 2 0
4 5 1 0
5 6 2 0
6 1 1 0
M END
""")
mol = Chem.RWMol(mol)
atom = Chem.Atom(0)
idx = mol.AddAtom(atom)
mol.AddBond(idx, 0)
Chem.SetTerminalAtomCoords(mol, idx, 0)
coord = mol.GetConformer().GetAtomPosition(idx)
self.assertAlmostEqual(coord.x, 2.5, 2)
self.assertAlmostEqual(coord.y, 0, 2)
self.assertAlmostEqual(coord.z, 0, 2)
def testSuppliersReadingDirectories(self):
# this is an odd one, basically we need to check that we don't hang
# which is pretty much a bad test in my opinion, but YMMV
d = tempfile.mkdtemp()
self.assertTrue(os.path.exists(d))
for supplier in [
Chem.SmilesMolSupplier,
Chem.SDMolSupplier,
Chem.TDTMolSupplier,
#Chem.CompressedSDMolSupplier,
]:
print("supplier:", supplier)
with self.assertRaises(OSError):
suppl = supplier(d)
if hasattr(Chem, 'MaeMolSupplier'):
with self.assertRaises(OSError):
suppl = Chem.MaeMolSupplier(d)
os.rmdir(d)
def testRandomSmilesVect(self):
m = Chem.MolFromSmiles("C1OCC1N(CO)(Cc1ccccc1NCCl)")
v = Chem.MolToRandomSmilesVect(m, 5, randomSeed=0xf00d)
self.assertEqual(v, [
"c1cc(CN(C2COC2)CO)c(cc1)NCCl", "N(CCl)c1c(CN(C2COC2)CO)cccc1", "N(CCl)c1ccccc1CN(C1COC1)CO",
"OCN(Cc1ccccc1NCCl)C1COC1", "C(N(C1COC1)Cc1c(cccc1)NCCl)O"
])
v = Chem.MolToRandomSmilesVect(m, 5, randomSeed=0xf00d, allHsExplicit=True)
self.assertEqual(v, [
"[cH]1[cH][c]([CH2][N]([CH]2[CH2][O][CH2]2)[CH2][OH])[c]([cH][cH]1)[NH][CH2][Cl]",
"[NH]([CH2][Cl])[c]1[c]([CH2][N]([CH]2[CH2][O][CH2]2)[CH2][OH])[cH][cH][cH][cH]1",
"[NH]([CH2][Cl])[c]1[cH][cH][cH][cH][c]1[CH2][N]([CH]1[CH2][O][CH2]1)[CH2][OH]",
"[OH][CH2][N]([CH2][c]1[cH][cH][cH][cH][c]1[NH][CH2][Cl])[CH]1[CH2][O][CH2]1",
"[CH2]([N]([CH]1[CH2][O][CH2]1)[CH2][c]1[c]([cH][cH][cH][cH]1)[NH][CH2][Cl])[OH]"
])
def testGithub3198(self):
ps = Chem.SmilesParserParams()
ps.removeHs = False
m = Chem.MolFromSmiles('[H]OC(F).[Na]', ps)
qa = rdqueries.AAtomQueryAtom()
self.assertEqual(tuple(x.GetIdx() for x in m.GetAtomsMatchingQuery(qa)), (1, 2, 3, 4))
qa = rdqueries.AHAtomQueryAtom()
self.assertEqual(tuple(x.GetIdx() for x in m.GetAtomsMatchingQuery(qa)), (0, 1, 2, 3, 4))
qa = rdqueries.QAtomQueryAtom()
self.assertEqual(tuple(x.GetIdx() for x in m.GetAtomsMatchingQuery(qa)), (1, 3, 4))
qa = rdqueries.QHAtomQueryAtom()
self.assertEqual(tuple(x.GetIdx() for x in m.GetAtomsMatchingQuery(qa)), (0, 1, 3, 4))
qa = rdqueries.XAtomQueryAtom()
