mmpdb
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Support for double-cut linkers with 0 atoms
I would like these two molecules to be identified as double-cut matched pairs (e.g. with exocyclic fragmentation):
The larger molecule has [*:1]C[*:2]
as the linker, which is fine:
$ mmpdb smifrag "c1ccccc1OC2CCCNC2" --cut-smarts "exocyclic"
|------------ variable ------------| |----------------------- constant ---------------------
#cuts | enum.label | #heavies | symm.class | smiles | order | #heavies | symm.class | smiles | with-H
------+------------+----------+------------+------------+-------+----------+------------+---------------------+----------
1 | N | 6 | 1 | *C1CCCNC1 | 0 | 7 | 1 | *Oc1ccccc1 | Oc1ccccc1
1 | N | 7 | 1 | *Oc1ccccc1 | 0 | 6 | 1 | *C1CCCNC1 | C1CCNCC1
2 | N | 1 | 11 | *O* | 01 | 12 | 12 | *C1CCCNC1.*c1ccccc1 | -
1 | N | 7 | 1 | *OC1CCCNC1 | 0 | 6 | 1 | *c1ccccc1 | c1ccccc1
1 | N | 6 | 1 | *c1ccccc1 | 0 | 7 | 1 | *OC1CCCNC1 | OC1CCCNC1
The smaller molecule should have [*:1][*:2]
as the linker, but nothing is found:
$ mmpdb smifrag "c1ccccc1C2CCCNC2" --cut-smarts "exocyclic"
|------------ variable -----------| |----------------- constant ----------------
#cuts | enum.label | #heavies | symm.class | smiles | order | #heavies | symm.class | smiles | with-H
------+------------+----------+------------+-----------+-------+----------+------------+-----------+---------
1 | N | 6 | 1 | *C1CCCNC1 | 0 | 6 | 1 | *c1ccccc1 | c1ccccc1
1 | N | 6 | 1 | *c1ccccc1 | 0 | 6 | 1 | *C1CCCNC1 | C1CCNCC1
I'm hoping there's a secret minsize somewhere I can change from 1 to 0, or is support for this likely to require much greater changes?