- 1.7
- 1.6
- 1.5
- Beta
- Examples (for 1.6a)
- Misc
Table of Contents
- 1. Disclaimer
- 2. Acknowledgements
- 3. Getting Started
- 4. Import / Export
- 5. The GUI
- 6. Command Language
- Command Language Overview
- Variable Types
- Command Reference
- Atom Commands
- Bond Commands
- Building Commands
- Cell Commands
- Charges Commands
- ColourScales Commands
- Disordered Commands
- Edit Commands
- Energy Commands
- Flow Commands
- Forcefield Commands
- Forces Commands
- Glyph Commands
- Grid Commands
- Image Commands
- Labeling Commands
- Math Commands
- Measuring Commands
- Messaging Commands
- Minimiser Commands
- Model Commands
- Monte Carlo Commands
- Pattern Commands
- Read / Write Commands
- Script Commands
- Selection Commands
- Site Commands
- String Commands
- System Commands
- Trajectory Commands
- Transform Commands
- View Commands
- 7. Topics of Interest
- 8. Forcefields and Typing
- Overview
- Supplied Forcefields
- Canongia-Lopes & Padua Ionic Liquids (cldp-il.ff)
- Youngs, Kohanoff, & Del Pópolo [dmim]Cl (dmimcl-fm.ff)
- Youngs & Hardacre [dmim]Cl (dmimcl-fm2.ff)
- Jorgensen at al. OPLS-AA (oplsaa.ff)
- Berensen et al.s Simple Point Charge Water (spc.ff)
- Berensen et al.s Extended Simple Point Charge Water (spce.ff)
- Rappe et al.s Universal Forcefield (testing/uff.ff)
- Mayo, Olafson & Goddard II's Generic Forcefield (testing/dreiding.ff)
- General Amber Forcefield (testing/gaff.ff)
- Liu, Wu & Wang's United-Atom Ionic Liquids Forcefield (lww-il.ff)
- Keyword Reference
- Rule-Based Forcefields
- Typing
- NETA Reference
- VDW Functional Forms
- Bond Functional Forms
- Angle Functional Forms
- Torsion Functional Forms
- 9. Methods
- 10. Enumerations
- 11. Changelogs
- Index
List of Figures
- 5.1. Atom List Window
- 5.2. Build Window, Add Atom Panel
- 5.3. Cell Definition Window
- 5.4. Cell Transform Window, Replicate Panel
- 5.5. Cell Transform Window, Scale Panel
- 5.6. Command Window, Scripts Panel
- 5.7. Command Window, Prompt Panel
- 5.8. Disordered Builder Window
- 5.9. Forcefield Window
- 5.10. Fragment Library Window
- 5.11. Geometry Window
- 5.12. Grids Window
- 5.13. Minimiser Window
- 5.14. Atom Position Window, Centre Panel
- 5.15. Atom Position Window, Flip Panel
- 5.16. Atom Position Window, Translate Panel
- 5.17. Atom Position Window, Shift Panel
- 5.18. Atom Position Window, Reposition Panel
- 5.19. Atom Transform Window, Rotate Panel
- 5.20. Atom Transform Window, Matrix Transform Panel
- 5.21. Atom Transform Window, Matrix Convert Panel
- 7.1. Pattern Example, System 1
- 7.2. Pattern Example, System 2
- 7.3. Pattern Example, System 3
- 7.4. Pattern Example, System 4
- 8.1. Water
- 8.2. 3-hydroxypropanoic acid
- 8.3. N,N,2,5-tetramethylpyridin-4-amine
List of Tables
- 4.1. Supported Model Formats
- 4.2. Supported Trajectory Formats
- 4.3. Supported Grid Data Formats
- 4.4. Supported Expression Data Formats
- 4.5. Filter properties
- 4.6. Filter types
- 4.7. Formatted output commands
- 4.8. Formatted input commands
- 4.9. Extra read/write specifiers
- 4.10. Escaped characters in format strings
- 4.11. Delimited read/write commands
- 5.1. Mouse Button Actions
- 5.2. Bonding Toolbar Icons
- 5.3. Build Toolbar Icons
- 5.4. Draw Style Toolbar Icons
- 5.5. Edit Toolbar Icons
- 5.6. File Toolbar Icons
- 5.7. Forcefield Toolbar Icons
- 5.8. Mouse Toolbar Icons
- 5.9. Mouse Toolbar Icons
- 5.10. Select Toolbar Icons
- 5.11. Tool Window Toolbar Icons
- 5.12. Trajectory Toolbar Icons
- 5.13.
- 5.14.
- 5.15.
- 5.16.
- 5.17.
- 5.18.
- 5.19.
- 5.20.
- 5.21.
- 6.1. Built-in Constants
- 6.2. Aten type members
- 6.3. Bond type functions
- 6.4. Atom type members
- 6.5. Bond type members
- 6.6. Bond type functions
- 6.7. Bound type members
- 6.8. Element type members
- 6.9. FFAtom type members
- 6.10. FFAtom type functions
- 6.11. FFBound type members
- 6.12. Forcefield type members
- 6.13. Glyph type members
- 6.14. Glyph type functions
- 6.15. GlyphData type members
- 6.16. Measurement type members
- 6.17. Model type members
- 6.18. Pattern type members
- 6.19. Prefs type members
- 6.20. Region type members
- 6.21. UnitCell type members
- 6.22. Vector type members
- 6.23. Test Operators
- 6.24. Autopolyhedra options
- 6.25. Newglyph options
- 6.26. Bitmap image formats
- 7.1. Pattern Examples
- 8.1. NETA keyword '~X' examples
- 8.2. NETA keyword '~X' examples
- 8.3. NETA keyword '-X' examples
- 8.4. NETA keyword '=X' examples
- 8.5. NETA keyword 'bond' examples
- 8.6. NETA keyword 'chain' examples
- 8.7. NETA keyword 'n' examples
- 8.8. NETA keyword 'nbonds' examples
- 8.9. NETA keyword 'nh' examples
- 8.10. NETA keyword 'aromatic' examples
- 8.11. NETA keyword 'noring' examples
- 8.12. NETA keyword 'planar' examples
- 8.13. NETA keyword 'ring' examples
- 8.14. NETA keyword 'size' examples
- 8.15. NETA geometry keywords
- 8.16. VDW Functional Forms
- 8.17. Bond Functional Forms
- 8.18. Angle Functional Forms
- 8.19. Torsion Functional Forms
- 9.1. Literature Methods
- 10.1. Bond type keywords
- 10.2. Cell type keywords
- 10.3. Colour scheme keywords
- 10.4. Combination Rules
- 10.5. Draw style keywords
- 10.6. Energy unit keywords
- 10.7. Glyph type keywords
- 10.8. Grid style keywords
- 10.9. Label type keywords
- 10.10. Output type keywords
- 10.11. Parse option keywords
- 10.12. Read/write return values
- 10.13. Region Shapes
- 10.14. View object keywords
- 10.15. Map type keywords