Thanks Noel, Greg...
Its always difficult to decide on what to do: should something wrong be
parsed leniently or should it fail with error. Its a philsophical debate as
well as technical one.
This argument comes up often enough with things like malformed XML - should
the parser fail with an error message or else go on reading the file on a
best effort basis (and possibly miss out on data because of, say, a broken
connection)
Anyways - thanks for your input. I did what I had to do. I used the
isomeric smiles representation found on the pdb.
On 23 November 2010 19:12, Greg Landrum <greg.land...@gmail.com> wrote:
> JP,
>
> Noel's summary below is, in my opinion, dead on: The molfile has problems:
> 1) there's a 4 coordinate neutral nitrogen
> 2) it's missing the "M END" line (maybe it's also missing the M CHG
> line that would fix the nitrogen?)
>
> OpenBabel takes the bad mol file and, faithfully, generates a SMILES
> that corresponds to it. The RDKit sees that valence violation and
> complains.
>
> -greg
>
>
>
> On Tue, Nov 23, 2010 at 11:25 AM, Noel O'Boyle <baoille...@gmail.com>
> wrote:
> > The mol file has a nitrogen with 4 hydrogens, but the nitrogen does
> > not have a positive charge. This is messed up. Either the nitrogen has
> > only 3 hydrogens (which is probably correct) or it has 4 and a
> > positive charge.
> >
> > The SMILES string from OpenBabel represents this MOL file accurately,
> > but OpenBabel should probably have given a warning when reading the
> > MOL file in the first place.
> >
> > - Noel
> >
> > On 23 November 2010 10:04, JP <jeanpaul.ebe...@inhibox.com> wrote:
> >>
> >> Hi there @OpenBabel and Greg
> >> I am using OpenBabel 2.3.0 and RDKit 201009 release and trying to get
> them
> >> if not work together at least live peacefully :)
> >> So I have a mol file coming from the pdb Astex Diverse Set (1hww.mol).
> I
> >> convert this to a smiles string using Openbabel
> >>>
> >>> babel -xn 1hww.mol 1hww.smiles
> >>
> >> (since I do not want to generate the name). I get the attached smiles
> file
> >> - [...@h]1(O)[...@h]2[n@H](CCC1)C[C@@H](O)[...@h]2o
> >> When I try to load this using RDKit
> (i.e. AllChem.MolFromSmiles(smiles)) I
> >> get
> >>>
> >>> [19:04:57] Explicit valence for atom # 3 N, 4, is greater than
> permitted
> >>
> >> If I copy the isomeric smiles
> >> (openeye) c1...@h]([C@@H]2[C@@H]([C@@H](c...@]2c1)O)O)O in the file
> instead
> >> of the openbabel generated smiles RDKit works fine...
> >> This is probably a simple chemistry problem, but I am a CS guy so please
> >> bear with me.
> >> Now my question is: Who is the culprit? (select one)
> >> a) No-one - The mol file is incorrect (but then again, why does
> Openbabel
> >> read it with an error message? Still I can read this directly through
> >> RDKit)
> >> b) Openbabel - it is generating an incorrect smiles string (and ideally
> this
> >> is now fixed and available in 2.3.1 :) )
> >> c) RDkit - The smiles is perfectly fine, please redirect your query
> >> elsewhere
> >> d) None of the above, the OS/hardware is playing tricks on you
> >> I appreciate any help and any light you can shed.
> >> Cheers
> >> JP
> >> PS These two frameworks are really great!! well done everyone!!
> >>
> >>
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>
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