#1308 cannot parse SMILES due to "SMILES strings cannot ring close two directly connected atoms"

cdk-1.4.x
closed
nobody
1
2013-06-28
2013-06-28
Martin Gütlein
No

beta-CYCLODEXTRIN (http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=160657156&viewopt=PubChem) could be parsed with 1.4.7, but fails with 1.4.14

new SmilesParser(DefaultChemObjectBuilder.getInstance()).parseSmiles("OC1O2O3(CO)O(O4(CO)O(O5C(CO)O(O6(CO)O(O7(CO)O(O8(CO)O(O1(O)2O)(O)8O)(O)7O)C(O)6O)(O)5O)(O)4O)(O)3O");

Related

Bugs: #1308

Discussion

  • correction: dont know about 1.4.14, but it fails with 1.4.18

     
  • John May
    John May
    2013-06-28

    Hi Martin,

    Daylight won't read it either.

    http://www.daylight.com/daycgi/depict?4f43314f324f3328434f294f284f3428434f294f284f354328434f294f284f3628434f294f284f3728434f294f284f3828434f294f284f31284f29324f29284f29384f29284f29374f2943284f29364f29284f29354f29284f29344f29284f29334f

    I'm guessing it was computed with CDK?

    Using the compound id smiles works okay: C(C1C2C(C(C(O1)OC3C(OC(C(C3O)O)OC4C(OC(C(C4O)O)OC5C(OC(C(C5O)O)OC6C(OC(C
    (C6O)O)OC7C(OC(C(C7O)O)OC8C(OC(O2)C(C8O)O)CO)CO)CO)CO)CO)CO)O)O)O

    from http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=444041

    Also, don't use DefaultChemObjectBuilder, SilentChemObjectBuilder is better (yes it should be other way round). The default one fires events on every update… which you don't need unless it's a GUI app. This can have massive hits in performance for some algorithms.

    J

    On 28 Jun 2013, at 14:03, "Martin Gütlein" martinguetlein@users.sf.net wrote:

    correction: dont know about 1.4.14, but it fails with 1.4.18

    [bugs:#1308] cannot parse SMILES due to "SMILES strings cannot ring close two directly connected atoms"

    Status: open
    Labels: parse smiles
    Created: Fri Jun 28, 2013 01:00 PM UTC by Martin Gütlein
    Last Updated: Fri Jun 28, 2013 01:00 PM UTC
    Owner: nobody

    beta-CYCLODEXTRIN (http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=160657156&viewopt=PubChem) could be parsed with 1.4.7, but fails with 1.4.14

    new SmilesParser(DefaultChemObjectBuilder.getInstance()).parseSmiles("OC1O2O3(CO)O(O4(CO)O(O5C(CO)O(O6(CO)O(O7(CO)O(O8(CO)O(O1(O)2O)(O)8O)(O)7O)C(O)6O)(O)5O)(O)4O)(O)3O");

    Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/cdk/bugs/1308/

    To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/

     

    Related

    Bugs: #1308

    • I'm guessing it was computed with CDK?

      Hmm, I don't actually know, I have it from a project partners database..

      Also, don't use DefaultChemObjectBuilder, SilentChemObjectBuilder is better

      Okay, I will switch to the Silent one. It does not read this specify compound as well, though

       
  • OpenBabel accepts it, BTW

     
  • okay, thanks, I think we have to fix the original smiles, then

    I dont know how to close this ticket, could you do that for me?

     
  • John May
    John May
    2013-06-28

    • status: open --> closed
     
  • John May
    John May
    2013-06-28

    Yeah, sourceforge change it so the submitter couldn't do that anymore - don't know why.