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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.
53 lines
1.5 KiB
C++
53 lines
1.5 KiB
C++
//
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// Writing molecules example5.cpp
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#include <fstream>
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#include <iostream>
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#include <sstream>
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#include <string>
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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/FileParsers/MolWriters.h>
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#include <boost/iostreams/device/file.hpp>
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#include <boost/iostreams/filtering_stream.hpp>
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#include <boost/iostreams/filter/gzip.hpp>
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#include <boost/iostreams/stream.hpp>
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int main( int argc , char **argv ) {
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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/5ht3ligs.sdf";
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bool takeOwnership = true;
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RDKit::SDMolSupplier mol_supplier( sdf_file , takeOwnership );
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std::vector<RDKit::ROMOL_SPTR> mols;
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while( !mol_supplier.atEnd() ) {
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RDKit::ROMOL_SPTR mol( mol_supplier.next() );
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if( mol ) {
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mols.push_back( mol );
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}
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}
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std::string pdb_file = file_root + "/data/5ht3ligs.pdb";
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RDKit::PDBWriter pdb_writer( pdb_file );
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for( std::size_t i = 0 , is = mols.size() ; i < is ; ++i ) {
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pdb_writer.write( *mols[i] );
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}
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std::ostringstream oss;
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// takeOwnership must be false for this, as we don't want the SDWriter trying
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// to delete the std::ostringstream.
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takeOwnership = false;
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boost::shared_ptr<RDKit::SDWriter> sdf_writer( new RDKit::SDWriter( &oss , takeOwnership ) );
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for( std::vector<RDKit::ROMOL_SPTR>::iterator it = mols.begin() ; it != mols.end() ; ++it ) {
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sdf_writer->write( *(*it) );
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}
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std::cout << oss.str() << std::endl;
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}
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