mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-04 21:54:27 +08:00
956fdf268c
* short test file for MolVS standardize_sm * short test file for MolVS fragment * short test file for MolVS metals * short test file for MolVS normalize * short test file for MolVS reionize * short test file for MolVS tautomer * short test file for MolVS validate * long test file for MolVS standardize smiles * long test file for MolVS fragment * long test file for MolVS metals * long test file for MolVS normalize * long test file for MolVS reionize * long test file for MolVS tautomer * long test file for MolVS validate * Unit tests for MolVS steps * dropping support for Python2 * molvs/__init__.py * molvs/charge.py * molvs/errors.py * molvs/fragment.py * molvs/metal.py * molvs/normalize.py * molvs/resonance.py * molvs/standardize.py * molvs/tautomer.py * molvs/utils.py * molvs/validate.py * molvs/validations.py * molvs/cli.py * adapted and renamed molvs/cli.py to work within $RDBASE/Contrib/MolVS/ * setup MolStandardize directories, source with empty cleanup function, header, CMake files * corrections to empty source, header and test1.cpp * adding empty functions and initializers to MolStandardize * empty Metal source, header and added test * added most of Metal.cpp functionality and made some more tests * empty functions and initializers to Normalize * empty functions and initializers to Validate * added most code for RDKitDefault mode, along with some tests * restructure for abstract base class ValidateMethod * written in isNoneValidation for MolVSValidation * took out isNoneValidation, put in noAtomValidation, neutralValidation, isotopeValidation for MolVSValidation * added in AllowedAtoms * added in disallowedAtoms * corrections to Validate * added code for FragmentRemover * extended fragment functionality to include choose largest fragment, added in tests for fragment catalog, fragment remover. Also added fragmentValidation method in MolStandardize * added another test to testValidate test_fragment * corrections to fragment * corrections to Metal * added code for Normalize * added normalize member function to MolStandardize and added tests * added multi fragment functionality to Normalize.cpp and additional tests * TransformCatalog * tests for Normalize.cpp * first bit of cleanup * added most of Charge functionality and some tests * some corrections to Charge.cpp and some more tests to testCharge.cpp * corrections to Charge.cpp * start of Tautomer Enumerate with some tests * added BondType option to Tautomer Enumeration * correcting for some memory leakage * a few alterations to formatting * sorting out some memory leaks * sorting out some memory leaks * some corrections for PCS test set * redo tests with updated RDKit * fixing memory leak * more fixes after 100kPCS set testing * using tab as delimiter in CSVs rather than comma * tutorial for MolStandardize * still working on Tautomer enumeration * deleted some empty tests * starting writing tautomer canonicalize * rename test_data -> data (the source still needs to be updated) * automatic source reformatting * adjust to directory rename * move the fragment catalog test into the MolStandardize directory do not create separate library for FragmentCatalog * stop building separate libraries for the catalogs * move the CleanupParameters into the MolStandardize namespace * first pass at python wrapper * move the py module to the correct dir; add some python tests; add standardizeSmiles to python wrapper * disabling the compareMolVSTest since that requires command line arguments to run * get this building on windows * put the python lib in the right place * further work on python wrapper for rdMolStandardize * added get and set functions to Metal and wrapped them * added get and set functions to Metal and wrapped them * changed construstor of Reionizer class and input args for reionize, wrapped this default * overload Reionizer constructor so user can input own AcidBaseFile from python * added Uncharger class to Charge and added test for Uncharger * wrapped Fragment, fixed some memory leakage, changed some args and return types, added some tests * wrapped Normalized and changed how Normalizer class is initiated * changing MolVSValidation structure so user can choose which MolVS submethod they want * starting to write Wrap for Validate * now it compiles with Wrap/Validate.cpp * a couple refactorings around validate * move the validate code into the rdMolStandardize module * make sure a valid pointer is returned for standardizeSmiles * rdMolStandardize.MolVSValidation done and tests added * half way through AllowedAtomsValidation * finished AllowedAtomsValidation and DisallowedAtomsValidation * moved charge, fragment, metal, normalize into the rdMolStandardize module * changed tutorial to use wrapped code * added copyrights * added copyrights * move the data files * modify source files to adjust to the move * added validateSmiles functionality * removed std::cout * redid some of the 100k PCS tests * working on the tutorial * adding some documentation * deleting some comment lines * some changes after pull review * More changes after pull review * start of trying to make java wrap * remove some warnings, add some questions * additional warning removals, a bit more reporting * some test cleanups * enable testing of the java code
317 lines
10 KiB
OpenEdge ABL
317 lines
10 KiB
OpenEdge ABL
/*
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*
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* Copyright (c) 2010, 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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%module RDKFuncs
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#if defined(SWIGWORDSIZE64)
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%{
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// There's a problem with SWIG, 64bit windows, and modern VC++ versions
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// This fine, fine piece of code fixes that.
