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
|
// $Id: SDMolSupplier.cpp 585 2008-03-30 13:36:56Z glandrum $
//
// Copyright (C) 2009 Greg Landrum
//
// @@ 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 <RDBoost/python.h>
#include <string>
#include <boost/iostreams/device/file.hpp>
#include <boost/iostreams/filtering_stream.hpp>
#include <boost/iostreams/filter/gzip.hpp>
#include <boost/iostreams/filter/bzip2.hpp>
#include <boost/algorithm/string.hpp>
namespace io = boost::iostreams;
// ours
#include <GraphMol/FileParsers/MolSupplier.h>
#include <GraphMol/Wrap/ContextManagers.h>
#include <GraphMol/RDKitBase.h>
#include <RDBoost/Wrap.h>
#include "MolSupplier.h"
namespace python = boost::python;
namespace RDKit {
// Note that this returns a pointer to the supplier itself, so be careful
// that it doesn't get deleted by python!
ForwardSDMolSupplier *MolSupplIter(ForwardSDMolSupplier *suppl) {
return suppl;
}
ROMol *MolSupplNext(ForwardSDMolSupplier *suppl) {
ROMol *res = 0;
if (!suppl->atEnd()) {
try {
res = suppl->next();
} catch (...) {
res = 0;
}
}
if (!res && suppl->atEnd()) {
PyErr_SetString(PyExc_StopIteration, "End of supplier hit");
throw boost::python::error_already_set();
}
return res;
}
ForwardSDMolSupplier *createForwardSupplier(std::string filename, bool sanitize,
bool removeHs) {
std::vector<std::string> splitName;
boost::split(splitName, filename, boost::is_any_of("."));
io::filtering_istream *strm = new io::filtering_istream();
if (splitName.back() == "sdf") {
} else if (splitName.back() == "gz") {
#ifndef RDK_NOGZIP
strm->push(io::gzip_decompressor());
#else
throw_value_error("gzip support not enabled");
#endif
} else if (splitName.back() == "bz2") {
#ifndef RDK_NOBZIP2
strm->push(io::bzip2_decompressor());
#else
throw_value_error("bzip2 support not enabled");
#endif
} else {
std::string errorTxt = "Unrecognized extension: " + splitName.back();
throw_value_error(errorTxt);
}
io::file_source fileSource(filename);
if (!fileSource.is_open()) {
std::string errorTxt = "could not open file: " + filename;
throw_value_error(errorTxt);
}
strm->push(fileSource);
ForwardSDMolSupplier *res =
new ForwardSDMolSupplier(strm, true, sanitize, removeHs);
return res;
}
std::string csdMolSupplierClassDoc =
"A class which supplies molecules from an SD file.\n\
\n\
Usage examples:\n\
\n\
1) Lazy evaluation: the molecules are not constructed until we ask for them:\n\n\
>>> suppl = SDMolSupplier('in.smi')\n\
>>> for mol in suppl:\n\
... mol.GetNumAtoms()\n\
\n\
Properties in the SD file are used to set properties on each molecule.\n\
The properties are accessible using the mol.GetProp(propName) method.\n\
\n";
struct compressedsdmolsup_wrap {
static void wrap() {
python::class_<ForwardSDMolSupplier, boost::noncopyable>(
"_CompressedSDMolSupplier", csdMolSupplierClassDoc.c_str(),
python::no_init)
.def("__iter__", &MolSupplIter<ForwardSDMolSupplier>,
python::return_internal_reference<1>())
.def("__enter__", &MolIOEnter<ForwardSDMolSupplier>,
python::return_internal_reference<>())
.def("__exit__", &MolIOExit<ForwardSDMolSupplier>)
.def("__next__", &MolSupplNext<ForwardSDMolSupplier>,
"Returns the next molecule in the file. Raises _StopIteration_ "
"on EOF.\n",
python::return_value_policy<python::manage_new_object>());
python::def("CompressedSDMolSupplier", createForwardSupplier,
(python::arg("fileName"), python::arg("sanitize") = true,
python::arg("removeHs") = true),
python::return_value_policy<python::manage_new_object>());
};
};
} // namespace RDKit
void wrap_compressedsdsupplier() { RDKit::compressedsdmolsup_wrap::wrap(); }
|
