|
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
|
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,
tiff=0,
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
|
|
|
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 )
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,
doModel=1,
)
Change model or residue 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' )
|
|
|
resrepr
|
resrepr ( 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 )
|
|
|
source
|
source ( filename )
|
|
|
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 )
|
|
|
unrescolor
|
unrescolor ( which, sel=None )
Clear atom 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 )
|
|