fixed indices of ladders
Thomas Forest
parent
182fee3f7a
commit
a242afd662
233
src/atom.py
233
src/atom.py
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@ -22,7 +22,7 @@ class Atom:
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self.coords = coordinates
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class Residue:
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def __init__(self, atoms_list):
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def __init__(self, atoms_list, indice):
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self.atoms = {}
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for atom in atoms_list:
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self.atoms[atom.atom_name] = atom
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@ -30,6 +30,7 @@ class Residue:
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self.res_name = atom.res_name
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self.chain_id = atom.chain_id
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self.insertion_code = atom.insertion_code
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self.indice = indice
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def h_bond(self, res2):
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@ -120,11 +121,12 @@ class Residue:
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# finally add the strongest bridge at i and j pos
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if(strongest_bridge):
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bridges[coord_bridge[0]] = (Bridge(strongest_bridge['btype'],
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strongest_bridge['ipos'],
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strongest_bridge['jpos']))
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strongest_bridge['ipos'],
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strongest_bridge['jpos']))
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bridges[coord_bridge[1]] = (Bridge(strongest_bridge['btype'],
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strongest_bridge['jpos'],
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strongest_bridge['ipos']))
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strongest_bridge['jpos'],
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strongest_bridge['ipos']))
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if(len(bridges)>0):
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return(bridges[coord_bridge[0]])
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else:
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@ -145,36 +147,6 @@ class Residue:
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return(self.get_turns(residues).turn_type, residues[i].resid)
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return(False)
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def get_helix2(self, residues):
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"""
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Return if there is an helix at a given residue,
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as well as its type.
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"""
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i = residues.index(self)
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# if there are no turns or it is the first residue, skip
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if i == 0:
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return False
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if(i in turns.keys() and i-1 in turns.keys()):
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print(turns[i].turn_type,"- HELIX at", residues[i].resid)
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return(turns[i].turn_type, residues[i].resid)
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return(False)
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def get_ladders(self, residues, ladders={}):
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#ladders = {}
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i = residues.index(self)
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if i != 0:
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if self.get_bridges(residues):
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if (residues[i-1].get_bridges(residues)):
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local_bridge = self.get_bridges(residues)
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consec_bridge = residues[i-1].get_bridges(residues)
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if local_bridge.bridge_type == consec_bridge.bridge_type:
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print("ladder", consec_bridge.res_num, local_bridge.res_num)
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ladders[i] = {'start':i-1,
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'end':i,
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'bridges':[consec_bridge, local_bridge]}
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return ladders
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def get_ladder(self, residues):
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#ladders = {}
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i = residues.index(self)
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@ -191,73 +163,109 @@ class Residue:
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return ladder
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return False
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def get_sheets(self, residues):
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"""
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Bridges between ladders.
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Check if 1 bridge between one ladder and one or more other ladders.
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Iterate over all residues of one ladder and check if bridge with other residues
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of the other ladders.
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"""
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sheets = {}
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sheet_start = residues.index(self)
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j=sheet_start
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k=2
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if(self.get_ladder(residues)):
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local_ladder = self.get_ladder(residues)
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while j < len(residues)-2:
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k = 2
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while residues[j+k].get_ladder(residues):
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if(residues[j+k].get_bridges(residues)):
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j = j+k
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k+=1
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if(k>):
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last = j
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j+=1
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print(j)
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if(k>2):
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sheet_end = last
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def get_bridges(residues):
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bridges = {}
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bridge = {}
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strongest_bridge = {}
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for i in range(1,len(residues)-4):
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E_min = 0
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for j in range(i+2,len(residues)-1):
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# select triplet with the minimal energy
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print("SHEET", sheet_start, sheet_end)
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if(residues[i-1].h_bond(residues[j])<-0.5
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and residues[j].h_bond(residues[i+1])<-0.5):
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bridge = {'res1':residues[i-1].h_bond(residues[j]),
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'res2':residues[j].h_bond(residues[i+1]),
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'ipos':residues[i].resid,
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'jpos':residues[j].resid,
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'i':residues[i].indice,
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'j':residues[j].indice,
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'btype':"para"}
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def get_sheets2(self):
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"""
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Bridges between ladders.
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Check if 1 bridge between one ladder and one or more other ladders.
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Iterate over all residues of one ladder and check if bridge with other residues
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of the other ladders.
