Creating OEDesignUnits from a PDB file

Preparation of a biological structure file (PDB, mmCIF) to a fully charged, hydrogenated, molecular componentized object (design unit; DU; OEDesignUnit) is one of the more advanced functionalities offered through Spruce TK. This example shows how to construct DUs using an input PDB file and the OEMakeDesignUnits function.

Command Line Interface

This example uses an input PDB file, and will output a set of DUs from it to a temporary directory (see OEMakeDesignUnits for details on the API).

prompt> make_design_units <input biomolecular PDB>

Code

Download code

make_design_units.py and 3tpp.pdb (the input PDB file)

Example

prompt> make_design_units.py 3tpp.pdb

will generate the following output:

DPI: 0.06, RFree: 0.18, Resolution: 1.60
Warning: Passing molecule through: no tautomer score for  OS(=O)(=O)O

Processing BU # 0 with title: BETA-SECRETASE 1
Warning: For residue ARG -4   A 1   removing clashing solvent molecule HOH 532   A 2
Warning: For residue ARG -4   A 1   removing clashing solvent molecule HOH 737   A 2
Warning: For residue ARG 7   A 1   removing clashing solvent molecule HOH 498   A 2
Warning: For residue ARG 7   A 1   removing clashing solvent molecule HOH 730   A 2
Warning: For residue ARG 7   A 1   removing clashing solvent molecule HOH 653   A 2
Warning: For residue ARG 128   A 1   removing clashing solvent molecule HOH 523   A 2
Warning: For residue ARG 128   A 1   removing clashing solvent molecule HOH 654   A 2
Warning: For residue LYS 142   A 1   removing clashing solvent molecule HOH 550   A 2
Warning: For residue LYS 142   A 1   removing clashing solvent molecule HOH 691   A 2
Warning: For residue ARG 205   A 1   removing clashing solvent molecule HOH 423   A 2
Warning: For residue ARG 205   A 1   removing clashing solvent molecule HOH 703   A 2
Warning: For residue LYS 256   A 1   removing clashing solvent molecule HOH 604 A A 1
DU: BETA-SECRETASE 1(A) > 5HA(A-999), Iridium Category: NA, LaD: 0.00, ASaD: 0.00, DPI: 0.06, POL: false, POAS: false, AltConfs: false, PackRes: false, Excp: false, IrrRFree: false, PossCov: false

Writing design unit 0 to /tmp/tmpw6_1wocm/3tpp_DU_0.oedu

See also