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projet_court
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attempt of NH-->O bonds discovery + correction of get_helix

master
Thomas Forest 2019-09-16 23:50:44 +02:00
parent bc420e4656
commit 583d7e33d8
2 changed files with 69 additions and 28 deletions
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31
src/dssp.py
View File

@ -3,6 +3,10 @@ import atom
import sys import sys
from structure import * from structure import *
def print_dssp():
empt_line=" " * 145
if(len(sys.argv)<2): if(len(sys.argv)<2):
print("Not enough arguments! Run with --help to learn more about proper" print("Not enough arguments! Run with --help to learn more about proper"
"call structure and parameters.") "call structure and parameters.")
@ -15,10 +19,29 @@ else:
#print(get_turns(pdb_file.residues)) #print(get_turns(pdb_file.residues))
#print(pdb_file.residues[27].h_bond(pdb_file.residues[28])) #print(pdb_file.residues[27].h_bond(pdb_file.residues[28]))
#print(get_bridges(pdb_file.residues)) #print(get_bridges(pdb_file.residues))
turns = get_turns(pdb_file.residues) turns = get_turns(pdb_file.residues)
get_helix(pdb_file.residues, turns) get_helix(pdb_file.residues, turns)
get_bends(pdb_file.residues) # get_bends(pdb_file.residues)
get_chirality(pdb_file.residues) # get_chirality(pdb_file.residues)
# bridges = get_bridges(pdb_file.residues)
# ladders = get_ladders(bridges)
# get_sheets(ladders)
# print("NBRIDGES",len(bridges))
bridges = get_bridges(pdb_file.residues) bridges = get_bridges(pdb_file.residues)
ladders = get_ladders(bridges)
get_sheets(ladders) get_bonds(pdb_file.residues)
print(pdb_file.residues[1].h_bond(pdb_file.residues[2]))
residues = pdb_file.residues
e_min = 0
for res in residues:
ene = residues[1].h_bond(res)
if ene <= e_min:
e_min = ene
best_res = res
print(residues[1].resid, best_res.resid,e_min)

