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# Copyright (c) 2017, Novartis Institutes for BioMedical Research Inc.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above
# copyright notice, this list of conditions and the following
# disclaimer in the documentation and/or other materials provided
# with the distribution.
# * Neither the name of Novartis Institutes for BioMedical Research Inc.
# nor the names of its contributors may be used to endorse or promote
# products derived from this software without specific prior written
# permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
# OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
from __future__ import print_function
import unittest
import os,sys, copy
from rdkit.six.moves import cPickle
from rdkit import rdBase
from rdkit import Chem
from rdkit.Chem.rdRGroupDecomposition import RGroupDecompose, RGroupDecomposition, RGroupDecompositionParameters
from collections import OrderedDict
class TestCase(unittest.TestCase) :
def atest_multicores(self):
cores_smi_easy = OrderedDict()
cores_smi_hard = OrderedDict()
#cores_smi_easy['cephem'] = Chem.MolFromSmiles('O=C1C([1*])[C@@H]2N1C(C(O)=O)=C([3*])CS2')
cores_smi_easy['cephem'] = Chem.MolFromSmarts('O=C1C([*:1])C2N1C(C(O)=O)=C([*:3])CS2')
cores_smi_hard['cephem'] = Chem.MolFromSmarts('O=C1C([2*])([1*])[C@@H]2N1C(C(O)=O)=C([3*])CS2')
#cores_smi_easy['carbacephem'] = Chem.MolFromSmiles('O=C1C([1*])[C@@H]2N1C(C(O)=O)=C([3*])CC2')
cores_smi_easy['carbacephem'] = Chem.MolFromSmarts('O=C1C([1*])C2N1C(C(O)=O)=C([3*])CC2')
cores_smi_hard['carbacephem'] = Chem.MolFromSmarts('O=C1C([2*])([1*])[C@@H]2N1C(C(O)=O)=C([3*])CC2')
#cores_smi_easy['oxacephem'] = Chem.MolFromSmiles('O=C1C([1*])[C@@H]2N1C(C(O)=O)=C([3*])CO2')
cores_smi_easy['oxacephem'] = Chem.MolFromSmarts('O=C1C([1*])C2N1C(C(O)=O)=C([3*])CO2')
cores_smi_hard['oxacephem'] = Chem.MolFromSmarts('O=C1C([2*])([1*])[C@@H]2N1C(C(O)=O)=C([3*])CO2')
#cores_smi_easy['carbapenem'] = Chem.MolFromSmiles('O=C1C([1*])[C@@H]2N1C(C(O)=O)=C([3*])C2')
cores_smi_easy['carbapenem'] = Chem.MolFromSmarts('O=C1C([1*])C2N1C(C(O)=O)=C([3*])C2')
cores_smi_hard['carbapenem'] = Chem.MolFromSmarts('O=C1C([2*])([1*])[C@@H]2N1C(C(O)=O)=C([3*])C2')
#cores_smi_easy['carbapenam'] = Chem.MolFromSmiles('O=C1C([1*])[C@@H]2N1C(C(O)=O)C([3*])([4*])C2')
cores_smi_easy['carbapenam'] = Chem.MolFromSmarts('O=C1C([1*])C2N1C(C(O)=O)C([3*])([4*])C2')
cores_smi_hard['carbapenam'] = Chem.MolFromSmarts('O=C1C([2*])([1*])[C@@H]2N1C(C(O)=O)C([3*])([4*])C2')
#cores_smi_easy['penem'] = Chem.MolFromSmiles('O=C1C([1*])[C@@H]2N1C(C(O)=O)=C([3*])S2')
cores_smi_easy['penem'] = Chem.MolFromSmarts('O=C1C([1*])C2N1C(C(O)=O)=C([3*])S2')
cores_smi_hard['penem'] = Chem.MolFromSmarts('O=C1C([2*])([1*])[C@@H]2N1C(C(O)=O)=C([3*])S2')
#cores_smi_easy['penam'] = Chem.MolFromSmiles('O=C1C([1*])[C@@H]2N1C(C(O)=O)C([3*])([4*])S2')
