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fcc2e226ff
* Start of GettingStartedInC++ documentation. * Changed GettingStartedInC++ from rst to markdown format. Added some more text. * Added Working with Molecules to GettingStartedInC++ * Expanded on behaviour of Kekulize wrt clearing aromatic flags on atoms and bonds. * Added section Modifying Molecules. * More plodding progress. * A load more documentation. * Undid change to global CMakeLists.txt * Minor editing of docs. * Changed examples so they use RDBASE to find test data rather than relative path. * Fixed use of -std=c++ in CMakeLists.txt. Extra waffling about memory. * Modifications to examples and documentation as requested. * Couple of minor changes. * Change to example11.cpp and associated text in docs.
49 lines
1.7 KiB
C++
49 lines
1.7 KiB
C++
//
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// Working with 3D molecules - example11.cpp
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#include <iostream>
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#include <map>
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#include <string>
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#include <vector>
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#include <Geometry/point.h>
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#include <GraphMol/GraphMol.h>
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#include <GraphMol/MolOps.h>
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#include <GraphMol/MolAlign/AlignMolecules.h>
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#include <GraphMol/DistGeomHelpers/Embedder.h>
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#include <GraphMol/ForceFieldHelpers/MMFF/MMFF.h>
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#include <GraphMol/ForceFieldHelpers/UFF/UFF.h>
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#include <GraphMol/SmilesParse/SmilesParse.h>
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int main( int main , char **argv ) {
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RDKit::ROMOL_SPTR mol( RDKit::SmilesToMol( "C1CCC1OC" ) );
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RDKit::ROMOL_SPTR mol1( RDKit::MolOps::addHs( *mol ) );
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// Original distance geometry embedding
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RDKit::DGeomHelpers::EmbedMolecule( *mol1 , 0 , 1234 );
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RDKit::UFF::UFFOptimizeMolecule( *mol1 );
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// new Riniker and Landrum CSD-based method
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// using the parameters class
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RDKit::DGeomHelpers::EmbedParameters params( RDKit::DGeomHelpers::ETKDG );
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params.randomSeed = 1234;
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RDKit::DGeomHelpers::EmbedMolecule( *mol2 , params );
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// Multiple conformations
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RDKit::INT_VECT mol1_cids = RDKit::DGeomHelpers::EmbedMultipleConfs( *mol1 , 10 );
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std::cout << "Number of conformations : " << mol1_cids.size() << std::endl;
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RDKit::INT_VECT mol2_cids;
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int numConfs = 20;
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RDKit::DGeomHelpers::EmbedMultipleConfs( *mol2 , mol2_cids , numConfs , params );
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std::cout << "Number of conformations : " << mol2_cids.size() << std::endl;
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std::vector<double> rms_list;
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std::vector<unsigned int> m2cids( mol2_cids.begin() , mol2_cids.end() );
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RDKit::MolAlign::alignMolConformers( *mol2 ,
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static_cast<const std::vector<unsigned int> *>( 0 ) ,
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&m2cids ,
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static_cast<const RDNumeric::DoubleVector *>( 0 ) ,
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false , 50 , &rms_list );
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}
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