Creating SMARTS from SMILES/InChI's - depends on canonical SMILES ?

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Creating SMARTS from SMILES/InChI's - depends on canonical SMILES ?

Steffen Neumann
Hi,

I've hit a problem using SMILES as SMARTS,
which in my case requires using *canonical* SMILES as input,
see the example below. The problem occurs both with ob-2.2.3
and todays SVN trunk.

Did I miss anything, or should I open a bug ?

Yours,
Steffen

#-------- Cut & Paste from here ------------

echo 'InChI=1S/C9H7N5O/c10-8-7-9(12-4-11-8)14(5-13-7)6-2-1-3-15-6/h2-6H,(H2,10,11,12)' | babel -i inchi - -o smi
#C1=CC(n2cnc3c(N)ncnc23)OC=1
#1 molecule converted
#1 info messages 25 audit log messages

echo 'O' |  babel -i smi - -s 'C1=CC(n2cnc3c(N)ncnc23)OC=1' -o smi -
#==============================
#*** Open Babel Error  in SMARTSError
#  SMARTS Error:
#C1=CC(n2cnc3c(N)ncnc23)OC=1
#                           ^

echo 'InChI=1S/C9H7N5O/c10-8-7-9(12-4-11-8)14(5-13-7)6-2-1-3-15-6/h2-6H,(H2,10,11,12)' | babel -i inchi - -o can
#Nc1ncnc2c1ncn2C1C=C=CO1
#1 molecule converted
#1 info messages 25 audit log messages

# Correct:
echo 'O' |  babel -i smi - -s 'Nc1ncnc2c1ncn2C1C=C=CO1' -o smi -
#0 molecules converted

--
IPB Halle                    AG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann          http://www.IPB-Halle.DE
Weinberg 3                   http://msbi.bic-gh.de
06120 Halle                  Tel. +49 (0) 345 5582 - 1470
                                  +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409


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Re: Creating SMARTS from SMILES/InChI's - depends on canonical SMILES ?

Steffen Neumann
On Mon, 2010-09-13 at 09:14 +0200, Steffen Neumann wrote:
...
> Did I miss anything, or should I open a bug ?
Added as #3065756

Yours,
Steffen

--
IPB Halle                    AG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann          http://www.IPB-Halle.DE
Weinberg 3                   http://msbi.bic-gh.de
06120 Halle                  Tel. +49 (0) 345 5582 - 1470
                                  +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409



------------------------------------------------------------------------------
Start uncovering the many advantages of virtual appliances
and start using them to simplify application deployment and
accelerate your shift to cloud computing.
http://p.sf.net/sfu/novell-sfdev2dev
_______________________________________________
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