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projet_court
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fixed indices of ladders

master
Thomas Forest 2019-09-18 03:34:06 +02:00
parent 182fee3f7a
commit a242afd662
4 changed files with 156 additions and 122 deletions
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195
src/atom.py
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@ -22,7 +22,7 @@ class Atom:
self.coords = coordinates
class Residue:
def __init__(self, atoms_list):
def __init__(self, atoms_list, indice):
self.atoms = {}
for atom in atoms_list:
self.atoms[atom.atom_name] = atom
@ -30,6 +30,7 @@ class Residue:
self.res_name = atom.res_name
self.chain_id = atom.chain_id
self.insertion_code = atom.insertion_code
self.indice = indice
def h_bond(self, res2):
@ -122,6 +123,7 @@ class Residue:
bridges[coord_bridge[0]] = (Bridge(strongest_bridge['btype'],
strongest_bridge['ipos'],
strongest_bridge['jpos']))
bridges[coord_bridge[1]] = (Bridge(strongest_bridge['btype'],
strongest_bridge['jpos'],
strongest_bridge['ipos']))
@ -145,36 +147,6 @@ class Residue:
return(self.get_turns(residues).turn_type, residues[i].resid)
return(False)
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):
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)
ladders[i] = {'start':i-1,
'end':i,
'bridges':[consec_bridge, local_bridge]}
return ladders
def get_ladder(self, residues):
#ladders = {}
i = residues.index(self)
@ -191,57 +163,82 @@ class Residue:
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
def get_bridges(residues):
bridges = {}
bridge = {}
strongest_bridge = {}
for i in range(1,len(residues)-4):
E_min = 0
for j in range(i+2,len(residues)-1):
# select triplet with the minimal energy
print("SHEET", sheet_start, sheet_end)
if(residues[i-1].h_bond(residues[j])<-0.5
and residues[j].h_bond(residues[i+1])<-0.5):
bridge = {'res1':residues[i-1].h_bond(residues[j]),
'res2':residues[j].h_bond(residues[i+1]),
'ipos':residues[i].resid,
'jpos':residues[j].resid,
'i':residues[i].indice,
'j':residues[j].indice,
'btype':"para"}
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")
if(residues[j-1].h_bond(residues[i])<-0.5
and residues[i].h_bond(residues[j+1])<-0.5):
bridge = {'res1':residues[j-1].h_bond(residues[i]),
'res2':residues[i].h_bond(residues[j+1]),
'ipos':residues[i].resid,
'jpos':residues[j].resid,
'i':residues[i].indice,
'j':residues[j].indice,
'btype':"para"}
if(residues[i].h_bond(residues[j])<-0.5
and residues[j].h_bond(residues[i])<-0.5):
bridge = {'res1':residues[i].h_bond(residues[j]),
'res2':residues[j].h_bond(residues[i]),
'ipos':residues[i].resid,
'jpos':residues[j].resid,
'i':residues[i].indice,
'j':residues[j].indice,
'btype':"anti"}
if(residues[i-1].h_bond(residues[j+1])<-0.5
and residues[j-1].h_bond(residues[i+1])<-0.5):
bridge = {'res1':residues[i-1].h_bond(residues[j+1]),
'res2':residues[j-1].h_bond(residues[i+1]),
'ipos':residues[i].resid,
'jpos':residues[j].resid,
'i':residues[i].indice,
'j':residues[j].indice,
'btype':"anti"}
def get_ladders2(self, bridges, residues):
if(bridge):
if(bridge['res1']+bridge['res2']<E_min):
E_min = bridge['res1']+bridge['res2']
strongest_bridge = bridge
coord_bridge = [i,j]
bridge = {}
# finally add the strongest bridge at i and j pos
if(strongest_bridge):
bridges[strongest_bridge['i']] = (Bridge(strongest_bridge['btype'],
strongest_bridge['ipos'],
strongest_bridge['jpos'],
[strongest_bridge['i'],
strongest_bridge['j']]))
bridges[strongest_bridge['j']] = (Bridge(strongest_bridge['btype'],
strongest_bridge['jpos'],
strongest_bridge['ipos'],
[strongest_bridge['i'],
strongest_bridge['j']]))
if(len(bridges)>0):
return(bridges)
else:
return(False)
def get_ladders(bridges, residues):
ladders = {}
i = residues.index(self)
if i != 0:
i = 1
while i < len(residues):
k = 1
if i in bridges.keys():
temp_bridges = [bridges[i]]
@ -250,15 +247,26 @@ class Residue:
temp_bridges.append(bridges[i+k])
k+=1
if k>1:
print("ladder", bridges[i].res_num, bridges[i+k-1].res_num)
#print("ladder", bridges[i].res_num, bridges[i+k-1].res_num)
ladders[i] = {'start':bridges[i].res_num,
'end':bridges[i+k-1].res_num,
'bridges':temp_bridges}
'bridges':temp_bridges,
'i':i,
'j':i+k-1}
i+=k-1
else:
i+=1
return ladders
def connected_ladders(ladd_1, ladd_2):
links = []
for bridge in ladd_1['bridges']:
if bridge.res_partner in res_list(ladd_2):
return([ladd_1['i'], ladd_1['j'], bridge.i, bridge.j,
ladd_2['i'], ladd_2['j']])
return False
def get_sheets(ladders):
"""
Bridges between ladders.
@ -266,15 +274,30 @@ def get_sheets(ladders):
Iterate over all residues of one ladder and check if bridge with other residues
of the other ladders.
"""
ladds = [ elem for elem in ladders.values() ]
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")
i = 0
while i < len(ladds):
j = i+1
ladd = ladds[i]
ladd1 = ladds[i]
ladd2 = ladds[j]
while j < len(ladds):
print(connected_ladders(ladd1, ladd2))
if connected_ladders(ladd1, ladd2)!=False:
ladd1 = ladd2
#print(connected_ladders(ladd1, ladd2)[4])
ladd2 = ladders[connected_ladders(ladd1, ladd2)[4]]
j+=1
print(ladd['i'], ladd2['i'])
i+=1
# for ladder in ladders:
# for ladd2 in ladders:
# if connected_ladders(ladders[ladder], ladders[ladd2]):
# pass
#print("ladder",ladders[ladder]['i'], ladders[ladder]['j'],"bridge",bridge.i, bridge.j,
# "ladder 2",ladders[ladd2]['i'], ladders[ladd2]['j'])
def res_list(ladder):
# TODO : method in ladder class

