[PyMOL] script to write down distances ligand-protein: need feedback

[Andrea S. <and...@gm...>]

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 =3D {}
    FileToOpen =3D 'Dist' + number=20
    DistOutput =3D open(FileToOpen,'w')
    DistOutput.write("ATOM_PROTEIN ATOM_LIGAND DISTANCE\n")
    out =3D open('cluster.out','r')
    pro_atoms =3D cmd.get_model("ref")
# read cluster file
    for i in out.readlines():
        i=3Dstring.strip(i)      =20
        tmp =3D string.split(i," ")
        index, elems =3D tmp[1], tmp[3:len(tmp)] =20
        HoL[index] =3D elems
# visualize the structures of cluster number
    for eachElem in HoL[number]:
        newElem =3D 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 =3D cmd.select('don','(elem n,o and (neighbor hydro))')
        Acc =3D cmd.select('acc','(elem o or (elem n and not (neighbor hydr=
o)))')
#     atoms_Don =3D cmd.index('don')
#     atoms_Acc =3D cmd.index('acc')
        HBA =3D cmd.distance('(lig and acc)','(active and don)',3.2)
        HBD =3D cmd.distance('(lig and don)','(active and acc)',3.2)
        cmd.align('ref',eachElem)
        DistOutput.write(" %14s  %14s %8.3f\n"%(Don,Acc,HBA))
    =20
    DistOutput.close()
=20
cmd.extend('read_cluster',read_cluster)
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