|
|
represent
|
represent ( style, sel=None )
|
Exceptions
|
|
|
MidasError( 'Unknown representation style "%s"' % style )
|
|
|
|
surfaceDelete
|
surfaceDelete ( category, sel=None )
|
|
|
chain
|
chain ( *args, *kw )
|
|
|
show
|
show ( sel=None, asChain=None )
|
|
|
move
|
move (
x=None,
y=None,
z=None,
frames=None,
)
|
|
|
focus
|
focus ( sel=None )
|
Exceptions
|
|
|
MidasError( "No displayed atoms/ribbons/surfaces specified" )
|
|
|
|
modeldisplay
|
modeldisplay ( sel=None )
|
|
|
modelcolor
|
modelcolor ( color, sel=None )
|
|
|
linewidth
|
linewidth ( width, sel=None )
|
|
|
rotation
|
rotation ( sel=None, reverse=None )
|
Exceptions
|
|
|
MidasError('Only two atoms must be selected.' ' You selected %d.' % len( atoms ) )
MidasError( 'Selected atoms are not connected' ' with a covalent bond' )
|
|
|
|
unribbon
|
unribbon ( sel=None )
|
|
|
ksdssp
|
ksdssp (
sel=None,
energy=None,
helixLen=None,
strandLen=None,
infoFile=None,
)
|
|
|
swapres
|
swapres (
newRes,
sel=None,
preserve=None,
bfactor=None,
)
|
Exceptions
|
|
|
MidasError( v )
MidasError( "No residues specified for swapping" )
|
|
|
|
ribrepr
|
ribrepr ( style, sel=None )
|
Exceptions
|
|
|
MidasError( 'Unknown representation style "%s"' % style )
|
|
|
|
setDc_color
|
setDc_color ( color )
|
|
|
rlabel
|
rlabel ( sel=None )
|
|
|
surfaceNew
|
surfaceNew (
category,
sel=None,
models=None,
)
|
|
|
ribcolor
|
ribcolor ( color, sel=None )
|
|
|
surfaceVisibilityByAtom
|
surfaceVisibilityByAtom ( atoms )
|
|
|
evalSpec
|
evalSpec ( spec )
|
|
|
undistance
|
undistance ( sel=None )
|
Exceptions
|
|
|
MidasError('Exactly two atoms must be selected. You ' 'selected %d.' % len( atoms ) )
MidasError( 'Error removing distance: %s.' % s )
|
|
|
|
ribbackbone
|
ribbackbone ( sel=None )
|
|
|
surfacetransparency
|
surfacetransparency ( val, sel=None )
|
|
|
matrixget
|
matrixget ( fileName )
|
|
|
vdwdensity
|
vdwdensity ( density, sel=None )
|
|
|
unribinsidecolor
|
unribinsidecolor ( which, sel=None )
|
|
|
setBg_color
|
setBg_color ( color )
|
|
|
atomMSMSModels
|
atomMSMSModels ( atoms )
|
|
|
rock
|
rock (
axis,
magnitude=None,
frequency=None,
frames=None,
)
|
|
|
colordef
|
colordef ( color, target )
|
Exceptions
|
|
|
MidasError( 'Color "%s" is undefined' % target )
MidasError( "Cannot define a color named '%s'" % color )
MidasError( 'Choose color in panel first' )
|
|
|
|
bond
|
bond ( sel=None )
|
Exceptions
|
|
|
MidasError("Choose only 2 atoms to bond (%d chosen)" % len( bonded ) )
|
|
|
|
textureUse
|
textureUse ( name )
|
Exceptions
|
|
|
KeyError, "No texture named '" + name + "' exists"
|
|
|
|
thickness
|
thickness ( delta, frames=None )
|
|
|
export
|
export (
filename=None,
format=None,
list=None,
)
|
Exceptions
|
|
|
MidasError( 'Unknown export format: %s' % format )
ValueError( "Cannot use argless 'export' command in nogui mode" )
|
|
|
|
ribinsidecolor
|
ribinsidecolor ( color, sel=None )
|
|
|
undisplay
|
undisplay ( sel=None )
|
|
|
close
|
close ( model, subid=None )
|
|
|
ribbon
|
ribbon ( sel=None )
|
|
|
rangeColor
|
rangeColor (
attrName,
colorItems,
wayPoints,
noValue,
sel=None,
)
|
|
|
scale
|
scale ( s, frames=None )
|
|
|
elementColor
|
elementColor ( element )
|
|
|
boundingSphere
|
boundingSphere ( sel )
|
|
|
section
|
section ( delta, frames=None )
|
|
|
label
|
label ( sel=None, warnLarge=None )
|
|
|
textureMap
|
textureMap ( **kw )
|
Exceptions
|
|
|
TypeError, "Unexpected keyword argument: " + key
IndexError, "Index (%d) out of bounds for current texture" % index
|
|
|
|
labelopt
|
labelopt ( opt, value )
|
|
|
x3dSave
|
