ds 1 7 scripting

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Scripting inDiscovery Studio

Daniel Berard

13 February 2007


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Outline

Part I Overview of DiscoveryScript Exposed functionality Example uses Contexts for running scripts

Part II Demo working examples Resources How to get started


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DiscoveryScript - Overview

DiscoveryScript is the scripting component in DS

Access to underlying data models in DS

Special File handlers Open, Insert files into the data model Save data models to various file formats

Modify, Extract data Create a molecule Modify display Calculate and extract data Study a ligand binding site

Visualization (when run within DS Visualizer Pro) View opened files Observe script operations


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DiscoveryScript - Environment

Exposed via Perl scripting language Implemented as an add-on to Perl

Why Choose Perl? Perl: well-known, mature scripting language Perl: full featured scripting language

Loops, tests, branching, subroutines, modules, objects

Can mix DiscoveryScript with other (non-Accelrys or Accelrys) Perlcomponents


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Exposed Data Model in DS 1.7

DS Visualizer Pro 1.7 exposes our Molecular Data Model (MDM)

Key objects For example Atom, Bond, Molecule, Residue, DistanceMonitor

Key commands (including corresponding ViewerPro commands) For example Rotate, Clean, Zoom

Most properties and key functions For example XYZ, ElementType, RemoveHydrogens

Constants and enumerated types For ease-of-use and clarity, such as Mdm::Hydrogen

Arrays and Filters For example, apply atom filter on a molecule to get all atoms in the

molecule


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DiscoveryScript - Uses

Scripting is a powerful tool for users

Automate repetitive tasks

Develop custom tools

Combine Accelrys and non-Accelrys tools through Perl

Incorporate DiscoveryScript into pipelines such as Pipeline Pilot

protocols


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Context 1: Stand-alone Scripting

Run from command window (Windows or Linux) Normal script output displayed in command window Scripts run without launching DS Client Full access to all DiscoveryScript capabilities Full access to Perl tools

such as for debugging scripts

How to run: Using Perl package with DS Visualizer Pro

Windows: p er l . b at Linux: sh p er l . sh cd to installation bi n folder (such as C:\Program

Files\Accelrys\Discovery Studio 1.7\bin) or have this in your PATH


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Context 2: DS Client Scripting

Seamless integration with DS: Ability to visualize molecule objects Views automatically updated when executing commands Manipulating objects directly requires explicit update command

How to run: File | Open Dialog Double-click the script file in the File Explorer Drag-and-drop into the DS Client


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Context 3: Pipeline Pilot

Seamless integration with Pipeline Pilot Professional Client Full access to Pipeline Pilot environment

Prepared for direct interactions between the scripts and the PipelinePilot data stream


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Examples

1. Minimal script - open molecular data file2. Stand-alone run - export data attributes from file3. DS Client open view on file, rotate4. Stand-alone/DS Client - Extract Chi angles5. DS Client - Render Ligand Cavity isolate, view and beautify

ligand binding site6. PP Protocol read MSV file, place conformation in PP data stream,

calculate CHARMm energy, save conformations as molecules mol2file


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Resources and Getting Started

Sample Scripts folder in the File Explorer, for example ExtractAngles.pl extracts valence or torsion angles from a set of

poses ExtractChiAngles.pl extracts chi angles from amino acids RenderLigand.pl isolates active binding site and beautifies

Accelrys Community Forum http://accelrys.org for more scripts

How to get started

Look at and modify existing example scripts Documentation Learning Perl lots of good books and courses!

ds 1 7 scripting

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