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// it's ok to think this is horrible, we won't mind
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#ifdef _MSC_VER
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#ifndef LONG_MAX
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#include <limits.h>
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#endif
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#if LONG_MAX==INT_MAX
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#define LONG_MAX (INT_MAX+1)
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#endif
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#endif
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%}
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#endif
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/* Suppress the unimportant warnings */
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#pragma SWIG nowarn=503,516
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%include <boost_shared_ptr.i>
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%{
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#include <boost/shared_ptr.hpp>
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#include <boost/shared_array.hpp>
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%}
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// The actual definition isn't in the top level hpp file!
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// The next two lines are to work around a problem caused by the fact that older versions of
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// SWIG don't work with newer versions of boost.
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#define BOOST_SP_NOEXCEPT
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#define BOOST_SP_NOEXCEPT_WITH_ASSERT
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#define BOOST_NOEXCEPT
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#define BOOST_NO_CXX11_RVALUE_REFERENCES
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#define BOOST_NO_CXX11_NULLPTR
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%include <boost/smart_ptr/shared_array.hpp>
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/* undefine RDKIT_<LIBNAME>_EXPORT macros */
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%include <RDGeneral/export.h>
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/* Include the base types before anything that will utilize them */
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#ifdef SWIGWIN
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%include "../msvc_stdint.i"
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#else
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%include "../stdint.i"
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#endif
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%include "std_string.i"
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%include "std_list.i"
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%include "extend_std_vector.i"
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%include "std_map.i"
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%include "std_pair.i"
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%include "carrays.i"
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/*
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* Custom handler for longs. The problem is described in swig-Bugs-2965875
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* and most of this solution is taken from the proposed patch in that bug report.
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* -------------------------------------------------------------------------
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* Define typemaps for `long`
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*
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* This is complicated by the fact `long` is 32-bits on some platforms
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* but is 64-bits on other platforms. We're just going to override the
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* important ones here.
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*/
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#if defined(SWIGWORDSIZE64)
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typedef long long int int64_t;
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typedef unsigned long long int uint64_t;
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typedef long long int int_least64_t;
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typedef unsigned long long int uint_least64_t;
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typedef long long int int_fast64_t;
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typedef unsigned long long int uint_fast64_t;
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typedef long long int intmax_t;
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typedef unsigned long long int uintmax_t;
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%apply long long { long };
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%apply const long long & { const long & };
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%apply unsigned long long { unsigned long };
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%apply const unsigned long long & { const unsigned long & };
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/*
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#elif defined(SWIGWORDSIZE32)
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%apply int { long };
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%apply const int & { const long & };
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%apply unsigned int { unsigned long };
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%apply const unsigned int & { const unsigned long & };
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#else
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#error "Neither SWIGWORDSIZE64 nor SWIGWORDSIZE32 is defined"
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*/
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#endif
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%shared_ptr(std::exception)
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%shared_ptr(RDKit::RDProps)
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%shared_ptr(RDKit::ROMol)
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%shared_ptr(RDKit::RWMol)
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%shared_ptr(RDKit::Atom)
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%shared_ptr(RDKit::Bond)
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%shared_ptr(RDKit::PeriodicTable)
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%shared_ptr(Canon::MolStackElem)
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%shared_ptr(RDKit::QueryAtom)
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%shared_ptr(RDKit::QueryBond)
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%shared_ptr(RDKit::QueryOps)
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%shared_ptr(RDKit::MolSanitizeException)
