Difference between revisions of "Script distance check.py"
From Bioinformatikpedia
(Created page with "<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 with actual coordina…") |
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Line 10: | Line 10: | ||
input=sys.argv[1]#contact.out |
input=sys.argv[1]#contact.out |
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− | in_pdb=sys.argv[2]#pdb file |
+ | in_pdb=sys.argv[2]#pdb file of reference structure |
residues=[] |
residues=[] |
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CN_dist=[]#[pos1, pos2, cn, state] state~TP or FP |
CN_dist=[]#[pos1, pos2, cn, state] state~TP or FP |
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+ | coordinates={}# contains x,y,z coordinates in a list of all atoms for every residue. {residue: [[x,y,z],[x,y,z],......]} |
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− | coordinates={} |
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#calculates euklidean distance between two atoms |
#calculates euklidean distance between two atoms |
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Line 34: | Line 34: | ||
return "FP" |
return "FP" |
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− | #checks TP |
+ | #checks TP or FP for all residue pairs |
def all_dist(res): |
def all_dist(res): |
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for i in res:#for every residue pair |
for i in res:#for every residue pair |
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− | if(i[5]>1 ): |
+ | if(i[5]>1 ): |
− | #print(i) |
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− | #print(coordinates.has_key(i[0])) |
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atoms1=coordinates[i[0]]#of all atoms of residue 1 (list of dictionarys) |
atoms1=coordinates[i[0]]#of all atoms of residue 1 (list of dictionarys) |
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atoms2=coordinates[i[2]]#of all atoms of residue 2 (list of dictionarys) |
atoms2=coordinates[i[2]]#of all atoms of residue 2 (list of dictionarys) |
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state=any_atom(atoms1, atoms2) |
state=any_atom(atoms1, atoms2) |
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− | |||
CN_dist.append([i[0],i[1],i[2],i[3],i[5],state]) |
CN_dist.append([i[0],i[1],i[2],i[3],i[5],state]) |
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+ | |||
+ | # stores all coordinates of all atoms of the structure |
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def read_pdb(): |
def read_pdb(): |
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file=open(in_pdb, 'r') |
file=open(in_pdb, 'r') |
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Line 59: | Line 58: | ||
else: |
else: |
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res_co.append({"x":float(info[6]),"y":float(info[7]),"z":float(info[8])}) |
res_co.append({"x":float(info[6]),"y":float(info[7]),"z":float(info[8])}) |
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+ | |||
− | |||
− | #print(info) |
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coordinates[int(info[5])]=res_co #key:aa position |
coordinates[int(info[5])]=res_co #key:aa position |
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− | |||
file.close() |
file.close() |
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+ | |||
#info[position1, residue1, position2, residue2, MI, CN] |
#info[position1, residue1, position2, residue2, MI, CN] |
Revision as of 21:50, 3 September 2013
<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>