def maxmins(atoms):
xmax = -999999999
xmin = 999999999
ymax = -999999999
ymin = 999999999
zmax = -99999999
zmin = 999999999
xs = 0
ys = 0
zs = 0
num = 0
nx = Atributs.atomt("xcoor")
ny = Atributs.atomt("ycoor")
nz = Atributs.atomt("zcoor")
for i in range(len(atoms) - 1):
linia = atoms[i]
x = linia[nx]
y = linia[ny]
z = linia[nz]
if x > xmax: xmax = x
if x <= xmin: xmin = x
if y > ymax: ymax = y
if y <= ymin: ymin = y
if z > zmax: zmax = z
if z <= zmin: zmin = z
num += 1
xs = xs + x
ys = ys + y
zs = zs + z
llista = [xmin, ymin, zmin], [xmax, ymax, zmax], [(round(xs / num, 4)),
round(ys / num, 4),
round(zs / num, 4)]
return (llista)
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 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()