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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
1.7 KiB
C++
57 lines
1.7 KiB
C++
//
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// Preserving molecules - example12.cpp
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#include <fstream>
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#include <iostream>
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#include <string>
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#include <GraphMol/GraphMol.h>
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#include <GraphMol/MolPickler.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/SmilesParse/SmilesWrite.h>
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int main( int argc , char **argv ) {
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RDKit::ROMOL_SPTR mol1( RDKit::SmilesToMol( "c1ccncc1" ) );
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std::string pickle;
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RDKit::MolPickler::pickleMol( *mol1 , pickle );
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RDKit::ROMol mol2;
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RDKit::MolPickler::molFromPickle( pickle , mol2 );
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std::cout << RDKit::MolToSmiles( mol2 ) << std::endl;
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// writing to pickle file
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std::string smi_file = getenv("RDBASE");
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smi_file += "/Code/GraphMol/test_data/canonSmiles.long.smi";
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std::string pkl_name = "canonSmiles.long.bin";
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// tab-delimited file, SMILES in column 0, name in 1, no title line
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RDKit::SmilesMolSupplier suppl( smi_file , "\t" , 0 , 1 , false );
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std::ofstream pickle_ostream( pkl_name.c_str() , std::ios_base::binary );
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int write_cnt = 0;
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while( !suppl.atEnd() ) {
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RDKit::ROMOL_SPTR mol( suppl.next() );
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RDKit::MolPickler::pickleMol( *mol , pickle_ostream );
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++write_cnt;
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}
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pickle_ostream.close();
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std::cout << "Wrote " << write_cnt << " molecules" << std::endl;
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// reading from pickle file
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std::ifstream pickle_istream( pkl_name.c_str() , std::ios_base::binary );
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int read_cnt = 0;
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while( !pickle_istream.eof() ) {
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RDKit::ROMol mol3;
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try {
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RDKit::MolPickler::molFromPickle( pickle_istream , mol3 );
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} catch( RDKit::MolPicklerException &e ) {
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break;
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}
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++read_cnt;
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}
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pickle_istream.close();
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std::cout << "Read " << read_cnt << " molecules." << std::endl;
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}
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