def plot_atoms(self):
xs = []
ys = []
zs = []
cs = []
watoms = []
if self.tipus == 1:
watoms = [
atom for atom in self.atoms
if atom[Atributs.atomt("idTAtom")] == True
]
if self.tipus == 2:
watoms = [
residu for residu in self.residus
if residu[Atributs.residut("idTResidu")] == True
]
self.tipus2 = 1
for linia in watoms:
if self.tipus == 1:
x = linia[Atributs.atomt("xcoor")]
y = linia[Atributs.atomt("ycoor")]
z = linia[Atributs.atomt("zcoor")]
if self.tipus == 2:
x = linia[Atributs.residut("xcoor")]
y = linia[Atributs.residut("ycoor")]
z = linia[Atributs.residut("zcoor")]
# Get color
chain = linia[Atributs.atomt("idChain")]
colors = Colors(chain, 1)
col = colors.color_molecula()
xs.append(x)
ys.append(y)
zs.append(z)
cs.append(col)
fig = plt.figure(figsize=(10, 5))
ax = fig.add_subplot(111, projection='3d')
ax.set_facecolor([0.98, 0.92, 0.84]) # blanc antic
ax.text2D(-0.10,
0.95,
self.capcalera,
horizontalalignment='left',
verticalalignment='top',
family='Serif',
size=9,
transform=ax.transAxes)
ax.scatter(xs, ys, zs, c=cs, marker='o', alpha=0.35)
ax.set_xlabel('Eix X')
ax.set_ylabel('Eix Y')
ax.set_zlabel('Eix Z')
plt.show()
def __init__(self, fitxer):
self.fitxer = fitxer
E = Entitat(self.fitxer)
self.linies = E.get_linies()
dadestotals = E.crear_entitat()
self.capcalera = dadestotals[0]
self.molecules = dadestotals[2]
self.residus = dadestotals[3]
self.atoms = dadestotals[4]
self.nom_taula = dadestotals[5]
self.nomResidu = Atributs.residut("nomResidu")
self.nomElement = Atributs.atomt("elemQuim")
self.idTResidu = Atributs.residut("idTResidu")
self.idTAtom = Atributs.atomt("idTAtom")
def plot_linies(self):
# Coordenades
tx = 0.0
ty = 0.0
tz = 0.0
txp = 0.0
typ = 0.0
tzp = 0.0
self.tipus2 = 2
fig = plt.figure(figsize=(11, 5))
ax = fig.add_subplot(111, projection='3d')
ax.set_facecolor([0.98, 0.92, 0.84]) # blanc antic
ax.text2D(-0.10,
0.95,
self.capcalera,
horizontalalignment='left',
verticalalignment='top',
family='Serif',
size=9,
transform=ax.transAxes)
# ax.text2D(0.05, 0.95, self.capcalera, transform=ax.transAxes)
# Posicions en el refistre de residus
chain = Atributs.residut("idChain")
s = Atributs.residut("idResidu")
amin = Atributs.residut("nomResidu")
x = Atributs.residut("xcoor")
y = Atributs.residut("ycoor")
z = Atributs.residut("zcoor")
prot = Atributs.residut("idTResidu")
# Vectors plot
punt_inici_x = []
punt_inici_y = []
punt_inici_z = []
punt_final_x = []
punt_final_y = []
punt_final_z = []
colamin = []
# Nomes aminoacids de la proteina residu[prot] == True
cadena = [residu for residu in self.residus if residu[prot] == True]
residus_net = cadena
n = len(residus_net) - 1
for i in range(n):
linia = residus_net[i]
chain1 = linia[chain]
amino = linia[amin]
tx = linia[x]
ty = linia[y]
tz = linia[z]
res1 = [chain1 + str(linia[s])]
if i < n:
liniapost = residus_net[i + 1]
chain2 = liniapost[chain]
txp = liniapost[x]
typ = liniapost[y]
tzp = liniapost[z]
res2 = [chain2 + str(liniapost[s])]
else:
pass
# Get color
if self.tipus == 1:
colors = Colors(chain1, 1)
cl = colors.color_molecula()
elif self.tipus == 2:
aminos = ('ALA', 'ARG', 'ASN', 'ASP', 'CYS', 'PHE', 'GLN',
'GLU', 'GLY', 'HIS', 'ILE', 'LEU', 'LYS', 'PRO',
'MET', 'SER', 'THR', 'TYR', 'TRP', 'VAL')
if amino in aminos:
ccolors = Colors(amino, 2)
cl = ccolors.color_tipus()
else:
cl = ('k')
else:
cl = ('c')
punt_inici_x.append(tx)
punt_inici_y.append(ty)
punt_inici_z.append(tz)
colamin.append(cl)
if i < n and chain1 == chain2:
punt_final_x.append(txp)
punt_final_y.append(typ)
punt_final_z.append(tzp)
else:
punt_final_x.append(tx)
punt_final_y.append(ty)
punt_final_z.append(tz)
for i in range(n):
xs = [punt_inici_x[i], punt_final_x[i]]
ys = [punt_inici_y[i], punt_final_y[i]]
zs = [punt_inici_z[i], punt_final_z[i]]
col = colamin[i]
ax.plot(xs, ys, zs, linewidth=2, color=col)
# linea = []
# linea = [x for x in punt_inici_x if x == 0]
# ax.set_xlabel('Eix X')
# ax.set_ylabel('Eix Y')
# ax.set_zlabel('Eix Z')
plt.show()
def plot2d_3d(self):
fig = plt.figure(figsize=(11, 5))
ax = fig.add_subplot(111, projection='3d')
ax.text2D(-0.10,
-0.10,
self.capcalera,
horizontalalignment='left',
verticalalignment='top',
family='Serif',
size=8,
transform=ax.transAxes)
self.tipus2 = 1
ax_xy = fig.add_subplot(331)
ax_xy.set_title('X/Y')
ax_xz = fig.add_subplot(333)
ax_xz.set_title('X/Z')
ax_zy = fig.add_subplot(334)
ax_zy.set_title('Z/Y')
ax.set_facecolor([0.98, 0.92, 0.84]) # blanc antic
zx, zy, zz = [], [], []
idchains = Atributs.residut("idChain")
idresidus = Atributs.residut("idResidu")
idresatom = Atributs.atomt("idResidu")
aprot = Atributs.atomt("idTAtom")
idx = Atributs.atomt("xcoor")
idy = Atributs.atomt("ycoor")
idz = Atributs.atomt("zcoor")
vella_mol = ""
for chain_id in self.molecules:
if chain_id != vella_mol:
atr = Colors(chain_id)
nom = atr.color_molecula()
vella_mol = chain_id
xs = []
ys = []
zs = []
wresidus = [
res for res in self.residus if res[idchains] == chain_id
]
for residu in wresidus:
watoms = []
watoms = [
atom for atom in self.atoms
if atom[idresatom] == residu[idresidus]
and atom[idchains] == chain_id and atom[aprot] == True
]
for atom in watoms:
x = atom[idx]
y = atom[idy]
z = atom[idz]
xs.append(x)
ys.append(y)
zs.append(z)
atr = Colors(chain_id, 1)
nom = atr.color_molecula()
ax.scatter(xs, ys, zs, marker='*', color=nom, alpha=0.35)
ax_xy.scatter(xs, ys, marker='.', color=nom, alpha=0.15)
ax_xz.scatter(xs, zs, marker='.', color=nom, alpha=0.15)
ax_zy.scatter(zs, ys, marker='.', color=nom, alpha=0.15)
# ax.text2D(0.05, 0.95, self.capcalera, transform=ax.transAxes)
# ax.text(9, 0, 0,self.capcalera , color='red')
plt.show()