self.assertEqual(tuple(x.GetIdx() for x in m.GetAtomsMatchingQuery(qa)), (3, ))
qa = rdqueries.XHAtomQueryAtom()
self.assertEqual(tuple(x.GetIdx() for x in m.GetAtomsMatchingQuery(qa)), (0, 3))
qa = rdqueries.MAtomQueryAtom()
self.assertEqual(tuple(x.GetIdx() for x in m.GetAtomsMatchingQuery(qa)), (4, ))
qa = rdqueries.MHAtomQueryAtom()
self.assertEqual(tuple(x.GetIdx() for x in m.GetAtomsMatchingQuery(qa)), (0, 4))
def testAdjustQueryPropertiesFiveRings(self):
mol = Chem.MolFromSmiles('c1cc[nH]c1')
nops = Chem.AdjustQueryParameters.NoAdjustments()
nmol = Chem.AdjustQueryProperties(mol, nops)
self.assertEqual(Chem.MolToSmarts(nmol), "[#6]1:[#6]:[#6]:[#7H]:[#6]:1")
nops.adjustConjugatedFiveRings = True
nmol = Chem.AdjustQueryProperties(mol, nops)
self.assertEqual(Chem.MolToSmarts(nmol), "[#6]1-,=,:[#6]-,=,:[#6]-,=,:[#7H]-,=,:[#6]-,=,:1")
def testFindPotentialStereo(self):
mol = Chem.MolFromSmiles('C[C@H](F)C=CC')
si = Chem.FindPotentialStereo(mol)
self.assertEqual(len(si), 2)
self.assertEqual(si[0].type, Chem.StereoType.Atom_Tetrahedral)
self.assertEqual(si[0].specified, Chem.StereoSpecified.Specified)
self.assertEqual(si[0].centeredOn, 1)
self.assertEqual(si[0].descriptor, Chem.StereoDescriptor.Tet_CCW)
self.assertEqual(list(si[0].controllingAtoms), [0, 2, 3])
self.assertEqual(si[1].type, Chem.StereoType.Bond_Double)
self.assertEqual(si[1].specified, Chem.StereoSpecified.Unspecified)
self.assertEqual(si[1].centeredOn, 3)
self.assertEqual(si[1].descriptor, Chem.StereoDescriptor.NoValue)
self.assertEqual(list(si[1].controllingAtoms),
[1, Chem.StereoInfo.NOATOM, 5, Chem.StereoInfo.NOATOM])
def testNewFindMolChiralCenters(self):
mol = Chem.MolFromSmiles('C[C@H](F)C=CC(F)Cl')
ctrs = Chem.FindMolChiralCenters(mol, useLegacyImplementation=False)
self.assertEqual(len(ctrs), 1)
self.assertEqual(ctrs, [(1, 'S')])
ctrs = Chem.FindMolChiralCenters(mol, useLegacyImplementation=False, includeCIP=False)
self.assertEqual(len(ctrs), 1)
self.assertEqual(ctrs, [(1, 'Tet_CCW')])
ctrs = Chem.FindMolChiralCenters(mol, useLegacyImplementation=False, includeUnassigned=True,
includeCIP=False)
self.assertEqual(len(ctrs), 2)
self.assertEqual(ctrs, [(1, 'Tet_CCW'), (5, '?')])
ctrs = Chem.FindMolChiralCenters(mol, useLegacyImplementation=False, includeUnassigned=True,
includeCIP=True)
self.assertEqual(len(ctrs), 2)
self.assertEqual(ctrs, [(1, 'S'), (5, '?')])
