# Scrip pdb distance check.py

<source lang="python">

1. !/usr/bin/python

import sys import os import re import numpy import math

input=sys.argv[1]#pdb file with coordinates

pdb_dist=[]#[pos1, pos2, 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 possible residue pairs

def all_dist():

```       checker=len(coordinates.keys())+1
for i in range(1,checker):#for every residue
for j in range(i,checker):
```
```                       atoms1=coordinates[i]#of all atoms of residue 1 (list of dictionarys)
atoms2=coordinates[j]#of all atoms of residue 2 (list of dictionarys)
```
```                       state=any_atom(atoms1, atoms2)
pdb_dist.append([i,j,state])
```

def read_pdb():

```       file=open(input, '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. writes CN_dist into file

def make_output(a):

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

if __name__ == '__main__':

```       read_pdb()
all_dist()
make_output(pdb_dist)
```

</source>