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
Distribute Jobs

Distributes a set of serial jobs to the desired host(s) using Job Control.

distribute_jobs.py
None
Compute Active Site Residue Identity and Homology

Takes a set of aligned proteins and computes the residue similarity and homology between the active sites of each structure.

active_site_identity.py
None
Command Line RMSD Calculation

Calculates the RMSD and maximum atom displacement between a pair of files. Options allow ASL selections and the ability to do either in-place or mobile RMSD.

rmsd.py
None
Merge CSV Properties into a Maestro File

Merge properties from a CSV file into a structure file and generate a new Maestro file. The structure file may be Maestro (including PV) or SDF format.

merge_csv_mae.py
None
Calculate Properties

Script for calculating various properties for the input structures, and adding a CT-level property for each.

calculate_properties.py
None
Measure by SMARTS

Measures distances, angles, or dihedral angles of substructures defined by the SMARTS pattern.

measure_by_smarts.py
None
WaterMap Kinetics

A script to identify those WaterMap hydration sites that are displaced by a ligand and calculate the various water transfer energies based on the criteria as described by Pearlstein et al., Proteins: Structure, Function, and Bioinformatics (2010), 78, 2571.

watermap_kinetics.py
WaterMap
Scale Simulation Box

Script for scaling the size of the simulation box and the coordinates.

This script scales the box size and the coordinates without regard for intramolecular constraints. The box shape is assumed to be orthorhombic. Three scaling methods are supported in order of precedence. 1. using an average volume per particle. 2. using separate scaling factors for the a, b, and c box vectors. 3. using a common scaling factor for the a, b, and c box vectors. Scaling factors are determined for the first structure in the file and then applied to all subsequent structures.

The output structure file is overwritten if it already exists.

scale_simulation_box.py
None
Integrate WaterMap

Script to integrate the thermodynamic properties of the hydration sites within the specified integration radius.

This script will integrate the thermodynamic properties of the hydration sites within the specified integration radius. The input files(s) should be either a single *wm.maegz file for a discrete approximation, or three *continuous*.cns files containing dH, -TdS and dH grid potential values for a continuous approximation.

integrate_wm.py
WaterMap
Compare Similar Proteins

Generates table for protein comparative structure analysis. Takes more than one Maestro or PDB file as input and generates a csv file.

compare_similar_proteins.py
None