Extracting Biounits from PDB Header Remarks

Biounit (BU) extraction is one of the more basic functionalities offered through the Spruce TK. This example shows how to extract BUs using the PDB header remarks.

Command Line Interface

This example takes in a PDB file, and optionally the maximum number of atoms to be considered a BU as well as a boolean flag to instruct the code to prefer author of software generated headers (see OEExtractBioUnits for details on the API).

prompt> extract_biounits_remarks <extract protein PDB> [max atoms] [prefer author]

Code

Download code

extract_biounits_remarks.py and 4re6.pdb (the extraction PDB file)

Example

prompt> extract_biounits_remarks.py 4re6.pdb

will generate the following output:

Writing biounit 0 to 4re6_BU_0.oeb.gz
Writing biounit 1 to 4re6_BU_1.oeb.gz

See also