HappyDoc Generated Documentation .\Midas

. / Midas 

Emulate UCSF Midas command set

Functions   
  represent 
represent ( style,  sel='sel' )
Exceptions   

MidasError( 'Unknown representation style "%s"' % style )

  surfaceDelete 
surfaceDelete ( category,  sel='sel' )
  chain 
chain ( *args,  *kw )
  show 
show ( sel='sel',  asChain=0 )
  move 
move (
        x=0,
        y=0,
        z=0,
        frames=None,
        )
  focus 
focus ( sel='sel' )

Window/cofr about displayed part of selection

Exceptions   

MidasError( "No displayed atoms/bonds/ribbons specified" )

  matrixget 
matrixget ( fileName )
  modeldisplay 
modeldisplay ( sel='sel' )
  modelcolor 
modelcolor ( color,  sel='sel' )

Change model color

Exceptions   

MidasError( e )

  linewidth 
linewidth ( width,  sel='sel' )
  unribbon 
unribbon ( sel='sel' )
  ksdssp 
ksdssp (
        sel='sel',
        energy=None,
        helixLen=None,
        strandLen=None,
        infoFile=None,
        )
  swapres 
swapres (
        newRes,
        sel='sel',
        preserve=0,
        bfactor=None,
        )
Exceptions   

MidasError( '"preserve" keyword not yet implemented' )
MidasError( "No residues specified for swapping" )

  ribrepr 
ribrepr ( style,  sel='sel' )
Exceptions   

MidasError( 'Unknown representation style "%s"' % style )

  setDc_color 
setDc_color ( color )
Exceptions   

MidasError( e )

  rlabel 
rlabel ( sel='sel' )

Display residue information as part of one atom label

  surfaceNew 
surfaceNew (
        category,
        sel='sel',
        models=None,
        )
  ribcolor 
ribcolor ( color,  sel='sel' )

Change ribbon color

Exceptions   

MidasError( e )

  surfaceCategory 
surfaceCategory ( category,  sel='sel' )
  save 
save ( filename )
  evalSpec 
evalSpec ( spec )
Exceptions   

MidasError, "mangled atom specifier"

  undistance 
undistance ( sel='sel' )

Remove distance monitor

Exceptions   

MidasError('Exactly two atoms must be selected. You ' 'selected %d.' % len( atoms ) )
MidasError( 'Error removing distance: %s.' % s )

  ribbackbone 
ribbackbone ( sel='sel' )
  rotation 
rotation ( sel='sel',  reverse=False )
Exceptions   

MidasError('Only two atoms must be selected.' ' You selected %d.' % len( atoms ) )
MidasError( 'Selected atoms are not connected' ' with a covalent bond' )

  rmsd 
rmsd ( f,  t )
  vdwdensity 
vdwdensity ( density,  sel='sel' )

Change vdw surface point density

  setBg_color 
setBg_color ( color )
Exceptions   

MidasError( e )

  unvdw 
unvdw ( sel='sel' )

Display point vdw surface of atoms

Atoms specification may come from either a selection or an osl string. If no atom specification is supplied, the current selection is displayed.

  rock 
rock (
        axis,
        magnitude=90,
        frequency=60,
        frames=-1,
        )
  colordef 
colordef ( color,  target )

Define RGB(A) color

Exceptions   

MidasError( 'Color "%s" is undefined' % target )
MidasError( "Cannot define a color named '%s'" % color )
MidasError( 'Choose color in panel first' )

  bond 
bond ( sel='sel' )
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 ()

Stop all motion

  undisplay 
undisplay ( sel='sel' )

Undisplay atoms

Atoms specification may come from either a selection or an osl string. If no atom specification is supplied, the current selection is undisplayed.

  close 
close ( model,  subid=None )
  ribbon 
ribbon ( sel='sel' )

