Merge pull request #82 from Avogadro/more-updates

Added previous version history (missing a few 1.9x betas still)
Avogadro · Feb 19, 2024 · 73ad44a · 73ad44a
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diff --git a/source/install/versions/index.md b/source/install/versions/index.md
@@ -1,15 +1,47 @@
-(install-versions)=
+(versions)=
 
 # Version History
 
+The list below includes versions of Avogadro v2 betas (1.9x) as well as
+previous versions of Avogadro (1.2 and older)
+
 ```{toctree}
 ---
-caption: Version History
+maxdepth: 1
 ---
+v199
+v1981
 v198
 v197
 v196
 v1951
 v195
 v194
+v193
+v192
+v191
+v190
+v120
+v111
+v110
+v103
+v102
+v101
+v100
+v099
+v098
+v097
+v096
+v095
+v094
+v093
+v092
+v091
+v090
+v081
+v080
+v061
+v060
+v020
+v010
 ```
diff --git a/source/install/versions/v010.md b/source/install/versions/v010.md
@@ -0,0 +1,93 @@
+(v010)=
+
+# Avogadro 0.1.0
+
+Avogadro version 0.1.0 was released on May 18, 2007.
+
+What Works
+----------
+
+-   Drawing of Molecules from scratch (Atoms, Bonds)
+-   Reading and Writing of over 80 chemical formats through [OpenBabel](https://openbabel.org)
+-   Manipulation of Molecule structures
+-   Geometric Optimization through OpenBabel forcefield support.
+-   Export to image.
+-   Engine overlay system allowing different three dimensional views;
+    -   Wireframe
+    -   Ball and Stick
+    -   Van Der Wall Spheres
+    -   Atom Labels
+-   Tools for interaction with the three dimensional representation;
+    -   Selection
+        -   Select Molecule
+        -   Select Atom
+        -   Select Area
+    -   Navigation
+        -   Scale (Zoom)
+        -   Rotation
+        -   Move
+    -   Draw
+        -   Draw Atom
+        -   Draw Bond
+        -   Change Atom Type
+        -   Delete Atom
+    -   Manipulation
+        -   Rotate Selection
+        -   Move Selection
+    -   Measure
+        -   Measure Distance
+        -   Measure Angle
+-   Extensions which easy extend the functionality of Avogadro (see below for more information)
+    -   Select by SMILES string
+    -   Add/Remove Hydrogens
+    -   Geometric Optimization of Molecule Structure using OpenBabel Forcefields
+    -   GAMESS Input Deck Generation
+
+Known Issues & Limitations
+--------------------------
+
+This release is an early beta release and is intended to gain feedback and interest in the project.
+
+The code currently expects to be editing one 3D molecule per file with one coordinate set. This means:
+
+-   No animations are currently supported (or molecular dynamics trajectories, movies, vibrations, etc.).
+-   Editing a multi-molecule file will only edit the first molecule. Saving will overwrite all records except the first.
+-   Opening a 2D file will not result in 3D coordinates. Opening a SMILES file will not create 3D coordinates either.
+-   Saving to a 2D format will not necessarily produce correct 2D stereochemistry.
+
+
+
+-   Only one color scheme is currently available, although the code allows different types to be implemented. Suggestions are welcome.
+-   Only one label scheme (by atom index) is currently available.
+-   No protein ribbon or cartoon render option is available.
+-   Surface rendering is not implemented.
+-   The underlying rendering engines support different rendering for individual atoms, bonds, residues, etc. This is not exposed in the user interface yet.
+-   The underlying code supports rendering crystallographic unit cells, but this is not exposed in the interface yet.
+-   Transparent spheres for selected atoms do not always appear transparent.
+
+
+
+-   Not all elements are available through the draw tool. A "periodic table" window will be implemented soon.
+-   A three-button mouse is required to use the tools. Mac users without a three-button mouse (ideally with scroll wheel) will have difficulty.
+-   The fragment library, protein and biomolecule builder features are not implemented yet.
+-   The "click measure" tool does not allow measuring 4-atom dihedral angles. All output is graphical, so it is not currently possible to copy the text to another program.
+-   The draw tool cannot delete a bond without deleting atoms.
+
+
+
+-   The Mac interface is not completely "native." A more unified, polished version is intended for the final release, without graphics in the menus and a "unified" toolbar look.
+-   The atom and bond list on the right side of the window only allows a list. It is not interactive -- for example, selecting an atom in the list will not select it in the view (or vice-versa). Only the atom and bond index are reported, nothing else yet.
+-   Views cannot yet be removed into separate windows. In future releases, you will be able to have separate views of the same molecule in separate windows.
+-   Export graphics will only save the current resolution in the window in bitmap form. Vector formats (SVG, PS, PDF) and other formats (POV-Ray) are intended to be implemented in the future.
