我试图使用 Numba 优化此功能，但我无法做到。我认为这没有可以加速的代码部分。如果有人可以帮助我优化这个版本，我的程序会变得非常快。请告知是否需要任何数据集或其他信息。当我对此直接应用@jit 时，它不起作用。
def c_a(x, y, z, counter, p_l):
# start = time.time()
if counter == 1:
l = x
m = y
n = z
path = "c_r.pdb"
global r_a_t
p = Bio.PDB.PDBParser()
structure = p.get_structure('mSN1', path)
c_r = [a.get_coord() for a in structure.get_atoms()]
lengthnew = len(c_r)
m_d = np.array([-45, -45, -45])
a_s_r = np.zeros((128, 128, 128), np.complex)
for i in range(0, lengthnew):
x = int(math.floor((c_r[i][0] - m_d[0]) / 1.2))
y = int(math.floor((c_r[i][1] - m_d[1]) / 1.2))
z = int(math.floor((c_r[i][2] - m_d[2]) / 1.2))
with open("Ei.txt", 'r') as ei_values:
for row in ei_values:
s_v = row.split()
if s_v[0] == r_a_t[i] :
a_s_r[x, y, z] = np.complex(s_v[1])
n_n = lambda x, y, z : [(x2, y2, z2) for x2 in range(x - 5, x + 6)
for y2 in range(y - 5, y + 6)
for z2 in range(z - 5, z + 6)
if (-1 < x < X and
-1 < y < Y and
-1 < z < Z and
(x != x2 or y != y2 or z != z2) and
(0 <= x2 < X) and
(0 <= y2 < Y) and
(0 <= z2 < Z) and
((( abs(x - x2)) ** 2 + (abs(y - y2)) ** 2 + (abs(z - z2)) ** 2 ) <= 25))]
m = n_n(l, m, n)
result = 0
for i in range(0, len(m)):
a = m[i][0]
b = m[i][1]
c = m[i][2]
result = result + a_s_r[a][b][c]
return result
else:
l = x
m = y
n = z
path = p_l
global l_a_t
p = Bio.PDB.PDBParser()
structure = p.get_structure('mSN1', path)
c_l = [a.get_coord() for a in structure.get_atoms()]
lengthnew = len(c_l)
m_d = np.array([-45, -45, -45])
a_s_l = np.zeros((128, 128, 128), np.complex)
for i in range(0, lengthnew):
x = int(math.floor((c_l[i][0] - m_d[0]) / 1.2))
y = int(math.floor((c_l[i][1] - m_d[1]) / 1.2))
z = int(math.floor((c_l[i][2] - m_d[2]) / 1.2))
with open("E.txt", 'r') as e_v:
for row in e_v:
s_v = row.split()
if s_v[0] == l_a_t[i] :
a_s_l[x, y, z] = np.complex(s_v[1])
n_n = lambda x, y, z : [(x2, y2, z2) for x2 in range(x - 5, x + 6)
for y2 in range(y - 5, y + 6)
for z2 in range(z - 5, z + 6)
if (-1 < x < X and
-1 < y < Y and
-1 < z < Z and
(x != x2 or y != y2 or z != z2) and
(0 <= x2 < X) and
(0 <= y2 < Y) and
(0 <= z2 < Z) and
(((abs(x - x2)) ** 2 + (abs(y - y2)) ** 2 + (abs(z - z2)) ** 2 ) <= 25))]
m = n_n(l, m, n)
result = 0
for i in range(0, len(m)):
a = m[i][0]
b = m[i][1]
c = m[i][2]
result = result + a_s_l[a][b][c]
# print "c_a : ", time.time() - start
return result