rdkit_chem 2019.03.3.1 → 2025.09.3.1

data/Code/RubyWrappers/gmwrapper/GraphMolRuby.i

@@ -0,0 +1,431 @@
+/*
+*
+*  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.
+*/
+%module RDKitChem
+
+#if defined(SWIGWORDSIZE64)
+%{
+// There's a problem with SWIG, 64bit windows, and modern VC++ versions
+//   This fine, fine piece of code fixes that.
+//   it's ok to think this is horrible, we won't mind
+#ifdef _MSC_VER
+
+#ifndef LONG_MAX
+#include <limits.h>
+#endif
+
+#if LONG_MAX==INT_MAX
+#define LONG_MAX (INT_MAX+1)
+#endif
+
+#endif
+%}
+#endif
+
+/* Suppress the unimportant warnings */
+#pragma SWIG nowarn=503,516
+
+// Ignore ostream operators globally - they cause redefinition errors and aren't useful in Ruby
+%ignore operator<<;
+
+%include <boost_shared_ptr.i>
+%{
+    #include <boost/shared_ptr.hpp>
+    #include <boost/shared_array.hpp>
+    #include <ForceField/UFF/Params.h>
+%}
+// The actual definition isn't in the top level hpp file!
+// The next two lines are to work around a problem caused by the fact that older versions of
+// SWIG don't work with newer versions of boost.
+#define BOOST_SP_NOEXCEPT
+#define BOOST_SP_NOEXCEPT_WITH_ASSERT
+#define BOOST_NOEXCEPT
+#define BOOST_NO_CXX11_RVALUE_REFERENCES
+#define BOOST_NO_CXX11_NULLPTR
+%include <boost/smart_ptr/shared_array.hpp>
+
+/* undefine RDKIT_<LIBNAME>_EXPORT macros */
+%include <RDGeneral/RDExportMacros.h>
+%include <RDGeneral/export.h>
+/* Include the base types before anything that will utilize them */
+#ifdef SWIGWIN
+%include "../msvc_stdint.i"
+#else
+%include "../stdint.i"
+#endif
+
+%include "std_string.i"
+%include "std_list.i"
+%include "std_vector.i"
+%include "extend_std_vector.i"
+%include "std_map.i"
+%include "std_pair.i"
+%include "carrays.i"
+
+/*
+ * Custom handler for longs.  The problem is described in swig-Bugs-2965875
+ * and most of this solution is taken from the proposed patch in that bug report.
+ * -------------------------------------------------------------------------
+ * Define typemaps for `long`
+ *
+ * This is complicated by the fact `long` is 32-bits on some platforms
+ * but is 64-bits on other platforms. We're just going to override the
+ * important ones here.
+ */
+#if defined(SWIGWORDSIZE64)
+typedef long long int		int64_t;
+typedef unsigned long long int	uint64_t;
+typedef long long int		int_least64_t;
+typedef unsigned long long int	uint_least64_t;
+typedef long long int		int_fast64_t;
+typedef unsigned long long int	uint_fast64_t;
+typedef long long int		intmax_t;
+typedef unsigned long long int	uintmax_t;
+
+%apply long long { long };
+%apply const long long & { const long & };
+%apply unsigned long long { unsigned long };
+%apply const unsigned long long & { const unsigned long & };
+
+/*
+#elif defined(SWIGWORDSIZE32)
+%apply int { long };
+%apply const int & { const long & };
+%apply unsigned int { unsigned long };
+%apply const unsigned int & { const unsigned long & };
+#else
+#error "Neither SWIGWORDSIZE64 nor SWIGWORDSIZE32 is defined"
+*/
+
+#endif
+
+// Tell SWIG that boost and std integer types are equivalent to standard types
+// This prevents duplicate swig::traits definitions
+%apply int { boost::int32_t };
+%apply const int & { const boost::int32_t & };
+%apply unsigned int { boost::uint32_t };
+%apply const unsigned int & { const boost::uint32_t & };
+%apply int { std::int32_t };
+%apply const int & { const std::int32_t & };
+%apply unsigned int { std::uint32_t };
+%apply const unsigned int & { const std::uint32_t & };
