# Difference between revisions of "Script distance check.py"

<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

```       file=open(in_pdb, 'r')
```
```       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]

```       file=open(input, 'r')
```
```       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()