On Fri, Jul 6, 2012 at 10:27 AM, JP <[email protected]> wrote: > Steifl -- that is a really crafty and less painful way how to go about it. > > The SMILES is in fact, a wget call away - since I am processing PDB > deposited structures. > http://www.rcsb.org/pdb/rest/describeHet?chemicalID=NAG
Do you want ideal ligand structures or those from the experimental PDB file? The ideal ones you can just download from PDBeChem (SDF). The Credo web service has a REST resource for downloading ligand structures in different formats (including SDF) - hopefully I will have a web server soon to make this publicly available. > Of course, this approach is not generally applicable (and for this you'd > need the perception code Greg mentioned). > Can I have a look at that code, just to see the amount of work involved -- > if nothing else? Just remember that those ligand structures are often far from perfect - the most common problems are missing atoms and dodgy geometries that affect bond order perception. Here are the two ligands (FRG) from PDB entry 1M48 for example: COC(=O)[C@H](Cc1ccc(cc1)C#Cc2ccccc2)NC(=O)C[C@H]3CCCN(C3)C(=[NH2+])N COC(=O)[C@H](Cc1ccc(cc1)C#Cc2ccccc2)NC(=O)C[C@H]3CC=CN(C3)C(=[NH2+])N The second one has a double bond because one of the rings does not have the same geometry as it does in the other ligand. > For the protein I can somehow "guess" the bonds. SanitizeMol takes around > 20 mins on my machine (I assume this is because of the massive size of the > molecule ~ 2000 atoms). > Jean-Paul Ebejer > Early Stage Researcher It might be easier to use Open Babel to load the PDB structure and extract just the binding site, which you could safe in a different format and use afterwards in RDKit. > > On 6 July 2012 07:33, Stiefl, Nikolaus <[email protected]> wrote: >> >> Hi JP, >> Not sure if this is of any help. If it's an pdb file from rcsb or an >> in-house one where you have a corresponding smiles available maybe you >> could use this information to properly setup the bond types using bond >> matches? I know the components.cif file still has quite a few errors - >> however, maybe it could be of help. >> Cheers >> Nik >> >> >> Maybe you could use the smiles information ion >> >> On 7/6/12 5:04 AM, "Greg Landrum" <[email protected]> wrote: >> >> >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. 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