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projet_court
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full output except STRUCTURE column

master
Thomas Forest 2019-09-18 12:56:41 +02:00
parent d745b942bd
commit 651f01f626
3 changed files with 119 additions and 34 deletions
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75
src/atom.py
View File

@ -28,10 +28,21 @@ class Residue:
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()):
@ -70,6 +81,18 @@ class Residue:
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))))
return angle
else:
return 360.0
def get_bridges(self, residues):
bridges = {}
bridge = {}
@ -163,6 +186,58 @@ class Residue:
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 = {}

73
src/dssp.py
View File

@ -13,22 +13,12 @@ if(len(sys.argv)<2):
"call structure and parameters.")
else:
pdb_file = pdb.PDBFile(sys.argv[1])
# print(pdb_file.residues[15].atoms["C"].coord_x)
#print(pdb_file.residues[2].atoms["N"].res_seq_nb, pdb_file.residues[2].atoms["N"].coord_x, pdb_file.residues[2].atoms["N"].coord_y, pdb_file.residues[2].atoms["N"].coord_z)
#print(pdb_file.residues[2].atoms["H"].coord_x)
#print(pdb_file.residues[2].h_bond(pdb_file.residues[40]))
#print(get_turns(pdb_file.residues))
#print(pdb_file.residues[27].h_bond(pdb_file.residues[28]))
#print(get_bridges(pdb_file.residues))
#turns = get_turns(pdb_file.residues)
#get_helix(pdb_file.residues, turns)
#get_bends(pdb_file.residues)
# get_chirality(pdb_file.residues)
bridges = get_bridges(pdb_file.residues)
ladders = get_ladders(bridges, pdb_file.residues)
sheets = get_sheets(ladders)
# print("NBRIDGES",len(bridges))
@ -36,32 +26,51 @@ else:
# get_bonds(pdb_file.residues)
residues = pdb_file.residues
e_min = 0
for res in residues:
ene = residues[1].h_bond(res)
if ene <= e_min:
e_min = ene
best_res = res
# e_min = 0
# for res in residues:
# ene = residues[1].h_bond(res)
# if ene <= e_min:
# e_min = ene
# best_res = res
#print(residues[1].resid, best_res.resid,e_min)
#get_phi_psi(residues)
#print(residues[2].atoms, residues[0].resid, residues[1].resid)
#print(get_TCO(residues[2],residues[3]))
# for i,ladder in enumerate(ladders.values()):
# print(chr(65+i))
# for ind, sheet in sheets.items():
# print(ind, sheet)
# for ladder in sheet:
# print(ladder['start'], ladder['end'])
################### OUTPUT ####################
# print DSSP-style formatted header of PDB file
for elem in pdb_file.get_header() :
print(pdb_file.get_header()[elem], end="")
# Get preliminary data for print loop
residues = pdb_file.residues
bridges = get_bridges(residues)
ladders = get_ladders(bridges, residues)
sheets = get_sheets(ladders)
# iterating over residues
for i,res in enumerate(residues):
#res.get_turns(residues, turns)
res.get_helix(residues)
#res.get_bridges(residues)
#res.get_ladders(residues, ladders)
#res.get_sheets(residues)
for i,ladder in enumerate(ladders.values()):
print(chr(65+i))
for ind, sheet in sheets.items():
print(ind, sheet)
for ladder in sheet:
print(ladder['start'], ladder['end'])
#res.get_helix(residues)
kappa = res.get_bends(residues)
t_co = res.get_tco(residues)
alpha = res.get_chirality(residues)[0]
phi = res.get_phi_psi(residues)[0]
psi = res.get_phi_psi(residues)[1]
x_ca = res.atoms["CA"].coord_x
y_ca = res.atoms["CA"].coord_y
z_ca = res.atoms["CA"].coord_z
print(i+1, res.resid, res.chain_id, res.res_letter, round(t_co, 3), round(kappa,1),
round(alpha, 1), round(phi, 1), round(psi,1), round(x_ca,1), round(y_ca,1), round(z_ca,1))

1
src/geom.py
View File

@ -1,4 +1,5 @@
import math
import numpy as np
def vector_from_pos(a, b):
xAB = b[0]-a[0]
yAB = b[1]-a[1]