#1225 ModelBuilder3D bug - incorrect MMFF94 N atom type

master
closed
5
2012-10-08
2012-05-09
Daniel Szisz
No

Incorrect MMFF94 atom type assigned to the second N atom in molecule CNC(=O)N(C)N=O. See the relevant test in ForceFieldConfiguratorTest class.

Discussion

  • Daniel Szisz
    Daniel Szisz
    2012-05-12

    Another molecule that exhibited the same failure is CCCC(C)(C)COC(N)=O. The N mmff94 atom type is N instead of NC=O. The corresponding N atom hoseCode is N-3;C(=OO/,C/).

     
  • Daniel Szisz
    Daniel Szisz
    2012-05-13

    The bug has been solved and a patch has been made for that. The problem was the not complete form of the mmff94 atom type pattern. Patch will be added tomorrow. See that and the relevant unit test.

     
  • Daniel Szisz
    Daniel Szisz
    2012-06-14

    Closed.

     
  • Applied to master now.

    Daniel, this patch too does not seem to have been applied to master yet. Bugs should not be closed until the fixes hit the main CDK repository.