def get_coord_nwchem(f):
"""
Extract XYZ coordinate from NWChem output file.
Parameters
----------
f : str
User input filename.
Returns
-------
atom : list
Full atomic labels of complex.
coord : ndarray
Full atomic coordinates of complex.
"""
nwchem_file = open(f, "r")
nline = nwchem_file.readlines()
start = 0
end = 0
atom, coord = [], []
for i in range(len(nline)):
if "Optimization converged" in nline[i]:
start = i
for i in range(len(nline)):
if "No. of atoms" in nline[i]:
end = int(nline[i].split()[4])
start = start + 18
end = start + end
# The 1st line of coordinate is at 18 lines next to 'Optimization converged'
for line in nline[start:end]:
dat = line.split()
dat1 = int(float(dat[2]))
coord_x = float(dat[3])
coord_y = float(dat[4])
coord_z = float(dat[5])
dat1 = elements.check_atom(dat1)
atom.append(dat1)
coord.append([coord_x, coord_y, coord_z])
nwchem_file.close()
coord = np.asarray(coord, dtype=np.float64)
return atom, coord
def get_coord_gaussian(f):
"""
Extract XYZ coordinate from Gaussian output file.
Parameters
----------
f : str
User input filename.
Returns
-------
atom : list
Full atomic labels of complex.
coord : ndarray
Full atomic coordinates of complex.
"""
gaussian_file = open(f, "r")
nline = gaussian_file.readlines()
start = 0
end = 0
atom, coord = [], []
for i in range(len(nline)):
if "Standard orientation:" in nline[i]:
start = i
for i in range(start + 5, len(nline)):
if "---" in nline[i]:
end = i
break
for line in nline[start + 5:end]:
data = line.split()
data1 = int(data[1])
coord_x = float(data[3])
coord_y = float(data[4])
coord_z = float(data[5])
data1 = elements.check_atom(data1)
atom.append(data1)
coord.append([coord_x, coord_y, coord_z])
gaussian_file.close()
coord = np.asarray(coord, dtype=np.float64)
return atom, coord
def on_pick(event):
"""
Pick point and get XYZ data
Parameters
----------
event : object
Event object for on-pick function.
Examples
--------
>>> def on_pick(event):
>>> ... ind = event.ind
>>> ... print("on_pick scatter:", ind, np.take(x, ind), np.take(y, ind))
"""
ind = event.ind[0]
x, y, z = event.artist._offsets3d
for i in range(len(self.atom)):
if x[ind] == self.coord[i][0]:
if y[ind] == self.coord[i][1]:
if z[ind] == self.coord[i][2]:
atom = self.atom[i]
break
results = f"{i + 1} {atom} : {x[ind]} {y[ind]} {z[ind]}"
coord = [x[ind], y[ind], z[ind]]
insert_text(results, coord, group)
# Highlight selected atom
index = elements.check_atom(atom)
ax.scatter(
x[ind],
y[ind],
z[ind],
marker="o",
linewidths=0.5,
edgecolors="orange",
picker=5,
alpha=0.5,
color="yellow",
s=elements.check_radii(index) * 400,
)
def octa_and_face(ao, co, save="not_save"):
"""
Display 3D structure of octahedral complex with 8 faces.
Parameters
----------
ao : list
Atomic labels of octahedral structure.
co : list
Atomic coordinates of octahedral structure.
save : str
Name of image file to save. If this argument is not set by user,
do not save a figure as image.
