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 > > > > ------------------------------------------------------------------------------ > Managing the Performance of Cloud-Based Applications > Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. > Read the Whitepaper. > http://pubads.g.doubleclick.net/gampad/clk?id=121051231&iu=/4140/ostg.clktrk > _______________________________________________ > OpenBabel-Devel mailing list > OpenBabel-Devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-devel > ------------------------------------------------------------------------------ Managing the Performance of Cloud-Based Applications Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. Read the Whitepaper. http://pubads.g.doubleclick.net/gampad/clk?id=121051231&iu=/4140/ostg.clktrk _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
