diff --git a/src/__pycache__/atom.cpython-37.pyc b/src/__pycache__/atom.cpython-37.pyc new file mode 100644 index 0000000..cf2b4a7 Binary files /dev/null and b/src/__pycache__/atom.cpython-37.pyc differ diff --git a/src/__pycache__/geom.cpython-37.pyc b/src/__pycache__/geom.cpython-37.pyc new file mode 100644 index 0000000..9e45ca8 Binary files /dev/null and b/src/__pycache__/geom.cpython-37.pyc differ diff --git a/src/__pycache__/pdb.cpython-37.pyc b/src/__pycache__/pdb.cpython-37.pyc new file mode 100644 index 0000000..cc64307 Binary files /dev/null and b/src/__pycache__/pdb.cpython-37.pyc differ diff --git a/src/__pycache__/structure.cpython-37.pyc b/src/__pycache__/structure.cpython-37.pyc new file mode 100644 index 0000000..ee79b27 Binary files /dev/null and b/src/__pycache__/structure.cpython-37.pyc differ diff --git a/src/atom.py b/src/atom.py index d3c7388..c3db1b2 100644 --- a/src/atom.py +++ b/src/atom.py @@ -243,7 +243,6 @@ def get_bridges(residues): bridges = {} bridge = {} strongest_bridge = {} - selected_bridges = [] for i in range(1,len(residues)-4): E_min = 0 for j in range(i+2,len(residues)-1): @@ -293,47 +292,23 @@ def get_bridges(residues): if(bridge['res1']+bridge['res2']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['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'], - 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']])) - 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'], - strongest_bridge['ipos'], - strongest_bridge['jpos'], - [strongest_bridge['i'], - strongest_bridge['j']])) + bridges[strongest_bridge['j']] = (Bridge(strongest_bridge['btype'], + strongest_bridge['ipos'], + strongest_bridge['jpos'], + [strongest_bridge['i'], + strongest_bridge['j']])) if(len(bridges)>0): return(bridges) else: @@ -366,12 +341,21 @@ def connected_ladders(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 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): """ Bridges between ladders. @@ -413,80 +397,19 @@ def get_sheets2(ladders): sheets = {} for ladder in ladders: for ladd2 in ladders: - if connected_ladders(ladders[ladder], ladders[ladd2]): - pass - print("ladder",ladders[ladder]['i'], ladders[ladder]['j'],"bridge",bridge.i, bridge.j, - "ladder 2",ladders[ladd2]['i'], ladders[ladd2]['j']) + 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): # TODO : method in ladder class l=[] - for i in range(ladder['start'], ladder['end']): + for i in range(ladder['i'], ladder['j']): l.append(i) 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): turns_3 = {} diff --git a/src/dssp.py b/src/dssp.py index 148f747..3f1c9a2 100644 --- a/src/dssp.py +++ b/src/dssp.py @@ -79,7 +79,6 @@ for i,res in enumerate(residues): turn_3 = print_turn_pattern(residues, res, turns[0]) turn_4 = print_turn_pattern(residues, res, turns[1]) turn_5 = print_turn_pattern(residues, res, turns[2]) - helix_3 = print_helix_pattern(residues, res, helix[0]) helix_4 = print_helix_pattern(residues, res, helix[1]) 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)) -for bridge in bridges: - print(bridges[bridge].i, bridges[bridge].j) +for ladd1 in ladders: + 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']) diff --git a/src/structure.py b/src/structure.py index ab6d585..1c206ad 100644 --- a/src/structure.py +++ b/src/structure.py @@ -14,19 +14,13 @@ class Turn(Structure): class Bridge(Structure): - def __init__(self, bridge_type, res_num, res_partner, indices, - second_bridge_type=None, second_resnum=None, - second_res_partner=None, second_indices=None): + def __init__(self, bridge_type, res_num, res_partner, indices): self.bridge_type = bridge_type self.res_num = res_num self.res_partner = res_partner Structure.res = res_num self.i = indices[0] 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):