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%shared_ptr(RDKit::SmilesParseException)
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%shared_ptr(RDKit::RingInfo)
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%shared_ptr(RDKit::ChemicalReaction)
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%shared_ptr(ForceFields::ForceFieldContrib);
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%shared_ptr(ForceFields::UFF::AngleBendContrib);
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%shared_ptr(ForceFields::UFF::BondStretchContrib);
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%shared_ptr(ForceFields::UFF::DistanceConstraintContrib);
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%shared_ptr(ForceFields::UFF::vdWContrib);
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%shared_ptr(ForceFields::UFF::TorsionAngleContrib);
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%shared_ptr(ForceFields::UFF::InversionContrib);
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%shared_ptr(RDKit::FilterCatalogEntry);
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/* Some utility classes for passing arrays in and out */
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%array_class(double, Double_Array);
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/* Since documentation management is deprecated in SWIG 1.3, we're using the suggested workarounds. Apply them
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here so that can be removed easily later */
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// Documentation
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%include "../Atom_doc.i"
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%include "../Bond_doc.i"
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%include "../BondIterators_doc.i"
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%include "../ChemReactions_doc.i"
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%include "../Conformer_doc.i"
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%include "../ExplicitBitVect_doc.i"
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%include "../PeriodicTable_doc.i"
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%include "../Point3D_doc.i"
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%include "../QueryAtom_doc.i"
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%include "../QueryBond_doc.i"
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%include "../RDKFuncs_doc.i"
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%include "../RingInfo_doc.i"
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%include "../ROMol_doc.i"
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%include "../RWMol_doc.i"
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%include "../SDMolSupplier_doc.i"
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%include "../SmilesMolSupplier_doc.i"
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%include "../SmilesWriter_doc.i"
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%include "../TDTMolSupplier_doc.i"
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%include "../TDTWriter_doc.i"
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%include "../Transform2D_doc.i"
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%include "../Transform3D_doc.i"
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%include "../FilterCatalog_doc.i"
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%include "../FilterCatalogParams_doc.i"
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%include "../FilterCatalogs_doc.i"
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// DO THIS BEFORE ANY OF THE OTHER INCLUDES
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%include "../RDKitExceptions.i"
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%include "../point.i"
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// Need the types wrapper or we get undefined errors for STR_VECT
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%include "../types.i"
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// Conformer seems to need to come before ROMol
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%include "../Conformer.i"
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%include "../Dict.i"
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%include "../RDProps.i"
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%include "../StereoGroup.i"
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%include "../ROMol.i"
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%include "../RWMol.i"
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%include "../Bond.i"
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%include "../BondIterators.i"
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%include "../Atom.i"
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%include "../AtomIterators.i"
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%include "../AtomPairs.i"
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%include "../Canon.i"
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%include "../Conformer.i"
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%include "../QueryAtom.i"
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%include "../QueryBond.i"
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%include "../QueryOps.i"
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%include "../MonomerInfo.i"
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%include "../PeriodicTable.i"
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%include "../SanitException.i"
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%include "../SmilesParse.i"
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%include "../SmilesWrite.i"
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%include "../SmartsWrite.i"
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%include "../MolOps.i"
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%include "../MolSupplier.i"
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%include "../MolWriters.i"
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%include "../RingInfo.i"
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%include "../ChemReactions.i"
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%include "../BitOps.i"
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%include "../ExplicitBitVect.i"
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%include "../Fingerprints.i"
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%include "../MorganFingerprints.i"
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%include "../ReactionFingerprints.i"
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%include "../Rings.i"
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%include "../transforms.i"
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%include "../DistGeom.i"
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%include "../ForceField.i"
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%include "../ChemTransforms.i"
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%include "../Subgraphs.i"
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%include "../MolTransforms.i"
