Finding pockets and their properties (like, Surface Area) from a PDB file¶

This example shows how to find pockets in an input PDB file using the OEFindPockets function. OEDesignUnit file (OEDesignUnit) can also be used as input to find the pockets.

Command Line Interface¶

This example uses an input PDB file, and will print surface area and list of residues for each found pocket in given PDB file.

prompt> findpockets <input protein molecule or DesignUnit file>

Code¶

Download code

findpockets.cpp and the 7mhf.pdb (the input PDB file),

Example¶

prompt> findpockets 7mhf.pdb

will generate the following output:

pockets count: 1
pocket_1Residues count: 22
pocket_1Residues:
HOH 623
GLY 143
ASN 142
HOH 502
DMS 404
MET 165
HOH 624
ASP 187
HOH 671
HOH 655
HOH 589
MET 49
HOH 782
ARG 188
THR 25
HIS 41
GLN 189
CYS 44
HOH 750
HOH 548
THR 45
SER 46
pocket_1 Surface Area: 211.091