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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.
57 lines
2.1 KiB
C++
57 lines
2.1 KiB
C++
//
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// Working with molecules example7.cpp
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#include <iostream>
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#include <GraphMol/GraphMol.h>
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#include <GraphMol/SmilesParse/SmilesParse.h>
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#include <GraphMol/MolOps.h>
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int main( int argc , char **argv ) {
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RDKit::ROMOL_SPTR mol( RDKit::SmilesToMol( "OC1C2C1CC2" ) );
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if( !mol->getRingInfo()->isInitialized() ) {
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RDKit::MolOps::findSSSR( *mol );
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}
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for( unsigned int i = 0 , is = mol->getNumAtoms() ; i < is ; ++i ) {
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const RDKit::Atom *atom = mol->getAtomWithIdx( i );
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std::cout << mol->getRingInfo()->numAtomRings( atom->getIdx() ) << " ";
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}
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std::cout << std::endl;
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for( unsigned int i = 0 , is = mol->getNumBonds() ; i < is ; ++i ) {
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const RDKit::Bond *bond = mol->getBondWithIdx( i );
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std::cout << mol->getRingInfo()->numBondRings( bond->getIdx() ) << " ";
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}
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std::cout << std::endl;
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const RDKit::Bond *bond = mol->getBondWithIdx( 1 );
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if( mol->getRingInfo()->numBondRings( bond->getIdx() )) {
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std::cout << "Bond " << bond->getIdx() << " is in a ring" << std::endl;;
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}
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std::cout << "Atom 2 is in ring of size 3 : "
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<< mol->getRingInfo()->isAtomInRingOfSize( 2 , 3 ) << std::endl;
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std::cout << "Atom 2 is in ring of size 4 : "
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<< mol->getRingInfo()->isAtomInRingOfSize( 2 , 4 ) << std::endl;
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std::cout << "Atom 2 is in ring of size 5 : "
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<< mol->getRingInfo()->isAtomInRingOfSize( 2 , 5 ) << std::endl;
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std::cout << "Bond 1 is in ring of size 3 : "
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<< mol->getRingInfo()->isBondInRingOfSize( 1 , 3 ) << std::endl;
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std::cout << "Atom 1 is in ring of size 5 : "
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<< mol->getRingInfo()->isAtomInRingOfSize( 1 , 5 ) << std::endl;
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RDKit::VECT_INT_VECT rings;
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RDKit::MolOps::symmetrizeSSSR( *mol , rings );
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std::cout << "Number of symmetric SSSR rings : " << rings.size() << std::endl;
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for( RDKit::VECT_INT_VECT::iterator it1 = rings.begin() , it1_end = rings.end() ; it1 != it1_end ; ++it1 ) {
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for( RDKit::INT_VECT::iterator it2 = it1->begin() , it2_end = it1->end() ; it2 != it2_end ; ++it2 ) {
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std::cout << *it2 << " ";
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}
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std::cout << std::endl;
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}
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std::cout << "Number of SSSR rings : " << RDKit::MolOps::findSSSR( *mol ) << std::endl;
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}
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