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new ladders print

master
Thomas Forest 2019-09-18 18:00:59 +02:00
parent de6f723d2f
commit 7f1ecf4472
7 changed files with 41 additions and 115 deletions
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131
src/atom.py
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@ -243,7 +243,6 @@ def get_bridges(residues):
bridges = {} bridges = {}
bridge = {} bridge = {}
strongest_bridge = {} strongest_bridge = {}
selected_bridges = []
for i in range(1,len(residues)-4): for i in range(1,len(residues)-4):
E_min = 0 E_min = 0
for j in range(i+2,len(residues)-1): for j in range(i+2,len(residues)-1):
@ -293,47 +292,23 @@ def get_bridges(residues):
if(bridge['res1']+bridge['res2']<E_min): if(bridge['res1']+bridge['res2']<E_min):
E_min = bridge['res1']+bridge['res2'] E_min = bridge['res1']+bridge['res2']
strongest_bridge = bridge strongest_bridge = bridge
if strongest_bridge not in selected_bridges:
selected_bridges.append(strongest_bridge)
coord_bridge = [i,j] coord_bridge = [i,j]
bridge = {} bridge = {}
# 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):
if(len(selected_bridges)>1):
bridges[strongest_bridge['i']] = (Bridge(strongest_bridge['btype'],
strongest_bridge['ipos'],
strongest_bridge['jpos'],
[strongest_bridge['i'],
strongest_bridge['j']],
selected_bridges[-2]['btype'],
selected_bridges[-2]['ipos'],
selected_bridges[-2]['jpos'],
[selected_bridges[-2]['i'],
selected_bridges[-2]['j']]))
bridges[strongest_bridge['j']] = (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']]))
selected_bridges[-2]['btype'],
selected_bridges[-2]['ipos'],
selected_bridges[-2]['jpos'],
[selected_bridges[-2]['i'],
selected_bridges[-2]['j']]))
else:
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'], bridges[strongest_bridge['j']] = (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']]))
if(len(bridges)>0): if(len(bridges)>0):
return(bridges) return(bridges)
else: else:
@ -366,12 +341,21 @@ def connected_ladders(ladd_1, ladd_2):
links = [] links = []
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_1['i'], ladd_1['j'], bridge.i, bridge.j,
# ladd_2['i'], ladd_2['j']])
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.
@ -413,81 +397,20 @@ def get_sheets2(ladders):
sheets = {} sheets = {}
for ladder in ladders: for ladder in ladders:
for ladd2 in ladders: for ladd2 in ladders:
if connected_ladders(ladders[ladder], ladders[ladd2]): if connected_ladders(ladders[ladder], ladders[ladd2]):
pass bridge_i = connected_ladders2(ladders[ladder], ladders[ladd2])[2]
print("ladder",ladders[ladder]['i'], ladders[ladder]['j'],"bridge",bridge.i, bridge.j, bridge_j = connected_ladders2(ladders[ladder], ladders[ladd2])[3]
"ladder 2",ladders[ladd2]['i'], ladders[ladd2]['j']) 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 # TODO : method in ladder class
l=[] l=[]
for i in range(ladder['start'], ladder['end']): for i in range(ladder['i'], ladder['j']):
l.append(i) l.append(i)
return(l) return(l)
def get_bends(residues):
bends = {}
for i in range(2,len(residues)-2):
angle = math.degrees(vector_angles(vectors_substr(position_vector(residues[i].atoms["CA"].coords),
position_vector(residues[i-2].atoms["CA"].coords)),
vectors_substr(position_vector(residues[i+2].atoms["CA"].coords),
position_vector(residues[i].atoms["CA"].coords))))
if(angle>70):
print("angle", residues[i].resid, angle)
bends[residues[i].resid] = angle
return(bends)
def get_chirality(residues):
for i in range(1,len(residues)-2):
chirality = {}
angle = calc_dihedral(residues[i-1].atoms["CA"].coords,
residues[i].atoms["CA"].coords,
residues[i+1].atoms["CA"].coords,
residues[i+2].atoms["CA"].coords)
if(angle>0 and angle<=180):
sign="+"
print("chirality", residues[i].resid, "+", angle)
if(angle<=0 and angle > -180):
sign="-"
print("chirality", residues[i].resid, "-", angle)
chirality[residues[i].resid] = sign
return chirality
def get_phi_psi(residues):
for i in range(len(residues)):
if(i==0):
phi = 360.0
else:
phi = calc_dihedral(residues[i-1].atoms["C"].coords,
residues[i].atoms["N"].coords,
residues[i].atoms["CA"].coords,
residues[i].atoms["C"].coords)
if(i==len(residues)-1):
psi = 360.0
else:
psi = calc_dihedral(residues[i].atoms["N"].coords,
residues[i].atoms["CA"].coords,
residues[i].atoms["C"].coords,
residues[i+1].atoms["N"].coords)
print("ANGLES", i, phi, psi)
def get_TCO(res1, res2):
CO_res1 = vector_from_pos(res1.atoms["C"].coords,
res1.atoms["O"].coords)
CO_res2 = vector_from_pos(res2.atoms["C"].coords,
res2.atoms["O"].coords)
angle = vector_angles(CO_res1, CO_res2)
return(math.cos(angle))
def build_turns_patterns(residues): def build_turns_patterns(residues):
turns_3 = {} turns_3 = {}
turns_4 = {} turns_4 = {}

