GChemPaint Manual V0.12.0

Jean Bréfort

GChemPaint allows you to draw and display 2D chemical structures.

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DOCUMENT AND MODIFIED VERSIONS OF THE DOCUMENT ARE PROVIDED UNDER THE TERMS OF THE GNU FREE DOCUMENTATION LICENSE WITH THE FURTHER UNDERSTANDING THAT:

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Feedback

To report a bug or make a suggestion regarding the GChemPaint application or this manual, go to the GChemPaint home page.


Table of Contents
Introduction
1. Getting started
1.1. To Start GChemPaint
1.2. When You Start GChemPaint
1.3. To Open a File
1.4. To Open Multiple Files from a Command Line
2. General operations
2.1. To Create a New File
2.2. To Save a File
2.3. To Edit the Document Properties
2.4. To Print the Document
2.4.1. The page setup dialog.
2.5. To Export an image
2.6. To Export an image suitable for Wikipedia publication.
2.7. To Edit the Preferences
2.7.1. Global settings
2.7.2. Editing Themes.
2.8. To Select and Move Objects
2.9. To Copy, Cut, and Paste Objects
2.10. To Undo or Redo Operations
2.11. To Delete Objects
2.12. To Flip or Rotate Objects
2.13. To Group and/or Align Objects
3. Editing molecules.
3.1. To Change the Current Element
3.1.1. Using the keyboard.
3.1.2. Using the Periodic Table Combo Button.
3.2. To Use or Manage Templates
3.2.1. Managing Templates
3.2.2. Adding a New Template
3.3. To Manage Residues
3.4. To Add or Modify an Atom
3.4.1. To Add or Modify an Single Atom
3.4.2. To Add or Modify a Group of Atoms
3.5. To Add or Modify a Local Charge
3.6. To Add Unbound Electrons to Atoms
3.7. To Add or Modify Orbitals representations
3.8. To Add or Modify a Bond
3.8.1. Bond tool
3.8.2. Stereo bond tools
3.8.3. Bond tools options
3.9. To Add a Chain
3.10. To Add a Cycle
3.10.1. Fixed size cycle tools
3.10.2. Variable size cycle tool
3.11. To Merge two Molecules
3.12. Using the Molecules contextual menu.
4. Other objects.
4.1. To Add an Arrow
4.2. To Attach an Object to a Reaction Arrow
4.3. To Add or Edit a Curved Arrow
4.4. To Add or Edit a Reaction
4.5. To Add or Edit a Mesomery Relationship
4.6. To Add or Edit a Retrosynthesis Pathway
4.7. To Add or Edit some Text
5. Support.
5.1. To Ask a Question
5.2. To Find the Gnome Chemistry Utils on the Web.
5.3. To Report a Bug
6. License
List of Tables
3-1. One character shortcuts for elements.
List of Figures
1-1. GChemPaint main window
1-2. GChemPaint toolbox
2-1. New File with Theme Dialog
2-2. Document Properties Dialog
2-3. The Page Setup tab.
2-4. The Print Scale tab.
2-5. Wikipedia Tool
2-6. Preferences Dialog
2-7. Arrows Page
2-8. Atoms Font Page
2-9. Atoms Extra Page
2-10. Bonds Page
2-11. Text Page
2-12. Selection Tool
2-13. GChemPaint toolbox when the selection tool is selected
2-14. Eraser Tool
2-15. Flip and Rotate Buttons
2-16. Group and/or Align Dialog Box.
3-1. Element popup menu.
3-2. Chosing an element
3-3. Templates Tool
3-4. GChemPaint toolbox when the templates tool is selected
3-5. New Template Dialog
3-6. Residues dialog
3-7. Phenyl residue
3-8. Phenyl structure
3-9. Element Tool
3-10. Hydrogen atoms position dialog box
3-11. Fragment Tool
3-12. Charge Tools
3-13. Electrons Tools
3-14. Orbital sample
3-15. Orbital tool
3-16. Toolbox with orbital tool selected
3-17. Orbital properties dialog
3-18. Bond Tool
3-19. Stereo Bond Tools
3-20. Inverted convention.
3-21. GChemPaint toolbox when a bond tool is selected
3-22. Fixed Size Cycle Tools buttons
3-23. GChemPaint toolbox when the chain tool is selected
3-24. Fixed Size Cycle Tool
3-25. GChemPaint toolbox when a cycle tool is selected
3-26. Variable Size Cycle Tool
3-27. GChemPaint toolbox when the variable size cycle tool is selected
3-28. Merge Button
3-29. Molecules contextual menu
3-30. Initial ghemical view.
3-31. After adding hydrogens
3-32. After geometry optimization.
4-1. Arrow Tools buttons
4-2. GChemPaint toolbox when an arrow tool is selected
4-3. GChemPaint toolbox when the reversible reaction arrow tool is selected
4-4. Object selection.
4-5. Contextual menu.
4-6. Dialog box.
4-7. Attached object.
4-8. Arrow Tools buttons
4-9. Toolbox when the full headed curved arrow tool is selected
4-10. Alternative positions.
4-11. Reaction Arrows Tools
4-12. Mesomery Arrow Tool
4-13. Creation of the molecules and arrows.
4-14. Selection of the popup menu entry.
4-15. Built mesomery relationship.
4-16. Retrosynthesis Arrow Tool
4-17. Creation of the molecules and arrows.
4-18. Selection of the popup menu entry.
4-19. Built retrosynthesis path.
4-20. Custom aligned retrosynthesis path.
4-21. GChemPaint toolbox when the text tool is selected
4-22. Text Tools Bar