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
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
|
//
// Copyright (C) 2018 Susan H. Leung
//
// @@ 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/Wrap.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/MolStandardize/Validate.h>
namespace python = boost::python;
using namespace RDKit;
namespace {
struct ValidationMethodWrap
: MolStandardize::ValidationMethod,
python::wrapper<MolStandardize::ValidationMethod> {
std::vector<MolStandardize::ValidationErrorInfo> validate(
const ROMol &mol, bool reportAllFailures) const override {
return this->get_override("validate")(mol, reportAllFailures);
}
std::shared_ptr<MolStandardize::ValidationMethod> copy() const override {
return this->get_override("copy")();
}
};
// Wrap ValidationMethod::validate and convert the returned
// vector into a python list of strings
python::list pythonValidateMethod(const MolStandardize::ValidationMethod &self,
const ROMol &mol, bool reportAllFailures) {
python::list res;
std::vector<MolStandardize::ValidationErrorInfo> errout =
self.validate(mol, reportAllFailures);
for (const auto &msg : errout) {
res.append(msg);
}
return res;
}
MolStandardize::MolVSValidation *getMolVSValidation(
python::object validations) {
std::vector<std::shared_ptr<MolStandardize::ValidationMethod>> vs;
auto pvect =
pythonObjectToVect<std::shared_ptr<MolStandardize::ValidationMethod>>(
validations);
if (!pvect) {
throw_value_error("validations argument must be non-empty");
}
for (auto v : *pvect) {
vs.push_back(v->copy());
}
return new MolStandardize::MolVSValidation(vs);
}
MolStandardize::AllowedAtomsValidation *getAllowedAtomsValidation(
python::object atoms) {
auto p_atomList = pythonObjectToVect<Atom *>(atoms);
if (!p_atomList) {
throw_value_error("allowedAtoms argument must be non-empty");
}
std::vector<std::shared_ptr<Atom>> satoms;
for (auto ap : *p_atomList) {
satoms.push_back(std::shared_ptr<Atom>(ap->copy()));
}
return new MolStandardize::AllowedAtomsValidation(satoms);
}
MolStandardize::DisallowedAtomsValidation *getDisallowedAtomsValidation(
python::object atoms) {
auto p_atomList = pythonObjectToVect<Atom *>(atoms);
if (!p_atomList) {
throw_value_error("disallowedAtoms must be non-empty");
}
std::vector<std::shared_ptr<Atom>> satoms;
for (auto ap : *p_atomList) {
satoms.push_back(std::shared_ptr<Atom>(ap->copy()));
}
return new MolStandardize::DisallowedAtomsValidation(satoms);
}
python::list standardizeSmilesHelper(const std::string &smiles) {
python::list res;
std::vector<MolStandardize::ValidationErrorInfo> errout =
MolStandardize::validateSmiles(smiles);
for (const auto &msg : errout) {
res.append(msg);
}
return res;
}
} // namespace
struct validate_wrapper {
static void wrap() {
std::string docString = "";
python::class_<ValidationMethodWrap, boost::noncopyable>("ValidationMethod")
.def("validate", pythonValidateMethod,
(python::arg("self"), python::arg("mol"),
python::arg("reportAllFailures") = false),
"");
python::class_<MolStandardize::RDKitValidation,
python::bases<MolStandardize::ValidationMethod>,
boost::noncopyable>("RDKitValidation")
.def(python::init<bool>(python::arg("allowEmptyMolecules") = false))
.def_readwrite("allowEmptyMolecules",
&MolStandardize::RDKitValidation::allowEmptyMolecules);
python::class_<MolStandardize::NoAtomValidation,
python::bases<MolStandardize::ValidationMethod>,
boost::noncopyable>("NoAtomValidation");
python::class_<MolStandardize::FragmentValidation,
python::bases<MolStandardize::ValidationMethod>,
boost::noncopyable>("FragmentValidation");
python::class_<MolStandardize::NeutralValidation,
