Contact Surface

Overview

This script calculates individual or global contact areas between a receptor molecule and a (multimodel) bundle of docked ligand structures. The exact contact surface area values (in Angstrom^2) are printed to the screen and also appended to a file called contactareas.txt If only a single global contact surface is calculated, a selection named "contact" is created that includes all receptor atoms within 3.9A of any ligand atom to illustrate the approximate contact surface.

The parameters are:

receptor (string)

The name of the selection/object representing the receptor protein

ligand (string)

The name of the selection/object representing the ligand

Note that this may be another protein!

receptor (string)

The name of the selection/object representing the receptor protein

states (integer), default:0

Calculate contact surface between the receptor and the first n states of the ligand.

If states = 0, the script calculates a global contact surface which takes all possible ligand states into account.

Usage

contact_surface receptor, ligand, [states=0]

The Code

#contact_surface v.3.0
#Copyleft Martin Christen, 2013

from pymol import cmd,stored
def contact_surface(receptor,ligand,states=0):

	"""
	AUTHOR
	Martin Christen
	
	DESCRIPTION
	This script calculates individual or global contact surfaces between a
	receptor molecule and a bundle of docked ligand structures (which have
	to be loaded into PyMOL as a multimodel object).
	
	The exact contact surface area values (in Angstrom^2) are printed to
	the screen and also appended to a file called contactareas.txt
	
	If only a single global contact surface is calculated, a selection
	named "contact" is created that includes all receptor atoms within
	3.9A of any ligand atom.
	
	USAGE
	contact_surface receptor, ligand, [states=0]
	
	PARAMETERS
	
	receptor (string)
	The name of the selection/object representing the receptor protein
	
	ligand (string)
	The name of the selection/object representing the ligand.
	Note that this may be another protein!
	
	states (integer)
	Calculate contact surface between the receptor and the first n states
	of the ligand. If states = 0 (default), the script calculates a global
	contact surface which takes  all possible ligand states into account.
	"""
	# sanity check the number of states
	states = abs(int(states))
	
	# make sure all atoms within an object occlude one another
	cmd.flag('ignore','none')
	
	# use solvent-accessible surface with high sampling density
	cmd.set('dot_solvent','1')
	cmd.set('dot_density','3')
	
	#if the 'states' parameter = 0 create a superposition of all ligand states
	if states == 0:
		cmd.split_states(ligand)
		cmd.group('ligandtemp',ligand+"_*")
		cmd.create(ligand+"_all",'ligandtemp')
		cmd.delete('ligandtemp')
		
		#create complex
		cmd.create('complextemp',ligand+"_all "+receptor)
	
		#measure area
		ligand_area=cmd.get_area(ligand+"_all")
		receptor_area=cmd.get_area(receptor)
		complex_area=cmd.get_area('complextemp')
		#normalize since the area is counted TWICE (once on receptor and once on ligand)
		contact_area=((ligand_area + receptor_area) - complex_area) / 2
		#delete complex
		cmd.delete('complextemp')
		
		#create the contact surface
		cmd.select('contact',"("+receptor+" and ("+ligand+"_all around 3.9))")
		
		#print contact surface area
		f=open('contactareas.txt','a')
		print "%s - %s : " % (receptor,ligand),
		print >>f, "%-s\t%-s\t" % (receptor,ligand),
		print >>f, "%-s" % (contact_area)
		print contact_area
		f.close()
		print "The GLOBAL contact area between "+receptor+ " and "+ligand+" is (A^2):"
		print ((ligand_area + receptor_area) - complex_area) / 2
	
	#If 'states' <> 0 calculate the contact areas to the first 'states' ligand states.
	#No individual contact surface objects are created to avoid overloading PyMOL.
	else:
		#create an object for each ligand state
		cmd.split_states(ligand)
		
		#sanity check: do not exceed that maximum number of states
		if states > cmd.count_states(ligand):
			states = cmd.count_states(ligand)
		
		#calculate contact surface area
		print "The contact areas between "+receptor+" and "+ligand+" [states 1 - "+str(states)+"] are (A^2):"
		#start looping
		#for s in range(1,cmd.count_states(ligand)+1):
		for s in range(1,states+1):
			#create complex
			cmd.create("tmp",ligand,s,1)
			cmd.create('complextemp',"tmp "+receptor)
			#measure areas
			ligand_area=cmd.get_area('tmp')
			receptor_area=cmd.get_area(receptor)
			complex_area=cmd.get_area('complextemp')
			#normalize since the area is counted TWICE (once on receptor and once on ligand)
			contact_area=((ligand_area + receptor_area) - complex_area)/2
			#delete temporary files
			cmd.delete('tmp')
			cmd.delete(ligand+"_*")
			cmd.delete('complextemp')
			#print contact surface area
			f=open('contactareas.txt','a')
			print "%s - %s_%-5s: " % (receptor,ligand,s),
			print >>f, "%-s\t%-s_%-5s\t" % (receptor,ligand,s),
			print >>f, "%-s" % (contact_area)
			print contact_area
			f.close()

cmd.extend("contact_surface",contact_surface)