Display residue as ribbon

  rangeColor 
rangeColor (
        attrName,
        colorItems,
        wayPoints,
        noValue,
        sel='#',
        )

color atom parts by attribute

attrName is a residue or atom attribute name. It can be prepended with atom. or residue. to resolve ambiguity if necessary. Otherwise, residue-level attributes win "ties".

colorItems is a comma-separated string of items to color (labels, surfaces, etc., as per the color command) or an empty string (color everything). In addition to the color command characters, the character r means to color ribbons.

wayPoints is a sequence of value/color tuples describing the color range layout. The values can be max, min, mid or numeric.

noValue is the color to apply to items missing the attribute. A value of None means to leave them unchanged.

  scale 
scale ( s,  frames=None )
  section 
section ( delta,  frames=None )
  label 
label ( sel='sel',  warnLarge=0 )

Add label to selected atoms

  textureMap 
textureMap ( **kw )
Exceptions   

TypeError, "Unexpected keyword argument: " + key
IndexError, "Index (%d) out of bounds for current texture" % index

  labelopt 
labelopt ( opt,  value )

change label display options

  x3dSave 
x3dSave ( filename )
  unlabel 
unlabel ( sel='sel' )

Add label to selected atoms

  deleteAtomsBonds 
deleteAtomsBonds ( atoms=[],  bonds=[] )

General utility functions

  convertColor 
convertColor ( color )
Exceptions   

RuntimeError, 'need a color'
UserError( 'Choose color in panel first' )
UserError( 'Color "%s" is undefined' % color )

  surfacerepresent 
surfacerepresent ( style,  sel='sel' )
Exceptions   

MidasError( 'Unknown surface representation style "%s"' % style )

  wait 
wait ( frames=-1 )
  objdisplay 
objdisplay ( sel='sel' )
  pdbrun 
pdbrun (
        cmd,
        all=0,
        conect=0,
        nouser=0,
        noobj=0,
        nowait=0,
        surface=0,
        mark=None,
        viewer=None,
        )
  longbond 
longbond ( ratio=2.5,  length=None )
  addaa 
addaa ( args )

add an amino acid to the last residue in a chain

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='sel' )
  color 
color ( color,  sel='sel' )

Change atom color

Exceptions   

MidasError( e )

  pop 
pop ( frames=None,  mode='linear' )
Exceptions   

MidasError( 'No pushed positions to pop' )
MidasError( "frame count must be positive" )

  unbondcolor 
unbondcolor ( sel='sel' )
  unribbackbone 
unribbackbone ( sel='sel' )
  open 
open (
        filename,
        filetype=None,
        model=chimera.OpenModels.Default,
        )
Exceptions   

MidasError(str( msg ) )

  select 
select ( sel='sel' )

Make selected models active

  unclip 
unclip ( plane )
  chirality 
chirality ( sel='sel' )
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='sel' )

Recompute window parameters

Exceptions   

MidasError( "Nothing to window" )

  unsetAutocolor 
unsetAutocolor ()
  unrlabel 
unrlabel ( sel='sel' )

Do not display residue information as part of any atom label

  surfacecolormode 
surfacecolormode ( style,  sel='sel' )
Exceptions   

MidasError( 'Unknown surface color mode "%s"' % style )

  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,
        )
  brotation 
brotation ( sel='sel' )

Setup backwards rotation

  uncofr 
uncofr ()
  reset 
reset (
        name='default',
        frames=None,
        mode='linear',
        )
Exceptions   

MidasError( "No saved position named '%s'" % name )
MidasError( "frame count must be positive" )

  distance 
distance ( sel='sel' )

Monitor distance between exactly two atoms

Exceptions   

MidasError('Exactly two atoms must be selected. You ' 'selected %d.' % len( atoms ) )
MidasError( 'Error adding distance: %s.' % s )

  unsurface 
unsurface ( sel='sel' )
  bondrepr 
bondrepr ( style,  sel='sel' )
Exceptions   