python::bases<MolStandardize::ValidationMethod>,
boost::noncopyable>("NeutralValidation");
python::class_<MolStandardize::IsotopeValidation,
python::bases<MolStandardize::ValidationMethod>,
boost::noncopyable>("IsotopeValidation")
.def(python::init<bool>(python::arg("strict") = false))
.def_readwrite("strict", &MolStandardize::IsotopeValidation::strict);
python::class_<MolStandardize::MolVSValidation,
python::bases<MolStandardize::ValidationMethod>,
boost::noncopyable>("MolVSValidation")
.def("__init__", python::make_constructor(&getMolVSValidation));
python::class_<MolStandardize::AllowedAtomsValidation,
python::bases<MolStandardize::ValidationMethod>,
boost::noncopyable>("AllowedAtomsValidation",
python::no_init)
.def("__init__", python::make_constructor(&getAllowedAtomsValidation));
python::class_<MolStandardize::DisallowedAtomsValidation,
python::bases<MolStandardize::ValidationMethod>,
boost::noncopyable>("DisallowedAtomsValidation",
python::no_init)
.def("__init__",
python::make_constructor(&getDisallowedAtomsValidation));
python::class_<MolStandardize::FeaturesValidation,
python::bases<MolStandardize::ValidationMethod>>(
"FeaturesValidation")
.def(python::init<bool, bool, bool, bool, bool, bool>(
(python::arg("allowEnhancedStereo") = false,
python::arg("allowAromaticBondType") = false,
python::arg("allowDativeBondType") = false,
python::arg("allowQueries") = false,
python::arg("allowDummmies") = false,
python::arg("allowAtomAliases") = false)))
.def_readwrite("allowEnhancedStereo",
&MolStandardize::FeaturesValidation::allowEnhancedStereo)
.def_readwrite(
"allowAromaticBondType",
&MolStandardize::FeaturesValidation::allowAromaticBondType)
.def_readwrite("allowDativeBondType",
&MolStandardize::FeaturesValidation::allowDativeBondType)
.def_readwrite("allowQueries",
&MolStandardize::FeaturesValidation::allowQueries)
.def_readwrite("allowDummies",
&MolStandardize::FeaturesValidation::allowDummies)
.def_readwrite("allowAtomAliases",
&MolStandardize::FeaturesValidation::allowAtomAliases);
python::class_<MolStandardize::DisallowedRadicalValidation,
python::bases<MolStandardize::ValidationMethod>,
boost::noncopyable>("DisallowedRadicalValidation");
python::class_<MolStandardize::Is2DValidation,
python::bases<MolStandardize::ValidationMethod>,
boost::noncopyable>("Is2DValidation")
.def(python::init<double>(python::arg("threshold") = 1e-3))
.def_readwrite("threshold", &MolStandardize::Is2DValidation::threshold);
python::class_<MolStandardize::Layout2DValidation,
python::bases<MolStandardize::ValidationMethod>,
boost::noncopyable>("Layout2DValidation")
.def(python::init<double, double, bool, bool, double>(
(python::arg("clashLimit") = 0.15,
python::arg("bondLengthLimit") = 25.,
python::arg("allowLongBondsInRings") = true,
python::arg("allowAtomBondClashExemption") = true,
python::arg("minMedianBondLength") = false)))
.def_readwrite("clashLimit",
&MolStandardize::Layout2DValidation::clashLimit)
.def_readwrite("bondLengthLimit",
&MolStandardize::Layout2DValidation::bondLengthLimit)
.def_readwrite(
"allowLongBondsInRings",
&MolStandardize::Layout2DValidation::allowLongBondsInRings)
.def_readwrite(
"allowAtomBondClashExemption",
&MolStandardize::Layout2DValidation::allowAtomBondClashExemption)
.def_readwrite(
"minMedianBondLength",
&MolStandardize::Layout2DValidation::minMedianBondLength);
python::class_<MolStandardize::StereoValidation,
python::bases<MolStandardize::ValidationMethod>,
boost::noncopyable>("StereoValidation");
python::def("ValidateSmiles", standardizeSmilesHelper, (python::arg("mol")),
docString.c_str());
}
};
void wrap_validate() { validate_wrapper::wrap(); }
|
