Re: [PyMOL] very slow script for distance calculation

[andrea s. <and...@gm...>]

Jules Jacobsen wrote:

> Hi Andrea,
>
> It depends on how you've written it.... It does sound more than a 
> little slow if you are just selecting a single residue. I had a script 
> which ended up looping through several sets of atoms which took ages 
> for larger models. I finally got fed-up with this and re-wrote it 
> properly. Now it's practically instantaneous. If you post the script 
> I'm sure someone will be able to offer you a pointer as to where you 
> might be going wrong.
>
> Jules

Hi Jules, here it is:
-------------------------------------------------
from pymol import cmd
import string, sys, os

if ("dist.out"):
    os.system("rm -f dist.out")
if ("full.out"):
    os.system("rm -f full.out")
nam = open("file.nam",'r')
KeepStruc = []
readnam = nam.readlines()
deep = int(15)
for j in range(0,deep):
    readnam[j] = string.strip(readnam[j])
    KeepStruc.append(readnam[j])

for i in KeepStruc:
    cmd.load(i,i)
    print i
    cmd.select("lig","segi B")
    cmd.select("pro","all and not segi B")
    amb = open("amb",'r')
    out = open("dist.out","a")
    full = open("full.out","a")
    out.write("%4s\n"%(i))
    full.write("%4s\n"%(i))
    count = 0
    for lines in amb.readlines():
        lines = string.strip(lines)
        tmp = string.split(lines,",")
        resname = tmp[0]
        atomtypes = tmp[1]
        tmp1 =string.split(atomtypes,":")
        atomlig = tmp1[0]
        atompro = tmp1[1]
        p = cmd.select("p","resi "+resname+" and name "+atompro+" and "+i)
        if (atomlig == "*"):
            ligand = cmd.select("ligand","segi B and "+i)
            atoms_lig = cmd.get_model('ligand')
            for atomsL in atoms_lig.atom:
                t = cmd.select("t","name "+atomsL.name)
                di = cmd.distance("di","t","p")
                
full.write("%4s%8s%8s%8.3f%12s\n"%(resname,atompro,atomsL.name,di,"DISTANCE"))
                if (di < 4):
                    count = count + 1
    #        print resname,atompro,count
            if (count == 0):
                
out.write("%4s%8s%8s%12s\n"%(resname,atompro,"*",">VIOLATED"))
            count = 0
        else:
            l = cmd.select("l","name "+atomlig+" and segi B and "+i)
            d = cmd.distance("dist_"+str(i),"p","l")
            
full.write("%4s%8s%8s%8.3f%12s\n"%(resname,atompro,atomlig,d,"DISTANCE"))
            if (d > 5):
                
out.write("%4s%8s%8s%8.3f%10s\n"%(resname,atompro,atomlig,d,"VIOLATED"))
       
       
out.close()
--------------------------------------------------
At the beginning I thought that problem was the memory because when I 
run it it starts fast and then aftr 4 structures it goes slowly slowly 
per every molecule, but I see my free memory always 50% and the cpu 
100%. I tried to empty the list in the script at end of each iteration 
but it didn't work.

thanks

andrea