mirror of
https://github.com/openbabel/openbabel.git
synced 2026-08-09 12:38:03 -05:00
Tim Vandermeersch
37fc3e40df
Out of 1M read SMILES, 3604 (0.3%) are not written out exactly the same but these are problems in the OBFormat, not the Smiley parser.
100 lines
2.3 KiB
C++
100 lines
2.3 KiB
C++
#include "obtest.h"
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#include <openbabel/mol.h>
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#include <openbabel/obconversion.h>
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using namespace std;
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using namespace OpenBabel;
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/*
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void dumpJSON(OBMol &mol)
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{
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mol.GetAtom(1)->GetHyb();
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mol.GetAtom(1)->GetType();
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FOR_ATOMS_OF_MOL (atom, mol)
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std::cout << " " << atom->JSON() << std::endl;
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}
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void compareJSON(OBMol &mol1, OBMol &mol2)
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{
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for (std::size_t i = 0; i < mol1.NumAtoms(); ++i) {
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std::string json1 = mol1.GetAtom(i+1)->JSON();
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std::string json2 = mol2.GetAtom(i+1)->JSON();
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OB_COMPARE(json1.substr(0, json1.find(", flags")) + " }", json2.substr(0, json2.find(", flags")) + " }");
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}
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}
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*/
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void test_parser(const std::string &smiles)
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{
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std::cout << "Testing: " << smiles << std::endl;
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OBConversion obConv, smileyConv;
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OB_REQUIRE(obConv.SetInFormat("smi"));
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OB_REQUIRE(obConv.SetOutFormat("smi"));
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OB_REQUIRE(smileyConv.SetInFormat("smy"));
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OBMol obMol, smileyMol;
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OB_REQUIRE(obConv.ReadString(&obMol, smiles));
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OB_REQUIRE(smileyConv.ReadString(&smileyMol, smiles));
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std::string obCanSmiles = obConv.WriteString(&obMol, true);
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std::string smileyCanSmiles = obConv.WriteString(&smileyMol, true);
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/*
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std::cout << "obMol:" << std::endl;
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dumpJSON(obMol);
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std::cout << "smileyMol:" << std::endl;
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dumpJSON(smileyMol);
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compareJSON(obMol, smileyMol);
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*/
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OB_COMPARE(obCanSmiles, smileyCanSmiles);
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}
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int main()
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{
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// simple test...
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test_parser("CCC");
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// test if aromaticity is working
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test_parser("c1ccccc1");
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test_parser("[nH]1cccc1");
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test_parser("c1ncncc1");
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// tetrahedral stereochemistry
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test_parser("C[C@](F)(Cl)Br");
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test_parser("C1CCCC[C@H]1[C@@H]1CCCCC1");
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test_parser("O=C1OC(=O)[C@@H]2[C@H]1C1C=CC2C1");
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test_parser("CO[C@@H](C)[C@@H](N)C(=O)O");
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// cis/trans stereochemistry
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test_parser("F/C=C/F");
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test_parser("F/C=C\\F");
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test_parser("F\\C=C/F");
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test_parser("F\\C=C\\F");
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test_parser("O=C1CCCC/C/1=N\\Nc1ccccc1");
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// mixed stereochemistry
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test_parser("CC(C)CCC[C@@H](C)[C@H]1CCC2C3CC=C4CC(CC[C@@]4(C)C3CC[C@@]12C)OC(=O)/C=C/c1ccccc1");
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// OB's smiles parser assigns hybridization 2 to 2nd O???
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test_parser("O=Nc1ccc(O)cc1");
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test_parser("Cn1nccc1");
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test_parser("NC1CC(C)(C)N([O])C(C)(C)C1");
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return 0;
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std::ifstream ifs("emolecules1M.smi");
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std::string line;
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while (std::getline(ifs, line))
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test_parser(line);
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return 0;
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}
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