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
|
//
// Copyright (C) 2005-2008 Greg Landrumm and 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.
//
#ifndef _RD_WRAP_MOLSUPPLIER_H_
#define _RD_WRAP_MOLSUPPLIER_H_
//! Template functions for wrapping suppliers as python iterators.
#include <RDBoost/python.h>
#include <GraphMol/RDKitBase.h>
#include <RDGeneral/FileParseException.h>
namespace RDKit {
// Note that this returns a pointer to the supplier itself, so be careful
// that it doesn't get deleted by python!
template <typename T>
T *MolSupplIter(T *suppl) {
suppl->reset();
return suppl;
}
template <typename T>
ROMol *MolSupplNext(T *suppl) {
ROMol *res = 0;
if (!suppl->atEnd()) {
try {
res = suppl->next();
} catch (...) {
res = 0;
}
}
// FIX: there is an edge case here that we ought to catch:
// suppliers where the last molecule has a chemistry problem
// With the current behavior, those empty molecules will not
// show up in the list
if (suppl->atEnd() && !res) {
PyErr_SetString(PyExc_StopIteration, "End of supplier hit");
throw boost::python::error_already_set();
}
return res;
}
template <typename T>
ROMol *MolSupplNextAcceptNullLastMolecule(T *suppl) {
ROMol *res = 0;
if (!suppl->atEnd()) {
try {
res = suppl->next();
} catch (...) {
res = 0;
}
} else {
PyErr_SetString(PyExc_StopIteration, "End of supplier hit");
throw boost::python::error_already_set();
}
return res;
}
template <typename T>
ROMol *MolSupplGetItem(T *suppl, int idx) {
ROMol *res = 0;
if (idx < 0) {
idx = suppl->length() + idx;
}
try {
res = (*suppl)[idx];
} catch (...) {
// it's kind of doofy that we can't just catch the FileParseException
// that is thrown when we run off the end of the supplier, but it seems
// that the cross-shared library exception handling thing is just too
// hard for me as of boost 1.35.0 (also 1.34.1) and g++ 4.1.x on linux
// this approach works as well:
if (suppl->atEnd()) {
PyErr_SetString(PyExc_IndexError, "invalid index");
throw boost::python::error_already_set();
} else {
res = 0;
}
}
return res;
}
}
#endif
|
