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#
# Copyright (C) 2019 Greg Landrum and T5 Informatics GmbH
# All Rights Reserved
#
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
import pickle
import unittest
from rdkit import Chem
from rdkit import RDConfig
from rdkit import rdBase
from rdkit.Chem.Scaffolds import rdScaffoldNetwork
rdBase.DisableLog("rdApp.info")
class TestScaffoldNetwork(unittest.TestCase):
def setUp(self):
pass
def test1Basics(self):
smis = ["c1ccccc1CC1NC(=O)CCC1", "c1cccnc1CC1NC(=O)CCC1"]
ms = [Chem.MolFromSmiles(x) for x in smis]
params = rdScaffoldNetwork.ScaffoldNetworkParams()
net = rdScaffoldNetwork.CreateScaffoldNetwork(ms, params)
self.assertEqual(len(net.nodes), 12)
self.assertEqual(len(net.edges), 13)
self.assertEqual(len(net.counts), len(net.nodes))
self.assertEqual(len([x for x in net.edges if x.type == rdScaffoldNetwork.EdgeType.Fragment]),
4)
self.assertEqual(len([x for x in net.edges if x.type == rdScaffoldNetwork.EdgeType.Generic]), 6)
self.assertEqual(
len([x for x in net.edges if x.type == rdScaffoldNetwork.EdgeType.RemoveAttachment]), 3)
net = rdScaffoldNetwork.ScaffoldNetwork()
rdScaffoldNetwork.UpdateScaffoldNetwork(ms, net, params)
self.assertEqual(len(net.nodes), 12)
self.assertEqual(len(net.edges), 13)
self.assertEqual(len([x for x in net.edges if x.type == rdScaffoldNetwork.EdgeType.Fragment]),
4)
self.assertEqual(len([x for x in net.edges if x.type == rdScaffoldNetwork.EdgeType.Generic]), 6)
self.assertEqual(
len([x for x in net.edges if x.type == rdScaffoldNetwork.EdgeType.RemoveAttachment]), 3)
def test2Basics(self):
smis = ["c1ccccc1CC1NC(=O)CCC1", "c1cccnc1CC1NC(=O)CCC1"]
ms = [Chem.MolFromSmiles(x) for x in smis]
params = rdScaffoldNetwork.ScaffoldNetworkParams()
params.includeScaffoldsWithoutAttachments = False
net = rdScaffoldNetwork.CreateScaffoldNetwork(ms, params)
self.assertEqual(len(net.nodes), 7)
self.assertEqual(len(net.edges), 7)
self.assertEqual(len([x for x in net.edges if x.type == rdScaffoldNetwork.EdgeType.Fragment]),
4)
self.assertEqual(len([x for x in net.edges if x.type == rdScaffoldNetwork.EdgeType.Generic]), 3)
def test3Update(self):
smis = ["c1ccccc1CC1NC(=O)CCC1", "c1cccnc1CC1NC(=O)CCC1"]
ms = [Chem.MolFromSmiles(x) for x in smis]
params = rdScaffoldNetwork.ScaffoldNetworkParams()
net = rdScaffoldNetwork.ScaffoldNetwork()
rdScaffoldNetwork.UpdateScaffoldNetwork(ms[0:1], net, params)
self.assertEqual(len(net.nodes), 9)
self.assertEqual(len(net.edges), 8)
self.assertEqual(len(net.counts), len(net.nodes))
self.assertEqual(list(net.counts).count(1), len(net.counts))
rdScaffoldNetwork.UpdateScaffoldNetwork(ms[1:2], net, params)
self.assertEqual(len(net.nodes), 12)
self.assertEqual(len(net.edges), 13)
self.assertEqual(len(net.counts), len(net.nodes))
self.assertEqual(len([x for x in net.edges if x.type == rdScaffoldNetwork.EdgeType.Fragment]),