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"""
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sheets = {}
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for ladder in ladders:
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for ladd2 in ladders:
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for bridge in ladders[ladder]['bridges']:
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if bridge.res_partner in res_list(ladders[ladd2]):
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print("ladder",ladders[ladder]['start'], ladders[ladder]['end'],"bridge",bridge.res_num, bridge.res_partner,
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"ladder 2",ladders[ladd2]['start'], ladders[ladd2]['end'])
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#print("stop ladder 2")
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print("stop ladder 1")
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if(residues[j-1].h_bond(residues[i])<-0.5
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and residues[i].h_bond(residues[j+1])<-0.5):
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bridge = {'res1':residues[j-1].h_bond(residues[i]),
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'res2':residues[i].h_bond(residues[j+1]),
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'ipos':residues[i].resid,
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'jpos':residues[j].resid,
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'i':residues[i].indice,
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'j':residues[j].indice,
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'btype':"para"}
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if(residues[i].h_bond(residues[j])<-0.5
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and residues[j].h_bond(residues[i])<-0.5):
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bridge = {'res1':residues[i].h_bond(residues[j]),
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'res2':residues[j].h_bond(residues[i]),
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'ipos':residues[i].resid,
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'jpos':residues[j].resid,
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'i':residues[i].indice,
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'j':residues[j].indice,
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'btype':"anti"}
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if(residues[i-1].h_bond(residues[j+1])<-0.5
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and residues[j-1].h_bond(residues[i+1])<-0.5):
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bridge = {'res1':residues[i-1].h_bond(residues[j+1]),
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'res2':residues[j-1].h_bond(residues[i+1]),
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'ipos':residues[i].resid,
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'jpos':residues[j].resid,
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'i':residues[i].indice,
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'j':residues[j].indice,
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'btype':"anti"}
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def get_ladders2(self, bridges, residues):
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ladders = {}
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i = residues.index(self)
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if i != 0:
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k = 1
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if i in bridges.keys():
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temp_bridges = [bridges[i]]
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while ((i+k in bridges.keys()) and
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(bridges[i].bridge_type == bridges[i+k].bridge_type)):
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temp_bridges.append(bridges[i+k])
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k+=1
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if k>1:
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print("ladder", bridges[i].res_num, bridges[i+k-1].res_num)
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ladders[i] = {'start':bridges[i].res_num,
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'end':bridges[i+k-1].res_num,
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'bridges':temp_bridges}
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i+=k-1
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else:
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i+=1
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return ladders
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if(bridge):
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if(bridge['res1']+bridge['res2']<E_min):
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E_min = bridge['res1']+bridge['res2']
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strongest_bridge = bridge
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coord_bridge = [i,j]
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bridge = {}
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# finally add the strongest bridge at i and j pos
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if(strongest_bridge):
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bridges[strongest_bridge['i']] = (Bridge(strongest_bridge['btype'],
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strongest_bridge['ipos'],
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strongest_bridge['jpos'],
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[strongest_bridge['i'],
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strongest_bridge['j']]))
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bridges[strongest_bridge['j']] = (Bridge(strongest_bridge['btype'],
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strongest_bridge['jpos'],
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strongest_bridge['ipos'],
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[strongest_bridge['i'],
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strongest_bridge['j']]))
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if(len(bridges)>0):
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return(bridges)
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else:
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return(False)
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def get_ladders(bridges, residues):
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ladders = {}
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i = 1
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while i < len(residues):
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k = 1
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if i in bridges.keys():
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temp_bridges = [bridges[i]]
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while ((i+k in bridges.keys()) and
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(bridges[i].bridge_type == bridges[i+k].bridge_type)):
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temp_bridges.append(bridges[i+k])
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k+=1
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if k>1:
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#print("ladder", bridges[i].res_num, bridges[i+k-1].res_num)
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ladders[i] = {'start':bridges[i].res_num,
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'end':bridges[i+k-1].res_num,
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'bridges':temp_bridges,
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'i':i,
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'j':i+k-1}
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i+=k-1
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else:
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i+=1
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return ladders
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def connected_ladders(ladd_1, ladd_2):
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links = []
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for bridge in ladd_1['bridges']:
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if bridge.res_partner in res_list(ladd_2):
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return([ladd_1['i'], ladd_1['j'], bridge.i, bridge.j,
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ladd_2['i'], ladd_2['j']])
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return False
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def get_sheets(ladders):
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"""
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@ -266,15 +274,30 @@ def get_sheets(ladders):
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Iterate over all residues of one ladder and check if bridge with other residues
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of the other ladders.
