The Windows error message are because your BABEL_DATADIR is not set correctly for OB2.3.1. The installer should have done it. Try "echo %BABEL_DATADIR%" at a command prompt.
- Noel On 25 June 2012 18:31, Dominique Massiot <dominique.mass...@cnrs-orleans.fr> wrote: > 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 > Directeur TGIR RMN Très Hauts Champs FR3050 > 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 > --------------------------------------------------------------------- > > > 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/OpenBabelCommandLine > 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 > > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
