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Class for presenting a Midas command line
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Methods
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NoStereo
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NoStereo (
self,
cmdName,
args,
)
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Exceptions
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IOError, 'Stereo must be be enabled at chimera startup ' 'with the --stereo command-line option. ' 'Stereo cannot be turned on and off within chimera. ' 'See the User\'s Guide for further information.'
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NoVdwopt
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NoVdwopt (
self,
cmdName,
args,
)
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Exceptions
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IOError, '"vdwopt" is not yet implemented.\n\n' 'However, "vdwopt density" is available as "vdwdensity"\n' 'and "vdwopt define" is available as "vdwdefine".'
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Unimplemented
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Unimplemented (
self,
cmdName,
args,
)
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Exceptions
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IOError, '"%s" is not yet implemented' %( cmdName )
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__init__
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__init__ ( self )
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activeHandler
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activeHandler (
self,
triggerName,
myData,
trigData,
)
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cmdClear
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cmdClear ( self, event=None )
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cmdReplace
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cmdReplace ( self, cmd )
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doAlias
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doAlias (
self,
cmdName,
args,
)
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Exceptions
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IOError, "No such alias: '%s'" % parts [ 0 ]
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doArglessFunc
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doArglessFunc (
self,
cmdName,
args,
)
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Exceptions
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IOError, "'%s' function takes no arguments" % cmdName
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doAtomSpecFunc
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doAtomSpecFunc (
self,
cmdName,
args,
)
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doCd
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doCd (
self,
cmdName,
args,
)
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doClip
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doClip (
self,
cmdName,
args,
)
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Exceptions
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IOError, '"Unit-less" clip not implemented'
IOError, 'clip plane must be "hither" or "yon"'
IOError, 'required clipping plane argument missing'
IOError, 'wait_frames argument not implemented'
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doClose
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doClose (
self,
cmdName,
args,
)
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Exceptions
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IOError, "argument must be model number or 'all'"
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doCofr
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doCofr (
self,
cmdName,
args,
)
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doColor
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doColor (
self,
cmdName,
args,
)
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doColordef
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doColordef (
self,
cmdName,
args,
)
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Exceptions
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IOError, "Too few arguments to colordef"
IOError, 'argument must be a color name, RGB, or RGBA value'
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doConic
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doConic (
self,
cmdName,
args,
)
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doCopy
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doCopy (
self,
cmdName,
args,
)
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Exceptions
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IOError, "%s keyword not implemented" % argWords [ 0 ]
IOError, "Keyword argument (to '%s') missing" % argWords [ 0 ]
IOError, "Unknown copy keyword '%s'" % argWords [ 0 ]
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doEcho
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doEcho (
self,
cmdName,
args,
)
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doHelp
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doHelp (
self,
cmdName,
args,
)
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Exceptions
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IOError, 'No help for topic "%s"' % args
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doKsdssp
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doKsdssp (
self,
cmdName,
args,
)
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doLabelopt
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doLabelopt (
self,
cmdName,
args,
)
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Exceptions
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IOError, 'unknown option "%s"' % argWords [ 0 ]
IOError, 'unknown value ("%s") for option "info"' % argWords [ 1 ]
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doLinewidth
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doLinewidth (
self,
cmdName,
args,
)
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Exceptions
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IOError, 'No linewidth specified'
IOError, 'width must be numeric'
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doLoad
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doLoad (
self,
cmdName,
args,
)
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doLongbond
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doLongbond (
self,
cmdName,
args,
)
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Exceptions
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IOError, 'argument to -l or -r must be numeric'
IOError, 'bad arguments: try "help longbond" for info'
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doMatch
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doMatch (
self,
cmdName,
args,
)
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Exceptions
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IOError, 'two separate atom specs required'
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doMatrixcopy
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doMatrixcopy (
self,
cmdName,
args,
)
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doModelFunc
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doModelFunc (
self,
cmdName,
args,
)
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doMove
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doMove (
self,
cmdName,
args,
)
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Exceptions
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IOError, 'required distance argument missing'
IOError, 'required motion axis argument missing'
IOError, 'wait_frames argument not implemented'
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doMsMs
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doMsMs (
self,
cmdName,
args,
)
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Exceptions
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IOError, 'missing category name'
IOError, 'unknown msms keyword "%s"' % argWords [ 0 ]
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doNeon
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doNeon (
self,
cmdName,
args,
)
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doOpen
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doOpen (
self,
cmdName,
args,
)
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Exceptions
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IOError, 'opening surfaces unimplemented'
IOError, 'required file name argument missing'
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doPdbrun
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doPdbrun (
self,
cmdName,
args,
)
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Exceptions
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IOError, "'mark=' not yet implemented"
IOError, "command to execute missing"
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doPreneon
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doPreneon (
self,
cmdName,
args,
)
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doRepr
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doRepr (
self,
cmdName,
args,
)
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Exceptions
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IOError, "missing representation argument"
IOError, 'unknown representation type ("%s")' % argWords [ 0 ]
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doReset
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doReset (
self,
cmdName,
args,
)
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doRibbonjr
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doRibbonjr (
self,
cmdName,
args,
)
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doRock
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doRock (
self,
cmdName,
args,
)
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Exceptions
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IOError, "axis must be 'x', 'y', or 'z'"
IOError, 'wait_frames argument not implemented'
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doRoll
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doRoll (
self,
cmdName,
args,
)
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Exceptions
