1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
|
//
// 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.
//
#include <RDBoost/python.h>
#include <GraphMol/GraphMol.h>
#include <RDBoost/Wrap.h>
#include <GraphMol/ScaffoldNetwork/ScaffoldNetwork.h>
namespace python = boost::python;
using namespace RDKit;
namespace {
ScaffoldNetwork::ScaffoldNetwork *createNetworkHelper(
python::object pmols,
const ScaffoldNetwork::ScaffoldNetworkParams ¶ms) {
auto mols = pythonObjectToVect<ROMOL_SPTR>(pmols);
ScaffoldNetwork::ScaffoldNetwork *res = new ScaffoldNetwork::ScaffoldNetwork;
if (mols) {
NOGIL gil;
updateScaffoldNetwork(*mols, *res, params);
}
return res;
}
void updateNetworkHelper(python::object pmols,
ScaffoldNetwork::ScaffoldNetwork &net,
const ScaffoldNetwork::ScaffoldNetworkParams ¶ms) {
auto mols = pythonObjectToVect<ROMOL_SPTR>(pmols);
if (mols) {
NOGIL gil;
updateScaffoldNetwork(*mols, net, params);
}
}
ScaffoldNetwork::ScaffoldNetworkParams *getBRICSParams() {
return new ScaffoldNetwork::ScaffoldNetworkParams(
ScaffoldNetwork::getBRICSNetworkParams());
}
} // namespace
#ifdef RDK_USE_BOOST_SERIALIZATION
struct scaffoldnetwork_pickle_suite : python::pickle_suite {
static python::tuple getinitargs(
const RDKit::ScaffoldNetwork::ScaffoldNetwork &self) {
std::stringstream oss;
boost::archive::text_oarchive oa(oss);
oa << self;
std::string res = oss.str();
return python::make_tuple(python::object(python::handle<>(
PyBytes_FromStringAndSize(res.c_str(), res.length()))));
};
};
#else
struct scaffoldnetwork_pickle_suite : python::pickle_suite {
static python::tuple getinitargs(
const RDKit::ScaffoldNetwork::ScaffoldNetwork &self) {
throw_runtime_error("Pickling of ScaffoldNetwork instances is not enabled");
};
};
#endif
BOOST_PYTHON_MODULE(rdScaffoldNetwork) {
python::scope().attr("__doc__") =
"Module containing functions for creating a Scaffold Network";
RegisterVectorConverter<ScaffoldNetwork::NetworkEdge>("NetworkEdge_VECT");
iterable_converter().from_python<std::vector<std::string>>();
python::class_<ScaffoldNetwork::ScaffoldNetworkParams>(
"ScaffoldNetworkParams", "Scaffold network parameters", python::init<>())
.def(python::init<const std::vector<std::string> &>(
(python::arg("bondBreakerSmartsList")),
"Constructor taking a list of Reaction SMARTS for the fragmentation "
"reactions"))
.def_readwrite(
"includeGenericScaffolds",
&ScaffoldNetwork::ScaffoldNetworkParams::includeGenericScaffolds,
"include scaffolds with all atoms replaced by dummies")
.def_readwrite(
"includeGenericBondScaffolds",
&ScaffoldNetwork::ScaffoldNetworkParams::includeGenericBondScaffolds,
"include scaffolds with all bonds replaced by single bonds")
.def_readwrite(
"includeScaffoldsWithoutAttachments",
&ScaffoldNetwork::ScaffoldNetworkParams::
includeScaffoldsWithoutAttachments,
"remove attachment points from scaffolds and include the result")
.def_readwrite(
"includeScaffoldsWithAttachments",
&ScaffoldNetwork::ScaffoldNetworkParams::
includeScaffoldsWithAttachments,
"Include the version of the scaffold with attachment points")
.def_readwrite(
"keepOnlyFirstFragment",
&ScaffoldNetwork::ScaffoldNetworkParams::keepOnlyFirstFragment,
"keep only the first fragment from the bond breaking rule")
.def_readwrite(
"pruneBeforeFragmenting",
&ScaffoldNetwork::ScaffoldNetworkParams::pruneBeforeFragmenting,
"Do a pruning/flattening step before starting fragmenting")
.def_readwrite("flattenIsotopes",
&ScaffoldNetwork::ScaffoldNetworkParams::flattenIsotopes,
"remove isotopes when flattening")
.def_readwrite("flattenChirality",
&ScaffoldNetwork::ScaffoldNetworkParams::flattenChirality,
"remove chirality and bond stereo when flattening")
.def_readwrite(
"flattenKeepLargest",
&ScaffoldNetwork::ScaffoldNetworkParams::flattenKeepLargest,
"keep only the largest fragment when doing flattening")
.def_readwrite("collectMolCounts",
&ScaffoldNetwork::ScaffoldNetworkParams::collectMolCounts,
"keep track of the number of molecules each scaffold was "
"found in");
python::enum_<ScaffoldNetwork::EdgeType>("EdgeType")
.value("Fragment", ScaffoldNetwork::EdgeType::Fragment)
.value("Generic", ScaffoldNetwork::EdgeType::Generic)
.value("GenericBond", ScaffoldNetwork::EdgeType::GenericBond)
.value("RemoveAttachment", ScaffoldNetwork::EdgeType::RemoveAttachment)
.value("Initialize", ScaffoldNetwork::EdgeType::Initialize);
python::class_<ScaffoldNetwork::NetworkEdge>(
"NetworkEdge", "A scaffold network edge", python::no_init)
.def_readonly("beginIdx", &ScaffoldNetwork::NetworkEdge::beginIdx,
"index of the begin node in node list")
.def_readonly("endIdx", &ScaffoldNetwork::NetworkEdge::endIdx,
"index of the end node in node list")
.def_readonly("type", &ScaffoldNetwork::NetworkEdge::type,
"type of the edge")
.def(python::self_ns::str(python::self_ns::self));
python::class_<ScaffoldNetwork::ScaffoldNetwork>(
"ScaffoldNetwork", "A scaffold network", python::init<>())
#ifdef RDK_USE_BOOST_SERIALIZATION
.def(python::init<const std::string &>())
// enable pickle support
.def_pickle(scaffoldnetwork_pickle_suite())
#endif
.def_readonly("nodes", &ScaffoldNetwork::ScaffoldNetwork::nodes,
"the sequence of SMILES defining the nodes")
.def_readonly("counts", &ScaffoldNetwork::ScaffoldNetwork::counts,
"the number of times each node was encountered while "
"building the network.")
.def_readonly("molCounts", &ScaffoldNetwork::ScaffoldNetwork::molCounts,
"the number of moleclues each node was found in.")
.def_readonly("edges", &ScaffoldNetwork::ScaffoldNetwork::edges,
"the sequence of network edges");
python::def("CreateScaffoldNetwork", &createNetworkHelper,
(python::arg("mols"), python::arg("params")),
"create (and return) a new network from a sequence of molecules",
python::return_value_policy<python::manage_new_object>());
python::def(
"UpdateScaffoldNetwork", &updateNetworkHelper,
(python::arg("mols"), python::arg("network"), python::arg("params")),
"update an existing network by adding molecules");
python::def("BRICSScaffoldParams", &getBRICSParams,
"Returns parameters for generating scaffolds using BRICS "
"fragmentation rules",
python::return_value_policy<python::manage_new_object>());
}
|
