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Cleaning commented artefacts

master
Thomas Forest 2019-09-18 18:56:27 +02:00
parent 314a12386b
commit 7f7d8aca98
2 changed files with 12 additions and 116 deletions
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124
src/chem.py
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@ -1,5 +1,4 @@
import math import math
#from structure import *
from geom import * from geom import *
class Atom: class Atom:
@ -107,7 +106,6 @@ class Residue:
if(self.h_bond(residues[i+j])<-0.5): if(self.h_bond(residues[i+j])<-0.5):
k = j k = j
if k != 0: if k != 0:
#print(k,"TURN", residues[i].resid, residues[i+k].resid)
return Turn(k,residues[i].resid) return Turn(k,residues[i].resid)
return False return False
@ -115,78 +113,17 @@ class Residue:
def get_bends(self, residues): def get_bends(self, residues):
i = residues.index(self) i = residues.index(self)
if i >=2 and i <len(residues)-2: if i >=2 and i <len(residues)-2:
angle = math.degrees(vector_angles(vectors_substr(position_vector(residues[i].atoms["CA"].coords), angle = math.degrees(vector_angles(
position_vector(residues[i-2].atoms["CA"].coords)), vectors_substr(position_vector(residues[i].atoms["CA"].coords),
vectors_substr(position_vector(residues[i+2].atoms["CA"].coords), position_vector(residues[i-2].atoms["CA"].coords)),
position_vector(residues[i].atoms["CA"].coords)))) vectors_substr(position_vector(residues[i+2].atoms["CA"].coords),
position_vector(residues[i].atoms["CA"].coords))))
if(angle>70): if(angle>70):
return [angle, 'S'] return [angle, 'S']
return [angle, ''] return [angle, '']
else: else:
return [360.0, ''] return [360.0, '']
def get_bridges(self, residues):
bridges = {}
bridge = {}
strongest_bridge = {}
i = residues.index(self)
if(i >= 1 and i < len(residues)-4):
E_min = 0
for j in range(i+2,len(residues)-1):
# select triplet with the minimal energy
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,
'btype':"para"}
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,
'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,
'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,
'btype':"anti"}
if(bridge):
if(bridge['res1']+bridge['res2']<E_min):
E_min = bridge['res1']+bridge['res2']
strongest_bridge = bridge
bridge = {}
coord_bridge = [i,j]
# finally add the strongest bridge at i and j pos
if(strongest_bridge):
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']))
if(len(bridges)>0):
return(bridges[coord_bridge[0]])
else:
return(False)
def get_helix(self, residues): def get_helix(self, residues):
""" """
Return if there is an helix at a given residue, Return if there is an helix at a given residue,
@ -198,12 +135,10 @@ class Residue:
return False return False
if(self.get_turns(residues) and residues[i-1].get_turns(residues)): if(self.get_turns(residues) and residues[i-1].get_turns(residues)):
#print(self.get_turns(residues).turn_type,"- HELIX at", residues[i].indice)
return(self.get_turns(residues).turn_type, residues[i].indice) return(self.get_turns(residues).turn_type, residues[i].indice)
return(False) return(False)
def get_ladder(self, residues): def get_ladder(self, residues):
#ladders = {}
i = residues.index(self) i = residues.index(self)
if i != 0: if i != 0:
if self.get_bridges(residues): if self.get_bridges(residues):
@ -211,7 +146,6 @@ class Residue:
local_bridge = self.get_bridges(residues) local_bridge = self.get_bridges(residues)
consec_bridge = residues[i-1].get_bridges(residues) consec_bridge = residues[i-1].get_bridges(residues)
if local_bridge.bridge_type == consec_bridge.bridge_type: 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, ladder = {'start':consec_bridge.res_num,
'end':local_bridge.res_num, 'end':local_bridge.res_num,
'bridges':[consec_bridge, local_bridge]} 'bridges':[consec_bridge, local_bridge]}
@ -278,7 +212,6 @@ def get_bridges(residues):
E_min = 0 E_min = 0
for j in range(i+2,len(residues)-1): for j in range(i+2,len(residues)-1):
# select triplet with the minimal energy # select triplet with the minimal energy
if(residues[i-1].h_bond(residues[j])<-0.5 if(residues[i-1].h_bond(residues[j])<-0.5
and residues[j].h_bond(residues[i+1])<-0.5): and residues[j].h_bond(residues[i+1])<-0.5):
bridge = {'res1':residues[i-1].h_bond(residues[j]), bridge = {'res1':residues[i-1].h_bond(residues[j]),
@ -328,13 +261,11 @@ def get_bridges(residues):
