My solution for the problem was the following:
qmol = Chem.MolFromMolBlock(molblock)
for atom in qmol.GetAtoms():
if atom.HasQuery():
continue
atom.SetNumExplicitHs(atom.GetTotalNumHs())
This gives a SMARTS like
this: [#7]1(-[#6](-[#6H2]-[#6,#8]-[#6H](-[#6H2]-1)-[*])=[#8])-[*]
This may be good enough for this specific user, however It doesn't solve
the problem of the [C,O] query atom [#6,#8]. If that is C, it would allow
additional substitution of this atom.
How is your solution handling it?
Best,
Peter
On Tue, Jun 7, 2016 at 1:06 AM Brian Kelley <fustiga...@gmail.com> wrote:
> An interesting conversation came up at work a few days ago regarding
> MolBlocks/CTABs with queries that behave in an unexpected manner. I'm
> tackling some of these issues when it comes to reaction processing .rxn
> based files and plan on contributing it relatively soon. However, I hadn't
> considered making it a generic Query based sanitization/processing.
>
>
> The basic question was "How do I get a MolBlock to only match the "R"'s
> and not allow substitutions anywhere else? like ChemAxon..."
>
>
> As it turns out, RDKit is very strict when it looks at RGroups. This was
> the initial issue with when i started Sanitizing RGroups. Basically there
> are several variants in the wild (ChemDraw/ICM) that make reactions that
> don't quite follow the CTAB spec. RDKit likes the atom labled R to (1)
> actually be in an "M RGP" tag and (2) have an atom mapping. If an atom is
> labeled "R" and not in a R_GRP it isn't considered a wild card for instance.
>
> Now queries don't really care about "M RGP", but they do care that it
> isn't a dummy atom. I'm listing below our current technique to fix these
> issues for CTAB queries and would like some feedback.
>
> Here is the workflow that we have been telling chemists during sketching:
>
> 1. Make a proper group. The marvin-sketch/Chemdraw "R" is not enough, you
> can replace it with "A", but R has special semantics and needs an RGroup
> label defined.
> 2. aromatize where appropriate
> 3. (optionally) protonate so only RGroups can match
>
> These line up with the following RDKit code snippets:
>
> 1. Fix the "R"s (note we probably should make proper RGroups, but this
> just add dummy matches)
>
> qmol = rdkit.Chem.MolFromMolblock(molblock)
> # first, change the "R"'s into matching any atoms
> from rdkit.Chem import rdqueries
> qmol = Chem.RWMol(qmol)
> for atom in newpat.GetAtoms():
> if atom.GetAtomicNum() == 0:
> qmol.ReplaceAtom(atom.GetIdx(),
> rdqueries.AtomNumGreaterQueryAtom(0))
>
>
> 2. aromatize - this might be good or might break things. It seems to work
> great, even with conditional logic i.e. [C,O] but I'm unsure which atom is
> actually being used to form the Pi electrons for aromaticity checking. I
> expect the First actually. In anycase, something needs to happen in
> general for random inputs, otherwise the matching doesn't really do what is
> expected.
>
> # We want to see if we can find aromaticity, this may be complicated with
> # query features [C,O] but it works ok.
> Chem.SanitizeMol(qmol, Chem.SANITIZE_SETAROMATICITY)
>
> 3. protonate if the desire is to only match RGroups
>
> # second, add explicit Hs so we only match the Rs
> # I'm unclear if this can fail in general, I would probably wrap this in
> # a try...except block
> Chem.SanitizeMol(qmol, Chem.SANITIZE_ADJUSTHS)
> qmol = Chem.MergeQueryHs(Chem.AddHs(qmol))
>
> This could be enabled with flags into a SanitizeQuery function, or perhaps
> a PrepareQuery function.
>
> Thoughts?
>
> Cheers,
> Brian
>
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