+-   No "preferences" are saved (e.g., rendering detail, default colors, etc.).
+
+
+
+A select list of commands is currently available, mostly as examples of what can be done using the Avogadro framework.
+
+-   Commands are only available in the "Tools" menu. Future releases will allow them to extend any menu or create new menus.
+-   The "Optimize Geometry" command uses the Ghemical force field, but offers no other options. It also does not display any feedback except in the "Messages" box.
+-   Only the GAMESS input generation is complete (as an example). Other programs are intended for support in future releases.
+-   No scripting support (for Python, Perl, Ruby, and shell scripting) is available. Future releases will allow users to add scripts for tasks such as submitting jobs to computational programs, changing molecular structure, or other uses. The entire engine will be scriptable through Avogadro and Open Babel scripting layers.
+-   A z-matrix builder command is intended for future releases.
+-   A unit cell / crystal builder is intended for future releases.
diff --git a/source/install/versions/v020.md b/source/install/versions/v020.md
@@ -0,0 +1,95 @@
+(v020)=
+
+# Avogadro 0.2.0
+
+Avogadro version 0.2.0 was released on October 23, 2007.
+
+What's New
+----------
+
+The following list includes some of the changes since [Avogadro 0.1.0](Avogadro 0.1.0 "wikilink").
+
+
+
+-   Support for rendering crystallographic cells and editing unit cell parameters.
+-   Flexible rendering, including multiple overlays, and per-atom and per-bond custom rendering.
+-   Flexible atom labeling schemes.
+-   Support for bond labeling.
+-   Axes engine to display x, y, z axes in the corner of the window.
+-   Improved transparency, including an adjustable transparent van der Waals sphere rendering option.
+-   Configuration options for rendering engines.
+-   A new flexible "painter" architecture, now allowing export to POV-Ray. In the future, support for PDF and SVG are planned.
+-   Multi-threaded rendering.
+
+
+
+-   A full periodic table for drawing and editing.
+-   New autorotate tool which will animate rotation of the molecule.
+-   New auto-optimize tool, which will continually optimize the geometry of the molecule as you draw or modify it.
+-   New "bond-centric" manipulation tool, which facilitates changing the bond length, angle, or dihedral angle of parts of a molecule.
+-   More visual feedback when using the mouse tools.
+
+
+
+-   Improved force field options, including calculating the energy, and conformational searching.
+-   Geometry optimization is threaded with a progress dialog.
+-   Improved speed of geometry optimization with Open Babel 2.2 builds. (Used on Mac and Windows binaries for Avogadro 0.2.)
+-   Adding/removing hydrogen atoms will now add to selected atoms only.
+-   New command to change hydrogen atoms (or only selected H atoms) to methyl groups.
+-   When pasting, the new atoms will be automatically selected for movement or manipulation.
+    -   We do not (yet) change tools, so you will likely wish to change to the manipulate tool after pasting atoms.
+-   Improved support for GAMESS advanced input generation (EFP and QM/MM).
+-   Command extensions can now go into any menu or submenu.
+
+
+
+-   Initial support for internationalization and translation.
+    -   Partial translations for French and German.
+-   Improved Mac support, including a unified toolbar look, use of a one-button mouse or trackpad (using the Option and Command keys as modifiers), and more.
+-   Many, many more enhancements and bug fixes.
+
+
+Known Issues & Limitations
+--------------------------
+
+This release is an early beta release and is intended to gain feedback and interest in the project.
+
+The code currently expects to be editing one 3D molecule per file with one coordinate set. This means:
+
+-   No animations are currently supported (or molecular dynamics trajectories, movies, vibrations, etc.).
+-   Editing a multi-molecule file will only edit the first molecule. Saving will overwrite all records except the first.
+-   Opening a 2D file will not result in 3D coordinates. Opening a SMILES file will not create 3D coordinates either.
+-   Saving to a 2D format will not necessarily produce correct 2D stereochemistry.
+
+
+
+-   Only one color scheme is currently available, although the code allows different types to be implemented. Suggestions are welcome.
+-   No protein ribbon or cartoon render option is available.
+-   Surface rendering is not implemented.
+
+
+
+-   The fragment library, protein and biomolecule builder features are not implemented yet.
+-   The "click measure" tool does not allow measuring 4-atom dihedral angles. All output is graphical, so it is not currently possible to copy the text to another program.
+-   The AutoOptimize tool causes crashes when mixing it with the Geometric Optimization extension available from the 'Tools' menu.
+
+
+
+-   The atom and bond list on the right side of the window only allows a list. It is not interactive -- for example, selecting an atom in the list will not select it in the view (or vice-versa). Only the atom and bond index are reported, nothing else yet.
+-   Views cannot yet be removed into separate windows. In future releases, you will be able to have separate views of the same molecule in separate windows.