def testMolFromPNG(self):
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'colchicine.png')
mol = Chem.MolFromPNGFile(fileN)
self.assertIsNotNone(mol)
self.assertEqual(mol.GetNumAtoms(), 29)
with open(fileN, 'rb') as inf:
d = inf.read()
mol = Chem.MolFromPNGString(d)
self.assertIsNotNone(mol)
self.assertEqual(mol.GetNumAtoms(), 29)
def testMolToPNG(self):
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'colchicine.no_metadata.png')
with open(fileN, 'rb') as inf:
d = inf.read()
mol = Chem.MolFromSmiles("COc1cc2c(c(OC)c1OC)-c1ccc(OC)c(=O)cc1[C@@H](NC(C)=O)CC2")
self.assertIsNotNone(mol)
self.assertEqual(mol.GetNumAtoms(), 29)
nd = Chem.MolMetadataToPNGString(mol, d)
mol = Chem.MolFromPNGString(nd)
self.assertIsNotNone(mol)
self.assertEqual(mol.GetNumAtoms(), 29)
nd = Chem.MolMetadataToPNGFile(mol, fileN)
mol = Chem.MolFromPNGString(nd)
self.assertIsNotNone(mol)
self.assertEqual(mol.GetNumAtoms(), 29)
def testMolsFromPNG(self):
refMols = [Chem.MolFromSmiles(x) for x in ('c1ccccc1', 'CCO', 'CC(=O)O', 'c1ccccn1')]
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'multiple_mols.png')
mols = Chem.MolsFromPNGFile(fileN)
self.assertEqual(len(mols), len(refMols))
for mol, refMol in zip(mols, refMols):
self.assertEqual(Chem.MolToSmiles(mol), Chem.MolToSmiles(refMol))
def testMetadataToPNG(self):
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'colchicine.png')
with open(fileN, 'rb') as inf:
d = inf.read()
mol = Chem.MolFromPNGString(d)
nd = Chem.MolMetadataToPNGString(mol, d)
vals = {'foo': '1', 'bar': '2'}
nd = Chem.AddMetadataToPNGString(vals, nd)
nvals = Chem.MetadataFromPNGString(nd)
self.assertTrue('foo' in nvals)
self.assertEqual(nvals['foo'], b'1')
self.assertTrue('bar' in nvals)
self.assertEqual(nvals['bar'], b'2')
nd = Chem.AddMetadataToPNGFile(vals, fileN)
nvals = Chem.MetadataFromPNGString(nd)
self.assertTrue('foo' in nvals)
self.assertEqual(nvals['foo'], b'1')
self.assertTrue('bar' in nvals)
self.assertEqual(nvals['bar'], b'2')
vals = {'foo': 1, 'bar': '2'}
with self.assertRaises(TypeError):
nd = Chem.AddMetadataToPNGString(vals, d)
def test_github3403(self):
core1 = "[$(C-!@[a])](=O)(Cl)"
sma = Chem.MolFromSmarts(core1)
m = Chem.MolFromSmiles("c1ccccc1C(=O)Cl")
self.assertFalse(m.HasSubstructMatch(sma, recursionPossible=False))
m = Chem.MolFromSmiles("c1ccccc1C(=O)Cl")
self.assertTrue(m.HasSubstructMatch(sma))
m = Chem.MolFromSmiles("c1ccccc1C(=O)Cl")
self.assertFalse(m.HasSubstructMatch(sma, recursionPossible=False))
def test_github3517(self):
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'NCI_aids_few.sdf')
sdSup = Chem.SDMolSupplier(fileN)
mols_list = list(sdSup)
mols_list_compr = [m for m in sdSup]
self.assertEqual(len(mols_list), len(mols_list_compr))
def test_github3492(self):
def read_smile(s):
m = Chem.MolFromSmiles(s)
rdkit.Chem.rdDepictor.Compute2DCoords(m)
return m
def sq_dist(a, b):
ab = [a[i] - b[i] for i, _ in enumerate(a)]
return sum([d * d for d in ab])
self.assertIsNotNone(Chem.MolFromSmiles("OCCN").GetAtoms()[0].GetOwningMol())
