User 3763398cd4
20-11-2008 20:19:35
I have noticed some strange behavior from Fragmenter. It seems to be denoting aromatic bonds to output fragments even though the original smiles input was not aromatic.
Example:
Fragmenter Input:
[H]C(=C(C([H])([H])[H])C([H])([H])[H])C([H])([H])c1c([H])c(C(N([H])C2=C(c3c([H])c([H])c(c(c3OC2=O)C([H])([H])[H])O[C@@]2([H])[C@@]([H])([C@@]([H])([C@]([H])(C(C([H])([H])[H])(C([H])([H])[H])O2)OC([H])([H])[H])OC(N([H])[H])=O)O[H])O[H])=O)c([H])c([H])c1O[H]
One Fragment Smiles from output:
[H]Nc1c(O[H])c2c([H])c([H])c(O[C@]3([H])OC(C([H])([H])[H])(C([H])([H])[H])[C@]([H])(OC([H])([H])[H])[C@@]([H])(OC(=O)N([H])[H])[C@@]3([H])O[H])c(c2oc1=O)C([H])([H])[H]
It turned the second half on the conjoined rings completely aromatic even though the original was not denoted as such. Is this working as intended?
Edit: Just to clarify, here is the smiles I was expecting to have returned.
[H]NC1=C(O[H])C2=C(OC1=O)C(=C(O[C@]1([H])OC(C([H])([H])[H])(C([H])([H])[H])[C@]([H])(OC([H])([H])[H])[C@@]([H])(OC(=O)N([H])[H])[C@@]1([H])O[H])C([H])=C2[H])C([H])([H])[H]
Example:
Fragmenter Input:
[H]C(=C(C([H])([H])[H])C([H])([H])[H])C([H])([H])c1c([H])c(C(N([H])C2=C(c3c([H])c([H])c(c(c3OC2=O)C([H])([H])[H])O[C@@]2([H])[C@@]([H])([C@@]([H])([C@]([H])(C(C([H])([H])[H])(C([H])([H])[H])O2)OC([H])([H])[H])OC(N([H])[H])=O)O[H])O[H])=O)c([H])c([H])c1O[H]
One Fragment Smiles from output:
[H]Nc1c(O[H])c2c([H])c([H])c(O[C@]3([H])OC(C([H])([H])[H])(C([H])([H])[H])[C@]([H])(OC([H])([H])[H])[C@@]([H])(OC(=O)N([H])[H])[C@@]3([H])O[H])c(c2oc1=O)C([H])([H])[H]
It turned the second half on the conjoined rings completely aromatic even though the original was not denoted as such. Is this working as intended?
Edit: Just to clarify, here is the smiles I was expecting to have returned.
[H]NC1=C(O[H])C2=C(OC1=O)C(=C(O[C@]1([H])OC(C([H])([H])[H])(C([H])([H])[H])[C@]([H])(OC([H])([H])[H])[C@@]([H])(OC(=O)N([H])[H])[C@@]1([H])O[H])C([H])=C2[H])C([H])([H])[H]