HappyDoc Generated Documentation ./Midas

. / Midas 

Functions   
  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 )
Exceptions   

MidasError( e )

  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 )
Exceptions   

MidasError( e )

  rlabel 
rlabel ( sel=None )
  surfaceNew 
surfaceNew (
        category,
        sel=None,
        models=None,
        )
  ribcolor 
ribcolor ( color,  sel=None )
Exceptions   

MidasError( e )

  surfaceVisibilityByAtom 
surfaceVisibilityByAtom ( atoms )
  save 
save ( filename )
  evalSpec 
evalSpec ( spec )
Exceptions   

MidasError, "mangled atom specifier"

  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 )
  rmsd 
rmsd ( f,  t )
  vdwdensity 
vdwdensity ( density,  sel=None )
  unribinsidecolor 
unribinsidecolor ( which,  sel=None )
  setBg_color 
setBg_color ( color )
Exceptions   

MidasError( e )

  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"

  version 
version ()
  thickness 
thickness ( delta,  frames=None )
  freeze 
freeze ()
  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 )
Exceptions   

MidasError( e )

  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 )
Exceptions   

MidasError( e )

  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,
        )
Exceptions   

MidasError(str( msg ) )

  select 
select ( sel=None )
  windowsize 
windowsize ( wh=None )
  unclip 
unclip ( plane )
  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 )
Exceptions   

MidasError( "Nothing to window" )

  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 )
  uncofr 
uncofr ()
  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"

  unscale 
unscale ()
  getcrd 
getcrd ( sel=None )
  rainbow 
rainbow ( sel=None,  **kw )
  vdw 
vdw ( sel=None )
  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,
        )
  unvdw 
unvdw ( sel=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 )
Exceptions   

MidasError( e )

  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 ()
  model 
model ( n )
  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 )
Exceptions   

MidasError( 'No atoms selected' )

  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 )

  push 
push ()
Classes   

MidasError

TooFewAtomsError

Python files   

ChimeraExtension.py

addAA.py

chiral.py

gui.py

midas_rainbow.py

midas_text.py

midas_ui.py


This document was automatically generated Wed Jul 9 15:49:38 2008 by HappyDoc version 3.1