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
|
/*
* Copyright (c) 2015, Novartis Institutes for BioMedical Research Inc.
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are
* met:
*
* * Redistributions of source code must retain the above copyright
* notice, this list of conditions and the following disclaimer.
* * Redistributions in binary form must reproduce the above
* copyright notice, this list of conditions and the following
* disclaimer in the documentation and/or other materials provided
* with the distribution.
* * Neither the name of Novartis Institutes for BioMedical Research Inc.
* nor the names of its contributors may be used to endorse or promote
* products derived from this software without specific prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
* "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
* LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
* A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
* OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
* SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
* LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
* DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
* THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
* OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
//%import "ROMol.i"
%include "std_vector.i"
%{
#include <GraphMol/SubstructLibrary/SubstructLibrary.h>
#include <GraphMol/TautomerQuery/TautomerQuery.h>
#include <GraphMol/GeneralizedSubstruct/XQMol.h>
using RDKit::GeneralizedSubstruct::ExtendedQueryMol;
%}
%shared_ptr(RDKit::TautomerQuery)
%shared_ptr(RDKit::MolHolderBase)
%shared_ptr(RDKit::MolHolder)
%shared_ptr(RDKit::CachedMolHolder)
%shared_ptr(RDKit::CachedSmilesMolHolder)
%shared_ptr(RDKit::CachedTrustedSmilesMolHolder)
%shared_ptr(RDKit::FPHolderBase)
%shared_ptr(RDKit::PatternHolder)
%shared_ptr(RDKit::TautomerPatternHolder)
%shared_ptr(RDKit::KeyHolderBase)
%shared_ptr(RDKit::KeyFromPropHolder)
%template(UChar_Vect) std::vector<unsigned char>;
%typemap(javacode) RDKit::SubstructLibrary %{
public static SubstructLibrary Deserialize(byte[] b) {
UChar_Vect vec = null;
try {
vec = new UChar_Vect();
vec.reserve(b.length);
for (int size=0;size<b.length;++size) {
vec.add((short)b[size]);
}
return new SubstructLibrary(vec);
} finally {
if (vec != null) {
vec.delete();
}
}
}
%}
%extend RDKit::SubstructLibrary {
SubstructLibrary(const std::vector<unsigned char> & data ) {
std::string str(data.begin(), data.end());
return new RDKit::SubstructLibrary(str);
}
static bool canSerialize() {
return RDKit::SubstructLibraryCanSerialize();
}
}
#ifdef SWIGJAVA
%typemap(jni) std::string RDKit::SubstructLibrary::Serialize "jbyteArray"
%typemap(jtype) std::string RDKit::SubstructLibrary::Serialize "byte[]"
%typemap(jstype) std::string RDKit::SubstructLibrary::Serialize "byte[]"
%typemap(javaout) std::string RDKit::SubstructLibrary::Serialize {
return $jnicall;
}
%typemap(out) std::string RDKit::SubstructLibrary::Serialize {
$result = JCALL1(NewByteArray, jenv, $1.size());
JCALL4(SetByteArrayRegion, jenv, $result, 0, $1.size(), (const jbyte*)$1.c_str());
}
#endif
%include <GraphMol/TautomerQuery/TautomerQuery.h>
%include <GraphMol/SubstructLibrary/SubstructLibrary.h>
%extend RDKit::SubstructLibrary {
%template(getMatches) getMatches<ROMol>;
%template(getMatches) getMatches<TautomerQuery>;
%template(getMatches) getMatches<RDKit::GeneralizedSubstruct::ExtendedQueryMol>;
%template(countMatches) countMatches<ROMol>;
%template(countMatches) countMatches<TautomerQuery>;
%template(countMatches) countMatches<ExtendedQueryMol>;
%template(hasMatch) hasMatch<ROMol>;
%template(hasMatch) hasMatch<TautomerQuery>;
%template(hasMatch) hasMatch<ExtendedQueryMol>;
}
%pragma(java) modulecode=%{
public static SubstructLibrary SubstructLibraryDeserialize(byte[] b) {
UChar_Vect vec = new UChar_Vect();
vec.reserve(b.length);
for (int size=0;size<b.length;++size) {
vec.add((short)b[size]);
}
return new SubstructLibrary(vec);
}
%}
|
