Difference between revisions of "Scripting"
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Chime's command language (see "About Chime" at http://molviz.org) is a superset of the [http://www.umass.edu/microbio/rasmol/getras.htm#rasmanual command language] of Roger Sayle's public domain application [http://www.umass.edu/microbio/rasmol/index2.htm RasMol]. (The command language of [http://www.rasmol.org/ open-source RasMol] has diverged somewhat from that in RasMol and Chime). The command language used by Jmol started with most of the Chime commands, but has outgrown it in a notable extent, allowing for many new capabilities. | Chime's command language (see "About Chime" at http://molviz.org) is a superset of the [http://www.umass.edu/microbio/rasmol/getras.htm#rasmanual command language] of Roger Sayle's public domain application [http://www.umass.edu/microbio/rasmol/index2.htm RasMol]. (The command language of [http://www.rasmol.org/ open-source RasMol] has diverged somewhat from that in RasMol and Chime). The command language used by Jmol started with most of the Chime commands, but has outgrown it in a notable extent, allowing for many new capabilities. | ||
<pre> | <pre> | ||
| − | *-RasMol (v | + | *-RasMol (v≤2.6) |
| + | | | ||
| + | |----Chime Takes nearly all RasMol 2.6 commands and adds a few. | ||
| + | | | | ||
| + | | ----Jmol (v≥10) Takes many RasMol 2.6 and Chime 2.6 commands and adds a few. | ||
| + | | | | ||
| + | | ---Jmol (v≥11) Adds many new commands. | ||
| + | | | ||
| + | -----OpenRasMol (v≥2.7) Takes all RasMol 2.6 commands and adds a few. | ||
| + | </pre> | ||
| + | |||
| + | = Transversal documentation = | ||
| + | Covering specific aspects or applications (not by command, and usually not exhaustive): | ||
| + | * [http://jmol.sourceforge.net/docs/surface/ Surfaces]. Jmol can calculate and render surfaces around a molecule, or part of it, representing its "true" shape and volume. Moreover, isosurfaces, atomic and molecular orbitals, and mathematically defined surfaces can also be rendered. | ||
| + | * [[Persistent Parameters|Persistent and nonpersistent "set" parameters]]. Some parameters defined using the "set" command are associated to the app/applet and hence maintained when a new molecule is loaded, while others are reset when the model is removed. | ||
Revision as of 18:44, 14 July 2007
- Description of files in Jmol+JSmol distribution
- File formats read or written by Jmol
- The Jmol scripting interface
- Scripting as a programming language
- Complete reference of scripting commands:
- Loading models directly from databases
- Mouse manual
- Default colors used by Jmol
- Atom sets predefined in Jmol
- Support for bond orders · isotopes · stereochemistry · hydrogen bonds
- Jmol as editor
- Multi-touch support
- Copying and pasting state scripts between applets.
- Backward compatibility (changes of behavior across versions)
- Features added since version 10
- Users mailing list (and a mirror)
The Jmol Application and Applet have a command language that grows on the base of command language of the browser plugin MDL Chime. A set of commands is called a command script, and writing such sets of commands or scripts is called scripting.
Documentation links
Documentation of Jmol's scripting language can be found here:
This is the official document. The style is encyclopedic, explaining each command in turn, as usual in reference manuals.
An introduction to Jmol scripting is available here:
A more user-friendly, but less thorough, basic guide by Nathan Silva and David Marcey; part of the Online Macromolecular Museum at California Lutheran University.
Similar but different scripting languages
Chime's command language (see "About Chime" at http://molviz.org) is a superset of the command language of Roger Sayle's public domain application RasMol. (The command language of open-source RasMol has diverged somewhat from that in RasMol and Chime). The command language used by Jmol started with most of the Chime commands, but has outgrown it in a notable extent, allowing for many new capabilities.
*-RasMol (v≤2.6) | |----Chime Takes nearly all RasMol 2.6 commands and adds a few. | | | ----Jmol (v≥10) Takes many RasMol 2.6 and Chime 2.6 commands and adds a few. | | | ---Jmol (v≥11) Adds many new commands. | -----OpenRasMol (v≥2.7) Takes all RasMol 2.6 commands and adds a few.
Transversal documentation
Covering specific aspects or applications (not by command, and usually not exhaustive):
- Surfaces. Jmol can calculate and render surfaces around a molecule, or part of it, representing its "true" shape and volume. Moreover, isosurfaces, atomic and molecular orbitals, and mathematically defined surfaces can also be rendered.
- Persistent and nonpersistent "set" parameters. Some parameters defined using the "set" command are associated to the app/applet and hence maintained when a new molecule is loaded, while others are reset when the model is removed.
