Scripts


All of the scripts listed on this page come pre-bundled with the latest Schrödinger Software release. To use any of these scripts simply use the following instructions:

Linux - In a Terminal Window type: $SCHRODINGER/run <script.py> -h
Mac - In a Terminal Window type: $SCHRODINGER/run <script.py> -h (Note: $SCHRODINGER Environment Variable must be set)
Windows - In a Schrödinger PowerShell Window or in the Schrödinger Command Prompt type: run <script.py> -h

For more information, please visit Knowledge Base Article 37 or view our Documentation on Running Jobs From the Command Line.
Script Requires
XP Atom Energies

Adds Glide XP terms from .xpdes file to a Maestro file as atom-level properties. These properties can be used to color and visualize atoms by the values.

xp_atom_energies.py
Glide
Create or Convert Pose Viewer Files

Converts pose viewer files into a series of complexes, and convert complexes into ligand-only, receptor-only, or pose viewer files.

pv_convert.py
None
Compute Entropy Associated with Each Energy Well

Computes a modified docking score based on work by A.M. Ruvinsky using the number of poses within each energy well. Poses are first clustered and then the entropy is computed for each cluster. Input poses should come from Glide saving 100 poses per ligand. The criteria for duplicate pose elimination should be reduced to zero (in the Clustering section under Advanced options in the Output tab of the Glide Docking panel) in order to ensure a full sampling of each energy well.

pose_entropy.py
Glide
Glide Cross Docking

Glide cross-docking application. Takes ligands, receptors, complexes, and grids as input. Generates grids for receptors and complexes, docks all ligands (including those from complexes) into all grids, and calculates RMSDs for docked ligand poses compared to their input references.

xglide.py
Glide
Print Grid Constraints

Print the constraints defined in a Glide grid (.grd or .zip).

print_grid_constraints.py
Glide
Sitemap Difference Maps

Given 2 SiteMap outputs, and for each result pair, generates a union of SiteMap points and surfaces, or optionally difference between them.

sitemap_difference_maps.py
SiteMap
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