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 >> > >> > >> > >> > >> > ------------------------------------------------------------------------------ >> > 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
