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Exposes substructlibrary to swig (#2337)

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* SWIG wrap SubstructLibrary

* Fix tests

* Fix virtual overload for tagAtoms

* Add SubstructLibrary to swig
This commit is contained in:
Brian Kelley
2019-03-12 11:35:22 -04:00
committed by Greg Landrum
parent 95eeec7b34
commit af6d413ccc
7 changed files with 352 additions and 2 deletions
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96
Code/JavaWrappers/SubstructLibrary.i Normal file
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/*
* 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>
%}
%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)
%template(UChar_Vect) std::vector<unsigned char>;
%typemap(javacode) RDKit::SubstructLibrary %{
public static SubstructLibrary Deserialize(byte[] b) {
UChar_Vect vec = new UChar_Vect();
vec.reserve(b.length);
for (int size=0;size<b.length;++size) {
vec.add(b[size]);
}
return new SubstructLibrary(vec);
}
%}
%extend RDKit::SubstructLibrary {
SubstructLibrary(const std::vector<unsigned char> & data ) {
std::string str(data.begin(), data.end());
return new RDKit::SubstructLibrary(str);
}
bool canSerialize() const {
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/SubstructLibrary/SubstructLibrary.h>
%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(b[size]);
}
return new SubstructLibrary(vec);
}
%}