self.assertEqual([Chem.MolFromSmiles("OCCN").GetAtoms()[i].GetAtomicNum() for i in range(4)],
[8, 6, 6, 7])
self.assertIsNotNone(Chem.MolFromSmiles("O=CCC=N").GetBonds()[0].GetOwningMol())
self.assertEqual(
[Chem.MolFromSmiles("O=CCC=N").GetBonds()[i].GetBondType() for i in range(4)],
[Chem.BondType.DOUBLE, Chem.BondType.SINGLE, Chem.BondType.SINGLE, Chem.BondType.DOUBLE])
self.assertIsNotNone(read_smile("CCC").GetConformers()[0].GetOwningMol())
pos = read_smile("CCC").GetConformers()[0].GetPositions()
self.assertAlmostEqual(sq_dist(pos[0], pos[1]), sq_dist(pos[1], pos[2]))
def test_github3553(self):
from io import StringIO
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'Wrap', 'test_data',
'github3553.sdf')
sdSup = Chem.SDMolSupplier(fileN)
for mol in sdSup:
pval = mol.GetProp('boiling.point.predicted')
sio = StringIO()
w = Chem.SDWriter(sio)
w.SetKekulize(True)
w.SetForceV3000(True)
w.write(mol)
w.flush()
txt = sio.getvalue()
self.assertTrue(pval in txt)
def test_github1631(self):
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'1CRN.pdb')
m = Chem.MolFromPDBFile(fileN)
info = m.GetAtomWithIdx(0).GetPDBResidueInfo()
self.assertEqual(info.GetName(), " N ")
self.assertEqual(info.GetResidueName(), "THR")
self.assertAlmostEqual(info.GetTempFactor(), 13.79, 2)
m2 = Chem.MolFromSmiles('CC(C(C(=O)O)N)O')
self.assertTrue(m2.GetAtomWithIdx(6).GetPDBResidueInfo() is None)
m2.GetAtomWithIdx(6).SetPDBResidueInfo(info)
info2 = m2.GetAtomWithIdx(6).GetPDBResidueInfo()
self.assertEqual(info2.GetName(), " N ")
self.assertEqual(info2.GetResidueName(), "THR")
self.assertAlmostEqual(info2.GetTempFactor(), 13.79, 2)
def testMolzip(self):
tests = [["C[*:1]", "N[*:1]", "CN", Chem.MolzipParams()]]
for a, b, res, params in tests:
self.assertEqual(
Chem.CanonSmiles(res),
Chem.MolToSmiles(Chem.molzip(Chem.MolFromSmiles(a), Chem.MolFromSmiles(b), params)))
# multiple arg test
a = Chem.MolFromSmiles('C=C[1*]')
b = Chem.MolFromSmiles('O/C=N/[1*]')
p = Chem.MolzipParams()
p.label = Chem.MolzipLabel.Isotope
c = Chem.molzip(a, b, p)
self.assertEqual(Chem.MolToSmiles(c), 'C=C/N=C/O')
# single argument test
a = Chem.MolFromSmiles('C=C[1*].O/C=N/[1*]')
p = Chem.MolzipParams()
p.label = Chem.MolzipLabel.Isotope
c = Chem.molzip(a, p)
self.assertEqual(Chem.MolToSmiles(c), 'C=C/N=C/O')
a = Chem.MolFromSmiles("[C@H]([Xe])(F)([V])")
b = Chem.MolFromSmiles("[Xe]N.[V]I")
p = Chem.MolzipParams()
p.label = Chem.MolzipLabel.AtomType
p.setAtomSymbols(["Xe", "V"])
c = Chem.molzip(a, b, p)
self.assertEqual(Chem.MolToSmiles(c), "N[C@@H](F)I")
a = Chem.MolFromSmiles("C(=[*:1])N")
b = Chem.MolFromSmiles("[*:1]-N=C")
p = Chem.MolzipParams()
p.enforceValenceRules = False
c = Chem.molzip(a, b, p)
def testContextManagers(self):
from rdkit import RDLogger
RDLogger.DisableLog('rdApp.*')
from io import StringIO
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'Wrap', 'test_data',
'github3553.sdf')
with Chem.SDMolSupplier(fileN) as suppl:
mols = [x for x in suppl if x is not None]
sio = StringIO()
with Chem.SDWriter(sio) as w:
for m in mols:
w.write(m)
txt = sio.getvalue()
self.assertEqual(txt.count('$$$$'), len(mols))
