mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-04 21:54:27 +08:00
add preliminary pass at a csharp wrapper.
this currently only will work using mono, visual studio integration still needs to be done
This commit is contained in:
Greg Landrum
290
Code/JavaWrappers/csharp_wrapper/GraphMolCSharp.i
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290
Code/JavaWrappers/csharp_wrapper/GraphMolCSharp.i
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@@ -0,0 +1,290 @@
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/*
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* $Id: GraphMolJava.i 2141 2012-07-27 06:16:45Z glandrum $
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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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/* 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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%include <boost/smart_ptr/shared_array.hpp>
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/* Include the base types before anything that will utilize them */
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%include "stdint.i"
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%include "std_string.i"
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%include "../gmwrapper/std_list.i"
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%include "../gmwrapper/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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// an extremely unsatisfying way of handling exceptions, but it's better than
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// crashing mono (which otherwise happened)
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%exception {
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try {
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$action
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}
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catch (RDKit::ChemicalReactionException &e) {
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std::string err="ChemicalReactionException: ";
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err+=e.message();
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SWIG_CSharpSetPendingException(SWIG_CSharpApplicationException, err.c_str());
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}
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catch (RDKit::ChemicalReactionParserException &e) {
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std::string err="ChemicalReactionParserException: ";
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err+=e.message();
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SWIG_CSharpSetPendingException(SWIG_CSharpApplicationException, err.c_str());
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}
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catch (RDKit::ConformerException &e) {
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std::string err="ConformerException: ";
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err+=e.message();
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SWIG_CSharpSetPendingException(SWIG_CSharpApplicationException, err.c_str());
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}
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catch (RDKit::MolPicklerException &e) {
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std::string err="MolPicklerException: ";
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err+=e.message();
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SWIG_CSharpSetPendingException(SWIG_CSharpApplicationException, err.c_str());
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}
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catch (RDKit::MolSanitizeException &e) {
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std::string err="MolSanitizeException: ";
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err+=e.message();
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SWIG_CSharpSetPendingException(SWIG_CSharpApplicationException, err.c_str());
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}
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catch (RDKit::SmilesParseException e) {
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std::string err="SmilesParseException: ";
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err+=e.message();
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SWIG_CSharpSetPendingException(SWIG_CSharpApplicationException, err.c_str());
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}
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catch (KeyErrorException e) {
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std::string err="KeyError: ";
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err+=e.key();
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SWIG_CSharpSetPendingException(SWIG_CSharpApplicationException, err.c_str());
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}
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catch (std::exception e) {
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SWIG_CSharpSetPendingException(SWIG_CSharpApplicationException, "error");
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}
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}
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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(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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/* 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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// 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 "../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 "../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 "../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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// 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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/* 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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(*($self))[i] = value;
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}
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}
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%include "../Descriptors.i"
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#ifdef BUILD_AVALON_SUPPORT
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%include "../AvalonLib.i"
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#endif
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#ifdef BUILD_INCHI_SUPPORT
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%include "../Inchi.i"
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#endif
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%include "../DiversityPick.i"
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%{
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#include <RDGeneral/versions.h>
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%}
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%include <RDGeneral/versions.h>
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16
Code/JavaWrappers/csharp_wrapper/README
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16
Code/JavaWrappers/csharp_wrapper/README
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To build on a linux system with mono installed:
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Run SWIG:
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---------
