Steifl -- that is a really crafty and less painful way how to go about it.
The SMILES is in fact, a wget call away - since I am processing PDB
deposited structures.
http://www.rcsb.org/pdb/rest/describeHet?chemicalID=NAG
Of course, this approach is not generally applicable (and for this you'd
need the perception code Greg mentioned).
Can I have a look at that code, just to see the amount of work involved --
if nothing else?
For the protein I can somehow "guess" the bonds. SanitizeMol takes around
20 mins on my machine (I assume this is because of the massive size of the
molecule ~ 2000 atoms).
-
Jean-Paul Ebejer
Early Stage Researcher
On 6 July 2012 07:33, Stiefl, Nikolaus <[email protected]> wrote:
> Hi JP,
> Not sure if this is of any help. If it's an pdb file from rcsb or an
> in-house one where you have a corresponding smiles available maybe you
> could use this information to properly setup the bond types using bond
> matches? I know the components.cif file still has quite a few errors -
> however, maybe it could be of help.
> Cheers
> Nik
>
>
> Maybe you could use the smiles information ion
>
> On 7/6/12 5:04 AM, "Greg Landrum" <[email protected]> wrote:
>
> >Hi JP,
> >
> >On Thu, Jul 5, 2012 at 7:07 PM, JP <[email protected]> wrote:
> >>
> >>
> >> I generate a RWMol instance from the HETATM portion of a PDB file. My
> >>atoms
> >> are currently only joined by a single bond as defined in the connect
> >>portion
> >> of the pdb file, e.g.
> >>
> >> CONECT 2235 2234 2236
> >> CONECT 2236 2231 2235 2251
> >> CONECT 2237 2238 2242
> >
> >ah, yes, the missing bond orders, one of the many reasons that I have
> >never done a PDB parser for the RDKit. :-S
> >
> >I think you're doing this work in C++, so I'm going to answer the rest
> >of the questions accordingly.
> >
> >> Are there any obvious rdkit ways how to detect :-
> >>
> >> 0. rings
> >
> >Sure.
> >
> >If you just want to know if each atom/ring is in a ring you can use
> >MolOps::fastFindRings and then mol.getRingInfo().numAtomRings(idx)>0
> >or mol.getRingInfo().numBondRings(idx)>0
> >
> >If you want to know what the SSSR rings are, then you should use
> >MolOps::symmetrizeSSSR(). You can pass that an extra argument where it
> >will return the rings as defined by atom indices. After calling this,
> >you can also get the set of atom rings using
> >mol.getRingInfo().atomRings() or the bond rings with
> >mol.getRingInfo().bondRings();
> >
> >> 1. aromatic rings/atoms
> >> 2. double/triple bonds
> >> 3. charges (if any)
> >
> >Here's where the trouble starts.
> >
> >I guess you want to perceive the bond types and atom hybridizations
> >from the geometry. From there you can get the charges. The RDKit does
> >not currently have anything to do this. There was a discussion on the
> >mailing list last year:
> >http://comments.gmane.org/gmane.science.chemistry.rdkit.user/85
> >where Geoff Hutchinson very kindly offered to donate the OpenBabel
> >bond perception code to the RDKit. He sent the code, but I've never
> >had the time to "port" it from OpenBabel to RDKit. If you're
> >interested in implementing this and were willing to do it in a way
> >that could be integrated into the main RDKit, I can send you the
> >donated code; it's about 300 lines of well-commented C++.
> >
> >>
> >> I would like to set these properties on every atom instance contained
> >>in my
> >> RWMol - so I generate a correct molecule representation.
> >> I assume sanitize would not clean these up for me? Correct?
> >
> >Correct. Sanitize uses the bond information that's there.
> >
> >-greg
> >
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