Thanks for your answer
The 3 first first lines are a single commented line (wrapped by the mailer)
I make progresses slowly the question is mostly "why is that working as a
command line under OsX and not Windows ? " and "why is that failing in a c++
call ?"
Thanks again
Dominique
---------------------------------------------------------------------
Dominique Massiot
Directeur CEMHTI-CNRS
http://cemhti.cnrs-orleans.fr <http://cemhti.cnrs-orleans.fr>
Directeur TGIR RMN Très Hauts Champs FR3050
http://www.tgir-rmn.org <http://www.tgir-rmn.org> /
Délégué Scientifique INC pour l'Interdisciplinarité
http://www.cnrs.fr/inc
1D avenue de la Recherche Scientifique
45071 Orléans cedex 2
France
tel[+33](0)238 25 55 18
fax[+33](0)238 63 81 03
e-mail : dominique.mass...@cnrs-orleans.fr
<mailto:dominique.mass...@cnrs-orleans.fr>
---------------------------------------------------------------------
De : Miguel Quirós Olozábal <mqui...@ugr.es>
Date : lundi 25 juin 2012 13:22
À : Dominique Massiot <dominique.mass...@cnrs-orleans.fr>
Cc : <openbabel-discuss@lists.sourceforge.net>
Objet : Re: [Open Babel] Converting CIF to XYZ - various errors commandline
or program call
El lun, 25-06-2012 a las 10:42 +0200, Dominique Massiot escribió:
> I am using Open Babel 2.3.1 on OsX and Windows and have various errors
> converting a cif file CIF to XYZ.
>
>
> Convert is done properly on OsX command line but fails in Windows
> commandline or program call OsX
>
>
> Advices or comments are welcome
>
>
> Thanks in advance
>
>
> -----------------
>
>
> Command line : obabel "obabel RbLaF4_Short.cif oxyz"
> OsX command line :
> conversion is done properly
> Windows commandline :
> C:\Users\massiot.CEMHTI\Dropbox\EXAVIZ\CIF Simple Examples>obabel
> RbLaF4_Short.c
> if -oxyz
> ==============================
> *** Open Babel Warning in OpenBabel::OBGlobalDataBase::Init
> Unable to open data file 'space-groups.txt'
> ==============================
> *** Open Babel Warning in OpenBabel::OBGlobalDataBase::Init
> Cannot initialize database
> ==============================
> *** Open Babel Warning in OpenBabel::SpaceGroup::Find
> Unknown space group (HM:,Hall:) with incomplete or wrong definition.
> ==============================
> *** Open Babel Warning in OpenBabel::CIFData::ExtractSpacegroup
> CIF Error: missing spacegroup description: defaulting to P1... (in
> data block:
> )
>
>
> OsX C++ program (runs properly for CML /SDF conversion
> Reads no molecules
>
>
>
> /Users/dominiquemassiot/Dropbox/EXAVIZ/OpenBabelCommandLine/build/Debug/OpenBa
> belCommandLine
>
> Test with link to OpenBabel
>
> ---------------------------
>
> Usage: ProgrameName InputFileName OutputFileName
>
> use default values for test
>
> Input file '/Users/dominiquemassiot/Dropbox/EXAVIZ/CIF Simple
> Examples/RbLaF4_Short.cif'
>
> Output file '/Users/dominiquemassiot/Dropbox/EXAVIZ/CIF Simple
> Examples/RbLaF4_Short.xyz'
>
> ==============================
>
> *** Open Babel Warning in ReadMolecule
>
> Problems reading a CIF file: no structure found !
>
> 0 molecules converted
>
> end
>
>
> Following is the CIF input file (very basic) RbLaF4_Short.cif
> ------------------
> # from //Crmht_10/Users/Mathieu
> ALLIX/1-Collaborations/ALR/LaRbF4/Publi LaRbF4/Affinement
> Publi/FINAL_COMBINED_WEIGHING250_TTANISO.EXP
> _audit_creation_date 2010-11-30T09:39:12
> _symmetry_space_group_name_H-M 'P n m a'
> _cell_length_a 6.462812
> _cell_length_b 3.864979
> _cell_length_c 16.176291
> _cell_angle_alpha 90.0000
> _cell_angle_beta 90.0000
> _cell_angle_gamma 90.0000
> loop_
> _atom_site_label
> _atom_site_type_symbol
> _atom_site_fract_x
> _atom_site_fract_y
> _atom_site_fract_z
> _atom_site_B_iso_or_equiv
> _atom_site_occupancy
> Rb RB+1 0.27509 0.75000 0.20070 0.713768584496 1.00000
> La1 LA+3 0.25179 0.25000 0.44119 0.535326438372 1.00000
> F1 F-1 0.13392 0.25000 0.03695 0.646892258051 1.00000
> F2 F-1 0.00067 0.75000 0.44397 0.706741438034 1.00000
> F3 F-1 0.39137 0.75000 0.36973 1.17724442421 1.00000
> F4 F-1 0.09340 0.25000 0.31114 1.19564133573 1.00000
> ------------------
>
Hello.
Looks like the data_ line at the beginning of the CIF file is missing.
If the two first line are comment inside the file they should be
preceded by a #.
Also symmetry operators are not present (not sure it they are neccessary
for the conversion, perhaps no). Also I would try put the element
symbols without charges (i.e. La instead of La+3).
Good luck.
--
Miguel Quirós Olozábal
Departamento de Química Inorgánica. Facultad de Ciencias.
Universidad de Granada. 18071 Granada. SPAIN.
email: mquiros<at>ugr<dot>es
mquiros<arroba>ugr<punto>es
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