+
+%shared_ptr(std::exception)
+%shared_ptr(RDKit::RDProps)
+%shared_ptr(RDKit::Conformer)
+%shared_ptr(RDKit::ROMol)
+%shared_ptr(RDKit::RWMol)
+%shared_ptr(RDKit::Atom)
+%shared_ptr(RDKit::Bond)
+%shared_ptr(RDKit::PeriodicTable)
+%shared_ptr(Canon::MolStackElem)
+%shared_ptr(RDKit::QueryAtom)
+%shared_ptr(RDKit::QueryBond)
+%shared_ptr(RDKit::QueryOps)
+%shared_ptr(RDKit::MolBundle)
+%shared_ptr(RDKit::FixedMolSizeMolBundle)
+%shared_ptr(RDKit::MolSanitizeException)
+%shared_ptr(RDKit::AtomSanitizeException)
+%shared_ptr(RDKit::AtomValenceException)
+%shared_ptr(RDKit::AtomKekulizeException)
+%shared_ptr(RDKit::KekulizeException)
+%shared_ptr(RDKit::SmilesParseException)
+%shared_ptr(RDKit::MolPicklerException)
+%shared_ptr(RDKit::RingInfo)
+%shared_ptr(RDKit::ChemicalReaction)
+%shared_ptr(ForceFields::ForceFieldContrib);
+%shared_ptr(ForceFields::UFF::AngleBendContrib);
+%shared_ptr(ForceFields::UFF::BondStretchContrib);
+%shared_ptr(ForceFields::DistanceConstraintContrib);
+%shared_ptr(ForceFields::UFF::vdWContrib);
+%shared_ptr(ForceFields::UFF::TorsionAngleContrib);
+%shared_ptr(ForceFields::UFF::InversionContrib);
+%shared_ptr(RDKit::FilterCatalogEntry);
+
+/* http://swig.10945.n7.nabble.com/std-containers-and-pointers-td3728.html */
+%{
+  /* template <> struct swig::traits<RDKit::ROMol> { */
+  /*   typedef pointer_category category; */
+  /*   static const char* type_name() */
+  /*   { */
+  /*     return "ROMol"; */
+  /*   } */
+  /* }; */
+
+  /* template <> struct swig::traits<ForceFields::UFF::AtomicParams> { */
+  /*   typedef pointer_category category; */
+  /*   static const char* type_name() */
+  /*   { */
+  /*     return "AtomicParams"; */
+  /*   } */
+  /* }; */
+%}
+
+/* Some utility classes for passing arrays in and out */
+%array_class(double, Double_Array);
+
+/* Since documentation management is deprecated in SWIG 1.3, we're using the suggested workarounds.  Apply them
+   here so that can be removed easily later */
+// Documentation
+
+// Create a class to throw various sorts of errors for testing.  Required for unit tests in ErrorHandlingTests.java
+/* #ifdef INCLUDE_ERROR_GENERATOR */
+/* %include "../ErrorGenerator.i" */
+/* #endif */
+
+// Fixes annoying compilation namespace issue
+typedef RDKit::MatchVectType MatchVectType;
+
+%define VVTEMPLATE_WRAP(name, T)
+%feature("ignore") std::vector< std::vector<T> >::append;
+%feature("ignore") std::vector< std::vector<T> >::assign;
+%feature("ignore") std::vector< std::vector<T> >::back;
+%feature("ignore") std::vector< std::vector<T> >::begin;
+%feature("ignore") std::vector< std::vector<T> >::capacity;
+%feature("ignore") std::vector< std::vector<T> >::clear;
+%feature("ignore") std::vector< std::vector<T> >::empty;
+%feature("ignore") std::vector< std::vector<T> >::end;
+%feature("ignore") std::vector< std::vector<T> >::equals;
+%feature("ignore") std::vector< std::vector<T> >::erase;
+%feature("ignore") std::vector< std::vector<T> >::front;
+%feature("ignore") std::vector< std::vector<T> >::get_allocator;
+%feature("ignore") std::vector< std::vector<T> >::insert;
+%feature("ignore") std::vector< std::vector<T> >::pop;
+%feature("ignore") std::vector< std::vector<T> >::pop_back;
+%feature("ignore") std::vector< std::vector<T> >::push_back;
+%feature("ignore") std::vector< std::vector<T> >::rbegin;
+%feature("ignore") std::vector< std::vector<T> >::rend;
+%feature("ignore") std::vector< std::vector<T> >::reserve;
+%feature("ignore") std::vector< std::vector<T> >::resize;
