Script distance check.py

This program check_distance> uses the pdb coordinates to calculate the distance between predicted contacts with an CN>1. Contacts with a distance >5 Angström are classified as FP, otherwise the are TP. The distances are calculated using the euklidean distance formula. <source lang="python">

1. !/usr/bin/python

import sys import os import re import numpy import math

input=sys.argv[1]#contact.out in_pdb=sys.argv[2]#pdb file of reference structure

residues=[] CN_dist=[]#[pos1, pos2, cn, state] state~TP or FP coordinates={}# contains x,y,z coordinates in a list of all atoms for every residue. {residue: [[x,y,z],[x,y,z],......]}

1. calculates euklidean distance between two atoms

def calc_dist(co1, co2):#dictionary with xyz

       p1=numpy.array((co1["x"],co1["y"],co1["z"]))
       p2=numpy.array((co2["x"],co2["y"],co2["z"]))

       dist=numpy.linalg.norm(p1-p2)
       return dist

1. checks distance between any atom of two residues

def any_atom(atom1_list, atom2_list):

               for a1 in atom1_list:
                       for a2 in atom2_list:
                               dist=calc_dist(a1,a2)
                               if(dist<5.0):
                                       return "TP"
               return "FP"

1. checks TP or FP for all residue pairs

def all_dist(res):

       for i in res:#for every residue pair
               if(i[5]>1 ):                                    
                       atoms1=coordinates[i[0]]#of all atoms of residue 1 (list of dictionarys)
                       atoms2=coordinates[i[2]]#of all atoms of residue 2 (list of dictionarys)

                       state=any_atom(atoms1, atoms2)
                       CN_dist.append([i[0],i[1],i[2],i[3],i[5],state])

1. stores all coordinates of all atoms of the structure

def read_pdb():

       file=open(in_pdb, 'r')
       lines=file.readlines()

       for line in lines:
               if(re.match("^ATOM",line)):
                       info=line.split()

                       if(info[2]=="N"):#every new residue starts with N
                               res_co=[{"x":float(info[6]),"y":float(info[7]),"z":float(info[8])}] #list of coordinates of all atoms
                       else:
                               res_co.append({"x":float(info[6]),"y":float(info[7]),"z":float(info[8])})
                      
                       coordinates[int(info[5])]=res_co #key:aa position
       file.close()

1. info[position1, residue1, position2, residue2, MI, CN]

def read_input():

       file=open(input, 'r')
       lines=file.readlines()

       for line in lines:
               text=line.lstrip().rstrip('\n')
               info=text.split()
               info[0]=int(info[0])
               info[2]=int(info[2])
               info[4]=float(info[4])
               info[5]=float(info[5])

               residues.append(info)
       file.close()

1. writes CN_dist into file

def make_output(a):

       file_name="corelations_%s"%(input)
       file=open(file_name, 'w')
       for i in a:
               file.write("%i %s %i %s %f %s\n"%(i[0],i[1],i[2],i[3],i[4],i[5]))
       file.close()

if __name__ == '__main__':

       read_input()
       read_pdb()
       all_dist(residues)
       make_output(CN_dist)

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