Pyadmin: 4 revisions

2014-03-28T01:43:28Z

4 revisions

MartinChristen: /* The Code */

2013-02-15T15:11:59Z

The Code

MartinChristen at 15:11, 15 February 2013

2013-02-15T15:11:12Z

MartinChristen at 15:10, 15 February 2013

2013-02-15T15:10:45Z

MartinChristen: Script to calculate and display the contact surface area between a receptor and one or more ligand molecules. ~~~~

2013-02-15T15:10:05Z

Script to calculate and display the contact surface area between a receptor and one or more ligand molecules. ~~~~

New page

= 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 =
<source lang="python">
contact_surface receptor, ligand, [states=0]
</source>

= The Code =
<source lang="python">
#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)
</source>

[[Category:Script_Library]]
[[Category:Math_Scripts]]
[[Category:Structural_Biology_Scripts]]

← Older revision	Revision as of 01:43, 28 March 2014
(No difference)

@@ Line 121: / Line 121: @@
 		print "The contact areas between "+receptor+" and "+ligand+" [states 1 - "+str(states)+"] are (A^2):"
 		#start looping
 		for s in range(1,states+1):
 			#create complex

@@ Line 14: / Line 14: @@
 :: Note that this may be another protein!
 '''states''' ''(integer)'', default:0
 :: Calculate contact surface between the receptor and the first n states of the ligand.

@@ Line 1: / Line 1: @@
 = 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
+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.

Contact Surface - Revision history

Pyadmin: 4 revisions

MartinChristen: /* The Code */

MartinChristen at 15:11, 15 February 2013

MartinChristen at 15:10, 15 February 2013

MartinChristen: Script to calculate and display the contact surface area between a receptor and one or more ligand molecules. ~~~~