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

[Norwid Behrnd]

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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