"Open Babel Error in LoadAllPlugins" Error

Cheminformatics Tutorials - Herong's Tutorial Examples

∟Open Babel: The Open Source Chemistry Toolbox

∟"Open Babel Error in LoadAllPlugins" Error

This section provides a tutorial example on how to resolve the 'Open Babel Error in LoadAllPlugins' error by adding the the BABEL_LIBDIR environment variable.

If you installed Open Babel from binary packages or source code files, you may see some errors when using Open Babel programs. Here is an example with Open Babel 3.1.1 on my CentOS system.

1. Check Open Babel installations.

herong$ dnf list installed | grep openbabel
  openbabel.x86_64        3.1.1-14.el8   @epel        
  openbabel-libs.x86_64   3.1.1-14.el8   @epel  

herong$ /usr/bin/obabel -V
  Open Babel 3.1.1 -- Sep 27 2022 -- 18:26:52

2. Generate the molecule structure in SVG format from a SMILES string.

herong$ /usr/bin/obabel -:c1ccccc1 -O out.svg
  1 molecule converted

3. Try to generate the molecule structure in SDF format from a SMILES string. I got an error.

herong$ /usr/bin/obabel -:c1ccccc1 -O out.sdf

*** Open Babel Error  in LoadAllPlugins
Unable to find OpenBabel plugins. Try setting the BABEL_LIBDIR environment variable. 
Missing or unknown output file or format spec or possibly a misplaced option. 
Options, other than -i -o -O -m, must come after the input files.

Open Babel 3.1.1 -- Sep 27 2022 -- 18:26:52
Usage:
obabel [-i<input-type>] <infilename> [-o<output-type>] -O<outfilename>
Try  -H option for more information.

4. Try to get help on the SDF format. I got an error.

herong$ /usr/bin/obabel -H sdf 
==============================
*** Open Babel Error  in LoadAllPlugins
Unable to find OpenBabel plugins. Try setting the BABEL_LIBDIR environment variable.
Format type:  was not recognized

5. Read the "Install Open Babel" document at https://openbabel.org/docs/dev/_sources/Installation/install.txt again. It contains the following question and answer:

What environment variables affect how Open Babel finds formats, plugins 
and libraries?

**LD_LIBRARY_PATH** - Used to find the :file:`libopenbabel.so` file.
  You should set this if you get error messages about not being able to 
  find :file:`libopenbabel.so`.

**BABEL_LIBDIR** - Used to find plugins such as the file formats
  If ``obabel -L formats`` does not list any file formats, then you need 
  to set this environment variable to the directory where the file formats 
  were installed, typically :file:`/usr/local/lib/openbabel/`.

**BABEL_DATADIR** - Used to find data files for fingerprints, forcefields,
  If you get errors about not being able to find some .txt files, then 
  you should set this to the name of the folder containing files such 
  as :file:`patterns.txt` and :file:`MACCS.txt`. These are typically 
  installed to :file:`/usr/local/share/openbabel`.

6. Locate the directory where file formats are installed.

herong$ rpm --query --list openbabel-libs

/usr/lib/.build-id
/usr/lib/.build-id/04
/usr/lib/.build-id/04/e9628013432e170e279512912c3f3c5cf50d58
/usr/lib/.build-id/0b
/usr/lib/.build-id/0b/c9fad959fb351db3b8df25cb4a44a8b112582f
...
/usr/lib64/libinchi.so.0
/usr/lib64/libinchi.so.0.4.1
/usr/lib64/libopenbabel.so.7.0.0
/usr/lib64/openbabel
/usr/lib64/openbabel/APIInterface.so
/usr/lib64/openbabel/CSRformat.so
/usr/lib64/openbabel/MCDLformat.so
/usr/lib64/openbabel/MNAformat.so
/usr/lib64/openbabel/PQSformat.so
...
/usr/lib64/openbabel/mdlformat.so
/usr/lib64/openbabel/mmcifformat.so
/usr/lib64/openbabel/mmodformat.so
/usr/lib64/openbabel/mol2format.so
...
/usr/lib64/openbabel/smilesformat.so
/usr/lib64/openbabel/smileyformat.so
/usr/lib64/openbabel/stlformat.so
/usr/lib64/openbabel/svgformat.so
...
/usr/share/doc/openbabel-libs
/usr/share/doc/openbabel-libs/AUTHORS
/usr/share/licenses/openbabel-libs/inchi-license-lgpl-2.1.txt
/usr/share/openbabel
/usr/share/openbabel/3.1.1
/usr/share/openbabel/3.1.1/MACCS.txt
/usr/share/openbabel/3.1.1/SMARTS_InteLigand.txt
/usr/share/openbabel/3.1.1/UFF.prm
...
/usr/share/openbabel/3.1.1/svgformat.script
/usr/share/openbabel/3.1.1/templates.sdf
/usr/share/openbabel/3.1.1/torlib.txt
/usr/share/openbabel/3.1.1/torsion.txt
/usr/share/openbabel/3.1.1/types.txt

7. Add BABEL_LIBDIR environment variable and generate SDF files again.

herong$ export BABEL_LIBDIR="/usr/lib64/openbabel/"

herong$ /usr/bin/obabel -:c1ccccc1 -O out.sdf --gen2D
1 molecule converted

herong$ /usr/bin/obabel "-:c1cc(ccc1CC(C(=O)O)N)O" -O tyrosine.sdf --gen3D
1 molecule converted

As you can see, the "Open Babel Error in LoadAllPlugins" error is resolved now. If you see other errors, you may need to set all 3 environment variables LD_LIBRARY_PATH, BABEL_LIBDIR and BABEL_DATADIR.

If you want to make "obabel" command available at /usr/local/bin/obabel, you can create a shell script there.

herong$ sudo vi /usr/local/bin/obabel
export BABEL_LIBDIR="/usr/share/openbabel/3.1.1"
source /usr/bin/obabel $1 $2 $3 $4 $5 $6 $7 $8

herong$ sudo chmod 755 /usr/local/bin/obabel