15
src/dssp.py
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@ -79,7 +79,6 @@ for i,res in enumerate(residues):
turn_3 = print_turn_pattern(residues, res, turns[0]) turn_3 = print_turn_pattern(residues, res, turns[0])
turn_4 = print_turn_pattern(residues, res, turns[1]) turn_4 = print_turn_pattern(residues, res, turns[1])
turn_5 = print_turn_pattern(residues, res, turns[2]) turn_5 = print_turn_pattern(residues, res, turns[2])
helix_3 = print_helix_pattern(residues, res, helix[0]) helix_3 = print_helix_pattern(residues, res, helix[0])
helix_4 = print_helix_pattern(residues, res, helix[1]) helix_4 = print_helix_pattern(residues, res, helix[1])
helix_5 = print_helix_pattern(residues, res, helix[2]) helix_5 = print_helix_pattern(residues, res, helix[2])
@ -91,5 +90,15 @@ for i,res in enumerate(residues):
round(alpha, 1), round(phi, 1), round(psi,1), round(x_ca,1), round(y_ca,1), round(z_ca,1)) round(alpha, 1), round(phi, 1), round(psi,1), round(x_ca,1), round(y_ca,1), round(z_ca,1))
for bridge in bridges: for ladd1 in ladders:
print(bridges[bridge].i, bridges[bridge].j) ladd_1 = ladders[ladd1]
for ladd2 in ladders:
ladd_2 = ladders[ladd2]
for bridge in ladd_1['bridges']:
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'])
# for ind, sheet in sheets.items():
# print(ind, sheet)
# for ladder in sheet:
# print(ladder['start'], ladder['end'])

8
src/structure.py
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@ -14,19 +14,13 @@ class Turn(Structure):
class Bridge(Structure): class Bridge(Structure):
def __init__(self, bridge_type, res_num, res_partner, indices, def __init__(self, bridge_type, res_num, res_partner, indices):
second_bridge_type=None, second_resnum=None,
second_res_partner=None, second_indices=None):
self.bridge_type = bridge_type self.bridge_type = bridge_type
self.res_num = res_num self.res_num = res_num
self.res_partner = res_partner self.res_partner = res_partner
Structure.res = res_num Structure.res = res_num
self.i = indices[0] self.i = indices[0]
self.j = indices[1] self.j = indices[1]
self.second_bridge_type = second_bridge_type
self.second_resnum = second_resnum
self.second_res_partner = second_res_partner
self.second_indices = second_indices
class Helix(Structure): class Helix(Structure):