CgoCircle

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.

• 

  Drawn circle.

• 

  CGO circle.

• 

  Circles of specified radius.

Usage

# Create a circle centered at X,Y,Z = (10,10,10) with radius=4
# and colored red/pink.
cgoCircle x=10, y=10, z=10, r=4, cr=1.0, cg=0.4, cb=0.9

# put a circle around residue 44
circleSelection i. 44

The Code

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):
  """
  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].
	  
  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))
  
  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)

  cmd.load_cgo( obj, "circle_" + str(random.randint(0,1000)))
  return obj


def circleSelection( selName, r=None, cr=1.0, cg=0.4, cb=0.8 ):
  """
  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 )
	
  
cmd.extend( "cgoCircle", cgoCircle )
cmd.extend( "circleSelection", circleSelection )