Re: [Joelib-devel] adding columns to the smiles output of Convert

[Joerg K. W. <we...@in...>]

Dear John Beaver,

> I've gotten JoeLib to convert an SDF file to a Smiles file using the 
> Convert program, but what is the best way to modify the default Smiles 
> output? Specifically, there are extra data elements in the SDF file of 
> the form...
> 
>    > <element1Name>
>    element1Value
> 
> ...beyond that needed to generate the Smiles, that I'd like to output 
> unmodified as additional columns in the Smiles file:
> 
>    smileString   |   element1Value   |   element2Value   |   ...
> 
> Does JoeLib store these somewhere? Would I need to edit the source, or 
> is there a standard way of changing output columns, such as editing the 
> joelib.properies file?
Yes !

If you got the instance for the Smiles writer this will initialize the 
output format.
The property, which is loaded by default is
joelib.io.types.Smiles.lineStructure=SMILES|TITLE
in the joelib.properties file

So one possibility is to change your required output there directly.

I've also implemented a command line option for
convertSkip.sh (joelib.test.ConvertSkip class)
which is
[+s<lineStructure>]     - Can be used for an alternate SMILES entry line 
structure

Here you have to quote your definition correcctly.

Finally, you can write your own class using one of the examples given in 
joelib/test to modify things to your requirements. E.g. using a 
descriptor file or whatever ...

Kind regards, Joerg


-- 
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW:    http://www-ra.informatik.uni-tuebingen.de
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