Bugs item #2923406, was opened at 2009-12-30 09:47
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Category: Command-line Tools
Group: 2.2.x
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Nobody/Anonymous (nobody)
Assigned to: Nobody/Anonymous (nobody)
Summary: Current openbabel install is non-functional for 10.6.2
Initial Comment:
The installer on the main site, used to install a fresh copy of openbabel on a
virgin 10.6.2 machine appears to install a broken version of openbabel that
appears to not be able to do anything. Additionally, babel mysteriously
reports it's version as 2.2.3
For example :
babel -H returns: (note the file formats supported)
Open Babel converts chemical structures from one file format to another
Usage: babel <input spec> <output spec> [Options]
Each spec can be a file whose extension decides the format.
Optionally the format can be specified by preceding the file by
-i<format-type> e.g. -icml, for input and -o<format-type> for output
See below for available format-types, which are the same as the
file extensions and are case independent.
If no input or output file is given stdin or stdout are used instead.
More than one input file can be specified and their names can contain
wildcard chars (* and ?).The molecules are aggregated in the output file.
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. Those with instances of sub-types
loaded are:
descriptors
fingerprints
forcefields
loaders
ops
When I try to use it for any common file types such as mol or cdx, it claims it
can either not read input file or write output file.
What's going on here ? Have I royally borked something somehow ? Install is
via the .pkg for 2.2.3 on the main wiki page.
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