Table of Contents

Module: __init__ Midas/__init__.py

Emulate UCSF Midas command set

Imported modules   
from StructMeasure import DistMonitor
import chimera
from chimera import selection, dialogs, elements, specifier, replyobj, misc
from chimera.colorTable import getColorByName
import chimera.match
from chimera.selection import YES, NO
import math
import os
import string
import sys
import tempfile
import types
Functions   
align
angle
brotation
center
clip
close
cofr
color
colordef
copy
display
distance
focus
freeze
getcrd
ksdssp
label
labelopt
linewidth
longbond
match
matrixcopy
model
modelcolor
modeldisplay
move
objdisplay
open
pdbrun
pop
push
rainbow
represent
rescolor
reset
ribbon
ribcolor
ribrepr
rock
roll
rotation
save
savepos
scale
section
select
setAutocolor
setIndependent
show
surface
surfaceCategory
surfaceDelete
surfaceNew
surfacecolormode
surfacerepresent
swapres
tColor
textureColor
textureMap
textureNew
textureUse
thickness
turn
unclip
uncofr
uncolor
undisplay
undistance
unlabel
unmodeldisplay
unobjdisplay
unribbon
unribcolor
unsavepos
unscale
unselect
unsetAutocolor
unsetIndependent
unsurface
unvdw
vdw
vdwdefine
vdwdensity
version
wait
window
write
  align 
align ( s )

  angle 
angle ( sel=None )

Report angle between three or four atoms

  brotation 
brotation ( sel=None )

Setup backwards rotation

  center 
center ( sel=None )

  clip 
clip (
        plane,
        delta,
        frames=1,
        )

  close 
close ( model )

  cofr 
cofr ( where='report' )

  color 
color ( color,  sel=None )

Change atom color

  colordef 
colordef ( color,  target )

Define RGB(A) color

  copy 
copy (
        printer=None,
        file=None,
        format=None,
        viewer=None,
        )

  display 
display ( sel=None )

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.

  distance 
distance ( sel=None )

Monitor distance between exactly two atoms

  focus 
focus ( sel=None )

Window/cofr about displayed part of selection

  freeze 
freeze ()

Stop all motion

  getcrd 
getcrd ( sel=None )

Print the coordinates of selected atoms

  ksdssp 
ksdssp (
        sel=None,
        energy=None,
        helixLen=None,
        strandLen=None,
        infoFile=None,
        )

  label 
label ( sel=None,  warnLarge=0 )

Add label to selected atoms

  labelopt 
labelopt ( opt,  value )

change label display options

  linewidth 
linewidth ( width,  sel=None )

  longbond 
longbond ( ratio=2.5,  length=None )

  match 
match (
        f,
        t,
        selected=0,
        )

Superposition the two specified sets of atoms

The specifications must be strings so we can guarantee that the order of atom selection is preserved

  matrixcopy 
matrixcopy ( f,  t )

  model 
model ( n )

  modelcolor 
modelcolor ( color,  sel=None )

Change model color

  modeldisplay 
modeldisplay ( sel=None )

  move 
move (
        x=0,
        y=0,
        z=0,
        frames=1,
        )

  objdisplay 
objdisplay ( sel=None )

  open 
open (
        filename,
        filetype=None,
        model=chimera.OpenModels.Default,
        )

  pdbrun 
pdbrun (
        cmd,
        all=0,
        conect=0,
        nouser=0,
        noobj=0,
        nowait=0,
        surface=0,
        mark=None,
        viewer=None,
        )

  pop 
pop ()

  push 
push ()

  rainbow 
rainbow ( sel=None )

Color selected models in rainbow pattern

  represent 
represent ( style,  sel=None )

  rescolor 
rescolor ( color,  sel=None )

  reset 
reset ( name='default' )

  ribbon 
ribbon ( sel=None )

Display residue as ribbon

  ribcolor 
ribcolor ( color,  sel=None )

Change ribbon color

  ribrepr 
ribrepr ( style,  sel=None )

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

  roll 
roll (
        axis,
        angle=3,
        frames=-1,
        )

  rotation 
rotation ( sel=None )

  save 
save ( filename )

  savepos 
savepos ( name='default' )

  scale 
scale ( s,  frames=1 )

  section 
section ( delta,  frames=1 )

  select 
select ( sel=None )

Make selected models active

  setAutocolor 
setAutocolor ()

  setIndependent 
setIndependent ()

  show 
show ( sel=None )

  surface 
surface ( atomSpec=None,  category=None )

  surfaceCategory 
surfaceCategory ( category,  sel=None )

  surfaceDelete 
surfaceDelete ( category,  sel=None )

  surfaceNew 
surfaceNew (
        category,
        sel=None,
        models=None,
        )

  surfacecolormode 
surfacecolormode ( style,  sel=None )

  surfacerepresent 
surfacerepresent ( style,  sel=None )

  swapres 
swapres (
        newRes,
        sel=None,
        preserve=0,
        )

  tColor 
tColor ( index,  sel=None )

  textureColor 
textureColor ( index,  color )

  textureMap 
textureMap ( **kw )

Exceptions   
IndexError, "Index (%d) out of bounds for current texture" % index
TypeError, "Unexpected keyword argument: " + key
  textureNew 
textureNew ( name,  numColors=5 )

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

Exceptions   
KeyError, "No texture named '" + name + "' exists"
  thickness 
thickness ( delta,  frames=1 )

  turn 
turn (
        axis,
        angle=3,
        frames=1,
        )

  unclip 
unclip ( plane )

  uncofr 
uncofr ()

  uncolor 
uncolor ( which,  sel=None )

Clear atom color

  undisplay 
undisplay ( sel=None )

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.

  undistance 
undistance ( sel=None )

Remove distance monitor

  unlabel 
unlabel ( sel=None )

Add label to selected atoms

  unmodeldisplay 
unmodeldisplay ( sel=None )

  unobjdisplay 
unobjdisplay ( sel )

  unribbon 
unribbon ( sel=None )

  unribcolor 
unribcolor ( which,  sel=None )

Clear ribbon color

  unsavepos 
unsavepos ( name )

  unscale 
unscale ()

  unselect 
unselect ( sel=None )

Make selected models inactive

  unsetAutocolor 
unsetAutocolor ()

  unsetIndependent 
unsetIndependent ()

  unsurface 
unsurface ( sel=None )

  unvdw 
unvdw ( sel=None )

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.

  vdw 
vdw ( sel=None )

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.

  vdwdefine 
vdwdefine (
        resType,
        atomName,
        radius,
        sel=None,
        increment=0,
        )

Change vdw radius of one type of atom

  vdwdensity 
vdwdensity ( density,  sel=None )

Change vdw surface point density

  version 
version ()

  wait 
wait ( frames=-1 )

  window 
window ( sel=None )

Recompute window parameters

  write 
write (
        writeModel,
        relModel,
        filename,
        )

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

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