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IOError, 'turning bond rotations not implemented'
IOError, 'wait_frames argument not implemented'
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doSave
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doSave (
self,
cmdName,
args,
)
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doSavepos
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doSavepos (
self,
cmdName,
args,
)
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doScale
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doScale (
self,
cmdName,
args,
)
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Exceptions
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IOError, 'required scaling factor argument missing'
IOError, 'wait_frames argument not implemented'
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doSection
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doSection (
self,
cmdName,
args,
)
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Exceptions
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IOError, 'required distance argument missing'
IOError, 'wait_frames argument not implemented'
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doSelect
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doSelect (
self,
cmdName,
args,
)
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doSet
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doSet (
self,
cmdName,
args,
)
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Exceptions
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IOError, "No keywords given to 'set' command"
IOError, 'no such "set" variable (or not implemented): %s' % argWords [ 0 ]
IOError, 'no value given for "set %s"' % argWords [ 0 ]
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doSleep
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doSleep (
self,
cmdName,
args,
)
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doSource
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doSource (
self,
cmdName,
args,
)
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Exceptions
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IOError, 'multiple source files not supported'
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doStop
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doStop (
self,
cmdName,
args,
)
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doSurface
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doSurface (
self,
cmdName,
args,
)
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doSurfaceCategory
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doSurfaceCategory (
self,
cmdName,
args,
)
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doSurfaceColor
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doSurfaceColor (
self,
cmdName,
args,
)
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Exceptions
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IOError, 'unknown surface color mode ("%s")' % argWords [ 0 ]
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doSurfaceDelete
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doSurfaceDelete (
self,
cmdName,
args,
)
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doSurfaceNew
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doSurfaceNew (
self,
cmdName,
args,
)
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doSurfaceRepr
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doSurfaceRepr (
self,
cmdName,
args,
)
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Exceptions
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IOError, 'unknown representation type ("%s")' % argWords [ 0 ]
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doSwapRes
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doSwapRes (
self,
cmdName,
args,
)
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Exceptions
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IOError, 'Usage: swapaa|swapna ' 'new_res_type[,preserve] atomspec'
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doSystem
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doSystem (
self,
cmdName,
args,
)
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doTColor
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doTColor (
self,
cmdName,
args,
)
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doTexture
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doTexture (
self,
cmdName,
args,
)
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Exceptions
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IOError, "Left side of map must be an integer"
IOError, "Too many arguments for texture new command"
IOError, 'No "=" found in assignment string'
IOError, 'unknown texture keyword "%s"' % argWords [ 0 ]
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doThickness
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doThickness (
self,
cmdName,
args,
)
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Exceptions
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IOError, 'clip plane separation reporting not implemented'
IOError, 'wait_frames argument not implemented'
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doUnalias
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doUnalias (
self,
cmdName,
args,
)
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doUnclip
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doUnclip (
self,
cmdName,
args,
)
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Exceptions
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IOError, 'required clipping plane argument missing'
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doUncolor
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doUncolor (
self,
cmdName,
args,
)
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doUndistance
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doUndistance (
self,
cmdName,
args,
)
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doUnsavepos
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doUnsavepos (
self,
cmdName,
args,
)
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doUnselect
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doUnselect (
self,
cmdName,
args,
)
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doUnset
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doUnset (
self,
cmdName,
args,
)
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Exceptions
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IOError, "No keywords given to 'set' command"
IOError, 'no such "unset" variable (or not implemented): %s' % argWords [ 0 ]
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doUnsurface
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doUnsurface (
self,
cmdName,
args,
)
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doVdwDefine
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doVdwDefine (
self,
cmdName,
args,
)
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Exceptions
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IOError, 'Usage: ' 'vdwdefine residueType atomName radius [atomSpec]'
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doVdwDensity
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doVdwDensity (
self,
cmdName,
args,
)
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Exceptions
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IOError, "missing density argument required"
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doWait
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doWait (
self,
cmdName,
args,
)
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doWindow
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doWindow (
self,
cmdName,
args,
)
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doWrite
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doWrite (
self,
cmdName,
args,
)
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Exceptions
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IOError, "usage: write [relative m] n filename"
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error
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error ( self, error )
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expandAliases
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expandAliases ( self, text )
expand aliases
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getSpecs
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getSpecs (
self,
args,
modelLevel=0,
)
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getWriteModel
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getWriteModel ( self, s )
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Exceptions
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IOError, "\"%s\" is not a model number" % s
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graphicsKeyboardCB
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graphicsKeyboardCB ( self, event )
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hide
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hide ( self )
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makeCommand
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makeCommand ( self, text )
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Exceptions
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IOError, 'Unrecognized command: "%s"' % cmd
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message
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message ( self, msg )
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processCommand
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processCommand ( self, eventOrString )
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selButtonPush
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selButtonPush ( self, which )
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show
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show ( self )
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sourceCallback
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sourceCallback ( self, filename )
called by Midas module's source function
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warn
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warn ( self, warning )
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