Hi,
Using RDKit 2013_09_1 binary Windows download with Python 2.7 on Windows 7.
from rdkit import Chem
m = Chem.MolFromPDBFile('C:/users/jhje/Desktop/1N8Z.pdb')
molfile = Chem.MolToMolBlock(m)
f = open("c:/temp/big.mol", "w")
f.write(molfile)
f.close()
The first lines of C:/temp/big.mol are:
HERCEPTIN FAB (ANTIBODY) - LIGHT CHAIN
RDKit 3D
78908023 0 0 0 0 0 0 0 0999 V2000
34.5390 88.7520 88.2980 N 0 0 0 0 0 0 0 0 0 0 0 0
34.7910 87.4610 89.0350 C 0 0 2 0 0 0 0 0 0 0 0 0
35.9070 86.7790 88.2540 C 0 0 0 0 0 0 0 0 0 0 0 0
which is unreadable since there are 7890 atoms and 8023 bonds and V2000
format supports max. 999 atoms/bonds. I would have expected RDKit to
switch to V3000 format automatically (?). I don't see any parameter in
MolToMolBlock() that can force V3000 output ?
Cheers
-- Jan
------------------------------------------------------------------------------
Rapidly troubleshoot problems before they affect your business. Most IT
organizations don't have a clear picture of how application performance
affects their revenue. With AppDynamics, you get 100% visibility into your
Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