+%feature("ignore") std::vector< std::vector<T> >::size;
+%feature("ignore") std::vector< std::vector<T> >::shift;
+%feature("ignore") std::vector< std::vector<T> >::swap;
+%feature("ignore") std::vector< std::vector<T> >::unshift;
+%template(name ## VectVect) std::vector< std::vector<T> >;
+%enddef
+
+%define VECTORTEMPLATE_WRAP(vectorname, T)
+%feature("ignore") std::vector<T>::append;
+%feature("ignore") std::vector<T>::assign;
+%feature("ignore") std::vector<T>::back;
+%feature("ignore") std::vector<T>::begin;
+%feature("ignore") std::vector<T>::capacity;
+%feature("ignore") std::vector<T>::clear;
+%feature("ignore") std::vector<T>::empty;
+%feature("ignore") std::vector<T>::end;
+%feature("ignore") std::vector<T>::erase;
+%feature("ignore") std::vector<T>::equals;
+%feature("ignore") std::vector<T>::front;
+%feature("ignore") std::vector<T>::get_allocator;
+%feature("ignore") std::vector<T>::insert;
+%feature("ignore") std::vector<T>::pop;
+%feature("ignore") std::vector<T>::pop_back;
+%feature("ignore") std::vector<T>::push_back;
+%feature("ignore") std::vector<T>::rbegin;
+%feature("ignore") std::vector<T>::rend;
+%feature("ignore") std::vector<T>::reserve;
+%feature("ignore") std::vector<T>::resize;
+%feature("ignore") std::vector<T>::size;
+%feature("ignore") std::vector<T>::shift;
+%feature("ignore") std::vector<T>::swap;
+%feature("ignore") std::vector<T>::unshift;
+%template(vectorname ## Vect) std::vector<T>;
+%enddef
+
+// DiceSimilarity template is instantiated in MorganFingerprints.i after SparseIntVect.h is included
+
+/* vector */
+%template(Int_Vect) std::vector<int>;
+%template(Byte_Vect) std::vector<signed char>;
+%template(Double_Vect) std::vector<double>;
+// Use base types (unsigned int) to avoid duplicate swig::traits definitions
+%template(UInt_Vect) std::vector<unsigned int>;
+%template(Str_Vect)  std::vector<std::string>;
+// Point vector templates removed - Ruby SWIG lacks swig::traits for custom types
+// %template(Point_Vect) std::vector<RDGeom::Point *>;
+// %template(Point2D_Vect) std::vector<RDGeom::Point2D *>;
+// %template(Point3D_Vect) std::vector<RDGeom::Point3D *>;
+// %template(Atomic_Params_Vect) std::vector<const ForceFields::UFF::AtomicParams *>;
+
+/* pair */
+// Use base types (int/unsigned int) to avoid duplicate swig::traits definitions
+%template(Int_Pair) std::pair<int, int>;
+%template(Double_Pair) std::pair<double,double>;
+%template(UInt_Pair) std::pair<unsigned int, int>;
+// Long_Pair removed - Ruby SWIG lacks swig::traits support for long long int
+
+/* map */
+%template(String_String_Map) std::map<std::string,std::string>;
+%template(Int_Int_Map) std::map<int,int>;
+// Point map templates removed - Ruby SWIG lacks swig::traits for custom types
+// %template(Int_Point2D_Map) std::map<int, RDGeom::Point2D>;
+// %template(Int_Point3D_Map) std::map<int, RDGeom::Point3D>;
+%template(Int_Int_Vect_List_Map) std::map<int,std::list<std::vector<int> > >;
+
+/* vector pair */
+// Use base types (int/unsigned int) to avoid duplicate swig::traits definitions
+%template(UInt_Pair_Vect) std::vector<std::pair<unsigned int,int> >;
+%template(Match_Vect) std::vector<std::pair<int,int> >;
+// Long_Pair_Vect removed - Ruby SWIG lacks swig::traits support for long long int
+
+/* vector vector */
+%template(Int_Vect_Vect) std::vector<std::vector<int> >;
+
+/* list */
+%template(Int_Vect_List) std::list<std::vector<int> >;
+%template(Int_List) std::list<int>;