MidasError( 'Unknown representation style "%s"' % style )

  align 
align ( sel )
Exceptions   

MidasError('Exactly two atoms must be selected. You ' 'selected %d.' % len( atoms ) )

  savepos 
savepos ( name='default' )
  unribcolor 
unribcolor ( which,  sel='sel' )

Clear ribbon color

  match 
match (
        f,
        t,
        selected=False,
        iterate=None,
        )

Superposition the two specified sets of atoms ("from" and "to")

if selected is true, transform all active models, not just the from model.

if iterate is not None or False, the matching will iterate (pruning poorly-matching atom pairs at each pass) until no pair distance exceeds the value assigned to iterate

Exceptions   

MidasError( "Iteration cutoff must be positive" )
TooFewAtomsError("Too few corresponding atoms" " (%d) to match models\n" % len( refAtoms ) )

  matrixset 
matrixset ( fileName )
Exceptions   

MidasError("Matrixset 'Model' line %d not of the" " form: Model number.number" %( i + 1 ) )
MidasError( "Matrixset file not composed of 4-line groups" " (model numbers each with a 3x4 matrix)" )
MidasError("Matrixset 3x4 matix line %d" " is not 4 numbers" %( j + 1 ) )

  display 
display ( sel='sel' )

Display atoms

Atoms specification may come from either a selection or an osl string. If no atom specification is supplied, the current selection is displayed.

  delete 
delete ( sel='sel' )

Delete atoms

  clip 
clip (
        plane,
        delta,
        frames=None,
        )
  surface 
surface ( atomSpec='sel',  category='main' )
  textureNew 
textureNew ( name,  numColors=5 )
Exceptions   

ValueError, "Number of colors for texture must be 4 or 5"
AttributeError, "Texture named " + name + " already exists"

  unscale 
unscale ()
  getcrd 
getcrd ( sel='sel' )

Print the coordinates of selected atoms

  rainbow 
rainbow ( sel='sel',  **kw )

Color selected models in rainbow pattern

  angle 
angle ( sel='sel' )

Report angle between three or four atoms

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=3,
        frames=None,
        )
  cofr 
cofr ( where='report' )
Exceptions   

MidasError( 'No atoms selected' )

  unsetIndependent 
unsetIndependent ()
  unbond 
unbond ( sel='sel' )
  vdwdefine 
vdwdefine (
        resType,
        atomName,
        radius,
        sel='sel',
        increment=0,
        )

Change vdw radius of one type of atom

  write 
write (
        writeModel,
        relModel,
        filename,
        allFrames=False,
        dispOnly=False,
        selOnly=False,
        )

write a PDB file

allFrames controls whether all frames of a trajectory are written out or just the current frame

dispOnly, if true, means to write only displayed atoms

selOnly, if true, means to write only selected atoms

Exceptions   

MidasError, "%d model ids match \"%s\"" %( len( mList ), s )

  vdw 
vdw ( sel='sel' )

Display point vdw surface of atoms

Atoms specification may come from either a selection or an osl string. If no atom specification is supplied, the current selection is displayed.

  bondcolor 
bondcolor ( color,  sel='sel' )
Exceptions   

MidasError( e )

  roll 
roll (
        axis,
        angle=3,
        frames=-1,
        )
  setAutocolor 
setAutocolor ()
  uncolor 
uncolor ( which,  sel='sel' )

Clear atom color

  unchimeraSelect 
unchimeraSelect ( sel='sel' )
  bonddisplay 
bonddisplay ( mode,  sel='sel' )
  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='sel' )
  center 
center ( sel='sel' )
Exceptions   

MidasError( 'No atoms selected' )

  unselect 
unselect ( sel='sel' )

Make selected models inactive

  textureColor 
textureColor ( index,  color )
  tColor 
tColor ( index,  sel='sel' )
Exceptions   

MidasError( 'Cannot texture color byatom (too many colors required)' )

  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 Thu Feb 02 15:18:29 2006 by HappyDoc version 3.0.a1