persistent error regarding smiles

User b4f15198ac

12-08-2014 02:36:09

Hello! I have been attempting to use jklustor on some ligands from rcsb's ligand expo, and keep getting back to this error.


Some features of the molecule which simplest SMILES representation is: [H][#8]-[#6](=O)C([H])([H])[#7]-1-[#6](=O)\[#6](\\[#7]=[#6]-1[C@@]([H])([#7;A]([H])[H])C([H])([H])[#8][H])=[#6](/[H])-c1c([H])[nH1]([H])c2c([H])c([H])c([H])c([H])c12 cannot be converted to smiles. Use the smarts or cxsmarts format.


This smile does not exist in my set!

I am running jkustor as follows:

jklustor -c mmds:5  Components-smiles-stereo-oe-edited.smi


I have also tried two work arounds:

1st) generating PF files with generatemd (no errors)

jklustor -c mmds:5

returns nothing,

2nd) standardize or molconvert to .sdf

same error

System Info:

Ubuntu 14.04

java version "1.6.0_45"

Java(TM) SE Runtime Environment (build 1.6.0_45-b06)

Java HotSpot(TM) 64-Bit Server VM (build 20.45-b01, mixed mode)


JKlustor - clustering command line frontend v0.07 


EDIT: converting to cxsmarts works without concern, but  jklustor -c mmds:5  ligands.cxsmarts still returns the same error

User b4f15198ac

12-08-2014 20:06:19

converted to sdf then tried again -> brought out the error message i needed:

"Molecule  has not supported feature at atom 3: atom has radical which would be lost.

Use the cxsmiles, smarts or cxsmarts format."


note that this did NOT show up when running jklustor on the original .smi file

using standardize fixed the problem.