Absolute SMILES Generation fails for reactions

[mrwns]

I noticed an issue when generating Absolute SMILES for reactions (which fails).

For the reactants and products individually, this works.

See example below, fails with 2.8 and 2.9 Snapshot.

        String reaction ="[CH3:9][O:8][C:7](=[O:10])[CH:6]([NH:11][C:12](=[O:13])[NH:14][C:15]1=[CH:16][C:17]([O:18][CH3:19])=[CH:20][C:21](=[C:26]1[OH:27])[C:22]([CH3:23])([CH3:24])[CH3:25])[C@@H:5]([F:38])[CH2:4][CH2:3][CH2:2][NH:1][C:29](=[O:28])[O:30][CH2:31][C:32]1=[CH:33][CH:34]=[CH:35][CH:36]=[CH:37]1>>[CH3:9][O:8][C:7](=[O:10])[CH:6]([NH:11][C:12](=[O:13])[NH:14][C:15]1=[CH:16][C:17]([O:18][CH3:19])=[CH:20][C:21](=[C:26]1[OH:27])[C:22]([CH3:23])([CH3:24])[CH3:25])[C@@H:5]([F:38])[CH2:4][CH2:3][CH2:2][NH2:1]";

        SmilesParser parser = new SmilesParser(SilentChemObjectBuilder.getInstance());

        SmilesGenerator gen1 = new SmilesGenerator(
                SmiFlavor.Absolute
        );

        // processing the individual reagents/products works
        for (String smiles : reaction.split(">>")){
            IAtomContainer mol = parser.parseSmiles(smiles);
            System.out.println(gen1.create(mol));

        }

        IReaction rxn = parser.parseReactionSmiles(reaction);

        //this fails for the whole reaction
        System.out.println(gen1.create(rxn));

[johnmay]

Doh! Easy fix, it's the empty agents. Perhaps something changed in the JNI/JNA inchi, should add a test case anyways.

[mrwns]

Thanks!

for note, I have the suspicion that SmiFlavor.AtomAtomMapRenumber does not work properly for reactions, as it re-numbers reactants and products independently (after a brief look into how the renumbering is called)

O=C(OCc1ccccc1)[NH:1][CH2:2][CH2:3][CH2:4][CH2:5][C@@H:6]([C:7]([O:8][CH3:9])=[O:10])[NH:11][C:12](=[O:13])[NH:14][c:15]1[cH:16][c:17]([O:18][CH3:19])[cH:20][c:21]([C:22]([CH3:23])([CH3:24])[CH3:25])[c:26]1[OH:27]>>[NH2:1][CH2:2][CH2:3][CH2:4][CH2:5][C@@H:6]([C:7]([O:8][CH3:9])=[O:10])[NH:11][C:12](=[O:13])[NH:14][c:15]1[cH:16][c:17]([O:18][CH3:19])[cH:20][c:21]([C:22]([CH3:23])([CH3:24])[CH3:25])[c:26]1[OH:27]

gets reassigned to

[O:1]=[C:2]([O:3][CH2:4][C:5]=1[CH:6]=[CH:7][CH:8]=[CH:9][CH:10]1)[NH:11][CH2:12][CH2:13][CH2:14][CH2:15][CH:16]([NH:17][C:18](=[O:19])[NH:20][C:21]2=[CH:22][C:23]([O:24][CH3:25])=[CH:26][C:27](=[C:28]2[OH:29])[C:30]([CH3:31])([CH3:32])[CH3:33])[C:34](=[O:35])[O:36][CH3:37]>>[O:1]=[C:2]([NH:3][C:4]1=[CH:5][C:6]([O:7][CH3:8])=[CH:9][C:10](=[C:11]1[OH:12])[C:13]([CH3:14])([CH3:15])[CH3:16])[NH:17][CH:18]([C:19](=[O:20])[O:21][CH3:22])[CH2:23][CH2:24][CH2:25][CH2:26][NH2:27]

[johnmay]

Will take a look