Returns
-------
None : None
"""
fig = plt.figure()
ax = Axes3D(fig)
# Plot atoms
for i in range(len(co)):
# Determine atomic number
n = elements.check_atom(ao[i])
ax.scatter(co[i][0],
co[i][1],
co[i][2],
marker='o',
linewidths=0.5,
edgecolors='black',
color=elements.check_color(n),
label=f"{ao[i]}",
s=elements.check_radii(n) * 300)
# Draw 8 faces
# Get atomic coordinates of octahedron
_, c_ref, _, _ = tools.find_faces_octa(co)
# Create array of vertices for 8 faces
vertices_list = []
for i in range(8):
get_vertices = c_ref[i].tolist()
x, y, z = zip(*get_vertices)
vertices = [list(zip(x, y, z))]
vertices_list.append(vertices)
# Added faces
color_list = [
"red", "blue", "green", "yellow", "violet", "cyan", "brown", "grey"
]
for i in range(len(vertices_list)):
ax.add_collection3d(
Poly3DCollection(vertices_list[i], alpha=0.5, color=color_list[i]))
# Draw line
for i in range(1, len(co)):
merge = list(zip(co[0], co[i]))
x, y, z = merge
ax.plot(x, y, z, 'k-', color="black", linewidth=2)
# Set legend
# Remove duplicate labels in legend.
# Ref.https://stackoverflow.com/a/26550501/6596684
handles, labels = ax.get_legend_handles_labels()
handle_list, label_list = [], []
for handle, label in zip(handles, labels):
if label not in label_list:
handle_list.append(handle)
label_list.append(label)
leg = plt.legend(handle_list,
label_list,
loc="lower left",
scatterpoints=1,
fontsize=12)
# Fixed size of point in legend
# Ref. https://stackoverflow.com/a/24707567/6596684
for i in range(len(leg.legendHandles)):
leg.legendHandles[i]._sizes = [90]
# Set axis
ax.set_xlabel(r'X', fontsize=15)
ax.set_ylabel(r'Y', fontsize=15)
ax.set_zlabel(r'Z', fontsize=15)
ax.set_title('Octahedral structure with faces', fontsize="12")
ax.grid(True)
# plt.axis('equal')
if save != "not_save":
plt.savefig('{0}.png'.format(save))
plt.show()
def all_atom(fal, fcl, save="not_save"):
"""
Display 3D structure of octahedral complex with label for each atoms.
Parameters
----------
fal : list
Atomic labels of full complex.
fcl : list
Atomic coordinates of full complex.
save : str
Name of image file to save. If this argument is not set by user,
do not save a figure as image.
Returns
-------
None : None
"""
fig = plt.figure()
ax = Axes3D(fig)
# ax = fig.add_subplot(111, projection='3d')
# Plot all atoms
for i in range(len(fcl)):
# Determine atomic number
n = elements.check_atom(fal[i])
ax.scatter(fcl[i][0],
fcl[i][1],
fcl[i][2],
marker='o',
linewidths=0.5,
edgecolors='black',
color=elements.check_color(n),
label=f"{fal[i]}",
s=elements.check_radii(n) * 300)
# Calculate distance
bond_list = tools.find_bonds(fal, fcl)
atoms_pair = []
for i in range(len(bond_list)):
get_atoms = bond_list[i]
x, y, z = zip(*get_atoms)
atoms = list(zip(x, y, z))
atoms_pair.append(atoms)
# Draw line
for i in range(len(atoms_pair)):
merge = list(zip(atoms_pair[i][0], atoms_pair[i][1]))
x, y, z = merge
ax.plot(x, y, z, 'k-', color="black", linewidth=2)
# Set legend
# Remove duplicate labels in legend.
# Ref.https://stackoverflow.com/a/26550501/6596684
handles, labels = ax.get_legend_handles_labels()
handle_list, label_list = [], []
for handle, label in zip(handles, labels):
if label not in label_list:
handle_list.append(handle)
label_list.append(label)
leg = plt.legend(handle_list,
label_list,
loc="lower left",
scatterpoints=1,
fontsize=12)
# Fixed size of point in legend
# Ref. https://stackoverflow.com/a/24707567/6596684
for i in range(len(leg.legendHandles)):
leg.legendHandles[i]._sizes = [90]
# Set axis
ax.set_xlabel(r'X', fontsize=15)
ax.set_ylabel(r'Y', fontsize=15)
ax.set_zlabel(r'Z', fontsize=15)
ax.set_title('Full complex', fontsize="12")
ax.grid(True)
# plt.axis('equal')
if save != "not_save":
plt.savefig('{0}.png'.format(save))
plt.show()
def octa(ao, co, save="not_save"):
"""
Display 3D structure of octahedral complex.
