Thanks! I feel rather stupid not checking for ConnectTheDots.
On Sun, Feb 9, 2014 at 6:18 AM, Noel O'Boyle <baoille...@gmail.com> wrote:
> I guessed that Roger will just call it ConnectTheDots...
>
> $ grep -i connectthedots `find . | grep cpp`
> ./Code/GraphMol/FileParsers/ProximityBonds.cpp:static void
> ConnectTheDots_Small(RWMol *mol)
> ./Code/GraphMol/FileParsers/ProximityBonds.cpp:static void
> ConnectTheDots_Medium(RWMol *mol)
> ./Code/GraphMol/FileParsers/ProximityBonds.cpp:static void
> ConnectTheDots_Large(RWMol *mol)
> ./Code/GraphMol/FileParsers/ProximityBonds.cpp:void ConnectTheDots(RWMol
> *mol)
> ./Code/GraphMol/FileParsers/ProximityBonds.cpp: ConnectTheDots_Large(mol);
> ./Code/GraphMol/FileParsers/PDBParser.cpp: ConnectTheDots(mol);
>
> - Noel
>
> On 9 February 2014 00:12, Patrick Fuller <patrickful...@gmail.com> wrote:
> > 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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>
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