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/ . / Midas / midas_text.py
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Functions
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doNeon
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doNeon ( cmdName, args )
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doPreneon
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doPreneon ( cmdName, args )
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doEcho
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doEcho ( cmdName, args )
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doSystem
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doSystem ( cmdName, args )
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NoVdwopt
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NoVdwopt ( cmdName, args )
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doSurfaceCategory
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doSurfaceCategory ( cmdName, args )
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doTexture
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doTexture ( cmdName, args )
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Exceptions
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MidasError, 'No "=" found in assignment string'
MidasError, 'unknown texture keyword "%s"' % argWords [ 0 ]
MidasError, "Too many arguments for texture new command"
MidasError, "Left side of map must be an integer"
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doSleep
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doSleep ( cmdName, args )
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Unimplemented
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Unimplemented ( cmdName, args )
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Exceptions
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MidasError, '"%s" is not yet implemented' %( cmdName )
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doStop
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doStop ( cmdName, args )
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doUnPerFrame
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doUnPerFrame ( cmdName, args )
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Exceptions
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MidasError( "No per-frame alias active" )
MidasError( "Usage: %s" % cmdName )
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doMatrixcopy
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doMatrixcopy ( cmdName, args )
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Exceptions
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MidasError, 'two model numbers required'
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doCopy
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doCopy ( cmdName, args )
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Exceptions
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MidasError, "%s keyword not implemented" % argWords [ 0 ]
MidasError, "Argument (to '%s') missing" % argWords [ 0 ]
MidasError, "supersample" " argument must be positive integer"
MidasError, "Unknown copy keyword '%s'" % argWords [ 0 ]
ValueError, ""
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doUnsurface
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doUnsurface ( cmdName, args )
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doNamesel
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doNamesel ( cmdName, args )
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doUnalias
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doUnalias ( cmdName, args )
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Exceptions
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MidasError, "No such alias ('%s)" % args
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doStart
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doStart ( cmdName, args )
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Exceptions
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MidasError, "Please specify the name of an extension"
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doSet
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doSet ( cmdName, args )
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Exceptions
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MidasError, 'no such "set" variable (or not implemented): %s' % argWords [ 0 ]
MidasError, "No keywords given to 'set' command"
MidasError, 'no value given for "set %s"' % argWords [ 0 ]
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doSource
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doSource ( cmdName, args )
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doMove
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doMove ( cmdName, args )
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Exceptions
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MidasError, 'required distance argument missing'
MidasError, 'required motion axis argument missing'
MidasError, 'wait_frames argument not implemented'
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doWait
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doWait ( cmdName, args )
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doLinewidth
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doLinewidth ( cmdName, args )
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Exceptions
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MidasError, 'No linewidth specified'
MidasError, 'width must be numeric'
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doSwapRes
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doSwapRes ( cmdName, args )
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Exceptions
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MidasError( 'Usage: swapna new_res_type[,preserve] atomspec' )
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doModelFunc
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doModelFunc ( cmdName, args )
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doSetAttr
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doSetAttr ( cmdName, args )
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doExport
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doExport ( cmdName, args )
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Exceptions
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MidasError("Extra export arguments '%s'" % ' '.join( argWords ) )
MidasError("Argument (to '%s') missing" % argWords [ 0 ] )
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doAlias
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doAlias ( cmdName, args )
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Exceptions
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MidasError, "No such alias: '%s'" % parts [ 0 ]
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doBondUncolor
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doBondUncolor ( cmdName, args )
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doAddAA
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doAddAA ( cmdName, args )
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doRMSD
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doRMSD ( cmdName, args )
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doOpen
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doOpen ( cmdName, args )
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Exceptions
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MidasError( "Cannot specify" " multiple model numbers" )
MidasError, 'No file chosen for open'
ValueError, "Cannot use argless 'open' command" "in nogui mode\n"
MidasError, 'opening surfaces unimplemented'
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doUnsavepos
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doUnsavepos ( cmdName, args )
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addCommand
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addCommand (
command,
cmdFunc,
revFunc=None,
help=None,
changesDisplay=None,
)
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doCofr
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doCofr ( cmdName, args )
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doBondDisplay
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doBondDisplay ( cmdName, args )
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doRepr
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doRepr ( cmdName, args )
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Exceptions
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MidasError, "missing representation argument"
MidasError, 'use "~ribbon" to undisplay ribbons'
MidasError, 'unknown representation type ("%s")' % argWords [ 0 ]
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doArglessFunc
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doArglessFunc ( cmdName, args )
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Exceptions
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MidasError, "'%s' function takes no arguments" % cmdName
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processCommandFile
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processCommandFile (
filename,
emulateRead=None,
usingString=None,
)
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doChirality
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doChirality ( cmdName, args )
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doClip
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doClip ( cmdName, args )
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Exceptions
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MidasError, '"Unit-less" clip not implemented'
MidasError, 'required clipping plane argument missing'
MidasError, 'wait_frames argument not implemented'
MidasError, 'clip plane must be "hither" or "yon"'
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expandAliases
