Re: [Joelib-help] joelib convert-calculateDescriptor

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

Dear JEAN-YVES,

> I'm still not exactly where I want with the joelib.
> I would like to generate a Text file with the native value descriptors
> corresponding to the structures in the SDF file.
> Running : sh convert.sh +d -oFLAT examples.SDF out.FLAT (I guess FLAT
> should be the correct format)
> Returns a file without any descriptors? (for the moment ,I get the results
> of the descriptor calculations only when choosing .SDF as output format.
 > When running  sh calculateDescriptor.sh +jcc examples.SDF out.FLAT
 > It returns an error message (even when adding -ap -SSKey).
 > -oFLAT seems also not to be recognized as a valid option.
Yes and no.
There are only 2 and 1/2 file formats which supports all possible 
descriptor types in JOELib, like values, arrays, matrices, atom-pairs 
and all the other stuff.

These file formats are:
SDF (import/export)
CML (import/export)
CTX (import only, CACTVS format of
              Wolf-Dietrich-Ihlenfeldt, Xchemistry GmbH
              Prof. Gasteiger, Molecular Networks)

So it is clear that it makes no sense to store all kind of descriptors 
in a flat file.

This explains your problems. Three solutions:

1. the default conversion mechanism requires a definition of the things 
to convert, so e.g. the SMILES and FLAT format have its definitions in 
joelib.properties.
If you want to change these settings you must change these properties 
there or you can change them by using the command line options.
I've added this option for the conversion mechanism only to the 
ConvertSkip-class, for which the shell script is convertSkip.sh

Here are the options and don't forget to quote these definitions.

  [+f<lineStructure>]     - Required if you use FLAT output format which 
other input format
  [+ff<lineStructureFile>]- Required if you use FLAT output format which 
other input format
  [+s<lineStructure>]     - Can be used for an alternate SMILES entry 
line structure

2. Use sh descSelection.sh
with flat-option and your preferred delimiter, this will be more or less 
analogue, but faster than the convertSkip routine.

3. Developer way. Calculate only the descriptors you need, so you can 
avoid temporary files :-)
For hints see the tutorial and all examples in joelib/test or write me 
an additional mail using the developer mailing list, then i can go into 
details. But the code i will give you there will be really similar to 
code fragments you can find in the joelib/test package.

Kind regards, Joerg


> 
> Best regards
> 
> Jean-Yves
> 
> 
> error message:
> 
> USING DEFAULT_ATOM_PROPERTIESUSING DEFAULT_ATOM_PROPERTIES15:50:36 [INFO ]
> joelib.test.DescriptorCalculation        - ... 115 molecules successful
> calculated in 242794 ms.15:50:36 [INFO ] joelib.test.DescriptorCalculation
> - Calculate binary SMARTS and fingerprints...15:50:36 [ERROR]
> joelib.io.types.MDLSD                    - Can not convert string 'Mol' to
> type 'int' in line: Molecule 2joelib.io.MoleculeIOException: Error in
> atom/bond definition line.        at
> joelib.io.types.MDLSD.readNumbers(MDLSD.java:1586)        at
> joelib.io.types.MDLSD.read(MDLSD.java:312)        at
> joelib.io.types.MDLSD.read(MDLSD.java:279)        at
> joelib.test.DescriptorCalculation.calculateNominalDescriptors(DescriptorCalculation.java:714)
>         at
> joelib.test.DescriptorCalculation.main(DescriptorCalculation.java:110)
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
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-- 
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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