Hi JP, On Tue, May 8, 2012 at 8:10 PM, JP <[email protected]> wrote: > Hi for the second time today, > > I am trying to generate a mol instance from the attached mol2 file (which > can be read by other tools). This is a format-converted receptor from the > DUD set - so huge in size compared to your average ligand (around 9000 > atoms). > > When I Chem.MolFromMol2File the file I get > > **** > Pre-condition Violation > cannot deal with more than 1000 atoms > Violation occurred on line 717 in file > /opt/RDKit_trunk/Code/GraphMol/Chirality.cpp > Failed Expression: mol.getNumAtoms()<1000 > **** > > I know what this means, but is there a work around I can use to read and > process the file? > Mol2 support is somewhat sketchy -- perhaps a conversion to sdf first would > make the trick? > (I tried that and it didn't quite work well) > > And I know RDKit is not meant to be a macromolecule toolkit (e.g. there is > no support for residues etc), but I thought to push it to the limit > nonetheless. :)
There are a couple of things going on here: 1) the immediate failure is caused by a test for maximum molecule size in Chirality.cpp that doesn't actually need to be there. You are perfectly safe commenting out line 717 in Chirality.cpp. I will do this in svn in the not-too-distant future. 2) even after that's removed, there's a kekulization failure for your molecule. I'm not quite sure what's causing this and, given the size of the molecule, it's pretty difficult to look at it and figure out what's going on. It's not being caused by the molecule size (I verified this by adding a test case for a 2500 atom molecule that needs to be kekulized... that works fine). A kekulization problem in something that comes from a mol2 file could be pointing to an atom-typing problem (never that surprising from mol2) or it could be a bug. Without a smaller molecule that shows the same problem it's going to be difficult to narrow this down further. Something of a side note that may help: given that this is a protein coming in from mol2, it may be safe to just turn off the kekulization and aromaticity perception bits of the sanitization process and see if you get further (you'll still need to fix the Chirality.cpp thing if you care about stereochemistry perception in this monster molecule). -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
