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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