#917 UIT should mention which Flags are used and overwritten

cdk-1.4.x
open
5
2012-11-03
2009-05-20
Egon Willighagen
No

On the cdk-devel ML today:

"I have a serious problem with the UniversalIsomorphismTester class. The substructure search generates correct data if I compare molecules which have no explicit H-atoms. But if I want to compare molecules with explicit H-atoms it generates wrong data. I have attached my source file and generated data to this document. Here is also the code which generates the incorrect results:"

Discussion

  • Update from the mailing list:

    I am using the UIT class to eliminate substructures from a given molecule. I
    have used the set/getFlags() method to flag atoms which were identified as a
    substrucure. Afterwards the flagged atoms were deleted. But I have not
    noticed that the UIT class also sets the flags. So there were more atoms
    deleted as it would make sense. That was the problem.

    OK, good. So the JavaDoc of UIT should explicitly state that the XXX
    flag is used by the algorithms, and reset when UIT methods are called.
    Right?

     
  • Downgrading this. I had a quick look at it, and it is not easy to recover from the source code.