rdkit_chem 2019.03.3.1 → 2025.09.3.1

data/Code/RubyWrappers/QueryBond.i

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+/*
+* $Id$
+*
+*  Copyright (c) 2010, 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.
+*/
+
+%{
+#include <GraphMol/QueryBond.h>
+%}
+
+%ignore RDKit::QueryBond::expandQuery;
+%ignore RDKit::QueryBond::setQuery;
+
+%include <GraphMol/QueryBond.h>
+
+%extend RDKit::QueryBond {
+	bool MatchBond(RDKit::Bond const *what) {
+		return ($self)->Match(what);
+	}
+}

data/Code/RubyWrappers/QueryOps.i

@@ -0,0 +1,44 @@
+/*
+* $Id$
+*
+*  Copyright (c) 2010, 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.
+*/
+
+%{
+#include <GraphMol/QueryOps.h>
+%}
+
+%ignore RDKit::RecursiveStructureQuery::d_mutex;
+%ignore RDKit::HasPropWithValueQuery::getPair;
+%ignore RDKit::HasPropWithValueQueryBase::getPair;
+
+%include <Query/QueryObjects.h>
+%include <Query/EqualityQuery.h>
+%include <GraphMol/QueryOps.h>

data/Code/RubyWrappers/RDKitExceptions.i

@@ -0,0 +1,75 @@
+/* 
+* $Id$
+*
+*  Copyright (c) 2010, 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.
+*/
+
+// Defines all of the C++ -> Java exception handling
+
+%{
+#include <RDGeneral/Exceptions.h>
+#include <RubyWrappers/GenericRDKitException.h>
+%}
+
+// Note that these files must follow the typemap declarations
+%include <RDGeneral/Exceptions.h>
+%include <RubyWrappers/GenericRDKitException.h>
+
+%exception {
+  try {
+     $action
+  } catch (RDKit::ChemicalReactionException &e) {
+    static VALUE exceptionError = rb_define_class("ChemicalReactionException", rb_eRuntimeError);
+    rb_raise(exceptionError, "%s", e.what());
+  } catch (RDKit::ChemicalReactionParserException &e) {
+    static VALUE exceptionError = rb_define_class("ChemicalReactionParserException", rb_eRuntimeError);
+    rb_raise(exceptionError, "%s", e.what());
+  } catch (RDKit::ConformerException &e) {
+    static VALUE exceptionError = rb_define_class("ConformerException", rb_eRuntimeError);
+    rb_raise(exceptionError, "%s", e.what());
+  } catch (RDKit::MolPicklerException &e) {
+    static VALUE exceptionError = rb_define_class("MolPicklerException", rb_eRuntimeError);
+    rb_raise(exceptionError, "%s", e.what());
+  } catch (RDKit::MolSanitizeException &e) {
+    static VALUE exceptionError = rb_define_class("MolSanitizeException", rb_eRuntimeError);
+    rb_raise(exceptionError, "%s", e.what());
+  } catch (RDKit::SmilesParseException &e) {
+    static VALUE exceptionError = rb_define_class("SmilesParseException", rb_eRuntimeError);
+    rb_raise(exceptionError, "%s", e.what());
+  } catch (KeyErrorException &e) {
+    static VALUE exceptionError = rb_define_class("KeyErrorException", rb_eRuntimeError);
+    rb_raise(exceptionError, "%s", e.what());
+
+  // Generic exception -- anything else
+  } catch (std::exception &e) {
+    static VALUE exceptionError = rb_define_class("GenericRDKitException", rb_eRuntimeError);
+    rb_raise(exceptionError, "%s", e.what());
+  }
+}