20
src/dssp.py
View File

@ -24,11 +24,11 @@ else:
#turns = get_turns(pdb_file.residues)
#get_helix(pdb_file.residues, turns)
get_bends(pdb_file.residues)
#get_bends(pdb_file.residues)
# get_chirality(pdb_file.residues)
# bridges = get_bridges(pdb_file.residues)
# ladders = get_ladders(bridges, pdb_file.residues)
# get_sheets(ladders)
bridges = get_bridges(pdb_file.residues)
ladders = get_ladders(bridges, pdb_file.residues)
get_sheets(ladders)
# print("NBRIDGES",len(bridges))
@ -47,13 +47,15 @@ else:
#get_phi_psi(residues)
#print(residues[2].atoms, residues[0].resid, residues[1].resid)
print(get_TCO(residues[2],residues[3]))
#print(get_TCO(residues[2],residues[3]))
#turns = {}
ladders = {}
for i,res in enumerate(residues):
# res.get_turns(residues, turns)
#res.get_helix(residues)
res.get_helix(residues)
#res.get_bridges(residues)
res.get_ladders(residues, ladders)
#res.get_ladders(residues, ladders)
#res.get_sheets(residues)
for i,ladder in enumerate(ladders.values()):
print(chr(65+i))

13
src/pdb.py
View File

@ -50,13 +50,20 @@ class PDBFile:
# get the current indice of atom
i = self.atoms.index(atom)
# if this is a brand new residue
if(len(self.atoms)>1 and
(atom.res_seq_nb == self.atoms[i-1].res_seq_nb
and atom.insertion_code!=self.atoms[i-1].insertion_code)):
self.residues.append(Residue(temp_atoms, len(self.residues)+1))
temp_atoms=[]
if(len(self.atoms)>1
and atom.res_seq_nb != self.atoms[i-1].res_seq_nb):
self.residues.append(Residue(temp_atoms))
and (atom.res_seq_nb != self.atoms[i-1].res_seq_nb)):
self.residues.append(Residue(temp_atoms, len(self.residues)+1))
temp_atoms=[]
temp_atoms.append(atom)
# last residue
self.residues.append(Residue(temp_atoms))
self.residues.append(Residue(temp_atoms, len(self.residues)))
# hydrogens should represent in average 50% of total atoms...
# We use 30% threshold...
if(count_h/len(temp_atoms)<0.30):

4
src/structure.py
View File

@ -14,11 +14,13 @@ class Turn(Structure):
class Bridge(Structure):
def __init__(self, bridge_type, res_num, res_partner):
def __init__(self, bridge_type, res_num, res_partner, indices):
self.bridge_type = bridge_type
self.res_num = res_num
self.res_partner = res_partner
Structure.res = res_num
self.i = indices[0]
self.j = indices[1]
class Helix(Structure):