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%include "../FMCS.i"
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%include "../MolDraw2D.i"
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%include "../FilterCatalog.i"
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%include "../Trajectory.i"
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%include "../MolStandardize.i"
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// Create a class to throw various sorts of errors for testing. Required for unit tests in ErrorHandlingTests.java
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#ifdef INCLUDE_ERROR_GENERATOR
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%include "../ErrorGenerator.i"
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#endif
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/* Done explicitly in BitOps.i
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%include <DataStructs/BitOps.h>
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%template(TanimotoSimilarityEBV) TanimotoSimilarity<ExplicitBitVect,ExplicitBitVect>;
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%template(DiceSimilarityEBV) DiceSimilarity<ExplicitBitVect,ExplicitBitVect>;
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*/
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%template(DiceSimilarity) RDKit::DiceSimilarity<boost::uint32_t>;
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/* vector */
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%template(Int_Vect) std::vector<int>;
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%template(Byte_Vect) std::vector<signed char>;
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%template(Double_Vect) std::vector<double>;
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%template(UInt_Vect) std::vector<boost::uint32_t>;
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%template(Str_Vect) std::vector<std::string> ;
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%template(Point_Vect) std::vector<RDGeom::Point *>;
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%template(Point2D_Vect) std::vector<RDGeom::Point2D *>;
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%template(Point3D_Vect) std::vector<RDGeom::Point3D *>;
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%template(Atomic_Params_Vect) std::vector<const ForceFields::UFF::AtomicParams *>;
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/* pair */
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%template(Int_Pair) std::pair<boost::int32_t, int >;
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%template(Double_Pair) std::pair<double,double>;
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%template(UInt_Pair) std::pair<boost::uint32_t, int >;
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%template(Long_Pair) std::pair<boost::int64_t,int>;
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/* map */
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%template(String_String_Map) std::map<std::string,std::string>;
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%template(Int_Int_Map) std::map<int,int>;
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%template(Int_Point2D_Map) std::map<int, RDGeom::Point2D>;
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%template(Int_Point3D_Map) std::map<int, RDGeom::Point3D>;
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%template(Int_Int_Vect_List_Map) std::map<int,std::list<std::vector<int> > >;
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/* vector pair */
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%template(UInt_Pair_Vect) std::vector<std::pair<boost::uint32_t,int> >;
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%template(Match_Vect) std::vector<std::pair<boost::int32_t,int> >;
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%template(Long_Pair_Vect) std::vector<std::pair<boost::int64_t,int> >;
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/* vector vector */
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%template(Int_Vect_Vect) std::vector<std::vector<int> >;
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/* list */
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%template(Int_Vect_List) std::list<std::vector<int> >;
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%template(Int_List) std::list<int>;
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%template(UInt_List) std::list<unsigned int>;
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/* other */
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%template(Match_Vect_Vect) std::vector<std::vector<std::pair<int,int> > >;
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%template(Flagged_Atomic_Params_Vect) std::pair<std::vector<const ForceFields::UFF::AtomicParams *>,bool>;
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%template(Shared_Int_Array) boost::shared_array<int>;
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%template(Shared_Double_Array) boost::shared_array<double>;
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// Methods to get at elements of shared arrays
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%extend boost::shared_array<double> {
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double getElement(int i) {
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return (*($self))[i];
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}
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double setElement(int i, double value) {
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(*($self))[i] = value;
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}
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}
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%extend boost::shared_array<int> {
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int getElement(int i) {
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return (*($self))[i];
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}
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int setElement(int i, int value) {
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(*($self))[i] = value;
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}
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}
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%include "../Descriptors.i"
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#ifdef RDK_BUILD_AVALON_SUPPORT
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%include "../AvalonLib.i"
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#endif
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#ifdef RDK_BUILD_INCHI_SUPPORT
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%include "../Inchi.i"
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#endif
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%include "../DiversityPick.i"
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%{
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#include <RDGeneral/versions.h>
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%}
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%include <RDGeneral/versions.h>
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