GChemPaint Manual V0.12.0

Jean Bréfort

  

Copyright © 2005-2010 Jean Bréfort

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

Permission is granted to copy, distribute and/or modify this document under the terms of the GNU Free Documentation License (GFDL), Version 1.1 or any later version published by the Free Software Foundation with no Invariant Sections, no Front-Cover Texts, and no Back-Cover Texts. You can find a copy of the GFDL at this link or in the file COPYING-DOCS distributed with this manual.

This manual is part of a collection of GNOME manuals distributed under the GFDL. If you want to distribute this manual separately from the collection, you can do so by adding a copy of the license to the manual, as described in section 6 of the license.

Many of the names used by companies to distinguish their products and services are claimed as trademarks. Where those names appear in any GNOME documentation, and the members of the GNOME Documentation Project are made aware of those trademarks, then the names are in capital letters or initial capital letters.

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

  1. DOCUMENT IS PROVIDED ON AN "AS IS" BASIS, WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES THAT THE DOCUMENT OR MODIFIED VERSION OF THE DOCUMENT IS FREE OF DEFECTS MERCHANTABLE, FIT FOR A PARTICULAR PURPOSE OR NON-INFRINGING. THE ENTIRE RISK AS TO THE QUALITY, ACCURACY, AND PERFORMANCE OF THE DOCUMENT OR MODIFIED VERSION OF THE DOCUMENT IS WITH YOU. SHOULD ANY DOCUMENT OR MODIFIED VERSION PROVE DEFECTIVE IN ANY RESPECT, YOU (NOT THE INITIAL WRITER, AUTHOR OR ANY CONTRIBUTOR) ASSUME THE COST OF ANY NECESSARY SERVICING, REPAIR OR CORRECTION. THIS DISCLAIMER OF WARRANTY CONSTITUTES AN ESSENTIAL PART OF THIS LICENSE. NO USE OF ANY DOCUMENT OR MODIFIED VERSION OF THE DOCUMENT IS AUTHORIZED HEREUNDER EXCEPT UNDER THIS DISCLAIMER; AND

  2. UNDER NO CIRCUMSTANCES AND UNDER NO LEGAL THEORY, WHETHER IN TORT (INCLUDING NEGLIGENCE), CONTRACT, OR OTHERWISE, SHALL THE AUTHOR, INITIAL WRITER, ANY CONTRIBUTOR, OR ANY DISTRIBUTOR OF THE DOCUMENT OR MODIFIED VERSION OF THE DOCUMENT, OR ANY SUPPLIER OF ANY OF SUCH PARTIES, BE LIABLE TO ANY PERSON FOR ANY DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES OF ANY CHARACTER INCLUDING, WITHOUT LIMITATION, DAMAGES FOR LOSS OF GOODWILL, WORK STOPPAGE, COMPUTER FAILURE OR MALFUNCTION, OR ANY AND ALL OTHER DAMAGES OR LOSSES ARISING OUT OF OR RELATING TO USE OF THE DOCUMENT AND MODIFIED VERSIONS OF THE DOCUMENT, EVEN IF SUCH PARTY SHALL HAVE BEEN INFORMED OF THE POSSIBILITY OF SUCH DAMAGES.

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
  Next
  Introduction