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Open Babel/en: Difference between revisions
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It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. | It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. | ||
On our | For further information on how to use Open Babel, please refer to the | ||
[https://openbabel.org/docs/ Open Babel User Guide]. | |||
On our clusters we have two kinds of modules for Open Babel installed: | |||
== <code>openbabel</code> == | == <code>openbabel</code> == | ||
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Notes: | Notes: | ||
* The <code>wget</code> command downloads <code>acetic_acid.mol</code> as an example file. | * The <code>wget</code> command downloads <code>acetic_acid.mol</code> as an example file. | ||
* The <code>obabel</code> command converts | * The <code>obabel</code> command converts the molecule described in 'acetic_acid.mol' from <code>.mol</code> format to <code>.pdb</code> format. | ||
== <code>openbabel-omp</code> == | == <code>openbabel-omp</code> == | ||
This is the | This is the version of Open Babel which has OpenMP parallelization enabled. | ||
{{box|<b>This module should not be used on login nodes,</b><br> | {{box|<b>This module should not be used on login nodes,</b><br> | ||
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==== Example ==== | ==== Example ==== | ||
The following job | The following job takes the [https://en.wikipedia.org/wiki/Chemical_table_file#SDF Structural Data File] <code>many_molecules.sdf</code>, | ||
which in this case should contain a database with many molecules and | which in this case should contain a database with many molecules, and generates Canonical [https://en.wikipedia.org/wiki/Simplified_molecular-input_line-entry_system SMILES] representations for each of them, using two CPU-cores. | ||
{{File | {{File | ||
|name=parallel_openbabel_job.sh | |name=parallel_openbabel_job.sh | ||
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Open Babel's functionality can be used from other languages such as Python. | Open Babel's functionality can be used from other languages such as Python. | ||
The [https://openbabel.org/docs/UseTheLibrary/Python.html Python interface for Open Babel] has been added to the both <code>openbabel</code> and <code>openbabel-omp</code> modules as extensions. | The [https://openbabel.org/docs/UseTheLibrary/Python.html Python interface for Open Babel] has been added to the both <code>openbabel</code> and <code>openbabel-omp</code> modules as extensions. | ||
Therefore both the <code>openbabel</code> and <code>pybel</code> packages can be used after loading both openbabel and a compatible Python module. | Therefore both the <code>openbabel</code> and <code>pybel</code> packages can be used after loading both <code>openbabel</code> and a compatible Python module. | ||
==== Example ==== | ==== Example ==== | ||