#1339 ModelBuilder3D: Symbol:O does not MATCH AtomType

cdk-1.0.x
open
nobody
None
1
2014-04-05
2014-04-05
SBeisken
No

The ModeBuilder3D fails for water (SMILES: O). Latest CDK nightly (1.5.x). Implicit hydrogens had been added to the atom-typed IAtomContainer.

Error: "Could not final configure atom due to problems with force field"
Atom is unkown: Symbol:O does not MATCH AtomType. HoseCode:O-2;(//)

Discussion

  • Yeah, some patch some long time ago messed up the atom type perception of the builder3d stack, way before it had good unit tests, and it went unnoticed :/

    This problem is known for some time now... no idea how to fix it; I had hoped to completely replace the custom perception stack, but the code is rather complex...