cores_smi_easy['penam'] = Chem.MolFromSmarts('O=C1C([*:1])C2N1C(C(O)=O)C([*:3])([*:4])S2')
cores_smi_hard['penam'] = Chem.MolFromSmarts('O=C1C([*:2])([*:1])[C@@H]2N1C(C(O)=O)C([*:3])([*:4])S2')
#cores_smi_easy['oxapenam'] = Chem.MolFromSmiles('O=C1C([1*])[C@@H]2N1C(C(O)=O)C([3*])([4*])O2')
cores_smi_easy['oxapenam'] = Chem.MolFromSmarts('O=C1C([1*])C2N1C(C(O)=O)C([3*])([4*])O2')
cores_smi_hard['oxapenam'] = Chem.MolFromSmarts('O=C1C([2*])([1*])[C@@H]2N1C(C(O)=O)C([3*])([4*])O2')
cores_smi_easy['monobactam'] = Chem.MolFromSmarts('O=C1C([1*])C([5*])N1')
cores_smi_hard['monobactam'] = Chem.MolFromSmarts('O=C1C([2*])([1*])C([6*])([5*])N1')
rg_easy = RGroupDecomposition(cores_smi_easy.values())
rg_stereo = RGroupDecomposition(cores_smi_hard.values())
def test_stereo(self):
smiles = """C1CCO[C@@H](N)1
C1CCO[C@H](N)1
C1CCO[C@@](N)(O)1
C1CCO[C@@](N)(P)1
C1CCO[C@@](N)(S)1
C1CCO[C@@H](O)1
C1CCO[C@H](O)1
C1CCO[C@@](O)(N)1
C1CCO[C@@](O)(P)1
C1CCO[C@@](O)(S)1
C1CCO[C@@H](P)1
C1CCO[C@H](P)1
C1CCO[C@@](P)(N)1
C1CCO[C@@](P)(O)1
C1CCO[C@@](P)(S)1
C1CCO[C@@H](S)1
C1CCO[C@H](S)1
C1CCO[C@@](S)(N)1
C1CCO[C@@](S)(O)1
C1CCO[C@@](S)(P)1
"""
mols = []
for smi in smiles.split():
m = Chem.MolFromSmiles(smi)
assert m, smi
mols.append(m)
core = Chem.MolFromSmarts("C1CCOC1")
rgroups = RGroupDecomposition(core)
for m in mols:
rgroups.Add(m)
rgroups.Process()
columns = rgroups.GetRGroupsAsColumns()
data = {}
for k,v in columns.items():
data[k] = [Chem.MolToSmiles(m,True) for m in v]
rgroups2,unmatched = RGroupDecompose([core], mols)
columns2,unmatched = RGroupDecompose([core], mols, asRows=False)
data2 = {}
for k,v in columns2.items():
data2[k] = [Chem.MolToSmiles(m,True) for m in v]
self.assertEqual(data, data2)
columns3, unmatched = RGroupDecompose([core], mols, asRows=False, asSmiles=True)
self.assertEqual(data, columns3)
def test_h_options(self):
core = Chem.MolFromSmiles("O=c1oc2ccccc2cc1")
smiles = ("O=c1cc(Cn2ccnc2)c2ccc(Oc3ccccc3)cc2o1",
"O=c1oc2ccccc2c(Cn2ccnc2)c1-c1ccccc1",
"COc1ccc2c(Cn3cncn3)cc(=O)oc2c1")
params = RGroupDecompositionParameters()
rgd = RGroupDecomposition(core,params)
for smi in smiles:
m = Chem.MolFromSmiles(smi)
rgd.Add(m)
rgd.Process()
columns = rgd.GetRGroupsAsColumns()
self.assertEqual(columns['R2'][0].GetNumAtoms(),12)
params.removeHydrogensPostMatch = True
rgd = RGroupDecomposition(core,params)
for smi in smiles:
m = Chem.MolFromSmiles(smi)
rgd.Add(m)
rgd.Process()
columns = rgd.GetRGroupsAsColumns()
self.assertEqual(columns['R2'][0].GetNumAtoms(),7)
def test_unmatched(self):
cores = [Chem.MolFromSmiles("N")]
mols = [Chem.MolFromSmiles("CC"),
Chem.MolFromSmiles("CC"),
Chem.MolFromSmiles("CC"),
Chem.MolFromSmiles("N"),
Chem.MolFromSmiles("CC")]
res, unmatched = RGroupDecompose(cores, mols)
self.assertEquals(len(res), 1)
self.assertEquals(unmatched, [0,1,2,4])
if __name__ == '__main__':
unittest.main()
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