doNeon ( cmdName,  args )

doPreneon ( cmdName,  args )

doEcho ( cmdName,  args )

doSystem ( cmdName,  args )

NoVdwopt ( cmdName,  args )

doSurfaceCategory ( cmdName,  args )

doTexture ( cmdName,  args )

doSleep ( cmdName,  args )

Unimplemented ( cmdName,  args )

doStop ( cmdName,  args )

doMatrixcopy ( cmdName,  args )

doCopy ( cmdName,  args )

clearError ()

doUnsurface ( cmdName,  args )

doUnalias ( cmdName,  args )

doSet ( cmdName,  args )

doSource ( cmdName,  args )

doMove ( cmdName,  args )

doWait ( cmdName,  args )

doLinewidth ( cmdName,  args )

doSwapRes ( cmdName,  args )

doModelFunc ( cmdName,  args )

doAlias ( cmdName,  args )

doBondUncolor ( cmdName,  args )

doAddAA ( cmdName,  args )

doRMSD ( cmdName,  args )

doOpen ( cmdName,  args )

doUnsavepos ( cmdName,  args )

addCommand (
        command,
        cmdFunc,
        revFunc=None,
        help=None,
        )

add a command to the interpreter

command is the command name; cmdFunc is the function to call when command is invoked, and revFunc (if any) is the function to call for ~command. cmdFunc and revFunc are both called with two string arguments: the command name and the argument string typed by the user. help is None if no help is provided, True if the command has help integrated with the other built-in commands (i.e. is listed in the User's Guide table of contents of commands), or is a string or tuple that can be used as an argument to chimera.help's display() function (an URL or package/URL tuple).

cmdFunc and revFunc are typically simple wrapper functions that in turn call the doExtensionFunc() command. See the doExtensionFunc doc string for details on usage.

One usually registers the new command from the extension's ChimeraExtension.py file so that it is available to the interpreter without the extension being imported. Don't import your extension directly from within your ChimeraExtension.py! Doing so will slow Chimera startup. Instead, you will import your extension from within your cmdFunc (and revFunc) functions. See FindHBond's ChimeraExtension.py for an example of typical usage [except for the help arg, since FindHBond's help is integrated with the built-in commands].

You will want to use the doExtensionFunc() command to handle parsing the text and calling your command. You may have to provide a shim function that works better (more "user friendly" keywords, etc.) than your normal API for use with doExtensionFunc(). See the doExtensionFunc() doc string for details.

doCofr ( cmdName,  args )

doBondDisplay ( cmdName,  args )

doRepr ( cmdName,  args )

doArglessFunc ( cmdName,  args )

processCommandFile (
        filename,
        emulateRead=0,
        usingString=False,
        )

called by source and read commands

doChirality ( cmdName,  args )

doClip ( cmdName,  args )

expandAliases ( text )

expand aliases

convertType ( value )

doLoad ( cmdName,  args )

doMsMs ( cmdName,  args )

doRoll ( cmdName,  args )

getSpecs ( args,  modelLevel=False )

doScale ( cmdName,  args )

doRibbonjr ( cmdName,  args )

message ( msg )

doBondColor ( cmdName,  args )

doUncolor ( cmdName,  args )

findQuoted ( text )

doUnset ( cmdName,  args )

doRock ( cmdName,  args )

doSection ( cmdName,  args )

doSurfaceColor ( cmdName,  args )

doWindow ( cmdName,  args )

doConic ( cmdName,  args )

doUnbond ( cmdName,  args )

doLongbond ( cmdName,  args )

doMatrixget ( cmdName,  args )

warn ( warning )

doSave ( cmdName,  args )

doRead ( cmdName,  args )

doVdwDensity ( cmdName,  args )

doSavepos ( cmdName,  args )

doKsdssp ( cmdName,  args )

doThickness ( cmdName,  args )

doClose ( cmdName,  args )

doBond ( cmdName,  args )

doSelect ( cmdName,  args )

doVdwDefine ( cmdName,  args )

error ( error )

doSurfaceDelete ( cmdName,  args )

doTColor ( cmdName,  args )

doMatrixset ( cmdName,  args )

makeCommand ( text )

doResrepr ( cmdName,  args )

doSurfaceRepr ( cmdName,  args )

doPop ( cmdName,  args )

doSurfaceNew ( cmdName,  args )

doAtomSpecFunc ( cmdName,  args )

doStereo ( cmdName,  args )

allModelSelect (
        activity,
        ids=None,
        id=None,
        subid=None,
        )

a select where all models with the proper ids are activated

activity: boolean controlled whether to activate or deactivate

ids: a string. Either all or comma-seperated model ids/subids; if all and activity is True, activate all models and remember previous activation states; if all and activity is False, restore remembered activation states; otherwise parsed into individual id/subids and this routine called again for each one

id: model id to activate/deactivate. If subid is None, then all' submodels. if None (and ids is None), then all models.

subid: used in tandem with id

doUnselect ( cmdName,  args )

doCd ( cmdName,  args )

doLabelopt ( cmdName,  args )

doMatch ( cmdName,  args )

doColor ( cmdName,  args )

doRainbow ( cmdName,  args )

doRescolor ( cmdName,  args )

doReset ( cmdName,  args )

doSurface ( cmdName,  args )

doRangeColor ( cmdName,  args )

doUnclip ( cmdName,  args )

doX3DSave ( cmdName,  args )

doUndistance ( cmdName,  args )

doHelp ( cmdName,  args )

getModelId ( s )

doWrite ( cmdName,  args )

doColordef ( cmdName,  args )

doLabel ( cmdName,  args )

doPdbrun ( cmdName,  args )

doExtensionFunc (
        extFunc,
        typed,
        invalid=[],
        specInfo=[],
        )

Call a function based on user-typed arguments

doExtensionFunc introspects the function extFunc to determine its positional and keyword arguments. The first arguments in the user-typed typed string are taken as the positional arguments, and the remainder of the string is assumed to be (space separated, quoting handled) key/value pairs and are matched up to the appropriate keywords. invalid is a list of arguments that are not valid for the user to provide and are therefore screened from the introspected arguments. specInfo is a list of 3-tuples specifying keyword (only) arguments that expect lists of atoms/residues/models as values and that therefore are typed as atom specifiers. Each 3-tuple consists of:

• The keyword the user types (should end in "spec") - The real keyword used by the function (this will automatically be added to invalid) - The method name applied to the selection generated by the specifier to extract the desired list (typically atoms, residues, molecules, or models)

Keyword argment names can be typed in any case by the user and will be matched to the appropriate keyword regardless of its case.

The user need only type enough characters to uniquely distinguish a keyword argument name. Nonetheless, you may want to provide a "front end" function to your actual workhorse function, where the keyword arguments have more user-friendly names.

Arguments values use some heuristic rules to convert to their most "natural" type. However, argument names can influence how the value is handled. In particular, if the argument name ends in...

• "color": the argument is treated as a color name and converted to a MaterialColor - "spec": the argument is assumed to be an atom specifier and the value type is a Selection - "file": the argument is file; the user can provide "browse" or "browser" as the typed value and get a file browser for choosing the file. If the argment name ends in "savefile", a save-style browser will be used.