I wonder if it is possible to automatically generate a covering Markush structure from a collection of compounds using the Java API.
I could think of a mechanism which combines MCS calculation with R-group decomposition.
Do you have any ideas or plans related to this issue?
Yes, it is possible if there is a common scaffold.
We are just adding a Markush output into R-group decomposition in version 5.3.
Sounds great to me! My main concern was how to generate the missing R1, R2, ... nodes for R-group decomposition, but this problem seems to be solved:
|As of JChem 5.3, a query without R-atoms will be automatically modified in|
setQuery(chemaxon.struc.Molecule): R-atoms will be added in place of
implicit hydrogens by addRGroups(chemaxon.struc.Molecule).
Can you give an estimation when 5.3 becomes available?