#576 CIF read crashes when _geom_bond_distance values start with decimal dot

[Andrius Merkys]

Jmol (as of SVN revision 21035) seems to crash when values of _geom_bond_distance CIF tag do not have initial digit (i.e. ".93(2)"), however, such values are valid CIF numbers.

Example of a real CIF file: http://www.crystallography.net/cod/2009633.cif@31976. After adding missing zeros to the values of _geom_bond_distance the file is read correctly.

[Bob Hanson]

Jmol.___JmolVersion="14.5.4_2016.03.30"

bug fix: _geom_bond_distance starting with "." halts CIF file reading

Will appear first as
http://chemapps.stolaf.edu/jmol/zip/jmol-14.5.4_2016.03.30.zip

BTW, not that it matters, but is there some particular reason the space
group information is at the end of the file? That's quite odd.
​

[Andrius Merkys]

Thanks for the prompt fix!

As for 2009633.cif, it seems that the symmetry information was derived later and appended to the end of the file. As far as I know, the order of tags in CIFs is not important (as in data hashes of JSON, Perl and PHP), thus such file is perfectly valid, although it's layout seems unusual.

[Bob Hanson]

Jmol.___JmolVersion="14.4.4_2016.03.31"
released

bug fix: _geom_bond_distance starting with "." halts CIF file reading

Looking for the latest version? * Download
Jmol-14.4.4_2016.03.31-binary.zip (61.3 MB)
https://sourceforge.net/projects/jmol/files/latest/download?source=files*

On Thu, Mar 31, 2016 at 1:25 AM, Andrius Merkys merkys@users.sf.net wrote:

Thanks for the prompt fix!

As for 2009633.cif, it seems that the symmetry information was derived
later and appended to the end of the file. As far as I know, the order of
tags in CIFs is not important (as in data hashes of JSON, Perl and PHP),
thus such file is perfectly valid, although it's layout seems unusual.

---

• [bugs:#576] https://sourceforge.net/p/jmol/bugs/576/ CIF read crashes
  when _geom_bond_distance values start with decimal dot*

Status: open
Group: v10
Labels: CIF
Created: Wed Mar 30, 2016 01:47 PM UTC by Andrius Merkys
Last Updated: Wed Mar 30, 2016 01:47 PM UTC
Owner: nobody

Jmol (as of SVN revision 21035) seems to crash when values of
_geom_bond_distance CIF tag do not have initial digit (i.e. ".93(2)"),
however, such values are valid CIF numbers.

Example of a real CIF file:
http://www.crystallography.net/cod/2009633.cif@31976. After adding
missing zeros to the values of _geom_bond_distance the file is read
correctly.

---

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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr

If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900