Script distance check.py
From Bioinformatikpedia
<source lang="python">
- !/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],......]}
- 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
- 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"
- 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])
- 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()
- 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()
- 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)
</source>