1 //
2 // Preserving molecules - example12.cpp
3
4 #include <fstream>
5 #include <iostream>
6 #include <string>
7 #include <GraphMol/GraphMol.h>
8 #include <GraphMol/MolPickler.h>
9 #include <GraphMol/FileParsers/MolSupplier.h>
10 #include <GraphMol/SmilesParse/SmilesParse.h>
11 #include <GraphMol/SmilesParse/SmilesWrite.h>
12
main(int argc,char ** argv)13 int main( int argc , char **argv ) {
14
15 std::shared_ptr<RDKit::ROMol> mol1( RDKit::SmilesToMol( "c1ccncc1" ) );
16 std::string pickle;
17 RDKit::MolPickler::pickleMol( *mol1 , pickle );
18 RDKit::ROMol mol2;
19 RDKit::MolPickler::molFromPickle( pickle , mol2 );
20 std::cout << RDKit::MolToSmiles( mol2 ) << std::endl;
21
22 // writing to pickle file
23 std::string smi_file = getenv("RDBASE");
24 smi_file += "/Code/GraphMol/test_data/canonSmiles.long.smi";
25 std::string pkl_name = "canonSmiles.long.bin";
26
27 // tab-delimited file, SMILES in column 0, name in 1, no title line
28 RDKit::SmilesMolSupplier suppl( smi_file , "\t" , 0 , 1 , false );
29 std::ofstream pickle_ostream( pkl_name.c_str() , std::ios_base::binary );
30 int write_cnt = 0;
31 while( !suppl.atEnd() ) {
32 std::shared_ptr<RDKit::ROMol> mol( suppl.next() );
33 // write all props (including _Name) to the pickle. Default is not to:
34 // RDKit::MolPickler::pickleMol( *mol , pickle_ostream);
35 // RDKit::MolPickler::pickleMol( *mol , pickle_ostream, RDKit::PicklerOps::NoProps);
36 RDKit::MolPickler::pickleMol( *mol , pickle_ostream, RDKit::PicklerOps::AllProps );
37 ++write_cnt;
38 }
39 pickle_ostream.close();
40 std::cout << "Wrote " << write_cnt << " molecules" << std::endl;
41
42 // reading from pickle file
43 std::ifstream pickle_istream( pkl_name.c_str() , std::ios_base::binary );
44 int read_cnt = 0;
45 while( !pickle_istream.eof() ) {
46 RDKit::ROMol mol3;
47 try {
48 RDKit::MolPickler::molFromPickle( pickle_istream , mol3 );
49 } catch( RDKit::MolPicklerException &e ) {
50 break;
51 }
52 if(!read_cnt) {
53 try {
54 std::cout << "Read mol of name : "
55 << mol3.getProp<std::string>("_Name") << std::endl;
56 } catch(KeyErrorException &e) {
57 std::cerr << "Pickle read error : " << e.what() << std::endl;
58 }
59 }
60 ++read_cnt;
61 }
62 pickle_istream.close();
63 std::cout << "Read " << read_cnt << " molecules." << std::endl;
64
65 }
66
67
68