Install Open Babel 2.4.1 from Source Code

Cheminformatics Tutorials - Herong's Tutorial Examples

∟Open Babel: The Open Source Chemistry Toolbox

∟Install Open Babel 2.4.1 from Source Code

This section provides a tutorial example on how to install Open Babel 2.4.1 from source code on CentOS 8 computers.

If for some reason, you have trouble to install Open Babel latest release from source code, you can try to install Open Babel 2.4.1 from source code on CentOS 8 as shown in this tutorial.

1. Go to Open Babel Code Repository at https://sourceforge.net/projects/openbabel/.

2. Open "Files > openbabel / 2.4.1" folder. And download openbabel-2.4.1.tar.gz.

3. Unzip and untar the download file. You should see a directory openbabel-2.4.1 with all source code.

4. Create a "build" sub-directory and configure the build system.

herong$ cd openbabel-2.4.1/

herong$ mkdir build
herong$ cd build

herong$ cmake ..
...
-- Checking for module 'cairo'
--   Package 'cairo', required by 'virtual:world', not found
-- Could NOT find Cairo (missing: CAIRO_LIBRARIES CAIRO_INCLUDE_DIRS)
-- Could NOT find Cairo. PNG output will NOT be supported.
...
-- Configuring done
-- Generating done
-- Build files have been written to: /home/herong/openbabel-2.4.1/build

5. Run the build process.

herong$ make -j2
Scanning dependencies of target inchi
Scanning dependencies of target openbabel
[  0%] Building CXX object src/CMakeFiles/openbabel.dir/alias.o
[  0%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/ichi_bns.o
[  0%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/ichi_io.o
...
[100%] Building CXX object test/CMakeFiles/test_runner.dir/unitcell.o
[100%] Building CXX object test/CMakeFiles/test_runner.dir/obtest.o
[100%] Linking CXX executable ../bin/test_runner
[100%] Built target test_runner

6. Run tests on the build result. You may see some failures.

herong$ make test
Running tests...
Test project /home/herong/openbabel-2.4.1/build
        Start   1: test_automorphism_1
  1/151 Test   #1: test_automorphism_1 ..............   Passed    0.01 sec
        Start   2: test_automorphism_2
  2/151 Test   #2: test_automorphism_2 ..............   Passed    0.01 sec
        Start   3: test_automorphism_3
        ...
150/151 Test #150: pytest_kekule ....................   Passed    0.32 sec
        Start 151: pytest_pdbformat
151/151 Test #151: pytest_pdbformat .................***Failed    0.03 sec

94% tests passed, 9 tests failed out of 151
Total Test time (real) =  21.85 sec

The following tests FAILED:
   42 - test_gzip_1 (Failed)
   53 - test_isomorphism_5 (Failed)
   54 - test_isomorphism_6 (Failed)
   57 - test_multicml_1 (Failed)
   64 - test_rotor_2 (Failed)
   65 - test_rotor_3 (Failed)
   66 - test_rotor_4 (Failed)
  146 - pytest_sym (Failed)
  151 - pytest_pdbformat (Failed)
Errors while running CTest
make: *** [Makefile:73: test] Error 8

7. Build final installation targets and install them to the default system location.

herong$ sudo make install
[ 14%] Built target openbabel
[ 16%] Built target plugin_descriptors
...
[100%] Built target test_runner
[100%] Built target roundtrip
Install the project...
-- Install configuration: "RelWithDebInfo"
-- Installing: /usr/local/include/openbabel-2.0/openbabel/babelconfig.h
-- Installing: /usr/local/lib/pkgconfig/openbabel-2.0.pc
...
-- Installing: /usr/local/bin/obgrep
-- Set runtime path of "/usr/local/bin/obgrep" to "/usr/local/lib"
-- Installing: /usr/local/bin/roundtrip
-- Set runtime path of "/usr/local/bin/roundtrip" to "/usr/local/lib"

7. Verify installation.

herong$ babel -V
Open Babel 2.4.1 -- May 25 2020 -- 08:24:13

8. Verify all commands provided by Open Babel.

herong$ cd /usr/local/bin
herong$ ls -l o*

-rwxr-xr-x. 1 root root  38624 May 25  2020 obabel
-rwxr-xr-x. 1 root root 342800 May 25  2020 obchiral
-rwxr-xr-x. 1 root root  24928 May 25  2020 obconformer
-rwxr-xr-x. 1 root root  29456 May 25  2020 obenergy
-rwxr-xr-x. 1 root root  34304 May 25  2020 obfit
-rwxr-xr-x. 1 root root  34112 May 25  2020 obfitall
-rwxr-xr-x. 1 root root  30136 May 25  2020 obgen
-rwxr-xr-x. 1 root root  29120 May 25  2020 obgrep
-rwxr-xr-x. 1 root root  30440 May 25  2020 obminimize
-rwxr-xr-x. 1 root root  38600 May 25  2020 obmm
-rwxr-xr-x. 1 root root  35480 May 25  2020 obprobe
-rwxr-xr-x. 1 root root  34536 May 25  2020 obprop
-rwxr-xr-x. 1 root root  34280 May 25  2020 obrotamer
-rwxr-xr-x. 1 root root  28728 May 25  2020 obrotate
-rwxr-xr-x. 1 root root  75808 May 25  2020 obspectrophore
-rwxr-xr-x. 1 root root  23968 May 25  2020 obsym
-rwxr-xr-x. 1 root root  24776 May 25  2020 obtautomer
-rwxr-xr-x. 1 root root  24184 May 25  2020 obthermo