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

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

Takes the <jobname>_match.csv file from a Scaffold Decomposition job and assigns structures to clusters according to their largest scaffold.

Given a match file <jobname>_match.csv from a Scaffold Decomposition job, this program produces a CSV file with structures clustered according to the largest scaffold they contain.
Shape Screen Cluster

This script is intended for use as a workflow for clustering based on shape_screen analysis (see usage example below). In addition to the shape_screen output files, clusters are written out as maestro files and a cluster_data.csv file containing the clusters as lists of structure titles.

Usage example: input.mae -JOB matrix -n 15
Shape Screening
Interaction Fingerprints

Provides a graphical interface to compute interaction fingerprints between a receptor and ligands similar to those described in Deng et al, J. Med Chem (2004), 47, 337.
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