x3dSave ( filename )
|
|
|
surfaceCategory
|
surfaceCategory ( category, sel=None )
|
|
|
unlabel
|
unlabel ( sel=None )
|
|
|
deleteAtomsBonds
|
deleteAtomsBonds ( atoms=None, bonds=None )
General utility functions
|
|
|
convertColor
|
convertColor ( color )
|
Exceptions
|
|
|
RuntimeError, 'need a color'
UserError( 'Choose color in panel first' )
UserError( 'Color "%s" is undefined' % color )
|
|
|
|
ribscale
|
ribscale ( name, sel=None )
|
Exceptions
|
|
|
MidasError( 'Unknown ribbon scaling "%s"' % name )
|
|
|
|
wait
|
wait ( frames=None )
|
|
|
objdisplay
|
objdisplay ( sel=None )
|
|
|
pdbrun
|
pdbrun (
cmd,
all=None,
conect=None,
nouser=None,
noobj=None,
nowait=None,
surface=None,
mark=None,
viewer=None,
)
|
|
|
longbond
|
longbond (
ratio=None,
length=None,
sel=None,
)
|
Exceptions
|
|
|
MidasError( "Missing segments already shown." " Use ~longbond to hide them." )
|
|
|
|
addaa
|
addaa ( args )
|
Exceptions
|
|
|
MidasError, "Exactly one residue must be selected. " "'%s' specifies %d residues." %(res_spec, len( residues ) )
MidasError, "Invalid number of arguments."
MidasError, "Missing residue type argument"
MidasError, "%s" % what
MidasError, "Not enough arguments. " "Require at least 'residue type' and 'residue sequence'"
MidasError, "Require either both phi and psi arguments or neither"
MidasError, "Too many arguments"
MidasError, "Missing residue sequence argument"
|
|
|
|
chimeraSelect
|
chimeraSelect ( sel=None )
|
|
|
color
|
color ( color, sel=None )
|
|
|
pop
|
pop ( frames=None, mode=None )
|
Exceptions
|
|
|
MidasError( 'No pushed positions to pop' )
MidasError( "frame count must be positive" )
|
|
|
|
unbondcolor
|
unbondcolor ( sel=None )
|
|
|
unribbackbone
|
unribbackbone ( sel=None )
|
|
|
open
|
open (
filename,
filetype=None,
model=None,
noprefs=None,
)
|
|
|
select
|
select ( sel=None )
|
|
|
windowsize
|
windowsize ( wh=None )
|
|
|
unvdwdefine
|
unvdwdefine ( sel=None )
|
|
|
chirality
|
chirality ( sel=None )
|
Exceptions
|
|
|
ChiralError("%s bonds to less than 4 atoms" % a.oslIdent() )
ChiralError( "No atoms specified" )
ChiralError("%s is not tetrahedral" % a.oslIdent() )
ChiralError("Unknown hybridization state for atom %s" % a.oslIdent() )
|
|
|
|
window
|
window ( sel=None )
|
|
|
unsetAutocolor
|
unsetAutocolor ()
|
|
|
unrlabel
|
unrlabel ( sel=None )
|
|
|
surfacecolormode
|
surfacecolormode ( style, sel=None )
|
Exceptions
|
|
|
MidasError( 'Unknown surface color mode "%s"' % style )
|
|
|
|
ringrepr
|
ringrepr ( style, sel=None )
|
Exceptions
|
|
|
MidasError( 'Unknown ring representation "%s"' % style )
|
|
|
|
namesel
|
namesel ( selName=None )
|
|
|
matrixcopy
|
matrixcopy ( f, t )
|
Exceptions
|
|
|
MidasError( 'Too many source models selected.' )
MidasError( 'No source models selected.' )
MidasError( 'No destination model(s) selected.' )
|
|
|
|
copy
|
copy (
printer=None,
file=None,
format=None,
viewer=None,
supersample=None,
raytrace=None,
rtwait=None,
rtclean=None,
)
|
|
|
brotation
|
brotation ( sel=None )
|
|
|
reset
|
reset (
name=None,
frames=None,
mode=None,
)
|
Exceptions
|
|
|
MidasError( "No saved position named '%s'" % name )
MidasError( "frame count must be positive" )
|
|
|
|
distance
|
distance ( sel=None )
|
Exceptions
|
|
|
MidasError('Exactly two atoms must be selected. You ' 'selected %d.' % len( atoms ) )
MidasError( 'Error adding distance: %s.' % s )
|
|
|
|
unsurface
|
unsurface ( sel=None )
|
|
|
bondrepr
|
bondrepr ( style, sel=None )
|
Exceptions
|
|
|
MidasError( 'Unknown representation style "%s"' % style )
|
|
|
|
align
|
align ( sel, sel2=None )