with self.assertRaises(RuntimeError):
w.write(mols[0])
with Chem.ForwardSDMolSupplier(fileN) as suppl:
mols = [x for x in suppl if x is not None]
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'first_200.tpsa.csv')
with Chem.SmilesMolSupplier(fileN, ",", 0, -1) as suppl:
ms = [x for x in suppl if x is not None]
sio = StringIO()
with Chem.SmilesWriter(sio) as w:
for m in mols:
w.write(m)
txt = sio.getvalue()
self.assertEqual(txt.count('\n'), len(mols) + 1)
with self.assertRaises(RuntimeError):
w.write(mols[0])
data = """$SMI<Cc1nnc(N)nc1C>
CAS<17584-12-2>
|
$SMI<Cc1n[nH]c(=O)nc1N>
CAS<~>
|
$SMI<Cc1n[nH]c(=O)[nH]c1=O>
CAS<932-53-6>
|
$SMI<Cc1nnc(NN)nc1O>
CAS<~>
|"""
with Chem.TDTMolSupplier() as suppl:
suppl.SetData(data, "CAS")
ms = [x for x in suppl if x is not None]
sio = StringIO()
with Chem.TDTWriter(sio) as w:
for m in mols:
w.write(m)
txt = sio.getvalue()
self.assertEqual(txt.count('$SMI'), len(mols))
with self.assertRaises(RuntimeError):
w.write(mols[0])
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'1CRN.pdb')
m = Chem.MolFromPDBFile(fileN)
mols = [m, m]
sio = StringIO()
with Chem.PDBWriter(sio) as w:
for m in mols:
w.write(m)
txt = sio.getvalue()
self.assertEqual(txt.count('COMPND CRAMBIN'), len(mols))
with self.assertRaises(RuntimeError):
w.write(mols[0])
if hasattr(Chem, 'MaeMolSupplier'):
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'NCI_aids_few.mae')
with Chem.MaeMolSupplier(fileN) as suppl:
ms = [x for x in suppl if x is not None]
RDLogger.EnableLog('rdApp.*')
def testInsertMol(self):
m = Chem.MolFromSmiles("CNO")
m2 = Chem.MolFromSmiles("c1ccccc1")
m3 = Chem.MolFromSmiles("C1CC1")
rwmol = Chem.RWMol(m)
rwmol.InsertMol(m2)
rwmol.InsertMol(m3)
self.assertEqual(Chem.MolToSmiles(rwmol), Chem.CanonSmiles("CNO.c1ccccc1.C1CC1"))
def testBatchEdits(self):
mol = Chem.MolFromSmiles("C1CCCO1")
for rwmol in [Chem.EditableMol(mol), Chem.RWMol(mol)]:
rwmol.BeginBatchEdit()
rwmol.RemoveAtom(2)
rwmol.RemoveAtom(3)
rwmol.CommitBatchEdit()
nmol = rwmol.GetMol()
self.assertEqual(Chem.MolToSmiles(nmol), "CCO")
for rwmol in [Chem.EditableMol(mol), Chem.RWMol(mol)]:
rwmol = Chem.EditableMol(mol)
rwmol.BeginBatchEdit()
rwmol.RemoveAtom(3)
rwmol.RemoveBond(4, 0)
rwmol.CommitBatchEdit()
nmol = rwmol.GetMol()
self.assertEqual(Chem.MolToSmiles(nmol), "CCC.O")
for rwmol in [Chem.EditableMol(mol), Chem.RWMol(mol)]:
rwmol.BeginBatchEdit()
rwmol.RemoveAtom(2)
rwmol.RemoveAtom(3)
rwmol.RollbackBatchEdit()
nmol = rwmol.GetMol()
self.assertEqual(Chem.MolToSmiles(nmol), "C1CCOC1")
def testBatchEditContextManager(self):
mol = Chem.MolFromSmiles("C1CCCO1")
with Chem.RWMol(mol) as rwmol:
rwmol.RemoveAtom(2)
rwmol.RemoveAtom(3)
# make sure we haven't actually changed anything yet:
self.assertEqual(rwmol.GetNumAtoms(), mol.GetNumAtoms())
self.assertEqual(rwmol.GetNumAtoms(), mol.GetNumAtoms() - 2)
# make sure no changes get made if we throw an exception
try:
with Chem.RWMol(mol) as rwmol:
rwmol.RemoveAtom(2)
rwmol.RemoveAtom(6)
except Exception:
pass
self.assertEqual(rwmol.GetNumAtoms(), mol.GetNumAtoms())
