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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.
69 lines
2.1 KiB
C++
69 lines
2.1 KiB
C++
//
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// Working with molecules example6.cpp
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#include <iostream>
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#include <GraphMol/GraphMol.h>
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#include <GraphMol/AtomIterators.h>
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#include <GraphMol/SmilesParse/SmilesParse.h>
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int main( int argc , char **argv ) {
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RDKit::ROMOL_SPTR mol( RDKit::SmilesToMol( "C1OC1" ) );
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RDKit::ROMol::VERTEX_ITER it , end;
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boost::tie( it , end ) = mol->getVertices();
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while( it != end ) {
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const RDKit::Atom *atom = (*mol)[*it].get();
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std::cout << atom->getAtomicNum() << " ";
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++it;
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}
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std::cout << std::endl;
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for( RDKit::ROMol::AtomIterator ai = mol->beginAtoms() ; ai != mol->endAtoms() ; ++ai) {
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std::cout << (*ai)->getAtomicNum() << " ";
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}
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std::cout << std::endl;
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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 << atom->getAtomicNum() << " ";
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}
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std::cout << std::endl;
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RDKit::ROMol::EDGE_ITER bond_it , bond_end;
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boost::tie( bond_it , bond_end ) = mol->getEdges();
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while( bond_it != bond_end ) {
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const RDKit::Bond *bond = (*mol)[*bond_it].get();
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std::cout << bond->getBondType() << " ";
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++bond_it;
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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 << bond->getIsAromatic() << " ";
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}
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std::cout << std::endl;
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RDKit::ROMOL_SPTR mol2( RDKit::SmilesToMol( "C1OC1Cl" ) );
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const RDKit::Bond *bond = mol2->getBondBetweenAtoms( 0 , 1 );
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std::cout << bond->getBeginAtomIdx() << " to "
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<< bond->getBeginAtomIdx() << " is "
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<< bond->getBondType() << std::endl;
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if( !mol2->getBondBetweenAtoms( 0 , 3 ) ) {
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std::cout << "No bond between 0 and 3" << std::endl;
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}
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const RDKit::Atom *atom = mol2->getAtomWithIdx( 2 );
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RDKit::ROMol::ADJ_ITER nbr , end_nbr;
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boost::tie( nbr , end_nbr ) = mol2->getAtomNeighbors( atom );
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while( nbr != end_nbr ) {
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const RDKit::Atom *nbr_atom = (*mol2)[*nbr].get();
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std::cout << nbr_atom->getIdx() << " : " << nbr_atom->getAtomicNum() << std::endl;
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++nbr;
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}
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}
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