+-   Export graphics will only save the current resolution in the window in bitmap form. Vector formats (SVG, PS, PDF) and other formats (POV-Ray) are intended to be implemented in the future.
+-   No "preferences" are saved (e.g., rendering detail, default colors, etc.).
+
+
+
+A select list of commands is currently available, mostly as examples of what can be done using the Avogadro framework.
+
+-   The "Optimize Geometry" command only supports the ghemical force field. Other force fields are intended in future releases.
+-   Only the GAMESS input generation is complete (as an example). Other programs are intended for support in future releases.
+-   No scripting support (for Python, Perl, Ruby, and shell scripting) is available. Future releases will allow users to add scripts for tasks such as submitting jobs to computational programs, changing molecular structure, or other uses. The entire engine will be scriptable through Avogadro and Open Babel scripting layers.
+-   A z-matrix builder command is intended for future releases.
+-   A unit cell / crystal builder is intended for future releases.
+
+
+
+-   The H2Methyl extension causes crashes always and so it was excluded from this build.
diff --git a/source/install/versions/v060.md b/source/install/versions/v060.md
@@ -0,0 +1,91 @@
+(v060)=
+
+# Avogadro 0.6.0
+
+Avogadro version 0.6.0 was released on February 29, 2008.
+
+What's New
+----------
+
+The following list includes some of the changes since [Avogadro 0.2.0](Avogadro 0.2.0 "wikilink"). The jump in version number indicates that Avogadro is rapidly reaching a stable 1.0 release series.
+
+
+
+-   Cloning render engines allowing parts of the molecule to be displayed using different styles etc.
+-   Protein ribbon engine to display secondary structure.
+-   Ring engine to highlight ring structures in molecules.
+-   Polyhedron engine highlighting metallic centers in molecules for example.
+-   Configurable color maps such as user specified colors.
+-   Added an isosurface generator using the marching cubes algorithm.
+-   New molecular orbitals engine that can display molecular orbitals and other surfaces from cube files.
+-   New Van der Waals surface engine generates a VdW surface with optional ESP coloring.
+
+
+
+-   An improved periodic table for drawing and editing.
+
+
+
+-   Selection menu
+    -   Add, remove, clear, invert selection.
+    -   Select by residue, chain, molecule (i.e., click on one atom, select a whole group or molecule).
+    -   Select by element, residue name, solvent.
+    -   Selections using SMARTS.
+
+
+
+-   Menu reorganization.
+-   Persistent window/tool settings.
+-   stacked widgets giving more space to the OpenGL window displaying the molecule.
+
+
+
+-   Improved force field options, including calculating the energy, and conformational searching.
+-   Geometry optimization is threaded with a progress dialog.
+-   Improved speed of geometry optimization with Open Babel 2.2 builds.
+
+
+
+-   Initial support for internationalization and translation.
+    -   Partial translations for French, German and British English.
+-   Many, many more enhancements and bug fixes.
+
+
+Known Issues & Limitations
+--------------------------
+
+This release is an early beta release and is intended to gain feedback and interest in the project.
+
+The code currently expects to be editing one 3D molecule per file with one coordinate set. This means:
+
+-   No animations are currently supported (or molecular dynamics trajectories, movies, vibrations, etc.).
+-   Editing a multi-molecule file will only edit the first molecule. Saving will overwrite all records except the first.
+-   Opening a 2D file will not result in 3D coordinates. Opening a SMILES file will not create 3D coordinates either.
+-   Saving to a 2D format will not necessarily produce correct 2D stereochemistry.
+
+
+
+-   Only one color scheme is currently available, although the code allows different types to be implemented. Suggestions are welcome.
+
+
+
+-   The fragment library, protein and biomolecule builder features are not implemented yet.
+
+
+
+-   The atom and bond list on the right side of the window only allows a list. It is not interactive -- for example, selecting an atom in the list will not select it in the view (or vice-versa). Only the atom and bond index are reported, nothing else yet.
+-   Views cannot yet be removed into separate windows. In future releases, you will be able to have separate views of the same molecule in separate windows.
+-   Export graphics will only save the current resolution in the window in bitmap form. Vector formats (SVG, PS, PDF) and other formats (POV-Ray) are intended to be implemented in the future.
+
+
+
+A select list of commands is currently available, mostly as examples of what can be done using the Avogadro framework.
+
+-   Only the GAMESS input generation is complete (as an example). Other programs are intended for support in future releases.
+-   No scripting support (for Python, Perl, Ruby, and shell scripting) is available. Future releases will allow users to add scripts for tasks such as submitting jobs to computational programs, changing molecular structure, or other uses. The entire engine will be scriptable through Avogadro and Open Babel scripting layers.
+-   A z-matrix builder command is intended for future releases.
+-   A unit cell / crystal builder is intended for future releases.
+
+
+
+-   The H2Methyl extension causes crashes always and so it was excluded from this build.