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//
// Preserving molecules - example12.cpp
#include <fstream>
#include <iostream>
#include <string>
#include <GraphMol/GraphMol.h>
#include <GraphMol/MolPickler.h>
#include <GraphMol/FileParsers/MolSupplier.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
int main(int argc, char **argv) {
std::shared_ptr<RDKit::ROMol> mol1(RDKit::SmilesToMol("c1ccncc1"));
std::string pickle;
RDKit::MolPickler::pickleMol(*mol1, pickle);
RDKit::ROMol mol2;
RDKit::MolPickler::molFromPickle(pickle, mol2);
std::cout << RDKit::MolToSmiles(mol2) << std::endl;
// writing to pickle file
std::string smi_file = getenv("RDBASE");
smi_file += "/Code/GraphMol/test_data/canonSmiles.long.smi";
std::string pkl_name = "canonSmiles.long.bin";
// tab-delimited file, SMILES in column 0, name in 1, no title line
RDKit::SmilesMolSupplier suppl(smi_file, "\t", 0, 1, false);
std::ofstream pickle_ostream(pkl_name.c_str(), std::ios_base::binary);
int write_cnt = 0;
while (!suppl.atEnd()) {
std::shared_ptr<RDKit::ROMol> mol(suppl.next());
// write all props (including _Name) to the pickle. Default is not to:
// RDKit::MolPickler::pickleMol( *mol , pickle_ostream);
// RDKit::MolPickler::pickleMol( *mol , pickle_ostream,
// RDKit::PicklerOps::NoProps);
RDKit::MolPickler::pickleMol(*mol, pickle_ostream,
RDKit::PicklerOps::AllProps);
++write_cnt;
}
pickle_ostream.close();
std::cout << "Wrote " << write_cnt << " molecules" << std::endl;
// reading from pickle file
std::ifstream pickle_istream(pkl_name.c_str(), std::ios_base::binary);
int read_cnt = 0;
while (!pickle_istream.eof()) {
RDKit::ROMol mol3;
try {
RDKit::MolPickler::molFromPickle(pickle_istream, mol3);
} catch (RDKit::MolPicklerException &e) {
break;
}
if (!read_cnt) {
try {
std::cout << "Read mol of name : " << mol3.getProp<std::string>("_Name")
<< std::endl;
} catch (KeyErrorException &e) {
std::cerr << "Pickle read error : " << e.what() << std::endl;
}
}
++read_cnt;
}
pickle_istream.close();
std::cout << "Read " << read_cnt << " molecules." << std::endl;
}
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