|
Exceptions
|
|
|
MidasError( 'Exactly two atoms must be selected' ' by atom spec or two atom specs provided.' )
MidasError( "Left atom spec (%s) selects no atoms" % sel1 )
MidasError( "Right atom spec (%s) selects no atoms" % sel2 )
|
|
|
|
savepos
|
savepos ( name=None )
|
|
|
unribcolor
|
unribcolor ( which, sel=None )
|
|
|
match
|
match (
f,
t,
selected=None,
iterate=None,
minPoints=None,
)
|
Exceptions
|
|
|
MidasError( "Iteration cutoff must be positive" )
TooFewAtomsError("Too few corresponding atoms" " (%d) to match models\n" % len( refAtoms ) )
|
|
|
|
unlongbond
|
unlongbond ()
|
Exceptions
|
|
|
MidasError( "Missing segments already hidden." " Use longbond to show them." )
|
|
|
|
surfacerepresent
|
surfacerepresent ( style, sel=None )
|
Exceptions
|
|
|
MidasError( 'Unknown surface representation style "%s"' % style )
|
|
|
|
matrixset
|
matrixset ( fileName )
|
Exceptions
|
|
|
MidasError( v )
MidasError("Matrixset 'Model' line %d not of the" " form: Model number.number" %( i + 1 ) )
MidasError("Matrixset 3x4 matrix line %d" " is not 4 numbers" %( j + 1 ) )
MidasError( "Matrixset file not composed of 4-line groups" " (model numbers each with a 3x4 matrix)" )
|
|
|
|
display
|
display ( sel=None )
|
|
|
delete
|
delete ( sel=None )
|
|
|
clip
|
clip (
plane,
delta,
frames=None,
)
|
|
|
surface
|
surface (
atomSpec=None,
category=None,
warnLarge=None,
)
|
|
|
textureNew
|
textureNew ( name, numColors=None )
|
Exceptions
|
|
|
ValueError, "Number of colors for texture must be 4 or 5"
AttributeError, "Texture named " + name + " already exists"
|
|
|
|
getcrd
|
getcrd ( sel=None )
|
|
|
rainbow
|
rainbow ( sel=None, **kw )
|
|
|
angle
|
angle ( sel=None )
|
Exceptions
|
|
|
MidasError('Three or four atoms must be selected. You ' 'selected %d.' % len( atoms ) )
|
|
|
|
unsavepos
|
unsavepos ( name )
|
Exceptions
|
|
|
MidasError( "No position named '%s'" % name )
|
|
|
|
turn
|
turn (
axis,
angle=None,
frames=None,
)
|
|
|
cofr
|
cofr ( where=None )
|
Exceptions
|
|
|
MidasError( 'No atoms or surfaces selected' )
|
|
|
|
unsetIndependent
|
unsetIndependent ()
|
|
|
unbond
|
unbond ( sel=None )
|
|
|
vdwdefine
|
vdwdefine (
radius,
sel=None,
increment=None,
)
|
|
|
write
|
write (
writeModel,
relModel,
filename,
allFrames=None,
dispOnly=None,
selOnly=None,
format=None,
)
|
Exceptions
|
|
|
MidasError( v )
MidasError( "Trajectories cannot be written in" " Mol2 format" )
MidasError, "%d model ids match \"%s\"" %( len( mList ), s )
|
|
|
|
unsetAttr
|
unsetAttr (
level,
name,
sel=None,
)
|
Exceptions
|
|
|
MidasError( "Cannot set attribute '%s' to None" % name )
|
|
|
|
bondcolor
|
bondcolor ( color, sel=None )
|
|
|
roll
|
roll (
axis,
angle=None,
frames=None,
)
|
|
|
setAutocolor
|
setAutocolor ()
|
|
|
setAttr
|
setAttr (
level,
name,
val,
sel=None,
)
|
|
|
uncolor
|
uncolor ( which, sel=None )
|
|
|
unchimeraSelect
|
unchimeraSelect ( sel=None )
|
|
|
bonddisplay
|
bonddisplay ( mode, sel=None )
|
|
|
unobjdisplay
|
unobjdisplay ( sel )
|
|
|
setIndependent
|
setIndependent ()
|
|
|
stereo
|
stereo ( mode )
|
Exceptions
|
|
|
MidasError( "Unknown stereo mode: %s" % mode )
MidasError( "Could not switch to stereo mode: %s" % mode )
|
|
|
|
unmodeldisplay
|
unmodeldisplay ( sel=None )
|
|
|
center
|
center ( sel=None )
|
|
|
unselect
|
unselect ( sel=None )
|
|
|
textureColor
|
textureColor ( index, color )
|
|
|
tColor
|
tColor ( index, sel=None )
|
Exceptions
|
|
|
MidasError( 'Cannot texture color byatom/byhet' ' (too many colors required)' )
UserError( 'Texture color "%s" is undefined' % index )
|
|
|