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
>
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