66
src/structure.py
View File

@ -34,7 +34,7 @@ def get_turns(residues):
if(i+j<len(residues)): if(i+j<len(residues)):
if(res.h_bond(residues[i+j])<-0.5): if(res.h_bond(residues[i+j])<-0.5):
print(j,"TURN", residues[i].resid, residues[i+j].resid) print(j,"TURN", residues[i].resid, residues[i+j].resid)
turns[residues[i].resid] = Turn(j,residues[i].resid) turns[i] = Turn(j,residues[i].resid)
return(turns) return(turns)
def get_bridges(residues): def get_bridges(residues):
@ -53,11 +53,6 @@ def get_bridges(residues):
'ipos':residues[i].resid, 'ipos':residues[i].resid,
'jpos':residues[j].resid, 'jpos':residues[j].resid,
'btype':"para"} 'btype':"para"}
# if(residues[i-1].h_bond(residues[j])+
# residues[j].h_bond(residues[i+1]))<E_min:
# E_min = residues[i-1].h_bond(residues[j])
# +residues[j].h_bond(residues[i+1])
# bridge_type = "para"
if(residues[j-1].h_bond(residues[i])<-0.5 if(residues[j-1].h_bond(residues[i])<-0.5
and residues[i].h_bond(residues[j+1])<-0.5): and residues[i].h_bond(residues[j+1])<-0.5):
@ -66,11 +61,6 @@ def get_bridges(residues):
'ipos':residues[i].resid, 'ipos':residues[i].resid,
'jpos':residues[j].resid, 'jpos':residues[j].resid,
'btype':"para"} 'btype':"para"}
# if(residues[j-1].h_bond(residues[i])+
# residues[i].h_bond(residues[j+1]))<E_min:
# E_min = residues[j-1].h_bond(residues[i])
# +residues[i].h_bond(residues[j+1])
# bridge_type = "para"
if(residues[i].h_bond(residues[j])<-0.5 if(residues[i].h_bond(residues[j])<-0.5
and residues[j].h_bond(residues[i])<-0.5): and residues[j].h_bond(residues[i])<-0.5):
@ -79,11 +69,6 @@ def get_bridges(residues):
'ipos':residues[i].resid, 'ipos':residues[i].resid,
'jpos':residues[j].resid, 'jpos':residues[j].resid,
'btype':"anti"} 'btype':"anti"}
# if(residues[i].h_bond(residues[j])+
# residues[j].h_bond(residues[i]))<E_min:
# E_min = residues[i].h_bond(residues[j])
# +residues[j].h_bond(residues[i])
# bridge_type = "anti"
if(residues[i-1].h_bond(residues[j+1])<-0.5 if(residues[i-1].h_bond(residues[j+1])<-0.5
and residues[j-1].h_bond(residues[i+1])<-0.5): and residues[j-1].h_bond(residues[i+1])<-0.5):
@ -92,11 +77,7 @@ def get_bridges(residues):
'ipos':residues[i].resid, 'ipos':residues[i].resid,
'jpos':residues[j].resid, 'jpos':residues[j].resid,
'btype':"anti"} 'btype':"anti"}
# if(residues[i-1].h_bond(residues[j+1])+
# residues[j-1].h_bond(residues[i+1]))<E_min:
# E_min = residues[i-1].h_bond(residues[j+1])
# +residues[j-1].h_bond(residues[i+1])
# bridge_type = "anti"
if(bridge): if(bridge):
if(bridge['res1']+bridge['res2']<E_min): if(bridge['res1']+bridge['res2']<E_min):
E_min = bridge['res1']+bridge['res2'] E_min = bridge['res1']+bridge['res2']
@ -107,14 +88,51 @@ def get_bridges(residues):
bridges[strongest_bridge['ipos']] = (Bridge(strongest_bridge['btype'], bridges[strongest_bridge['ipos']] = (Bridge(strongest_bridge['btype'],
strongest_bridge['ipos'], strongest_bridge['ipos'],
strongest_bridge['jpos'])) strongest_bridge['jpos']))
bridges[strongest_bridge['jpos']] = (Bridge(strongest_bridge['btype'], # bridges[strongest_bridge['jpos']] = (Bridge(strongest_bridge['btype'],
strongest_bridge['jpos'], # strongest_bridge['jpos'],
strongest_bridge['ipos'])) # strongest_bridge['ipos']))
if(len(bridges)>0): if(len(bridges)>0):
return(bridges) return(bridges)
else: else:
return(False) return(False)
# def get_bonds(residues):
# for i,res1 in enumerate(residues):
# E_min = 0
# strongest_bridge = []
# for j in range(-5,6):
# if(i+j < len(residues)):
# res2 = residues[i+j]
# if(res1.h_bond(res2)<-0.5) and (res1.h_bond(res2)<E_min):
# E_min = res1.h_bond(res2)
# strongest_bridge = [res1, res2]
# if(len(strongest_bridge)>0):
# diff = strongest_bridge[0].resid - strongest_bridge[1].resid
# if( abs (diff) > 1 and abs(diff)<=5):
# print(diff)
def get_bonds(residues):
bonds = {}
k = 0
for i,res in enumerate(residues):
E_min = 0
for j in range(-5,-2):
if(i+j<len(residues)):
if(residues[i+j].h_bond(res)<-0.5):
k+=1
#if(res.h_bond(residues[i+j])<E_min):
E_min = res.h_bond(residues[i+j])
res_a = res
res_b = residues[i+j]
if j not in bonds:
bonds[j] = []
bonds[j].append([res_a.resid, res_b.resid])
#turns[residues[i].resid] = Turn(j,residues[i].resid)
for key in bonds.keys():
print(key, len(bonds[key]))
print("LH",k)
def get_helix(residues, turns): def get_helix(residues, turns):
i = 1 i = 1
helix = [] helix = []