def testGithub4138(self):
m = Chem.MolFromSmiles('C1CCCO1')
q = Chem.MolFromSmarts('')
self.assertFalse(m.HasSubstructMatch(q))
self.assertEqual(m.GetSubstructMatch(q), ())
self.assertEqual(m.GetSubstructMatches(q), ())
m = Chem.MolFromSmiles('')
q = Chem.MolFromSmarts('C')
self.assertFalse(m.HasSubstructMatch(q))
self.assertEqual(m.GetSubstructMatch(q), ())
self.assertEqual(m.GetSubstructMatches(q), ())
def testGithub4144(self):
''' the underlying problem with #4144 was that the
includeRings argument could not be passed to ClearComputedProps()
from Python. Make sure that's fixed
'''
m = Chem.MolFromSmiles('c1ccccc1')
self.assertEqual(m.GetRingInfo().NumRings(), 1)
m.ClearComputedProps(includeRings=False)
self.assertEqual(m.GetRingInfo().NumRings(), 1)
m.ClearComputedProps()
with self.assertRaises(RuntimeError):
m.GetRingInfo().NumRings()
def testAddWavyBondsForStereoAny(self):
m = Chem.MolFromSmiles('CC=CC')
m.GetBondWithIdx(1).SetStereo(Chem.BondStereo.STEREOANY)
m2 = Chem.Mol(m)
Chem.AddWavyBondsForStereoAny(m2)
self.assertEqual(m2.GetBondWithIdx(1).GetStereo(), Chem.BondStereo.STEREONONE)
self.assertEqual(m2.GetBondWithIdx(0).GetBondDir(), Chem.BondDir.UNKNOWN)
m2 = Chem.Mol(m)
Chem.AddWavyBondsForStereoAny(m2, clearDoubleBondFlags=False)
self.assertEqual(m2.GetBondWithIdx(1).GetStereo(), Chem.BondStereo.STEREOANY)
self.assertEqual(m2.GetBondWithIdx(0).GetBondDir(), Chem.BondDir.UNKNOWN)
m = Chem.MolFromSmiles("CC=CC=CC=CC")
m.GetBondWithIdx(1).SetStereoAtoms(0, 3)
m.GetBondWithIdx(1).SetStereo(Chem.BondStereo.STEREOCIS)
m.GetBondWithIdx(3).SetStereo(Chem.BondStereo.STEREOANY)
m.GetBondWithIdx(5).SetStereoAtoms(4, 7)
m.GetBondWithIdx(5).SetStereo(Chem.BondStereo.STEREOCIS)
m2 = Chem.Mol(m)
Chem.AddWavyBondsForStereoAny(m2)
self.assertEqual(m2.GetBondWithIdx(3).GetStereo(), Chem.BondStereo.STEREOANY)
self.assertEqual(m2.GetBondWithIdx(0).GetBondDir(), Chem.BondDir.NONE)
Chem.AddWavyBondsForStereoAny(
m2, addWhenImpossible=Chem.StereoBondThresholds.DBL_BOND_SPECIFIED_STEREO)
self.assertEqual(m2.GetBondWithIdx(3).GetStereo(), Chem.BondStereo.STEREONONE)
self.assertEqual(m2.GetBondWithIdx(2).GetBondDir(), Chem.BondDir.UNKNOWN)
def testSmartsParseParams(self):
smi = "CCC |$foo;;bar$| ourname"
m = Chem.MolFromSmarts(smi)
self.assertTrue(m is not None)
ps = Chem.SmartsParserParams()
ps.allowCXSMILES = False
ps.parseName = False
m = Chem.MolFromSmarts(smi, ps)
self.assertTrue(m is None)
ps.allowCXSMILES = True
ps.parseName = True
m = Chem.MolFromSmarts(smi, ps)
self.assertTrue(m is not None)
self.assertTrue(m.GetAtomWithIdx(0).HasProp('atomLabel'))
self.assertEqual(m.GetAtomWithIdx(0).GetProp('atomLabel'), "foo")
self.assertTrue(m.HasProp('_Name'))
self.assertEqual(m.GetProp('_Name'), "ourname")
self.assertEqual(m.GetProp("_CXSMILES_Data"), "|$foo;;bar$|")
def testSmilesWriteParams(self):
m = Chem.MolFromSmiles('C[C@H](F)Cl')
ps = Chem.SmilesWriteParams()
ps.rootedAtAtom = 1
self.assertEqual(Chem.MolToSmiles(m, ps), "[C@@H](C)(F)Cl")
self.assertEqual(Chem.MolToCXSmiles(m, ps), "[C@@H](C)(F)Cl")
def testCXSmilesOptions(self):
