[Cod-bugs] update suggest cod-tools, bash script molcif2sdf

Antanas Vaitkus antanas.vaitkus90 at gmail.com
Fri May 8 16:28:39 EEST 2020


Dear Norwid,

thank you for the report. It seems strange that the script did not work on
your system, since 'babel' is an old version of 'obabel' [1] which still
comes
packaged with the Debian 10 installation of the 'openbabel' package [2].

However, I do agree with your suggestion to replace 'babel' with 'obabel'
since the same approach is also suggested by the openbabel developers [2].
This change will be included in the next release of 'cod-tools'.

[1] https://openbabel.org/docs/dev/Command-line_tools/babel.html
[2] https://packages.debian.org/buster/openbabel

Sincerely,
Antanas

On Thu, 7 May 2020 at 22:21, Norwid Behrnd <nbehrnd at yahoo.com> wrote:

> Dear Ladies and Gentlemen,
>
> based on an observation I would like to suggest an update of bash
> script molcif2sdf (last public edit by 2019-12-06) at line #114; namely,
> the substitution of «babel» by «obabel»
>
>
> During a session of Linux Debian 10, backed by openbabel (release
> 3.0.0), I aimed for the conversion of file 1501905.cif into a .sdf
> suitable for DataWarrior with cod-tools' codcif2sdf.  The conversion
> failed and indicated bash script molcif2sdf as possible cause:
>
> norwid at carnot2:~/Desktop$ codcif2sdf 1501905.cif
> /usr/bin/cif_molecule: 1501905.cif data_1501905: WARNING, multiplicity
> ratios are given instead of multiplicities for 61 atoms -- taking
> calculated values.
> /usr/bin/molcif2sdf: 114: babel: not found
> norwid at carnot2:~/Desktop$ codcif2sdf --version
> cod-tools version 2.10
>
>
> A fresh re-installation from Debian's testing repositories did not
> improve the situation, by label they are the same as the tools offered
> by your page as tar.gz.  Tentatively, I substituted «babel» by «obabel»
> in line #114 of molcif2sdf and found obtained the .sdf as expected.
>
> norwid at carnot2:~/Desktop$ codcif2sdf 1501905.cif > so.sdf
> /usr/bin/cif_molecule: 1501905.cif data_1501905: WARNING, multiplicity
> ratios are given instead of multiplicities for 61 atoms -- taking
> calculated values. 1 molecule converted
> norwid at carnot2:~/Desktop$
>
> Starting .cif, successfully converted .sdf and modified bash script,
> each appended by .txt to pass the email, are provided as attachment to
> this email.
>
> With best regards,
>
> Norwid Behrnd
>
>  ---- 8>< ---- md5sum ---- ---- attached file ----
> d5dac2ef4c96a1c852e34c58e052c48b  1501905.cif.txt
> 5946d1cd9694511d76007cd3c9458cb5  so.sdf.txt
> 1daf86169048b51a20ef808805569b6c  molcif2sdf_modified_line_114.txt
>  ----
>
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-- 
Antanas Vaitkus,
PhD student at Vilnius University Institute of Biotechnology,
room V325, Saulėtekio al. 7,
LT-10257 Vilnius, Lithuania

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