Difference between revisions of "Scripting"
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| − | + | The Jmol [[Jmol_Application|Application]] and [[Jmol_Applet|Applet]] have a command language that grows on the base of [http://www.mdl.com/support/developer/chime/developer_tools.jsp command language] of the browser plugin [http://www.mdl.com/ 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:''' | '''Documentation of Jmol's scripting language can be found here:''' | ||
* http://www.stolaf.edu/academics/chemapps/jmol/ | * http://www.stolaf.edu/academics/chemapps/jmol/ | ||
| + | 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:''' | '''An introduction to Jmol scripting is available here:''' | ||
| − | * http://www. | + | * http://www.callutheran.edu/Academic_Programs/Departments/BioDev/omm/scripting/molmast.htm |
| + | 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 [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> | ||
| + | *-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 20:51, 13 February 2007
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.
