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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_string.i"
%include "std_vector.i"
%{
#include <../RDGeneral/Dict.h>
#include <../Catalogs/Catalog.h>
#include <../Catalogs/CatalogParams.h>
#include <GraphMol/FilterCatalog/FilterMatcherBase.h>
#include <GraphMol/FilterCatalog/FilterCatalogEntry.h>
#include <GraphMol/FilterCatalog/FilterCatalog.h>
// bug fix for swig, it removes these from their namespaces
typedef RDCatalog::Catalog<RDKit::FilterCatalogEntry, RDKit::FilterCatalogParams>::paramType_t paramType_t;
typedef RDCatalog::Catalog<RDKit::FilterCatalogEntry, RDKit::FilterCatalogParams>::entryType_t entryType_t;
typedef std::vector<std::string> STR_VECT;
%}
%template(FilterCatalogEntry_Vect) std::vector< boost::shared_ptr<RDKit::FilterCatalogEntry> >;
%template(FilterCatalogEntryVect) std::vector< const RDKit::FilterCatalogEntry* >;
%template(UChar_Vect) std::vector<unsigned char>;
%template(FilterMatch_Vect) std::vector<RDKit::FilterMatch>;
%include "enums.swg"
%include <../RDGeneral/Dict.h>
%include <../Catalogs/Catalog.h>
%include <../Catalogs/CatalogParams.h>
%include <GraphMol/Substruct/SubstructMatch.h>
%typemap(javacode) RDKit::FilterCatalog %{
public static FilterCatalog 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 FilterCatalog(vec);
}
%}
%extend RDKit::FilterMatch {
MatchVectType getAtomMatches() {
return ($self)->atomPairs;
}
}
%newobject RDKit::FilterCatalogEntry::getProp;
%extend RDKit::FilterCatalogEntry {
std::string getProp(const std::string key){
std::string res;
($self)->getProp(key, res);
return res;
}
std::vector<RDKit::FilterMatch> getFilterMatches(const ROMol &mol) {
std::vector<RDKit::FilterMatch> matches;
($self)->getFilterMatches(mol, matches);
return matches;
}
}
%extend RDKit::FilterCatalog {
FilterCatalog(const std::vector<unsigned char> & data ) {
std::string str(data.begin(), data.end());
return new RDKit::FilterCatalog(str);
}
bool canSerialize() const {
return RDKit::FilterCatalogCanSerialize();
}
// boost does a bad job of wrapping shared_ptr<const T> so we will do the
// unthinkable and cast away const.
// Also we can't use FilterCatalog::SENTRY because swig thinks it is a new
// type. Bad swig!
boost::shared_ptr<RDKit::FilterCatalogEntry> getFirstMatch(const ROMol &mol) {
RDKit::FilterCatalog::CONST_SENTRY res = self->getFirstMatch(mol);
return boost::const_pointer_cast<RDKit::FilterCatalogEntry>(res);
}
std::vector<boost::shared_ptr<RDKit::FilterCatalogEntry> > getMatches(const ROMol &mol) {
std::vector<RDKit::FilterCatalog::CONST_SENTRY> matches = self->getMatches(mol);
std::vector<RDKit::FilterCatalog::SENTRY> res;
res.reserve(matches.size());
for (size_t i=0; i< matches.size(); ++i) {
res.push_back( boost::const_pointer_cast<RDKit::FilterCatalogEntry>(matches[i]) );
}
return res;
}
// re-wrap swig is making duplicate entries for some strange reason
unsigned int addEntry(boost::shared_ptr<RDKit::FilterCatalogEntry> entry) {
return self->addEntry(entry);
}
bool removeEntry(boost::shared_ptr<RDKit::FilterCatalogEntry> entry) {
return self->removeEntry(entry);
}
// swig const-ptr shenanigans again
boost::shared_ptr<RDKit::FilterCatalogEntry> getEntry(unsigned int idx) const {
return boost::const_pointer_cast<RDKit::FilterCatalogEntry>(
self->getEntry(idx));
}
unsigned int getIdxForEntry(const boost::shared_ptr<FilterCatalogEntry> &entry) const {
return self->getIdxForEntry(entry);
}
}
%ignore RDKit::FilterCatalog(const std::string &);
%ignore RDKit::FilterCatalog::getFirstMatch;
%ignore RDKit::FilterCatalog::getMatches;
%ignore RDKit::FilterCatalog::addEntry;
%ignore RDKit::FilterCatalog::removeEntry;
%ignore RDKit::FilterCatalog::setCatalogParams;
%ignore RDKit::FilterCatalog::getIdxForEntry;
%ignore RDKit::FilterCatalog::getEntryWithIdx;
%ignore RDKit::FilterMatch::operator==;
%ignore std::vector<RDKit::FilterMatch>::operator==;
//%ignore RDKit::FilterCatalogEntry::getPropList;
%ignore RDKit::Dict::getPropList;
#ifdef SWIGJAVA
%typemap(jni) std::string RDKit::FilterCatalog::Serialize "jbyteArray"
%typemap(jtype) std::string RDKit::FilterCatalog::Serialize "byte[]"
%typemap(jstype) std::string RDKit::FilterCatalog::Serialize "byte[]"
%typemap(javaout) std::string RDKit::FilterCatalog::Serialize {
return $jnicall;
}
%typemap(out) std::string RDKit::FilterCatalog::Serialize {
$result = JCALL1(NewByteArray, jenv, $1.size());
JCALL4(SetByteArrayRegion, jenv, $result, 0, $1.size(), (const jbyte*)$1.c_str());
}
#endif
%include <GraphMol/FilterCatalog/FilterMatcherBase.h>
%include <GraphMol/FilterCatalog/FilterCatalogEntry.h>
%include <GraphMol/FilterCatalog/FilterCatalog.h>
%pragma(java) modulecode=%{
public static FilterCatalog FilterCatalogDeserialize(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 FilterCatalog(vec);
}
%}
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