Noel - Thanks for the link to that presentation! It's useful to see
information from someone who's clearly looked into this sort of thing. That
being said, I'm having no luck grepping around RDKit's source for the bond
inference algorithm. Do you know where to look for this?
Thanks,
Pat
On Mon, Feb 3, 2014 at 3:17 PM, Noel O'Boyle <baoille...@gmail.com> wrote:
> FYI, Roger added a connect the dots to RDKit a few months back for a
> PDB parser. You can see his discussion of various algorithms at the
> end of http://www.slideshare.net/NextMoveSoftware/rdkit-gems. We could
> repurpose this code considering the licence.
>
> - Noel
>
> On 3 February 2014 19:58, Patrick Fuller <patrickful...@gmail.com> wrote:
> > So you can use -ab or -aB if you want to ignore ConnectTheDots.
> >
> > Good to know, thanks!
> >
> > The biggest talk has largely centered on PerceiveBondOrders and Kekule /
> > aromatic detection, which are usually slower than ConnectTheDots. If
> you'd
> > like to take a stab at an improved implementation of ConnectTheDots
> > (octree?) for larger systems, that would certainly be well received.
> Since
> > the number of atoms is known before CTD is called, the method could
> choose
> > implementations as needed.
> >
> > Sounds like fun - I'll take a stab at it in the coming weeks.
> >
> > Pat
> >
> >
> >
> > On Mon, Feb 3, 2014 at 9:54 AM, Geoffrey Hutchison
> > <geoff.hutchi...@gmail.com> wrote:
> >>
> >> Looking through the source, it seems that the crash is due to automatic
> >> O(N^2) bond inference on crystals. I was able to verify this by manually
> >> parsing the cif and building an OBMol from scratch (just adding atoms).
> >>
> >>
> >> From the documentation for cif (and most formats):
> >>
> >> Read Options e.g. -ab:
> >> v Verbose CIF conversion
> >> s Output single bonds only
> >> b Disable bonding entirely
> >> B Use bonds listed in CIF file from _geom_bond_etc records (overrides
> >> option b)
> >>
> >> So you can use -ab or -aB if you want to ignore ConnectTheDots.
> >>
> >> I don't want to make a bond-disabling API change just to fix a corner
> >> case. Instead, has there been any talk about making ConnectTheDots
> O(NlogN)?
> >> I feel like it could be construed as a graph search problem.
> >>
> >>
> >> The biggest talk has largely centered on PerceiveBondOrders and Kekule /
> >> aromatic detection, which are usually slower than ConnectTheDots. If
> you'd
> >> like to take a stab at an improved implementation of ConnectTheDots
> >> (octree?) for larger systems, that would certainly be well received.
> Since
> >> the number of atoms is known before CTD is called, the method could
> choose
> >> implementations as needed.
> >>
> >> Cheers,
> >> -Geoff
> >
> >
> >
> >
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