Contents

Table of contents

• 1. Getting Started
• 2. File Compatibility
• 3. Command Language
• 4. Forcefields / Atom Typing
• 5. Other Topics
• 6. Legacy Documentation (up to v1.1)
• 7. Notes

1. Getting Started

• Compilation - Compilation guides for various platforms
• Installation? - Installation notes
• FAQ - Common problems and known issues
• The Command Line - Command-line options, and how to use Aten as a batch tool
• The GUI - Layout and function of the GUI

2. File Compatibility

• CompatibilityNotes - Read this first!
• Supported File Formats - List of file formats supported out-of-the-box
• Filters - How they work, and how to write them
• Trajectory Files - Specific details on how trajectory files are handled
• Reading and Writing Data
  • Formatting Strings - overview of C-style formatted reading and writing
  • Delimited Reading and Writing - How delimited reading and writing works
  • Unformatted Reading and Writing? - Working with binary data

3. Command Language

• Command Language - Language basics
• Command Reference - Descriptions of every script command available in Aten
  • Skip to section: Atoms Bonding Building Cell Charges Colourscales Disordered Energies Edit Flow Forcefields Forces Glyphs Grids Image Labeling Math Measuring Messaging Minimiser Models Monte Carlo Pattern Patterns Prefs Read Write Scripts Selection Sites String System Trajectory Transformation View
• Command Index - Index of all available commands
• Variables - Variable types
• Paths and Subvariables - Subvariable access

4. Forcefields / Atom Typing

• Forcefield Files - Forcefield file format, and currently-implemented functional forms
• Functional Forms - All functional forms currently implemented in Aten
  • VDW Functional Forms - Short-range interatomic interactions
  • Bond Functional Forms? - Bond (i-j) intramolecular interactions
  • Angle Functional Forms? - Angle (i-j-k) intramolecular interactions
  • Torsion Functional Forms? - Torsion/Dihedral (i-j-k-l) intramolecular interactions
• Atom Typing - Concepts of atom typing
• NETA - Describing atom types with the Nested English Typing Approach
• NETA Reference - Reference for the NETA language

5. Other Topics

• Colourscales? - Using colourscales to colour objects and surfaces
• Methods - Descriptions of various algorithms and methods used within Aten

6. Legacy Documentation (up to v1.1)

• Command Reference v1.1 - Descriptions of every script command available in Aten
• Filters v1.1 - How they work, and how to write them
• Variables v1.1 - How variables are used in Aten, and how data is accessed

7. Notes

Aten uses Space Group Info (c) 1994-96 Ralf W. Grosse-Kunstleve.
Aten also uses other free software such as the Qt toolkit and readline.

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