+%template(UInt_List) std::list<unsigned int>;
+
+/* other */
+%template(Match_Vect_Vect) std::vector<std::vector<std::pair<int,int> > >;
+// Flagged_Atomic_Params_Vect removed - Ruby SWIG lacks swig::traits for custom types
+// %template(Flagged_Atomic_Params_Vect) std::pair<std::vector<const ForceFields::UFF::AtomicParams *>,bool>;
+%template(Shared_Int_Array) boost::shared_array<int>;
+%template(Shared_Double_Array) boost::shared_array<double>;
+
+// These methods are renamed to valid method names
+%rename(inc)   *::operator++;
+%rename(good)  *::operator bool;
+%rename(deref) *::operator->;
+%rename(add)  *::operator+=;
+%rename(idx)  *::operator[];
+
+// Methods to get at elements of shared arrays
+%extend boost::shared_array<double> {
+  double getElement(int i) {
+    return (*($self))[i];
+  }
+  void setElement(int i, double value) {
+    (*($self))[i] = value;
+  }
+}
+%extend boost::shared_array<int> {
+  int getElement(int i) {
+    return (*($self))[i];
+  }
+  void setElement(int i, int value) {
+    (*($self))[i] = value;
+  }
+}
+
+// This requires SWIG 4.2 or higher - must be before RDKitExceptions.i
+%include "std_string_view.i"
+
+// DO THIS BEFORE ANY OF THE OTHER INCLUDES
+%include "../RDKitExceptions.i"
+
+%include "../point.i"
+// Need the types wrapper or we get undefined errors for STR_VECT
+%include "../types.i"
+// Conformer seems to need to come before ROMol
+%include "../Conformer.i"
+%include "../Dict.i"
+%include "../RDLogger.i"
+%include "../RDProps.i"
+%include "../StereoGroup.i"
+%include "../ROMol.i"
+%include "../RWMol.i"
+%include "../Bond.i"
+%include "../BondIterators.i"
+%include "../Atom.i"
+%include "../AtomIterators.i"
+%include "../AtomPairs.i"
+%include "../Canon.i"
+%include "../Conformer.i"
+%include "../QueryAtom.i"
+%include "../QueryBond.i"
+%include "../QueryOps.i"
+%include "../MolBundle.i"
+%include "../MonomerInfo.i"
+%include "../PeriodicTable.i"
+%include "../SanitException.i"
+%include "../SmilesParse.i"
+%include "../SmilesWrite.i"
+%include "../SmartsWrite.i"
+%include "../MolOps.i"
+%include "../MolSupplier.i"
+%include "../MolWriters.i"
+%include "../RingInfo.i"
+%include "../ChemReactions.i"
+%include "../BitOps.i"
+%include "../ExplicitBitVect.i"
+%include "../Fingerprints.i"
+%include "../MorganFingerprints.i"
+%include "../ReactionFingerprints.i"
+%include "../Rings.i"
+%include "../transforms.i"
+%include "../DistGeom.i"
+%include "../ForceField.i"
+%include "../ChemTransforms.i"
+%include "../Subgraphs.i"
+%include "../MolTransforms.i"
+%include "../FMCS.i"
+%include "../MolDraw2D.i"
+%include "../FilterCatalog.i"
+%include "../Trajectory.i"
+%include "../MolStandardize.i"
+%include "../SubstructLibrary.i"
+%include "../RGroupDecomposition.i"
+%include "../ScaffoldNetwork.i"
+%include "../TautomerQuery.i"
+%include "../SubstanceGroup.i"
+%include "../MolEnumerator.i"
+%include "../MolHash.i"
+%include "../Abbreviations.i"
+%include "../Streams.i"
+%include "../GeneralizedSubstruct.i"
+%include "../RascalMCES.i"
+%include "../Queries.i"
+%include "../Subset.i"
+
+%include "../Descriptors.i"
+
+#ifdef RDK_BUILD_AVALON_SUPPORT
+%include "../AvalonLib.i"
+#endif
+#ifdef RDK_BUILD_INCHI_SUPPORT
+%include "../Inchi.i"
+#endif
+#ifdef RDK_BUILD_CHEMDRAW_SUPPORT
+%include "../ChemDraw.i"
+#endif
+
+%include "../DiversityPick.i"
+
+%{
+#include <RDGeneral/versions.h>
+%}
+
+%immutable RDKit::rdkitVersion;
+%immutable RDKit::boostVersion;
+%immutable RDKit::rdkitBuild;
+
+%include <RDGeneral/versions.h>

