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- import math
- from structure import *
- class Atom:
-
- def dist_atoms(self, atom2):
- return(math.sqrt((self.coord_x-atom2.coord_x)**2 +
- (self.coord_y-atom2.coord_y)**2 +
- (self.coord_z-atom2.coord_z)**2))
-
-
- def __init__(self, atom_id, atom_name, res_name, chain_id,
- res_seq_nb, insertion_code, coordinates):
- self.atom_id = atom_id
- self.atom_name = atom_name
- self.res_name = res_name
- self.chain_id = chain_id
- self.res_seq_nb = res_seq_nb
- self.insertion_code = insertion_code
- self.coord_x = coordinates[0]
- self.coord_y = coordinates[1]
- self.coord_z = coordinates[2]
- self.coords = coordinates
-
- class Residue:
- def __init__(self, atoms_list, indice):
- self.atoms = {}
- for atom in atoms_list:
- self.atoms[atom.atom_name] = atom
- self.resid = atom.res_seq_nb
- self.res_name = atom.res_name
- self.res_letter = self.get_amino_letter(atom.res_name)
- self.chain_id = atom.chain_id
- self.insertion_code = atom.insertion_code
- self.indice = indice
-
- def get_amino_letter(self, res_name):
- code3 = ['ALA', 'ARG', 'ASN', 'ASP', 'CYS', 'GLU', 'GLN', 'GLY',
- 'HIS', 'ILE', 'LEU', 'LYS', 'MET', 'PHE', 'PRO', 'SER',
- 'THR', 'TRP', 'TYR', 'VAL']
-
-
- code1 = ['A','R','N','D','C','E','Q','G','H','I','L','K','M','F','P',
- 'S','T','W','Y','V']
-
- return code1[code3.index(res_name)]
-
- def h_bond(self, res2):
- if("H" not in res2.atoms.keys()):
- return(False)
- # dimensionnal factor, in kcal/mole
- f = 332
- # partial charges
- q1 = 0.42
- q2 = 0.20
- # distance between O-N atoms, in angströms
- r_ON = self.atoms["O"].dist_atoms(res2.atoms["N"])
- # distance between C-H atoms, in angströms
- r_CH = self.atoms["C"].dist_atoms(res2.atoms["H"])
- # distance between O-H atoms, in angströms
- r_OH = self.atoms["O"].dist_atoms(res2.atoms["H"])
- # distance between C-N atoms, in angströms
- r_CN = self.atoms["C"].dist_atoms(res2.atoms["N"])
- # electrostatic interaction energy, in kcal/mole
- E = q1*q2*(1/r_ON + 1/r_CH - 1/r_OH - 1/r_CN)*f
- return(E)
-
- def get_turns(self, residues):
- """
- Get all the turns from a specific residue.
- """
- turns = {}
- i = residues.index(self)
- k = 0
- for j in range(3,6):
- if(i+j<len(residues)):
- if(self.h_bond(residues[i+j])<-0.5):
- k = j
- if k != 0:
- #print(k,"TURN", residues[i].resid, residues[i+k].resid)
- return Turn(k,residues[i].resid)
-
- return False
-
- def get_bends(self, residues):
- i = residues.index(self)
- if i >=2 and i <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):
- return [angle, 'S']
- return [angle, '']
- else:
- 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):
- """
- Return if there is an helix at a given residue,
- as well as its type.
