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
|
//
// Copyright (C) 2020 Shrey Aryan
//
// @@ 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.
//
#ifdef RDK_BUILD_THREADSAFE_SSS
#define NO_IMPORT_ARRAY
#include <RDBoost/python.h>
#include <string>
// ours
#include <GraphMol/FileParsers/MultithreadedSmilesMolSupplier.h>
#include <GraphMol/RDKitBase.h>
#include <RDGeneral/FileParseException.h>
#include <GraphMol/Wrap/ContextManagers.h>
#include "MolSupplier.h"
#include "MultithreadedMolSupplier.h"
namespace python = boost::python;
namespace RDKit {
std::string multiSmilesMolSupplierClassDoc =
"A class which concurrently supplies molecules from a text file.\n\
Please note that this class is still a bit experimental and the API may\n\
change in future releases.\n\
\n\
Usage examples:\n\
\n\
1) Lazy evaluation: the molecules might not be constructed until we ask for them:\n\n\
>>> suppl = MultithreadedSmilesMolSupplier('in.smi')\n\
>>> for mol in suppl:\n\
... if(mol):\n\
... mol.GetNumAtoms()\n\
\n\
2) Lazy evaluation 2:\n\n\
>>> suppl = MultithreadedSmilesMolSupplier('in.smi')\n\
>>> while (!suppl.atEnd()):\n\
... mol = next(mol)\n\
... if(mol):\n\
... mol.GetNumAtoms()\n\
\n";
std::string multiSmsDocStr =
"Constructor\n\n\
ARGUMENTS: \n\
\n\
- fileName: name of the file to be read\n\
\n\
- delimiter: (optional) text delimiter (a string). Defauts to ' \t'.\n\
\n\
- smilesColumn: (optional) index of the column containing the SMILES\n\
data. Defaults to 0.\n\
\n\
- nameColumn: (optional) index of the column containing molecule names.\n\
Defaults to 1.\n\
\n\
- titleLine: (optional) set this toggle if the file contains a title line.\n\
Defaults to true.\n\
\n\
- sanitize: (optional) toggles sanitization of molecules as they are read.\n\
Defaults to true.\n\
\n\
- numWriterThreads: (optional) number of writer threads. Defaults to 1.\n\
\n\
- sizeInputQueue: (optional) size of input/reader queue. Defaults to 5.\n\
\n\
- sizeOutputQueue: (optional) size of output/writer queue. Defaults to 5.\n\
\n";
struct multiSmiMolSup_wrap {
static void wrap() {
python::class_<MultithreadedSmilesMolSupplier, boost::noncopyable>(
"MultithreadedSmilesMolSupplier",
multiSmilesMolSupplierClassDoc.c_str(),
python::init<>(python::args("self")))
.def(python::init<std::string, std::string, int, int, bool, bool,
unsigned int, size_t, size_t>(
(python::arg("self"), python::arg("fileName"),
python::arg("delimiter") = " \t", python::arg("smilesColumn") = 0,
python::arg("nameColumn") = 1, python::arg("titleLine") = true,
python::arg("sanitize") = true,
python::arg("numWriterThreads") = 1,
python::arg("sizeInputQueue") = 5,
python::arg("sizeOutputQueue") = 5),
multiSmsDocStr.c_str()))
.def("__iter__",
(MultithreadedSmilesMolSupplier *
(*)(MultithreadedSmilesMolSupplier *)) &
MTMolSupplIter,
python::return_internal_reference<1>(), python::args("self"))
.def("__enter__",
(MultithreadedSmilesMolSupplier *
(*)(MultithreadedSmilesMolSupplier *)) &
MolIOEnter,
python::return_internal_reference<>())
.def("__exit__",
(bool (*)(MultithreadedSmilesMolSupplier *, python::object,
python::object, python::object)) &
MolIOExit)
.def("__next__",
(ROMol * (*)(MultithreadedSmilesMolSupplier *)) &
MolForwardSupplNext,
"Returns the next molecule in the file. Raises _StopIteration_ "
"on EOF.\n",
python::return_value_policy<python::manage_new_object>(),
python::args("self"))
.def("atEnd", &MultithreadedSmilesMolSupplier::atEnd,
python::args("self"),
"Returns true if we have read all records else false.\n")
.def("GetLastRecordId",
(unsigned int (*)(MultithreadedSmilesMolSupplier *)) &
MTMolSupplLastId,
python::args("self"),
"Returns the record id for the last extracted item.\n")
.def("GetLastItemText",
(std::string(*)(MultithreadedSmilesMolSupplier *)) &
MTMolSupplLastItem,
python::args("self"),
"Returns the text for the last extracted item.\n");
};
};
} // namespace RDKit
void wrap_multiSmiSupplier() { RDKit::multiSmiMolSup_wrap::wrap(); }
#endif
|
