Hi JP, On Thu, Jul 5, 2012 at 7:07 PM, JP <[email protected]> wrote: > > > I generate a RWMol instance from the HETATM portion of a PDB file. My atoms > are currently only joined by a single bond as defined in the connect portion > of the pdb file, e.g. > > CONECT 2235 2234 2236 > CONECT 2236 2231 2235 2251 > CONECT 2237 2238 2242
ah, yes, the missing bond orders, one of the many reasons that I have never done a PDB parser for the RDKit. :-S I think you're doing this work in C++, so I'm going to answer the rest of the questions accordingly. > Are there any obvious rdkit ways how to detect :- > > 0. rings Sure. If you just want to know if each atom/ring is in a ring you can use MolOps::fastFindRings and then mol.getRingInfo().numAtomRings(idx)>0 or mol.getRingInfo().numBondRings(idx)>0 If you want to know what the SSSR rings are, then you should use MolOps::symmetrizeSSSR(). You can pass that an extra argument where it will return the rings as defined by atom indices. After calling this, you can also get the set of atom rings using mol.getRingInfo().atomRings() or the bond rings with mol.getRingInfo().bondRings(); > 1. aromatic rings/atoms > 2. double/triple bonds > 3. charges (if any) Here's where the trouble starts. I guess you want to perceive the bond types and atom hybridizations from the geometry. From there you can get the charges. The RDKit does not currently have anything to do this. There was a discussion on the mailing list last year: http://comments.gmane.org/gmane.science.chemistry.rdkit.user/85 where Geoff Hutchinson very kindly offered to donate the OpenBabel bond perception code to the RDKit. He sent the code, but I've never had the time to "port" it from OpenBabel to RDKit. If you're interested in implementing this and were willing to do it in a way that could be integrated into the main RDKit, I can send you the donated code; it's about 300 lines of well-commented C++. > > I would like to set these properties on every atom instance contained in my > RWMol - so I generate a correct molecule representation. > I assume sanitize would not clean these up for me? Correct? Correct. Sanitize uses the bond information that's there. -greg ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