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"""
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ladds = [ elem for elem in ladders.values() ]
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sheets = {}
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for ladder in ladders:
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for ladd2 in ladders:
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for bridge in ladders[ladder]['bridges']:
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if bridge.res_partner in res_list(ladders[ladd2]):
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print("ladder",ladders[ladder]['start'], ladders[ladder]['end'],"bridge",bridge.res_num, bridge.res_partner,
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"ladder 2",ladders[ladd2]['start'], ladders[ladd2]['end'])
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#print("stop ladder 2")
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print("stop ladder 1")
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i = 0
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while i < len(ladds):
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j = i+1
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ladd = ladds[i]
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ladd1 = ladds[i]
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ladd2 = ladds[j]
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while j < len(ladds):
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print(connected_ladders(ladd1, ladd2))
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if connected_ladders(ladd1, ladd2)!=False:
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ladd1 = ladd2
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#print(connected_ladders(ladd1, ladd2)[4])
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ladd2 = ladders[connected_ladders(ladd1, ladd2)[4]]
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j+=1
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print(ladd['i'], ladd2['i'])
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i+=1
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# for ladder in ladders:
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# for ladd2 in ladders:
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# if connected_ladders(ladders[ladder], ladders[ladd2]):
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# pass
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#print("ladder",ladders[ladder]['i'], ladders[ladder]['j'],"bridge",bridge.i, bridge.j,
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# "ladder 2",ladders[ladd2]['i'], ladders[ladd2]['j'])
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def res_list(ladder):
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# TODO : method in ladder class
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20
src/dssp.py
20
src/dssp.py
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@ -24,11 +24,11 @@ else:
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#turns = get_turns(pdb_file.residues)
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#get_helix(pdb_file.residues, turns)
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get_bends(pdb_file.residues)
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#get_bends(pdb_file.residues)
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# get_chirality(pdb_file.residues)
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# bridges = get_bridges(pdb_file.residues)
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# ladders = get_ladders(bridges, pdb_file.residues)
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# get_sheets(ladders)
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bridges = get_bridges(pdb_file.residues)
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ladders = get_ladders(bridges, pdb_file.residues)
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get_sheets(ladders)
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# print("NBRIDGES",len(bridges))
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@ -47,13 +47,15 @@ else:
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#get_phi_psi(residues)
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#print(residues[2].atoms, residues[0].resid, residues[1].resid)
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print(get_TCO(residues[2],residues[3]))
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#print(get_TCO(residues[2],residues[3]))
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#turns = {}
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ladders = {}
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for i,res in enumerate(residues):
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# res.get_turns(residues, turns)
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#res.get_helix(residues)
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res.get_helix(residues)
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#res.get_bridges(residues)
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res.get_ladders(residues, ladders)
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#res.get_ladders(residues, ladders)
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#res.get_sheets(residues)
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for i,ladder in enumerate(ladders.values()):
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print(chr(65+i))
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13
src/pdb.py
13
src/pdb.py
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@ -50,13 +50,20 @@ class PDBFile:
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# get the current indice of atom
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i = self.atoms.index(atom)
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# if this is a brand new residue
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if(len(self.atoms)>1 and
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(atom.res_seq_nb == self.atoms[i-1].res_seq_nb
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and atom.insertion_code!=self.atoms[i-1].insertion_code)):
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self.residues.append(Residue(temp_atoms, len(self.residues)+1))
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temp_atoms=[]
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if(len(self.atoms)>1
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and atom.res_seq_nb != self.atoms[i-1].res_seq_nb):
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self.residues.append(Residue(temp_atoms))
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and (atom.res_seq_nb != self.atoms[i-1].res_seq_nb)):
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self.residues.append(Residue(temp_atoms, len(self.residues)+1))
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temp_atoms=[]
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temp_atoms.append(atom)
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# last residue
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self.residues.append(Residue(temp_atoms))
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self.residues.append(Residue(temp_atoms, len(self.residues)))
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# hydrogens should represent in average 50% of total atoms...
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# We use 30% threshold...
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if(count_h/len(temp_atoms)<0.30):
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@ -14,11 +14,13 @@ class Turn(Structure):
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class Bridge(Structure):
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def __init__(self, bridge_type, res_num, res_partner):
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def __init__(self, bridge_type, res_num, res_partner, indices):
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self.bridge_type = bridge_type
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self.res_num = res_num
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self.res_partner = res_partner
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Structure.res = res_num
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self.i = indices[0]
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self.j = indices[1]
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class Helix(Structure):
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