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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.
86 lines
2.9 KiB
C++
86 lines
2.9 KiB
C++
//
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// Substructure searching - example14.cpp
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#include <iostream>
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#include <vector>
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#include <GraphMol/GraphMol.h>
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#include <GraphMol/FileParsers/MolSupplier.h>
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#include <GraphMol/SmilesParse/SmilesParse.h>
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#include <GraphMol/Substruct/SubstructMatch.h>
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int main( int argc , char **argv ) {
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RDKit::ROMOL_SPTR mol1( RDKit::SmilesToMol( "c1ccccc1O" ) );
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RDKit::RWMOL_SPTR patt( RDKit::SmartsToMol( "ccO" ) );
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RDKit::MatchVectType res;
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if( RDKit::SubstructMatch( *mol1 , *patt , res ) ) {
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std::cout << "Pattern matched molecule : " << std::endl;
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for( size_t i = 0 ; i < res.size() ; ++i ) {
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std::cout << "(" << res[i].first << "," << res[i].second << ")";
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}
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std::cout << std::endl;
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}
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std::vector<RDKit::MatchVectType> hits_vect;
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if( RDKit::SubstructMatch( *mol1 , *patt , hits_vect ) ) {
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for( size_t i = 0 ; i < hits_vect.size() ; ++i ) {
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std::cout << "Match " << i + 1 << " : ";
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for( size_t j = 0 ; j < hits_vect[i].size() ; ++j ) {
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std::cout << "(" << hits_vect[i][j].first << ","
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<< hits_vect[i][j].second << ")";
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}
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std::cout << std::endl;
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}
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}
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std::string file_root = getenv( "RDBASE" );
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file_root += "/Docs/Book";
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std::string sdf_file = file_root + "/data/actives_5ht3.sdf";
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RDKit::SDMolSupplier mol_supplier( sdf_file , true );
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RDKit::RWMOL_SPTR patt1( RDKit::SmartsToMol( "c[NH1]" ) );
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std::vector<RDKit::ROMOL_SPTR> matches;
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while( !mol_supplier.atEnd() ) {
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RDKit::ROMOL_SPTR mol3( mol_supplier.next() );
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if( mol3 && RDKit::SubstructMatch( *mol3 , *patt1 , res ) ) {
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matches.push_back( mol3 );
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}
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}
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std::cout << "There were " << matches.size() << " hits in the file." << std::endl;
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RDKit::ROMOL_SPTR mol4( RDKit::SmilesToMol( "C1=CC=CC=C1OC" ) );
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RDKit::RWMOL_SPTR smi_mol1( RDKit::SmilesToMol( "CO" ) );
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if( RDKit::SubstructMatch( *mol4 , *smi_mol1 , res ) ) {
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std::cout << "SMILES match" << std::endl;
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} else {
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std::cout << "Not SMILES match" << std::endl;
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}
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RDKit::RWMOL_SPTR smt_mol1( RDKit::SmartsToMol( "CO" ) );
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if( RDKit::SubstructMatch( *mol4 , *smt_mol1 , res ) ) {
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std::cout << "SMARTS match" << std::endl;
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} else {
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std::cout << "Not SMARTS match" << std::endl;
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}
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RDKit::RWMOL_SPTR smi_mol2( RDKit::SmilesToMol( "COC" ) );
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if( RDKit::SubstructMatch( *mol4 , *smi_mol2 , res ) ) {
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std::cout << "SMILES match" << std::endl;
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} else {
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std::cout << "Not SMILES match" << std::endl;
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}
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RDKit::RWMOL_SPTR smt_mol2( RDKit::SmartsToMol( "COC" ) );
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if( RDKit::SubstructMatch( *mol4 , *smt_mol2 , res ) ) {
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std::cout << "SMARTS match" << std::endl;
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} else {
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std::cout << "Not SMARTS match" << std::endl;
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}
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// Needs aromatic C
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RDKit::RWMOL_SPTR smt_mol3( RDKit::SmartsToMol( "COc" ) );
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if( RDKit::SubstructMatch( *mol4 , *smt_mol3 , res ) ) {
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std::cout << "SMARTS match" << std::endl;
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} else {
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std::cout << "Not SMARTS match" << std::endl;
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}
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}
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