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Before go back to bridges and ladders methods

master
Thomas Forest 2019-09-17 22:57:47 +02:00
parent 2505792465
commit 182fee3f7a
2 changed files with 100 additions and 15 deletions
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106
src/atom.py
View File

@ -52,16 +52,22 @@ class Residue:
E = q1*q2*(1/r_ON + 1/r_CH - 1/r_OH - 1/r_CN)*f
return(E)
def get_turns(self, residues, turns):
def get_turns(self, residues):
"""
Get all the turns from a specific residue.
"""
turns = {}
i = residues.index(self)
k = 0
for j in range(3,6):
if(i+j<len(residues)):
if(self.h_bond(residues[i+j])<-0.5):
print(j,"TURN", residues[i].resid, residues[i+j].resid)
turns[i] = Turn(j,residues[i].resid)
k = j
if k != 0:
#print(k,"TURN", residues[i].resid, residues[i+k].resid)
return Turn(k,residues[i].resid)
return False
def get_bridges(self, residues):
bridges = {}
@ -124,22 +130,38 @@ class Residue:
else:
return(False)
def get_helix(self, residues, turns):
def get_helix(self, residues):
"""
Return if there is an helix at a given residue,
as well as its type.
"""
i = residues.index(self)
# if there are no turns or it is the first residue, skip
if not turns or i == 0:
if i == 0:
return False
if (i <= len(residues)):
if(i in turns.keys() and i-1 in turns.keys()):
print(turns[i].turn_type,"- HELIX at", residues[i].resid)
return(turns[i].turn_type, residues[i].resid)
if(self.get_turns(residues) and residues[i-1].get_turns(residues)):
print(self.get_turns(residues).turn_type,"- HELIX at", residues[i].resid)
return(self.get_turns(residues).turn_type, residues[i].resid)
return(False)
def get_ladders(self, residues, ladders):
def get_helix2(self, residues):
"""
Return if there is an helix at a given residue,
as well as its type.
"""
i = residues.index(self)
# if there are no turns or it is the first residue, skip
if i == 0:
return False
if(i in turns.keys() and i-1 in turns.keys()):
print(turns[i].turn_type,"- HELIX at", residues[i].resid)
return(turns[i].turn_type, residues[i].resid)
return(False)
def get_ladders(self, residues, ladders={}):
#ladders = {}
i = residues.index(self)
if i != 0:
if self.get_bridges(residues):
@ -151,6 +173,70 @@ class Residue:
ladders[i] = {'start':i-1,
'end':i,
'bridges':[consec_bridge, local_bridge]}
return ladders
def get_ladder(self, residues):
#ladders = {}
i = residues.index(self)
if i != 0:
if self.get_bridges(residues):
if (residues[i-1].get_bridges(residues)):
local_bridge = self.get_bridges(residues)
consec_bridge = residues[i-1].get_bridges(residues)
if local_bridge.bridge_type == consec_bridge.bridge_type:
#print("ladder", consec_bridge.res_num, local_bridge.res_num)
ladder = {'start':consec_bridge.res_num,
'end':local_bridge.res_num,
'bridges':[consec_bridge, local_bridge]}
return ladder
return False
def get_sheets(self, residues):
"""
Bridges between ladders.
Check if 1 bridge between one ladder and one or more other ladders.
Iterate over all residues of one ladder and check if bridge with other residues
of the other ladders.
"""
sheets = {}
sheet_start = residues.index(self)
j=sheet_start
k=2
if(self.get_ladder(residues)):
local_ladder = self.get_ladder(residues)
while j < len(residues)-2:
k = 2
while residues[j+k].get_ladder(residues):
if(residues[j+k].get_bridges(residues)):
j = j+k
k+=1
if(k>):
last = j
j+=1
print(j)
if(k>2):
sheet_end = last
print("SHEET", sheet_start, sheet_end)
def get_sheets2(self):
"""
Bridges between ladders.
Check if 1 bridge between one ladder and one or more other ladders.
Iterate over all residues of one ladder and check if bridge with other residues
of the other ladders.
"""
sheets = {}
for ladder in ladders:
for ladd2 in ladders:
for bridge in ladders[ladder]['bridges']:
if bridge.res_partner in res_list(ladders[ladd2]):
print("ladder",ladders[ladder]['start'], ladders[ladder]['end'],"bridge",bridge.res_num, bridge.res_partner,
"ladder 2",ladders[ladd2]['start'], ladders[ladd2]['end'])
#print("stop ladder 2")
print("stop ladder 1")
def get_ladders2(self, bridges, residues):
ladders = {}

9
src/dssp.py
View File

@ -49,12 +49,11 @@ else:
#print(residues[2].atoms, residues[0].resid, residues[1].resid)
print(get_TCO(residues[2],residues[3]))
turns = {}
#turns = {}
ladders = {}
for i,res in enumerate(residues):
# res.get_turns(residues, turns)
# res.get_helix(residues, turns)
res.get_bridges(residues)
#res.get_helix(residues)
#res.get_bridges(residues)
res.get_ladders(residues, ladders)
#res.get_sheets(residues)