Symmetric variable fragments are not replaced in both possible directions #78

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opened 2025-10-14 17:06:09 -06:00 by navan · 0 comments

navan commented

2025-10-14 17:06:09 -06:00

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Originally created by @KramerChristian on 5/9/2018

When running the transform query, the enumerator only creates one out of the several possible compounds if a fragment to be replaced is symmetric.

Here is a simplified example:
Running a transform query with this input compound

C1CCC1CCN2CC2

yields (among others) this fragmentation:

constant: C1CCC1*.C2CN2*
variable: CC

Note that the variable linker is symmetric.
The MMP database now contains transformations like

CC >> C(C)C

which should produce these two compounds:

C1CCC1C(C)CN2CC2
C1CCC1CC(C)N2CC2

, depending on which way round the transformation is applied. However, it only produces one of them. (The other one is produced too, but based on a different rule with much less pairs.)

*Originally created by @KramerChristian on 5/9/2018* When running the transform query, the enumerator only creates one out of the several possible compounds if a fragment to be replaced is symmetric. Here is a simplified example: Running a transform query with this input compound C1CCC1CCN2CC2 yields (among others) this fragmentation: constant: C1CCC1*.C2CN2* variable: *CC* Note that the variable linker is symmetric. The MMP database now contains transformations like *CC* >> *C(C)C* which should produce these two compounds: C1CCC1C(C)CN2CC2 C1CCC1CC(C)N2CC2 , depending on which way round the transformation is applied. However, it only produces one of them. (The other one is produced too, but based on a different rule with much less pairs.)