Hi guys,
I am trying to make a script to automatize a procedure. I have got a
file where I can pick up the structure of protein-ligand complexes
cluster
The script below read the number of the cluster and then visualize
them align with a protein reference. Everything is fine except I'd
like write on a file the distances between some residues of each
structure with the ligand but I cannot figure out how do it. I read
different post but it seems that I missing something.
thanks a lot
Regards,
andrea
##### CUT HERE #####
from pymol import cmd
import string, sys, os
def read_cluster(number):
cmd.reinitialize()
cmd.load('/home/pippo/ref.pdb','ref')
cmd.select('Refactive','resi 17+20+23+25+26+43+44 in ref')
HoL = {}
FileToOpen = 'Dist' + number
DistOutput = open(FileToOpen,'w')
DistOutput.write("ATOM_PROTEIN ATOM_LIGAND DISTANCE\n")
out = open('cluster.out','r')
pro_atoms = cmd.get_model("ref")
# read cluster file
for i in out.readlines():
i=string.strip(i)
tmp = string.split(i," ")
index, elems = tmp[1], tmp[3:len(tmp)]
HoL[index] = elems
# visualize the structures of cluster number
for eachElem in HoL[number]:
newElem = eachElem + '.pdb'
cmd.load(newElem.strip(),eachElem)
cmd.select('active','resi 17+20+23+25+26+43+44')
cmd.select('lig','resn CBO')
cmd.select('ligDon','(elem n,o and (neighbor hydro) in lig)')
cmd.select('ligAcc','(elem o or (elem n and not (neighbor
hydro)) in lig)')
Don = cmd.select('don','(elem n,o and (neighbor hydro))')
Acc = cmd.select('acc','(elem o or (elem n and not (neighbor hydro)))')
# atoms_Don = cmd.index('don')
# atoms_Acc = cmd.index('acc')
HBA = cmd.distance('(lig and acc)','(active and don)',3.2)
HBD = cmd.distance('(lig and don)','(active and acc)',3.2)
cmd.align('ref',eachElem)
DistOutput.write(" %14s %14s %8.3f\n"%(Don,Acc,HBA))
DistOutput.close()
cmd.extend('read_cluster',read_cluster)
########## CUT HERE ################
