Scripts
Command-line only Scripts
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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 |