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
|
//
// 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/Normalize.h>
#include <sstream>
namespace python = boost::python;
using namespace RDKit;
namespace {
ROMol *normalizeHelper(MolStandardize::Normalizer &self, const ROMol &mol) {
return self.normalize(mol);
}
void normalizeInPlaceHelper(MolStandardize::Normalizer &self, ROMol &mol) {
self.normalizeInPlace(static_cast<RWMol &>(mol));
}
MolStandardize::Normalizer *normalizerFromDataAndParams(
const std::string &data, const MolStandardize::CleanupParameters ¶ms) {
std::istringstream sstr(data);
return new MolStandardize::Normalizer(sstr, params.maxRestarts);
}
} // namespace
struct normalize_wrapper {
static void wrap() {
python::scope().attr("__doc__") =
"Module containing tools for normalizing molecules defined by SMARTS "
"patterns";
std::string docString = "";
python::class_<MolStandardize::Normalizer, boost::noncopyable>(
"Normalizer", python::init<>(python::args("self")))
.def(python::init<std::string, unsigned int>(
python::args("self", "normalizeFilename", "maxRestarts")))
.def("normalize", &normalizeHelper,
(python::arg("self"), python::arg("mol")), "",
python::return_value_policy<python::manage_new_object>())
.def("normalizeInPlace", &normalizeInPlaceHelper,
(python::arg("self"), python::arg("mol")),
"modifies the input molecule");
python::def(
"NormalizerFromData", &normalizerFromDataAndParams,
(python::arg("paramData"), python::arg("params")),
"creates a Normalizer from a string containing normalization SMARTS",
python::return_value_policy<python::manage_new_object>());
python::def("NormalizerFromParams", &MolStandardize::normalizerFromParams,
(python::arg("params")),
"creates a Normalizer from CleanupParameters",
python::return_value_policy<python::manage_new_object>());
}
};
void wrap_normalize() { normalize_wrapper::wrap(); }
|