# finally add the strongest bridge at i and j pos # finally add the strongest bridge at i and j pos
if(strongest_bridge): if(strongest_bridge):
bridges[strongest_bridge['i']] = (Bridge(strongest_bridge['btype'], bridges[strongest_bridge['i']] = (Bridge(strongest_bridge['btype'],
strongest_bridge['ipos'], strongest_bridge['ipos'],
strongest_bridge['jpos'], strongest_bridge['jpos'],
[strongest_bridge['i'], [strongest_bridge['i'],
strongest_bridge['j']])) strongest_bridge['j']]))
bridges[strongest_bridge['j']] = (Bridge(strongest_bridge['btype'], bridges[strongest_bridge['j']] = (Bridge(strongest_bridge['btype'],
strongest_bridge['ipos'], strongest_bridge['ipos'],
strongest_bridge['jpos'], strongest_bridge['jpos'],
@ -357,7 +288,6 @@ def get_ladders(bridges, residues):
temp_bridges.append(bridges[i+k]) temp_bridges.append(bridges[i+k])
k+=1 k+=1
if k>1: if k>1:
#print("ladder", bridges[i].res_num, bridges[i+k-1].res_num)
ladders[i] = {'start':bridges[i].res_num, ladders[i] = {'start':bridges[i].res_num,
'end':bridges[i+k-1].res_num, 'end':bridges[i+k-1].res_num,
'bridges':temp_bridges, 'bridges':temp_bridges,
@ -373,20 +303,8 @@ def connected_ladders(ladd_1, ladd_2):
for bridge in ladd_1['bridges']: for bridge in ladd_1['bridges']:
if bridge.res_partner in res_list(ladd_2): if bridge.res_partner in res_list(ladd_2):
return ladd_2 return ladd_2
return False return False
def connected_ladders2(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 ladd_2
return False
def get_sheets(ladders): def get_sheets(ladders):
""" """
Bridges between ladders. Bridges between ladders.
@ -396,7 +314,6 @@ def get_sheets(ladders):
""" """
ladds = [ elem for elem in ladders.values() ] ladds = [ elem for elem in ladders.values() ]
sheets = {} sheets = {}
corresp = {} corresp = {}
for ladd1 in ladds: for ladd1 in ladds:
for ladd2 in ladds: for ladd2 in ladds:
@ -414,29 +331,10 @@ def get_sheets(ladders):
corresp[ladd2['i']] = corresp[ladd1['i']] corresp[ladd2['i']] = corresp[ladd1['i']]
elif ladd1 not in corresp_list and ladd2 in corresp_list: elif ladd1 not in corresp_list and ladd2 in corresp_list:
sheets[corresp[ladd2['i']]].append(ladd1) sheets[corresp[ladd2['i']]].append(ladd1)
corresp[ladd1['i']] = corresp[ladd2['i']] corresp[ladd1['i']] = corresp[ladd2['i']]
return sheets return sheets
def get_sheets2(ladders):
"""
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:
if connected_ladders(ladders[ladder], ladders[ladd2]):
bridge_i = connected_ladders2(ladders[ladder], ladders[ladd2])[2]
bridge_j = connected_ladders2(ladders[ladder], ladders[ladd2])[3]
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): def res_list(ladder):
# TODO : method in ladder class
l=[] l=[]
for i in range(ladder['i'], ladder['j']): for i in range(ladder['i'], ladder['j']):
l.append(i) l.append(i)
@ -467,7 +365,6 @@ def build_helix_patterns(residues):
if(helix): if(helix):
helix_type = residues[i].get_helix(residues)[0] helix_type = residues[i].get_helix(residues)[0]
helix_pos = residues[i].get_helix(residues)[1] helix_pos = residues[i].get_helix(residues)[1]
#print("TYPE", helix_type)
for k in range(helix_type): for k in range(helix_type):
if helix_type == 3: if helix_type == 3:
helix_3[i+1+k] = "G" helix_3[i+1+k] = "G"
@ -475,7 +372,6 @@ def build_helix_patterns(residues):
helix_4[i+1+k] = "H" helix_4[i+1+k] = "H"
if helix_type == 5: if helix_type == 5:
helix_5[i+1+k] = "I" helix_5[i+1+k] = "I"
#print(helix_3)
return[helix_3, helix_4, helix_5] return[helix_3, helix_4, helix_5]
def print_helix_pattern(residues, res, helix): def print_helix_pattern(residues, res, helix):
@ -503,5 +399,7 @@ def raw_ladders_print(ladders, ):
ladd_2 = ladders[ladd2] ladd_2 = ladders[ladd2]
for bridge in ladd_1['bridges']: for bridge in ladd_1['bridges']:
if bridge.j in res_list(ladd_2): if bridge.j in res_list(ladd_2):
print("ladder", ladd_1['i'],"-",ladd_1['j'], "|", bridge.i, "...", bridge.j, "| ladder", ladd_2['i'], ladd_2['j']) print("ladder", ladd_1['i'],"-", ladd_1['j'], "|",
bridge.i, "...", bridge.j, "| ladder",
ladd_2['i'], ladd_2['j'])

4
src/pdb.py
View File

@ -110,6 +110,4 @@ class PDBFile:
self.rawLines = self.get_content(filename) self.rawLines = self.get_content(filename)
self.metadata = self.get_header() self.metadata = self.get_header()
self.get_atoms(filename) self.get_atoms(filename)
# for elem in self.metadata :
# print(self.metadata[elem], end="")