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https://github.com/rdkit/rdkit.git
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c8aa10c80f
* Fixes #3797 * [WIP] Add tautomer queries to the substruct library * Add TautomerQuery to CMake * Add missing TautomerQuery functions, python wrapper and tests * Add python wrappers for Substruct Library Tautomer Queries * Explictly label non-const pattern function now that we have both * Use boost::shared_ptr not std::shared_ptr * Fix java builds * One more try to fix java builds * Fix Java Tests * Run clang format * Reenable tests * Fix annoyingly stupid bug and annoying commit of debug code * Fix documentation * reenable ifdef threadsafe check * Throw warning and perform tautomer search instead of bailing with incorrect fingerprints * Simplfy api with templates * Fix SubstructLibrary java issues * minor API cleanup * simplify the SWIG wrappers Co-authored-by: Brian Kelley <bkelley@relaytx.com> Co-authored-by: greg landrum <greg.landrum@gmail.com>
113 lines
4.0 KiB
OpenEdge ABL
113 lines
4.0 KiB
OpenEdge ABL
/*
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* Copyright (c) 2015, Novartis Institutes for BioMedical Research Inc.
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* All rights reserved.
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*
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are
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* met:
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*
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* * Redistributions of source code must retain the above copyright
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* notice, this list of conditions and the following disclaimer.
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* * Redistributions in binary form must reproduce the above
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* copyright notice, this list of conditions and the following
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* disclaimer in the documentation and/or other materials provided
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* with the distribution.
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* * Neither the name of Novartis Institutes for BioMedical Research Inc.
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* nor the names of its contributors may be used to endorse or promote
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* products derived from this software without specific prior written permission.
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*
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
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* "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
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* LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
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* A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
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* OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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* SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
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* LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
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* DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
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* THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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* OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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*/
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//%import "ROMol.i"
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%include "std_vector.i"
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%{
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#include <GraphMol/SubstructLibrary/SubstructLibrary.h>
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#include <GraphMol/TautomerQuery/TautomerQuery.h>
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%}
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%shared_ptr(RDKit::TautomerQuery)
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%shared_ptr(RDKit::MolHolderBase)
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%shared_ptr(RDKit::MolHolder)
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%shared_ptr(RDKit::CachedMolHolder)
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%shared_ptr(RDKit::CachedSmilesMolHolder)
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%shared_ptr(RDKit::CachedTrustedSmilesMolHolder)
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%shared_ptr(RDKit::FPHolderBase)
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%shared_ptr(RDKit::PatternHolder)
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%shared_ptr(RDKit::TautomerPatternHolder)
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%template(UChar_Vect) std::vector<unsigned char>;
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%typemap(javacode) RDKit::SubstructLibrary %{
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public static SubstructLibrary Deserialize(byte[] b) {
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UChar_Vect vec = new UChar_Vect();
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vec.reserve(b.length);
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for (int size=0;size<b.length;++size) {
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vec.add(b[size]);
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}
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return new SubstructLibrary(vec);
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}
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%}
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%extend RDKit::SubstructLibrary {
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SubstructLibrary(const std::vector<unsigned char> & data ) {
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std::string str(data.begin(), data.end());
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return new RDKit::SubstructLibrary(str);
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}
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bool canSerialize() const {
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return RDKit::SubstructLibraryCanSerialize();
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}
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}
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#ifdef SWIGJAVA
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%typemap(jni) std::string RDKit::SubstructLibrary::Serialize "jbyteArray"
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%typemap(jtype) std::string RDKit::SubstructLibrary::Serialize "byte[]"
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%typemap(jstype) std::string RDKit::SubstructLibrary::Serialize "byte[]"
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%typemap(javaout) std::string RDKit::SubstructLibrary::Serialize {
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return $jnicall;
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}
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%typemap(out) std::string RDKit::SubstructLibrary::Serialize {
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$result = JCALL1(NewByteArray, jenv, $1.size());
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JCALL4(SetByteArrayRegion, jenv, $result, 0, $1.size(), (const jbyte*)$1.c_str());
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}
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#endif
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%include <GraphMol/TautomerQuery/TautomerQuery.h>
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%include <GraphMol/SubstructLibrary/SubstructLibrary.h>
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%extend RDKit::SubstructLibrary {
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%template(getMatches) getMatches<ROMol>;
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%template(getMatches) getMatches<TautomerQuery>;
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%template(countMatches) countMatches<ROMol>;
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%template(countMatches) countMatches<TautomerQuery>;
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%template(hasMatch) hasMatch<ROMol>;
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%template(hasMatch) hasMatch<TautomerQuery>;
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}
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%pragma(java) modulecode=%{
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public static SubstructLibrary SubstructLibraryDeserialize(byte[] b) {
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UChar_Vect vec = new UChar_Vect();
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vec.reserve(b.length);
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for (int size=0;size<b.length;++size) {
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vec.add(b[size]);
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}
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return new SubstructLibrary(vec);
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}
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%}
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