Working with a fresh OpenBabel 2.2.3 installation... There are no diferences related with BABEL* variables, they are not defined. PATH: i "force" to run the same executable (there is one babel installation at this time), and i retrieve different outputs with different users.
A problem detected: with a non-root user, i retrieve a "formats is not a recognized plugin type" with babel -H command --- --- ---With a non-root user, /usr/local/bin/babel -H Open Babel converts chemical structures from one file format to another Usage: babel <input spec> <output spec> [Options] Conversion options -f <#> Start import at molecule # specified -l <#> End import at molecule # specified -e Continue with next object after error, if possible -z Compress the output with gzip -k Attempt to translate keywords -H Outputs this help text -Hxxx (xxx is file format ID e.g. -Hcml) gives format info -Hall Outputs details of all formats -V Outputs version number -L <BaseType> Lists plugin classes of this type e.g. <fingerprints>, or <plugins> for a list of BaseTypes -m Produces multiple output files, to allow: Splitting: e.g. babel infile.mol new.smi -m puts each molecule into new1.smi new2.smi etc Batch conversion: e.g. babel *.mol -osmi -m converts each input file to a .smi file The following file formats are recognized: formats is not a recognized plugin type [<= HERE HERE HERE] Those with instances of sub-types loaded are: descriptors fingerprints forcefields loaders ops See further specific info and options using -H<format-type>, e.g. -Hcml El mié, 24-03-2010 a las 07:09 -0700, Craig A. James escribió: > On 3/24/10 2:24 AM, David García Aristegui wrote: > > Same input file prop.smi (CCC), and in the examples of my user > prop.smi > > is owned by "aristegui" > > > > With root: > > > > r...@thema:/tmp/test_dir_1# babel --gen3D -ismi prop.smi -osdf > prop.sdf > > 1 molecule converted > > 1 info messages 55 audit log messages 1 debugging messages > > > > and a proper prop.sdf with 3D coordinates is generated > > > > With my user: > > > > ariste...@thema:/tmp/test_dir_2$ /usr/bin/babel --gen3D -ismi > prop.smi > > -osdf prop.sdf > > > > babel: cannot read input format! > > Open Babel 2.2.0 -- Jul 17 2008 -- 11:53:19 > > Usage: babel [-i<input-type>]<name> [-o<output-type>]<name> > > Try -H option for more information. > > > > ariste...@thema:/tmp/test_dir_2$ /usr/local/bin/babel --gen3D -ismi > > prop.smi -osdf prop.sdf > > > > babel: cannot read input format! > > Open Babel 2.2.3 -- Jan 18 2010 -- 13:11:01 > > Usage: babel [-i<input-type>]<name> [-o<output-type>]<name> > > Try -H option for more information. > > > > babel: cannot read input format! > > Open Babel 2.2.0 -- Jul 17 2008 -- 11:53:19 > > Usage: babel [-i<input-type>]<name> [-o<output-type>]<name> > > Try -H option for more information. > > > > Thank you for your help!!! > > > > El mar, 23-03-2010 a las 20:39 +0100, Tim Vandermeersch escribió: > >> On Tue, Mar 23, 2010 at 8:08 PM, David GarcÃa Aristegui > >> <ariste...@cbm.uam.es> wrote: > >>> Hello, OB is installed on /usr/bin/babel /usr/local/bin/babel > >>> The BABEL_LIBDIR is not set (for root or the others). > >> > >> Sorry for all the questions, but it's hard to guess what's wrong... > >> > >> Do you have two versions of OB installed? > >> Does "/usr/bin/babel -H" produce the same results as > >> "/usr/local/bin/babel -H"? > >> Does /usr/local/bin versus /usr/bin have the same priority for > user& > >> root? (i.e. are they in the same order in PATH env. var.) > >> > >>> Best regards. > >>> > >>> El mar, 23-03-2010 a las 20:03 +0100, Tim Vandermeersch escribió: > >>>> Hi, > >>>> > >>>> On Tue, Mar 23, 2010 at 7:29 PM, David GarcÃa Aristegui > >>>> <ariste...@cbm.uam.es> wrote: > >>>>> Hello, i have a strange problem with non-root users and > >> OpenBabel, > >>>> and > >>>>> tested with two different versions of the program: > >>>>> > >>>>> Open Babel 2.2.3 -- Jan 18 2010 > >>>>> Open Babel 2.2.0 -- Jul 17 2008 > >>>>> > >>>>> OB is installed in a PC with Ubuntu 8x (Hardy Neron) > >>>>> Linux 2.6.27-14-server (the root account is activated). > >>>>> > >>>>> My problem: with non-root users i always retrieve an > >>>>> "babel: cannot read input format!" error, even if the file is > > As root, then a regular user, type: > > env | sort > > and look for differences. The environment variables of interest are > > BABEL_* (any variable with BABEL_ prefix) > LD_LIBRARY_PATH > PATH > > Or alternatively, look for these same variables in your > shell-initialization scripts (.cshrc for csh, .bash_profile > and .bash_rc for bash, but I don't remember which one Cygwin uses). > > Craig > ------------------------------------------------------------------------------ Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss