"obabel -s ..." Command - Substructure Search

Cheminformatics Tutorials - Herong's Tutorial Examples

∟"obabel -s ..." Command - Substructure Search

This section provides a tutorial example on how to use 'obabel ... -s ...' command to do substructure search with Open Babel.

Substructure search is a common task in cheminformatics studies. The objective of substructure search is to evaluate whether or not a given molecule structure contains a given substructure pattern.

You can do substructure search with Open Babel using the "obabel ... -s ..." command with the following syntax:

babel input_section output_section -s smarts_string

The smarts_string specifies a SMARTS string that represents a molecule pattern. "obabel" command will apply this pattern to each molecule in the input data source. If the the pattern matches a substructure of the molecule, it will be written to the output. Otherwise, it will be skipped.

Substructure search is also called substructure filtering or substructure matching.

Here are some examples of substructure matching with a single atom as the molecule pattern:

herong$ # methane molecule contains an aliphatic carbon
herong$ obabel -:C -o smiles -s C
C
1 molecule converted

herong$ # methane molecule contains no aromatic carbon
herong$ obabel -:C -o smiles -s c
0 molecules converted

herong$ # benzene molecule contains an aromatic carbon
herong$ obabel -:c1ccccc1 -o smiles -s c
c1ccccc1
1 molecule converted

herong$ # benzene molecule contains no aliphatic carbon
herong$ obabel -:c1ccccc1 -o smiles -s C
0 molecules converted

Here is another group of examples of substructure matching with a single bond as the molecule pattern:

herong$ # tyrosine molecule contains a two-aromatic-carbon bond
herong$ obabel "-:c1cc(ccc1CC(C(=O)O)N)O" -o smiles -s cc
c1cc(ccc1CC(C(=O)O)N)O
1 molecule converted

herong$ # tyrosine molecule contains an aromatic-carbon-aliphatic-carbon bond
herong$ obabel "-:c1cc(ccc1CC(C(=O)O)N)O" -o smiles -s cC
c1cc(ccc1CC(C(=O)O)N)O
1 molecule converted

herong$ # tyrosine molecule contains no aromatic-carbon-nitrogen bond
herong$ obabel "-:c1cc(ccc1CC(C(=O)O)N)O" -o smiles -s cN
0 molecules converted

herong$ # tyrosine molecule contains an aliphatic-carbon-nitrogen bond
herong$ obabel "-:c1cc(ccc1CC(C(=O)O)N)O" -o smiles -s CN
c1cc(ccc1CC(C(=O)O)N)O
1 molecule converted