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expandAliases ( text, doReport )
expand aliases
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convertType
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convertType ( value )
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doUnsetAttr
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doUnsetAttr ( cmdName, args )
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Exceptions
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MidasError( "Usage: %s atom|residue|molecule" " attrName atomspec" % cmdName )
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doLoad
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doLoad ( cmdName, args )
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Exceptions
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MidasError, 'No file chosen for load'
ValueError, "Cannot use argless 'load' command" "in nogui mode\n"
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doMsMs
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doMsMs ( cmdName, args )
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Exceptions
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MidasError, 'missing category name'
MidasError, 'unknown msms keyword "%s"' % argWords [ 0 ]
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doRoll
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doRoll ( cmdName, args )
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Exceptions
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MidasError, 'turning bond rotations not implemented'
MidasError, 'wait_frames argument not implemented'
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getSpecs
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getSpecs ( args, modelLevel=None )
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doScale
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doScale ( cmdName, args )
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Exceptions
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MidasError, 'required scaling factor argument missing'
MidasError, 'wait_frames argument not implemented'
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doSurface
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doSurface ( cmdName, args )
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doBondColor
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doBondColor ( cmdName, args )
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doUncolor
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doUncolor ( cmdName, args )
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findQuoted
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findQuoted ( text )
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Exceptions
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MidasError, "Unmatched quote in %s" % text
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doUnset
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doUnset ( cmdName, args )
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Exceptions
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MidasError, "No keywords given to 'set' command"
MidasError, 'no such "unset" variable (or not implemented): %s' % argWords [ 0 ]
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doRock
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doRock ( cmdName, args )
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Exceptions
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MidasError, "axis must be 'x', 'y', or 'z'"
MidasError, 'wait_frames argument not implemented'
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doSection
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doSection ( cmdName, args )
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Exceptions
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MidasError, 'required distance argument missing'
MidasError, 'wait_frames argument not implemented'
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doSurfaceColor
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doSurfaceColor ( cmdName, args )
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Exceptions
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MidasError( "No surface-coloring mode specified" )
MidasError('unknown surface coloring mode ("%s")' % argWords [ 0 ] )
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doWindow
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doWindow ( cmdName, args )
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doConic
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doConic ( cmdName, args )
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doUnbond
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doUnbond ( cmdName, args )
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doUnsurfaceTransparency
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doUnsurfaceTransparency ( cmdName, args )
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doLongbond
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doLongbond ( cmdName, args )
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Exceptions
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MidasError( "'longbond' command no longer takes arguments" )
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doMatrixget
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doMatrixget ( cmdName, args )
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Exceptions
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ValueError( "Cannot use argless 'matrixget'" " command in nogui mode" )
MidasError, 'No file chosen for matrixget'
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doSave
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doSave ( cmdName, args )
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Exceptions
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ValueError, "Cannot use argless 'save' command" "in nogui mode\n"
MidasError, 'No file chosen for save'
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doRead
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doRead ( cmdName, args )
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doVdwDensity
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doVdwDensity ( cmdName, args )
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Exceptions
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MidasError, "missing density argument required"
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doSavepos
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doSavepos ( cmdName, args )
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doKsdssp
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doKsdssp ( cmdName, args )
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doThickness
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doThickness ( cmdName, args )
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Exceptions
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MidasError( 'clip plane separation reporting not implemented' )
MidasError, 'wait_frames argument not implemented'
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doClose
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doClose ( cmdName, args )
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Exceptions
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MidasError( "argument must be model" " number, 'session' or 'all'" )
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doBond
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doBond ( cmdName, args )
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doSelect
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doSelect ( cmdName, args )
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doVdwDefine
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doVdwDefine ( cmdName, args )
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Exceptions
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MidasError( 'Usage: vdwdefine [+/-]radius [atomSpec]' )
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doSurfaceTransparency
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doSurfaceTransparency ( cmdName, args )
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Exceptions
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MidasError( "Transparency value must be between" " 0 and 100 (inclusive)" )
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doSurfaceDelete
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doSurfaceDelete ( cmdName, args )
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doTColor
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doTColor ( cmdName, args )
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Exceptions
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MidasError, 'No texture color specified'
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doMatrixset
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doMatrixset ( cmdName, args )
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Exceptions
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ValueError( "Cannot use argless 'matrixset'" " command in nogui mode" )
MidasError, 'No file chosen for matrixset'
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makeCommand
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makeCommand ( text, reportAliasExpansion=None )
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Exceptions
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MidasError, 'Unrecognized command: "%s"' % cmd
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doResrepr
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doResrepr ( cmdName, args )
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Exceptions
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MidasError, "Resrepr command removed. Use ribbon command to show ribbons. Use ribrepr command to set ribbon styles."