data/Code/RubyWrappers/gmwrapper/std_list.i

@@ -0,0 +1,65 @@
+/* -----------------------------------------------------------------------------
+ * See the LICENSE file for information on copyright, usage and redistribution
+ * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ *
+ * std_list.i
+ * ----------------------------------------------------------------------------- */
+
+%include <std_common.i>
+
+%{
+#include <list>
+#include <stdexcept>
+%}
+
+namespace std {
+    
+    template<class T> class list {
+      public:
+        typedef size_t size_type;
+        typedef T value_type;
+        typedef const value_type& const_reference;
+        list();
+        size_type size() const;
+        %rename(isEmpty) empty;
+        bool empty() const;
+        void clear();
+        %rename(add) push_back;
+        void push_back(const value_type& x);
+        %extend {
+            const_reference get(int i) throw (std::out_of_range) {
+                int size = int(self->size());
+                int j;
+                if (i>=0 && i<size) {
+                  std::list< T >::const_iterator p;  
+                  p=self->begin(); 
+                  for (j=0; j<i; j++) {p++;}
+                  return (*p);   
+                }
+                else
+                    throw std::out_of_range("list index out of range");
+            }
+
+            bool equals(const list<T> &o){
+              if(self->size()==o.size()){
+                std::list< T >::const_iterator sIt=self->begin();
+                std::list< T >::const_iterator oIt=o.begin();
+                while(sIt != self->end()){
+                  if(*sIt != *oIt) return false;
+                  ++sIt;
+                  ++oIt;
+                }
+                return true;
+              } else {
+                return false;
+              }
+            }
+
+        }
+   };
+}
+
+%define specialize_std_list(T)
+#warning "specialize_std_list - specialization for type T no longer needed"
+%enddef
+

data/Code/RubyWrappers/point.i

@@ -0,0 +1,56 @@
+/* 
+* $Id$
+*
+*  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 <Geometry/point.h>
+%}
+
+// Ignore ostream operators to prevent redefinition errors
+%ignore RDGeom::operator<<;
+
+%include <Geometry/point.h>
+
+
+%extend RDGeom::Point3D {
+	RDGeom::Point3D* RDGeom::Point3D::minus(const RDGeom::Point3D &other) {
+		RDGeom::Point3D* diff = new RDGeom::Point3D(*($self) - other);
+		return diff;
+	}
+}
+
+%extend RDGeom::Point2D {
+	RDGeom::Point2D* RDGeom::Point2D::minus(const RDGeom::Point2D &other) {
+		RDGeom::Point2D* diff = new RDGeom::Point2D(*($self) - other);
+		return diff;
+	}
+}
+

data/Code/RubyWrappers/transforms.i

@@ -0,0 +1,60 @@
+/* 
+* $Id$
+*
+*  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 <Numerics/SquareMatrix.h>
+#include <Geometry/Transform.h>
+#include <Geometry/Transform2D.h>
+#include <Geometry/Transform3D.h>
+#include <Numerics/SymmMatrix.h>
+%}
+
+
+%include <Numerics/Vector.h>
+%include <Numerics/Matrix.h>
+%include <Numerics/SquareMatrix.h>
+%include <Numerics/SymmMatrix.h>
+
+/* These template definitions need to come after the C++ template definition code, but before the
+   instantiation by other modules. */
+
+%template(IntMatrix) RDNumeric::Matrix<int>;
+%template(DoubleMatrix) RDNumeric::Matrix<double>;
+%template(IntSymmMatrix) RDNumeric::SymmMatrix<int>;
+%template(DoubleSymmMatrix) RDNumeric::SymmMatrix<double>;
+%template(DoubleSquareMatrix) RDNumeric::SquareMatrix<double>;
+
+%include <Geometry/Transform.h>
+%include <Geometry/Transform2D.h>
+%include <Geometry/Transform3D.h>
+

data/Code/RubyWrappers/types.i

@@ -0,0 +1,40 @@
+/* 
+* $Id$
+*
+*  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 <RDGeneral/types.h>
+%}
+
+
+
+%include <RDGeneral/types.h>

data/README.md

@@ -0,0 +1,24 @@
+
+# rdkit-chem gem
+
+GEM for [RDKIT](http://rdkit.org/), an Open-Source Cheminformatics Software
+
+## Environment
+
+### Prerequisites
+  * cmake 3.8 or later
+  * curl
+  * tar, sed, make (those should be present anyway)
+  * SWIG 2 or later
+  * python header (`python-dev`)
+  * sqlite (`sqlite3-dev`)
+  * boost > 1.58 (`libboost-all-dev`)
+  * gcc
+  
+
+## Install
+`gem install rdkit_chem`
+
+It downloads the sources, compiles and installs RDKIT with the ruby bindings.
+The installation may last very long - please be patient.
+