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. :)
The file I am trying to process may be found at
http://dl.dropbox.com/u/13990555/rec.mol2 (it is relatively large, so I
have not attached it)
-
Jean-Paul Ebejer
Early Stage Researcher
------------------------------------------------------------------------------
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