4)
self.assertEqual(len([x for x in net.edges if x.type == rdScaffoldNetwork.EdgeType.Generic]), 6)
self.assertEqual(
len([x for x in net.edges if x.type == rdScaffoldNetwork.EdgeType.RemoveAttachment]), 3)
net = rdScaffoldNetwork.CreateScaffoldNetwork(ms[0:1], params)
rdScaffoldNetwork.UpdateScaffoldNetwork(ms[1:2], net, params)
self.assertEqual(len(net.nodes), 12)
self.assertEqual(len(net.edges), 13)
self.assertEqual(len([x for x in net.edges if x.type == rdScaffoldNetwork.EdgeType.Fragment]),
4)
self.assertEqual(len([x for x in net.edges if x.type == rdScaffoldNetwork.EdgeType.Generic]), 6)
self.assertEqual(
len([x for x in net.edges if x.type == rdScaffoldNetwork.EdgeType.RemoveAttachment]), 3)
def test4Str(self):
smis = ["c1ccccc1CC1NC(=O)CCC1"]
ms = [Chem.MolFromSmiles(x) for x in smis]
params = rdScaffoldNetwork.ScaffoldNetworkParams()
net = rdScaffoldNetwork.CreateScaffoldNetwork(ms, params)
self.assertEqual(len(net.nodes), 9)
self.assertEqual(len(net.edges), 8)
self.assertEqual(str(net.edges[0]), "NetworkEdge( 0->1, type:Fragment )")
def test5FragmentationReactions(self):
smis = ["c1c(CC2CC2)cc(NC2CC2)cc1OC1CC1"]
ms = [Chem.MolFromSmiles(x) for x in smis]
params = rdScaffoldNetwork.ScaffoldNetworkParams(
["[!#0;R:1]-!@[O:2]>>[*:1]-[#0].[#0]-[*:2]", "[!#0;R:1]-!@[N:2]>>[*:1]-[#0].[#0]-[*:2]"])
params.includeScaffoldsWithoutAttachments = False
params.includeGenericScaffolds = False
net = rdScaffoldNetwork.CreateScaffoldNetwork(ms, params)
self.assertEqual(len(net.nodes), 5)
self.assertEqual(len(net.edges), 7)
def test6Options(self):
smis = ["C1OC1Cc1ccccc1"]
ms = [Chem.MolFromSmiles(x) for x in smis]
params = rdScaffoldNetwork.ScaffoldNetworkParams()
net = rdScaffoldNetwork.CreateScaffoldNetwork(ms, params)
self.assertEqual(len(net.nodes), 9)
self.assertEqual(len(net.edges), 8)
params = rdScaffoldNetwork.ScaffoldNetworkParams()
params.keepOnlyFirstFragment = False
net = rdScaffoldNetwork.CreateScaffoldNetwork(ms, params)
self.assertEqual(len(net.nodes), 19)
self.assertEqual(len(net.edges), 23)
params = rdScaffoldNetwork.ScaffoldNetworkParams()
params.includeGenericScaffolds = False
net = rdScaffoldNetwork.CreateScaffoldNetwork(ms, params)
self.assertEqual(len(net.nodes), 5)
self.assertEqual(len(net.edges), 4)
params = rdScaffoldNetwork.ScaffoldNetworkParams()
params.includeGenericBondScaffolds = True
net = rdScaffoldNetwork.CreateScaffoldNetwork(ms, params)
self.assertEqual(len(net.nodes), 11)
self.assertEqual(len(net.edges), 10)
def test7Github3177(self):
smis = ["C1OC1Cc1ccccc1"]
ms = [Chem.MolFromSmiles(x) for x in smis]
ms.append(None)
params = rdScaffoldNetwork.ScaffoldNetworkParams()
with self.assertRaises(ValueError):
net = rdScaffoldNetwork.CreateScaffoldNetwork(ms, params)
if __name__ == '__main__':
unittest.main()
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