Generate Szmap points and probe orientations at ligand atoms

A program that generates 3D conformations of probe molecules and Szmap points at each ligand atom coordinate.

See also

• OESzmapEngine class

• OESzmapResults class

• OECalcSzmapValue function

• OEIsClashing function

• OEEnsemble namespace

• OEComponent namespace

Command Line Interface

A description of the command line interface can be obtained by executing the program with the –help argument.

prompt> java SzmapBestOrientations --help

will generate the following output:

Simple parameter list
 -l : Input ligand coordinates for calculations
 -o : Output file for points and probes molecules
 -p : Input protein (or other) context mol
 -prob : Cutoff for cumulative probability of probes

Code

Download code

SzmapBestOrientations.java

Examples

prompt> java SzmapBestOrientations -l 4std_lig.oeb.gz -p 4std_prot.oeb.gz -o SzmapBestOrientations.oeb.gz