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doSurfaceRepr
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doSurfaceRepr ( cmdName, args )
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Exceptions
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MidasError("Must specify repr type (one of: %s)" % ", ".join( styles ) )
MidasError('Unknown representation type ("%s")' % argWords [ 0 ] )
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doPop
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doPop ( cmdName, args )
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doSurfaceNew
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doSurfaceNew ( cmdName, args )
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doAtomSpecFunc
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doAtomSpecFunc ( cmdName, args )
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doStereo
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doStereo ( cmdName, args )
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Exceptions
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MidasError, 'Unrecognized stereo mode: %s' % args
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allModelSelect
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allModelSelect (
activity,
ids=None,
id=None,
subid=None,
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Exceptions
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MidasError, "Could not parse model list"
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doUnselect
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doUnselect ( cmdName, args )
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doCd
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doCd ( cmdName, args )
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doLabelopt
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doLabelopt ( cmdName, args )
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Exceptions
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MidasError, "too many arguments to labelopt"
MidasError, 'unknown option "%s"' % argWords [ 0 ]
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doMatch
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doMatch ( cmdName, args )
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Exceptions
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MidasError( "'iterate' argument must be" " a number" )
MidasError( "'iterate' keyword requires" " cutoff distance argument" )
MidasError( "'iterate' argument must be" " a positive number" )
MidasError, 'missing atom spec'
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doColor
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doColor ( cmdName, args )
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doRainbow
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doRainbow ( cmdName, args )
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doRescolor
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doRescolor ( cmdName, args )
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Exceptions
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MidasError, "Rescolor command removed. Use ribcolor command to set ribbon colors."
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doReset
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doReset ( cmdName, args )
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doPerFrame
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doPerFrame ( cmdName, args )
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Exceptions
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MidasError( "Usage: %s alias_name [field_width]" % cmdName )
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doWindowsize
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doWindowsize ( cmd_name, args )
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Exceptions
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MidasError, 'Syntax error: %s [ ]' % cmd_name
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testPath
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testPath ( text, wildcarding )
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doRangeColor
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doRangeColor ( cmdName, args )
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Exceptions
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MidasError, "Missing required args (try 'help %s')" % cmdName
MidasError, "Less than two value/color pairs provided (try 'help %s')" % cmdName
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doUnclip
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doUnclip ( cmdName, args )
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Exceptions
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MidasError, "mangled clipping plane name: %s" % args
MidasError, 'required clipping plane argument missing'
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doLabel
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doLabel ( cmdName, args )
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doX3DSave
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doX3DSave ( cmdName, args )
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Exceptions
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ValueError, "Cannot use argless 'x3dsave' " "command in nogui mode\n"
MidasError, 'No file chosen for save'
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doUndistance
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doUndistance ( cmdName, args )
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doHelp
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doHelp ( cmdName, args )
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Exceptions
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MidasError, "Cannot provide help for unknown command '%s'" % args
MidasError, 'No help available for "%s"' % args
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getModelId
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getModelId ( s )
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Exceptions
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MidasError, "\"%s\" is not a model number" % s
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doPreset
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doPreset ( cmdName, args )
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Exceptions
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MidasError, s
MidasError, "unknown subcommand '%s' for 'preset'" % cmd
MidasError( "usage: preset apply|list ..." )
MidasError( "usage: preset apply type number" )
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doWrite
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doWrite ( cmdName, args )
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Exceptions
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MidasError, "writing surfaces not yet supported"
MidasError, 'No file chosen for write'
ValueError, "Cannot use argless 'write' command" "in nogui mode\n"
MidasError( "Must supply model number as an argument" )
MidasError( "'format' value must either" " be 'pdb' or 'mol2'" )
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doColordef
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doColordef ( cmdName, args )
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Exceptions
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MidasError, "Too few arguments to colordef"
MidasError, 'argument must be a color name, RGB, or RGBA value'
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doPdbrun
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doPdbrun ( cmdName, args )
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Exceptions
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MidasError, "'mark=' not yet implemented"
MidasError, "command to execute missing"
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doExtensionFunc
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doExtensionFunc (
extFunc,
typed,
invalid=None,
specInfo=None,
)
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Exceptions
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MidasError, "Missing required argument(s): %s" %(", ".join( missingTyped ) )
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