# just checking that the fields parameter gets used.
# we've tested the individual values on the C++ side
m = Chem.MolFromSmiles("OC1CCC(F)C1 |LN:1:1.3.2.6|")
ps = Chem.SmilesWriteParams()
ps.rootedAtAtom = 1
self.assertEqual(
Chem.MolToCXSmiles(m, ps, (Chem.CXSmilesFields.CX_ALL ^ Chem.CXSmilesFields.CX_LINKNODES)),
"C1(O)CCC(F)C1")
def testKekulizeIfPossible(self):
m = Chem.MolFromSmiles('c1cccn1', sanitize=False)
m.UpdatePropertyCache(strict=False)
Chem.KekulizeIfPossible(m)
for atom in m.GetAtoms():
self.assertTrue(atom.GetIsAromatic())
for bond in m.GetBonds():
self.assertTrue(bond.GetIsAromatic())
self.assertEqual(bond.GetBondType(), Chem.BondType.AROMATIC)
def testgithub4992(self):
if not hasattr(Chem, "Chem.MultithreadedSDMolSupplier"):
return
good1 = Chem.MolFromSmiles('C')
#good1.SetProp('molname', 'good1')
good2 = Chem.MolFromSmiles('CC')
#good2.SetProp('molname', 'good2')
good3 = Chem.MolFromSmiles('CCC')
#good3.SetProp('molname', 'good3')
bad = Chem.MolFromSmiles('CN(C)(C)C', sanitize=False)
#bad.SetProp('molname', 'bad')
with Chem.SDWriter("good1_good2_good3.sdf") as w:
w.write(good1)
w.write(good2)
w.write(good3)
w.write(good1)
w.write(good2)
w.write(good3)
with Chem.SDWriter("good1_good2_good3_bad.sdf") as w:
w.write(good1)
w.write(good2)
w.write(good3)
w.write(bad)
with Chem.SDWriter("good1_good2_bad_good3.sdf") as w:
w.write(good1)
w.write(good2)
w.write(bad)
w.write(good3)
with Chem.SDWriter("bad_good1_good2_good3.sdf") as w:
w.write(bad)
w.write(good1)
w.write(good2)
w.write(good3)
def read_mols(supplier, filename):
i = 0
with supplier(filename) as sdSuppl:
count = -1
for count, mol in enumerate(sdSuppl):
if mol is not None:
i += 1
return i
counts = []
for i, s in enumerate((Chem.SDMolSupplier, Chem.MultithreadedSDMolSupplier)):
for j, f in enumerate(('good1_good2_good3.sdf', 'good1_good2_bad_good3.sdf',
'good1_good2_bad_good3.sdf', 'bad_good1_good2_good3.sdf')):
print(f'---------------\n{s.__name__} {f}')
if i == 0:
counts.append(read_mols(s, f))
else:
self.assertEqual(counts[j], read_mols(s, f))
def test_blocklogs(self):
with capture_logging(logging.INFO) as log_stream:
# Logging is known to be problematic with static linked libs
# so let's skip the test if we can't see the expected error
# log before we block logging.
Chem.MolFromSmiles('garbage_0')
if 'garbage_0' not in log_stream.getvalue():
self.skipTest('cannot fetch log msgs')
else:
log_stream.truncate(0)
with rdBase.BlockLogs():
Chem.MolFromSmiles('garbage_1')
self.assertNotIn('garbage_1', log_stream.getvalue())
Chem.MolFromSmiles('garbage_2')
self.assertIn('garbage_2', log_stream.getvalue())
log_stream.truncate(0)
block = rdBase.BlockLogs()
self.assertIsNotNone(block)
Chem.MolFromSmiles('garbage_3')
self.assertNotIn('garbage_3', log_stream.getvalue())
del block
Chem.MolFromSmiles('garbage_4')
self.assertIn('garbage_4', log_stream.getvalue())
log_stream.truncate(0)
if __name__ == '__main__':
if "RDTESTCASE" in os.environ:
suite = unittest.TestSuite()
testcases = os.environ["RDTESTCASE"]
for name in testcases.split(':'):
suite.addTest(TestCase(name))
runner = unittest.TextTestRunner()
runner.run(suite)
else:
unittest.main()
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