new ladders print
Thomas Forest
parent
de6f723d2f
commit
7f1ecf4472
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131
src/atom.py
131
src/atom.py
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@ -243,7 +243,6 @@ def get_bridges(residues):
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bridges = {}
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bridge = {}
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strongest_bridge = {}
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selected_bridges = []
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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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@ -293,47 +292,23 @@ def get_bridges(residues):
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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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if strongest_bridge not in selected_bridges:
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selected_bridges.append(strongest_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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if(len(selected_bridges)>1):
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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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selected_bridges[-2]['btype'],
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selected_bridges[-2]['ipos'],
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selected_bridges[-2]['jpos'],
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[selected_bridges[-2]['i'],
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selected_bridges[-2]['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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[strongest_bridge['i'],
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strongest_bridge['j']],
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selected_bridges[-2]['btype'],
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selected_bridges[-2]['ipos'],
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selected_bridges[-2]['jpos'],
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[selected_bridges[-2]['i'],
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selected_bridges[-2]['j']]))
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else:
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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['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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[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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[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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@ -366,12 +341,21 @@ 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 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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@ -413,81 +397,20 @@ def get_sheets2(ladders):
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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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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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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['start'], ladder['end']):
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for i in range(ladder['i'], ladder['j']):
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l.append(i)
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return(l)
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def get_bends(residues):
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bends = {}
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for i in range(2,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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if(angle>70):
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print("angle", residues[i].resid, angle)
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bends[residues[i].resid] = angle
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return(bends)
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def get_chirality(residues):
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for i in range(1,len(residues)-2):
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chirality = {}
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angle = calc_dihedral(residues[i-1].atoms["CA"].coords,
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residues[i].atoms["CA"].coords,
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residues[i+1].atoms["CA"].coords,
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residues[i+2].atoms["CA"].coords)
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if(angle>0 and angle<=180):
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sign="+"
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print("chirality", residues[i].resid, "+", angle)
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if(angle<=0 and angle > -180):
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sign="-"
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print("chirality", residues[i].resid, "-", angle)
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chirality[residues[i].resid] = sign
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return chirality
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def get_phi_psi(residues):
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for i in range(len(residues)):
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if(i==0):
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phi = 360.0
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else:
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phi = calc_dihedral(residues[i-1].atoms["C"].coords,
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residues[i].atoms["N"].coords,
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residues[i].atoms["CA"].coords,
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residues[i].atoms["C"].coords)
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if(i==len(residues)-1):
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psi = 360.0
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else:
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psi = calc_dihedral(residues[i].atoms["N"].coords,
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residues[i].atoms["CA"].coords,
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residues[i].atoms["C"].coords,
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residues[i+1].atoms["N"].coords)
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print("ANGLES", i, phi, psi)
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def get_TCO(res1, res2):
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CO_res1 = vector_from_pos(res1.atoms["C"].coords,
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res1.atoms["O"].coords)
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CO_res2 = vector_from_pos(res2.atoms["C"].coords,
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res2.atoms["O"].coords)
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angle = vector_angles(CO_res1, CO_res2)
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return(math.cos(angle))
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def build_turns_patterns(residues):
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turns_3 = {}
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turns_4 = {}
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15
src/dssp.py
15
src/dssp.py
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@ -79,7 +79,6 @@ for i,res in enumerate(residues):
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turn_3 = print_turn_pattern(residues, res, turns[0])
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turn_4 = print_turn_pattern(residues, res, turns[1])
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turn_5 = print_turn_pattern(residues, res, turns[2])
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helix_3 = print_helix_pattern(residues, res, helix[0])
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helix_4 = print_helix_pattern(residues, res, helix[1])
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helix_5 = print_helix_pattern(residues, res, helix[2])
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@ -91,5 +90,15 @@ for i,res in enumerate(residues):
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round(alpha, 1), round(phi, 1), round(psi,1), round(x_ca,1), round(y_ca,1), round(z_ca,1))
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for bridge in bridges:
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print(bridges[bridge].i, bridges[bridge].j)
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for ladd1 in ladders:
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ladd_1 = ladders[ladd1]
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for ladd2 in 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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# for ind, sheet in sheets.items():
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# print(ind, sheet)
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# for ladder in sheet:
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# print(ladder['start'], ladder['end'])
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@ -14,19 +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, indices,
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second_bridge_type=None, second_resnum=None,
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second_res_partner=None, second_indices=None):
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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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self.second_bridge_type = second_bridge_type
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self.second_resnum = second_resnum
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self.second_res_partner = second_res_partner
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self.second_indices = second_indices
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class Helix(Structure):
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