- """
- i = residues.index(self)
- # if there are no turns or it is the first residue, skip
- if i == 0:
- return False
-
- 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(False)
-
- def get_ladder(self, residues):
- #ladders = {}
- i = residues.index(self)
- if i != 0:
- if self.get_bridges(residues):
- if (residues[i-1].get_bridges(residues)):
- local_bridge = self.get_bridges(residues)
- consec_bridge = residues[i-1].get_bridges(residues)
- 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,
- 'end':local_bridge.res_num,
- 'bridges':[consec_bridge, local_bridge]}
- return ladder
- return False
-
- def get_tco(self, residues):
- i = residues.index(self)
- if(i!=0):
- res2 = residues[i-1]
- CO_res1 = vector_from_pos(self.atoms["C"].coords,
- self.atoms["O"].coords)
- CO_res2 = vector_from_pos(res2.atoms["C"].coords,
- res2.atoms["O"].coords)
- angle = vector_angles(CO_res1, CO_res2)
- else:
- angle = math.pi/2
- return(math.cos(angle))
-
- def get_chirality(self, residues):
- i = residues.index(self)
- if (i >=1 and i < 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="+"
-
- if(angle<=0 and angle > -180):
- sign="-"
-
- else:
- angle = 360.0
- sign = ''
-
- return [angle, sign]
-
- def get_phi_psi(self, residues):
- i = residues.index(self)
- 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)
-
- return((phi, psi))
- def get_bridges(residues):
- bridges = {}
- bridge = {}
- strongest_bridge = {}
- for i in range(1,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,
- 'i':residues[i].indice,
- 'j':residues[j].indice,
- '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,
- 'i':residues[i].indice,
- 'j':residues[j].indice,
- '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,
- 'i':residues[i].indice,
- 'j':residues[j].indice,
- '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,
- 'i':residues[i].indice,
- 'j':residues[j].indice,
- 'btype':"anti"}
-
- if(bridge):
- if(bridge['res1']+bridge['res2']<E_min):
- E_min = bridge['res1']+bridge['res2']
- strongest_bridge = bridge
- coord_bridge = [i,j]
- bridge = {}
-
- # finally add the strongest bridge at i and j pos
- if(strongest_bridge):
-
- 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']]))
- if(len(bridges)>0):
- return(bridges)
- else:
- return(False)
-
- def get_ladders(bridges, residues):
- ladders = {}
- i = 1
- while i < len(residues):
- k = 1
- if i in bridges.keys():
- temp_bridges = [bridges[i]]
- while ((i+k in bridges.keys()) and
- (bridges[i].bridge_type == bridges[i+k].bridge_type)):
- temp_bridges.append(bridges[i+k])
- k+=1
- if k>1:
- #print("ladder", bridges[i].res_num, bridges[i+k-1].res_num)
- ladders[i] = {'start':bridges[i].res_num,
- 'end':bridges[i+k-1].res_num,
- 'bridges':temp_bridges,
- 'i':i,
- 'j':i+k-1}
- i+=k-1
- else:
- i+=1
- return ladders
-
- 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_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.
- 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.
- """
- ladds = [ elem for elem in ladders.values() ]
- sheets = {}
-
- corresp = {}
- for ladd1 in ladds:
- for ladd2 in ladds:
- if connected_ladders(ladd1, ladd2)!=False:
- corresp_list = [ elem for elem in corresp.keys() ]
- if ladd1['i'] not in corresp_list and ladd2['i'] not in corresp_list:
- ind = len(sheets.keys())
- sheets[ind] = []
- sheets[ind].append(ladd1)
- sheets[ind].append(ladd2)
- corresp[ladd1['i']] = ind
- corresp[ladd2['i']] = ind
- elif ladd2 not in corresp_list and ladd1 in corresp_list:
- sheets[corresp[ladd1['i']]].append(ladd2)
- corresp[ladd2['i']] = corresp[ladd1['i']]
- elif ladd1 not in corresp_list and ladd2 in corresp_list:
- sheets[corresp[ladd2['i']]].append(ladd1)
- corresp[ladd1['i']] = corresp[ladd2['i']]
-
- 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):
- # TODO : method in ladder class
- l=[]
- for i in range(ladder['i'], ladder['j']):
- l.append(i)
- return(l)
-
- def build_turns_patterns(residues):
- turns_3 = {}
- turns_4 = {}
- turns_5 = {}
- for i,res in enumerate(residues):
- turn = residues[i].get_turns(residues)
- if(turn):
- for k in range(turn.turn_type):
- if turn.turn_type == 3:
- turns_3[i+1+k] = turn.turn_type
- if turn.turn_type == 4:
- turns_4[i+1+k] = turn.turn_type
- if turn.turn_type == 5:
- turns_5[i+1+k] = turn.turn_type
- return[turns_3, turns_4, turns_5]
-
- def build_helix_patterns(residues):
- helix_3 = {}
- helix_4 = {}
- helix_5 = {}
- for i,res in enumerate(residues):
- helix = residues[i].get_helix(residues)
- if(helix):
- helix_type = residues[i].get_helix(residues)[0]
- helix_pos = residues[i].get_helix(residues)[1]
- #print("TYPE", helix_type)
- for k in range(helix_type):
- if helix_type == 3:
- helix_3[i+1+k] = "G"
- if helix_type == 4:
- helix_4[i+1+k] = "H"
- if helix_type == 5:
- helix_5[i+1+k] = "I"
- #print(helix_3)
- return[helix_3, helix_4, helix_5]
-
- def print_helix_pattern(residues, res, helix):
- i = residues.index(res)+1
- if i in helix.keys():
- return (helix[i])
- else:
- return(' ')
-
- def print_turn_pattern(residues, res, turns):
- i = residues.index(res)+1
- if i in turns.keys() and not i-1 in turns.keys():
- return(">")
- elif i in turns.keys() and i-1 in turns.keys():
- return(turns[i])
- elif i not in turns.keys() and i-1 in turns.keys():
- return("<")
- else:
- return(' ')
-
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