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swig -c++ -csharp -namespace GraphMolWrap -DBUILD_AVALON_SUPPORT -DBUILD_INCHI_SUPPORT -DSWIGWORDSIZE64 -outdir ./swig_csharp -I/usr/include -I/usr/local/include -I$RDBASE/Code -I$RDBASE/Code/JavaWrappers -I$RDBASE/External -o GraphMolCSharp_wrap.cxx ./GraphMolCSharp.i
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Compile and link the shared library:
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------------------------------------
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g++ -DGraphMolWrap_EXPORTS -DRDK_64BIT_BUILD -O3 -DNDEBUG -fPIC -I/usr/local/include -I$RDBASE/Code -I$RDBASE/Code/JavaWrappers -I$RDBASE/External -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -o GraphMolCSharp_wrap.cxx.o -c GraphMolCSharp_wrap.cxx
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g++ -fPIC -O3 -DNDEBUG -shared -Wl,-soname,libRDKFuncs.so -o libRDKFuncs.so GraphMolCSharp_wrap.cxx.o -L/usr/local/lib $RDBASE/lib/libAvalonLib_static.a $RDBASE/lib/libavalon_clib_static.a $RDBASE/lib/libRDInchiLib_static.a $RDBASE/lib/libInchi_static.a $RDBASE/lib/libFileParsers_static.a $RDBASE/lib/libSmilesParse_static.a $RDBASE/lib/libDepictor_static.a $RDBASE/lib/libSubstructMatch_static.a $RDBASE/lib/libChemReactions_static.a $RDBASE/lib/libFingerprints_static.a $RDBASE/lib/libChemTransforms_static.a $RDBASE/lib/libSubgraphs_static.a $RDBASE/lib/libGraphMol_static.a $RDBASE/lib/libDataStructs_static.a $RDBASE/lib/libDescriptors_static.a $RDBASE/lib/libPartialCharges_static.a $RDBASE/lib/libMolTransforms_static.a $RDBASE/lib/libDistGeomHelpers_static.a $RDBASE/lib/libDistGeometry_static.a $RDBASE/lib/libForceFieldHelpers_static.a $RDBASE/lib/libForceField_static.a $RDBASE/lib/libEigenSolvers_static.a $RDBASE/lib/libOptimizer_static.a $RDBASE/lib/libMolAlign_static.a $RDBASE/lib/libAlignment_static.a $RDBASE/lib/libSimDivPickers_static.a $RDBASE/lib/libRDGeometryLib_static.a $RDBASE/lib/libRDGeneral_static.a -lboost_thread-mt -lboost_system-mt -lpthread
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Build and test the csharp code:
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-------------------------------
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gmcs -out:RDKFuncs.dll -t:library swig_csharp/*.cs
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gmcs -out:test.exe -addmodule:./RDKFuncs.dll test.cs
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mono test.exe
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76
Code/JavaWrappers/csharp_wrapper/test.cs
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76
Code/JavaWrappers/csharp_wrapper/test.cs
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@@ -0,0 +1,76 @@
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using System;
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using GraphMolWrap;
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public class rdktest
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{
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// static void rxnTest() {
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// Console.WriteLine( "Reaction tests" );
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// var rxn = ChemicalReaction.ReactionFromSmarts("[N:1][C:2].[OH][C:3]=[O:4]>>[C:2][N:1][C:3]=[O:4]");
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// var amine = RWMol.MolFromSmiles("CCCN");
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// var acid = RWMol.MolFromSmiles("C1CC1CC(=O)O");
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// ROMol[] rs = {amine,acid};
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// ROMol_Vect rv = new ROMol_Vect(rs);
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// for(var i=0;i<100000;i++){
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// var ps=rxn.runReactants(rv);
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// if(i%100 == 0) {
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// Console.WriteLine( "\t{0}", i );
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// }
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// }
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// Console.WriteLine( "Goodbye" );
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// }
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// static void smiTest() {
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// Console.WriteLine( "repeatedly from smiles" );
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// for(var i=0;i<1000000;i++){
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// ROMol m1=RDKFuncs.MolFromSmiles("c1ccccc1");
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// if(i%1000 == 0) {
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// Console.WriteLine( "\t{0}", i );
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// }
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// }
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// Console.WriteLine( "Goodbye" );
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// }
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static void morganTest()
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{
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// ----- Object creation -----
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Console.WriteLine( "Creating some objects:" );
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ROMol m1=RWMol.MolFromSmiles("c1ccccc1");
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Console.WriteLine(" mol: "+m1+" "+m1.getNumAtoms());
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ROMol m2=RWMol.MolFromSmiles("c1ccccn1");
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var fp1=RDKFuncs.MorganFingerprintMol(m1,2);
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var fp2=RDKFuncs.MorganFingerprintMol(m2,2);
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Console.WriteLine(" sim: "+RDKFuncs.DiceSimilarity(fp1,fp2));
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}
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static void Main()
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{
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// ----- Object creation -----
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Console.WriteLine( "Creating some objects:" );
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ROMol m1=RWMol.MolFromSmiles("c1ccccc1");
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Console.WriteLine(" mol: "+m1+" "+m1.getNumAtoms());
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ROMol m2=RWMol.MolFromSmiles("c1ccccn1");
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Console.WriteLine(" smi: "+m1+" "+m1.MolToSmiles());
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Console.WriteLine(" smi2: "+m2+" "+m2.MolToSmiles());
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ExplicitBitVect fp1=RDKFuncs.LayeredFingerprintMol(m1);
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ExplicitBitVect fp2=RDKFuncs.LayeredFingerprintMol(m2);
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Console.WriteLine(" sim: "+RDKFuncs.TanimotoSimilarityEBV(fp1,fp2));
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//rxnTest();
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//smiTest();
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morganTest();
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ROMol m3=RWMol.MolFromSmiles("c1cccc1");
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Console.WriteLine( "Goodbye" );
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}
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}
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