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
|
// $Id: ChemicalFeatureUtils.cpp 1528 2010-09-26 17:04:37Z glandrum $
//
// Copyright (C) 2006 Rational Discovery LLC
//
// @@ 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.
//
#define NO_IMPORT_ARRAY
#include <boost/python.hpp>
#include <boost/dynamic_bitset.hpp>
#include <GraphMol/RDKitBase.h>
#include <RDGeneral/types.h>
#include <GraphMol/MolChemicalFeatures/MolChemicalFeature.h>
#include <GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.h>
#include <ChemicalFeatures/FreeChemicalFeature.h>
namespace python = boost::python;
namespace RDKit {
python::object GetAtomMatch(python::object featMatch,int maxAts=1024){
python::list res;
unsigned int nEntries=python::extract<unsigned int>(featMatch.attr("__len__")());
boost::dynamic_bitset<> indices(maxAts);
for(unsigned int i=0;i<nEntries;++i){
MolChemicalFeature *feat=python::extract<MolChemicalFeature *>(featMatch[i]);
const MolChemicalFeature::AtomPtrContainer &atoms = feat->getAtoms();
MolChemicalFeature::AtomPtrContainer_CI aci;
python::list local;
for(aci=atoms.begin();aci!=atoms.end();++aci){
unsigned int idx=(*aci)->getIdx();
if(indices[idx]){
return python::list();
} else {
indices[idx]=1;
}
local.append(idx);
}
res.append(local);
}
return res;
}
#if 0
// defined in MolChemicalFeatureFactory.cpp
python::tuple getFeatsForMol(const MolChemicalFeatureFactory &factory,
const ROMol &mol,
std::string includeOnly);
// Moving this into C++ didn't provide any speed improvement in our profiling,
// so, rather than adding additional complications to the wrapper interface,
// we'll just leave it out
//
// In the event it should be re-integrated, here's the def:
//python::def("GetFeatureMatchDict",GetFeatMatchDict,(python::arg("mol"),
// python::arg("factory"),
// python::arg("feats")),
// );
python::dict GetFeatMatchDict(const ROMol *mol,const MolChemicalFeatureFactory *factory,
python::object feats){
python::dict res;
unsigned int nEntries=python::extract<unsigned int>(feats.attr("__len__")());
for(unsigned int i=0;i<nEntries;++i){
const char *family;
python::extract<MolChemicalFeature *> cfX(feats[i]);
if(cfX.check()){
family=cfX()->getFamily().c_str();
} else {
python::extract<ChemicalFeatures::FreeChemicalFeature *> fcfX(feats[i]);
family=fcfX()->getFamily().c_str();
}
if(!res.has_key(family)){
res[family] = getFeatsForMol(factory,mol,family);
}
}
return res;
}
#endif
struct ChemicalFeatureUtils_wrapper {
static void wrap() {
python::def("GetAtomMatch",GetAtomMatch,(python::arg("featMatch"),python::arg("maxAts")=1024),
"Returns an empty list if any of the features passed in share an atom.\n\
Otherwise a list of lists of atom indices is returned.\n");
}
};
} // end of namespace RDKit
void wrap_ChemicalFeatureUtils() {
RDKit::ChemicalFeatureUtils_wrapper::wrap();
}
|
