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66 lines
2.2 KiB
C++
66 lines
2.2 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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std::shared_ptr<RDKit::ROMol> 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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std::shared_ptr<RDKit::ROMol> mol(suppl.next());
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// write all props (including _Name) to the pickle. Default is not to:
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// RDKit::MolPickler::pickleMol( *mol , pickle_ostream);
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// RDKit::MolPickler::pickleMol( *mol , pickle_ostream,
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// RDKit::PicklerOps::NoProps);
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RDKit::MolPickler::pickleMol(*mol, pickle_ostream,
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RDKit::PicklerOps::AllProps);
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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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if (!read_cnt) {
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try {
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std::cout << "Read mol of name : " << mol3.getProp<std::string>("_Name")
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<< std::endl;
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} catch (KeyErrorException &e) {
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std::cerr << "Pickle read error : " << e.what() << std::endl;
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}
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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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