data/Code/RubyWrappers/RDLogger.i

@@ -0,0 +1,74 @@
+/*
+*
+*  Copyright (c) 2010-2023, Novartis Institutes for BioMedical Research Inc.
+*   and other RDKit contributors
+*  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.
+*/
+%ignore boost::logging::rdLogger::SetTee(std::ostream &stream);
+%ignore rdAppLog;
+%ignore rdDebugLog;
+%ignore rdInfoLog;
+%ignore rdErrorLog;
+%ignore rdWarningLog;
+%ignore rdStatusLog;
+%{
+#include <RDGeneral/RDLog.h>
+boost::logging::rdLogger& getRdAppLog() {
+  return *rdAppLog;
+}
+
+boost::logging::rdLogger& getRdDebugLog() {
+  return *rdDebugLog;
+}
+
+boost::logging::rdLogger& getRdErrorLog() {
+  return *rdErrorLog;
+}
+
+boost::logging::rdLogger& getRdInfoLog() {
+  return *rdInfoLog;
+}
+
+boost::logging::rdLogger& getRdWarningLog() {
+  return *rdWarningLog;
+}
+
+boost::logging::rdLogger& getRdStatusLog() {
+  return *rdStatusLog;
+}
+%}
+%include <RDGeneral/RDLog.h>
+
+boost::logging::rdLogger& getRdAppLog();
+boost::logging::rdLogger& getRdDebugLog();
+boost::logging::rdLogger& getRdErrorLog();
+boost::logging::rdLogger& getRdInfoLog();
+boost::logging::rdLogger& getRdWarningLog();
+boost::logging::rdLogger& getRdStatusLog();

data/Code/RubyWrappers/RDProps.i

@@ -0,0 +1,44 @@
+/*
+*
+*  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.
+*/
+
+%{
+#include <RDGeneral/types.h>
+#include <RDGeneral/RDProps.h>
+%}
+
+
+%include <RDGeneral/RDProps.h>
+
+%template(setProp)  RDKit::RDProps::setProp<std::string>;
+%template(setIntProp) RDKit::RDProps::setProp<int>;
+%template(setBoolProp) RDKit::RDProps::setProp<bool>;
+%template(setDoubleProp) RDKit::RDProps::setProp<double>;

data/Code/RubyWrappers/RGroupDecomposition.i

@@ -0,0 +1,52 @@
+/*
+*
+*  Copyright (c) 2019, Greg Landrum
+*  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.
+*
+*/
+%{
+#include <GraphMol/RGroupDecomposition/RGroupDecompParams.h>
+#include <GraphMol/RGroupDecomposition/RGroupDecompJSONParsers.h>
+#include <GraphMol/RGroupDecomposition/RGroupDecomp.h>
+typedef std::vector<std::string> STR_VECT;
+%}
+
+%include "std_string.i"
+
+// SparseIntVect64 removed - Ruby SWIG lacks swig::traits for long long int (already defined in AtomPairs.i for 32-bit versions)
+
+%template(ROMol_Vect) std::vector<boost::shared_ptr<RDKit::ROMol>>;
+%template(StringMolMap_Vect) std::vector<std::map<std::string, boost::shared_ptr<RDKit::ROMol>>>;
+%template(StringROMol_VectMap) std::map<std::string,std::vector<boost::shared_ptr<RDKit::ROMol>>>;
+
+
+%extend std::map<std::string, boost::shared_ptr<RDKit::ROMol>> {
+  std::vector<std::string> keys() {
+    std::vector<std::string> _keys;
+    for(auto it : *self) {
+      std::cerr << "* '" << it.first << "'" << std::endl;
+      _keys.push_back(it.first);
+    }
+    return _keys;
+  }
+}
+
+%extend std::map<std::string,std::vector<boost::shared_ptr<RDKit::ROMol>>> {
+  std::vector<std::string> keys() {
+    std::vector<std::string> _keys;
+    for(auto it : *self) {
+      _keys.push_back(it.first);
+    }
+    return _keys;
+  }
+}
+
+%include <RDGeneral/BetterEnums.h>
+%include <GraphMol/RGroupDecomposition/RGroupDecompParams.h>
+%include <GraphMol/RGroupDecomposition/RGroupDecompJSONParsers.h>
+%include <GraphMol/RGroupDecomposition/RGroupDecomp.h>