You have confused formal charges with atomic charges. SMARTS matching is
for formal charges. Your example molecule according to Open Babel is
O[N](=O)C, and so the SMARTS matching is correct. It's possible that Open
Babel is reading the MOL2 file incorrectly (I'm not really familiar with
the details of MOL2 - the reliance on atom types complicates
reading/writing MOL2 files - I recommend you use a MOL file instead of MOL2
files unless required.)
- Noel
On 12 April 2014 04:05, Igor Leontyev <i.leont...@gmail.com> wrote:
> Dear OpenBabel community:
> I'm faced with a problem of selecting atoms by SMARTS patterns that
> include charge descriptor "+/-" such as '[O-][N+](=O)C'. The pattern
> matching does not work properly unless the molecular structure is given
> in the smile format. To localize the problem I have tested different
> smarts with "obgrep" application by searching in Nitromethane.mol2
> structure. The mol2-format is used because it provides atomic charge
> information. (Mol and hin-formats were also tested and resulted in the
> same problem.) All patterns with charge descriptor result in no matches
> in Nitromethane (canonical smile C[N+](=O)[O-]):
> 'C[N+](=O)[O-]'
> 'C-[N+]([O-])=O'
> 'C-[N]([O-])=O'
> '[O-][N+](=O)C'
> 'O[N+](=O)C'
> are failed. The only successful patterns are that which have no charge
> descriptors. For example, the command:
> obgrep -imol2 'C-[N]([O])=O' Nitromethane.mol2
> has a match and outputs the structure:
>
> @<TRIPOS>MOLECULE
> Nitromethane.hin
> 7 6 0 0 0
> SMALL
> GASTEIGER
>
> @<TRIPOS>ATOM
> 1 O 1.4119 0.9932 -0.0000 O.2 1 LIG11 -0.5820
> 2 O 1.3830 -1.0017 -0.0000 O.2 1 LIG11 0.0340
> 3 N 0.7869 0.0029 -0.0000 N.pl3 1 LIG11 0.0348
> 4 C -0.6030 0.0054 0.0000 C.3 1 LIG11 0.1981
> 5 H -0.9794 -0.5079 0.8877 H 1 LIG11 0.1050
> 6 H -0.9794 -0.5079 -0.8877 H 1 LIG11 0.1050
> 7 H -1.0199 1.0160 0.0000 H 1 LIG11 0.1050
> @<TRIPOS>BOND
> 1 1 3 1
> 2 2 3 2
> 3 3 4 1
> 4 4 5 1
> 5 4 6 1
> 6 4 7 1
>
> Does OBabel support smarts charge-descriptors for matching 3D
> structures? Or what I am I doing wrong? (In my tests matching works only
> for smi-files).
>
> Thank you,
> Igor
>
>
>
> ------------------------------------------------------------------------------
> Learn Graph Databases - Download FREE O'Reilly Book
> "Graph Databases" is the definitive new guide to graph databases and their
> applications. Written by three acclaimed leaders in the field,
> this first edition is now available. Download your free book today!
> http://p.sf.net/sfu/NeoTech
> _______________________________________________
> OpenBabel-discuss mailing list
> OpenBabel-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
------------------------------------------------------------------------------
Start Your Social Network Today - Download eXo Platform
Build your Enterprise Intranet with eXo Platform Software
Java Based Open Source Intranet - Social, Extensible, Cloud Ready
Get Started Now And Turn Your Intranet Into A Collaboration Platform
http://p.sf.net/sfu/ExoPlatform
_______________________________________________
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
