Cleaning commented artefacts
Thomas Forest
parent
314a12386b
commit
7f7d8aca98
118
src/chem.py
118
src/chem.py
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@ -1,5 +1,4 @@
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import math
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#from structure import *
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from geom import *
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class Atom:
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@ -107,7 +106,6 @@ class Residue:
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if(self.h_bond(residues[i+j])<-0.5):
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k = j
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if k != 0:
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#print(k,"TURN", residues[i].resid, residues[i+k].resid)
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return Turn(k,residues[i].resid)
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return False
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@ -115,78 +113,17 @@ class Residue:
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def get_bends(self, residues):
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i = residues.index(self)
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if i >=2 and i <len(residues)-2:
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angle = math.degrees(vector_angles(vectors_substr(position_vector(residues[i].atoms["CA"].coords),
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position_vector(residues[i-2].atoms["CA"].coords)),
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vectors_substr(position_vector(residues[i+2].atoms["CA"].coords),
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position_vector(residues[i].atoms["CA"].coords))))
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angle = math.degrees(vector_angles(
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vectors_substr(position_vector(residues[i].atoms["CA"].coords),
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position_vector(residues[i-2].atoms["CA"].coords)),
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vectors_substr(position_vector(residues[i+2].atoms["CA"].coords),
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position_vector(residues[i].atoms["CA"].coords))))
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if(angle>70):
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return [angle, 'S']
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return [angle, '']
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else:
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return [360.0, '']
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def get_bridges(self, residues):
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bridges = {}
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bridge = {}
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strongest_bridge = {}
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i = residues.index(self)
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if(i >= 1 and i < 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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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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'btype':"para"}
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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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'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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'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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'btype':"anti"}
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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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bridge = {}
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coord_bridge = [i,j]
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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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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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if(len(bridges)>0):
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return(bridges[coord_bridge[0]])
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else:
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return(False)
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def get_helix(self, residues):
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"""
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Return if there is an helix at a given residue,
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@ -198,12 +135,10 @@ class Residue:
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return False
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if(self.get_turns(residues) and residues[i-1].get_turns(residues)):
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#print(self.get_turns(residues).turn_type,"- HELIX at", residues[i].indice)
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return(self.get_turns(residues).turn_type, residues[i].indice)
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return(False)
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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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if i != 0:
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if self.get_bridges(residues):
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@ -211,7 +146,6 @@ class Residue:
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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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ladder = {'start':consec_bridge.res_num,
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'end':local_bridge.res_num,
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'bridges':[consec_bridge, local_bridge]}
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@ -278,7 +212,6 @@ def get_bridges(residues):
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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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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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@ -328,13 +261,11 @@ def get_bridges(residues):
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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['ipos'],
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strongest_bridge['jpos'],
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@ -357,7 +288,6 @@ def get_ladders(bridges, residues):
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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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@ -373,20 +303,8 @@ def connected_ladders(ladd_1, ladd_2):
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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_2
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return False
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def connected_ladders2(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 ladd_2
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return False
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def get_sheets(ladders):
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"""
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Bridges between ladders.
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@ -396,7 +314,6 @@ def get_sheets(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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corresp = {}
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for ladd1 in ladds:
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for ladd2 in ladds:
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@ -415,28 +332,9 @@ def get_sheets(ladders):
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elif ladd1 not in corresp_list and ladd2 in corresp_list:
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sheets[corresp[ladd2['i']]].append(ladd1)
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corresp[ladd1['i']] = corresp[ladd2['i']]
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return sheets
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def get_sheets2(ladders):
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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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if connected_ladders(ladders[ladder], ladders[ladd2]):
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bridge_i = connected_ladders2(ladders[ladder], ladders[ladd2])[2]
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bridge_j = connected_ladders2(ladders[ladder], ladders[ladd2])[3]
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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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l=[]
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for i in range(ladder['i'], ladder['j']):
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l.append(i)
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@ -467,7 +365,6 @@ def build_helix_patterns(residues):
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if(helix):
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helix_type = residues[i].get_helix(residues)[0]
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helix_pos = residues[i].get_helix(residues)[1]
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#print("TYPE", helix_type)
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for k in range(helix_type):
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if helix_type == 3:
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helix_3[i+1+k] = "G"
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@ -475,7 +372,6 @@ def build_helix_patterns(residues):
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helix_4[i+1+k] = "H"
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if helix_type == 5:
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helix_5[i+1+k] = "I"
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#print(helix_3)
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return[helix_3, helix_4, helix_5]
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def print_helix_pattern(residues, res, helix):
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@ -503,5 +399,7 @@ def raw_ladders_print(ladders, ):
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ladd_2 = ladders[ladd2]
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for bridge in ladd_1['bridges']:
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if bridge.j in res_list(ladd_2):
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print("ladder", ladd_1['i'],"-",ladd_1['j'], "|", bridge.i, "...", bridge.j, "| ladder", ladd_2['i'], ladd_2['j'])
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print("ladder", ladd_1['i'],"-", ladd_1['j'], "|",
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bridge.i, "...", bridge.j, "| ladder",
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ladd_2['i'], ladd_2['j'])
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@ -110,6 +110,4 @@ class PDBFile:
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self.rawLines = self.get_content(filename)
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self.metadata = self.get_header()
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self.get_atoms(filename)
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# for elem in self.metadata :
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# print(self.metadata[elem], end="")
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