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2014-03-28T01:49:14Z

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= Overview =
This script will create a CGO circle with the origin at the specified X,Y,Z coordinates. Also, you can specify the radius and the colors. See the examples.

If you want to draw a circle around an object or selection, use '''circleSelection'''. If you want pure flexibility over your circle then use '''cgoCircle'''.

'''There are two functions here:'''

'''cgoCircle'''
::— creates a CGO circle at some user-specified location
'''circleSelection'''
::—creates a circle around the named object or selection.

<gallery heights=200px widths=300px perrow=3>
Image:Circle1.png|Drawn circle.
Image:Circle2.png|CGO circle.
Image:Circle3.png|Circles of specified radius.
Image:CircleR.png|Circle with specified width.
Image:CircleR2.png|Circle with a line width of 150. Pores anyone?
</gallery>

= Usage =
<source lang="python">
import math
import pymol
from pymol.cgo import *
import random

def cgoCircle(x, y, z, r=8.0, cr=1.0, cg=0.4, cb=0.8, w=2.0):
"""
Create a CGO circle

PARAMS
x, y, z
X, Y and Z coordinates of the origin

r
Radius of the circle

cr, cg, cb
Color triplet, [r,g,b] where r,g,b are all [0.0,1.0].

w
Line width of the circle

RETURNS
the CGO object (it also loads it into PyMOL, too).

"""
x = float(x)
y = float(y)
z = float(z)
r = abs(float(r))
cr = abs(float(cr))
cg = abs(float(cg))
cb = abs(float(cb))
w = float(w)

obj = [ BEGIN, LINES, COLOR, cr, cg, cb ]
for i in range(180):
obj.append( VERTEX )
obj.append(r*math.cos(i) + x )
obj.append(r*math.sin(i) + y )
obj.append(z)
obj.append( VERTEX )
obj.append(r*math.cos(i+0.1) + x )
obj.append(r*math.sin(i+0.1) + y )
obj.append(z)
obj.append(END)

cName = cmd.get_unused_name("circle_")
cmd.load_cgo( obj, cName )
cmd.set("cgo_line_width", w, cName )
return obj

def circleSelection( selName, r=None, cr=1.0, cg=0.4, cb=0.8, w=2.0 ):
"""
circleSelection -- draws a cgo circle around a given selection or object

PARAMS
selName
Name of the thing to encircle.

r
Radius of circle.
DEFAULT: This cript automatically defines the radius for you. If
you select one atom and the resultant circle is too small, then
you can override the script's calculation of r and specify your own.

cr, cg, cb
red, green and blue coloring, each a value in the range [0.0, 1.0]

RETURNS
The circle object.

"""
((minX, minY, minZ), (maxX, maxY, maxZ)) = cmd.get_extent(selName)

if r==None:
r = max( [maxX-minX, maxY-minY, maxZ-minZ] )

stored.coords = []
cmd.iterate_state(1, selName, "stored.coords.append([x,y,z])")
l = len(stored.coords)

centerX = sum(map(lambda x: x[0], stored.coords)) / l
centerY = sum(map(lambda x: x[1], stored.coords)) / l
centerZ = sum(map(lambda x: x[2], stored.coords)) / l

return cgoCircle( centerX, centerY, centerZ, r, cr, cg, cb, w )

cmd.extend( "cgoCircle", cgoCircle )
cmd.extend( "circleSelection", circleSelection )
</source>

= Updates =
* Line width option
* better circle naming

[[Category:Script_Library]]
[[Category:Math_Scripts]]
[[Category:CGO]]

CgoCircle - Revision history

Pyadmin: 5 revisions