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
Grid Generation from Poseviewer File

Generates a Glide grid from a poseviewer file. The ligand in the poseviewer file is used to determine the center of the Glide grid box.

grid_gen_from_pv.py
Glide
Create Glide Simplified Input File

Takes command line options and creates a Glide simplified input file (SIF).

glide_sif.py
Glide
Calculate Entropy

Calculates the entropy and Boltzmann-weighted energy (in kJ/mol) for a multi-entry file. The temperature (in K) can be adjusted and the relative energy property can be specified.

entropy_calc.py
None
Compare Ligand Ranks

Compare ranks of compounds in structure files that are ordered in ascending rank (best first).

pose_rank_and_rmsd_analysis.py
None
Split Structure by Substructure

Splits structures by chain, molecule, residue, ligand or PDB.

split_structure.py
None
Compute Ligand Volume

Computes the volume for each ligand or active site in a file.

volume_calc.py
None
Find Receptor-ligand Interactions

Detect interactions between a receptor and a set of ligands in a poseviewer file. The script lists each H-bond and contact (good, bad, or ugly) along with a summary reporting the number of ligands forming each kind of interaction with each receptor residue. The script also detects hydrophobic, salt-bridge, pi-cation, and pi-pi interactions.

poseviewer_interactions.py
None
Block-sort Glide Results

A command-line script for block-sorting Glide results, in which the results for each ligand are grouped and sorted by Emodel (HTVS/SP) or the XP pose rank, and then the ligand blocks are sorted according to the GlideScore of the top member.

glide_blocksort.py
Glide
Compute SASA of Ligands in a Complex

Estimates the solvent accessible surface area (SASA) of a ligand or pose in the context of a receptor.

atomic_sasa.py
None
Binding SASA

Calculates SASA of ligand and receptor before and after receptor-ligand binding.

binding_sasa.py
None