Parameters
----------
ao : list
Atomic labels of octahedral structure.
co : list
Atomic coordinates of octahedral structure.
save : str
Name of image file to save. If this argument is not set by user,
do not save a figure as image.
Returns
-------
None : None
"""
fig = plt.figure()
ax = Axes3D(fig)
# Plot atoms
for i in range(len(co)):
# Determine atomic number
n = elements.check_atom(ao[i])
ax.scatter(co[i][0],
co[i][1],
co[i][2],
marker='o',
linewidths=0.5,
edgecolors='black',
color=elements.check_color(n),
label=f"{ao[i]}",
s=elements.check_radii(n) * 300)
# Draw line
for i in range(1, len(co)):
merge = list(zip(co[0], co[i]))
x, y, z = merge
ax.plot(x, y, z, 'k-', color="black", linewidth=2)
# Set legend
# Remove duplicate labels in legend.
# Ref.https://stackoverflow.com/a/26550501/6596684
handles, labels = ax.get_legend_handles_labels()
handle_list, label_list = [], []
for handle, label in zip(handles, labels):
if label not in label_list:
handle_list.append(handle)
label_list.append(label)
leg = plt.legend(handle_list,
label_list,
loc="lower left",
scatterpoints=1,
fontsize=12)
# Fixed size of point in legend
# Ref. https://stackoverflow.com/a/24707567/6596684
for i in range(len(leg.legendHandles)):
leg.legendHandles[i]._sizes = [90]
# Set axis
ax.set_xlabel(r'X', fontsize=15)
ax.set_ylabel(r'Y', fontsize=15)
ax.set_zlabel(r'Z', fontsize=15)
ax.set_title('Octahedral structure', fontsize="12")
ax.grid(True)
# plt.axis('equal')
if save != "not_save":
plt.savefig('{0}.png'.format(save))
plt.show()
def find_metal(atom=None, coord=None):
"""
Count the number of metal center atom in complex.
Parameters
----------
atom : list, None
Full atomic labels of complex.
coord : array_like, None
Full atomic coordinates of complex.
Returns
-------
total_metal : int
The total number of metal center atom.
atom_metal : list
Atomic labels of metal center atom.
coord_metal : ndarray
Atomic coordinates of metal center atom.
See Also
--------
octadist.src.elements.check_atom :
Convert atomic number to atomic symbol and vice versa.
Examples
--------
>>> atom = ['Fe', 'N', 'N', 'N', 'N', 'N', 'N']
>>> coord = [[-1.95348286e+00, 4.51770478e+00, 1.47855811e+01],
[-1.87618286e+00, 4.48070478e+00, 1.26484811e+01],
[-3.90128286e+00, 5.27750478e+00, 1.40814811e+01],
[-4.88286000e-03, 3.69060478e+00, 1.42392811e+01],
[-2.18698286e+00, 4.34540478e+00, 1.69060811e+01],
[-1.17538286e+00, 6.38340478e+00, 1.56457811e+01],
[-2.75078286e+00, 2.50260478e+00, 1.51806811e+01]]
>>> total_metal, atom_metal, coord_metal = find_metal(atom, coord)
>>> total_metal
1
>>> atom_metal
['Fe']
>>> coord_metal
[[-1.95348286 4.51770478 14.78558113]]
"""
if atom is None or coord is None:
raise TypeError("find_metal needs two arguments: atom, coord")
total_metal = 0
atom_metal = []
coord_metal = []
for i in range(len(atom)):
number = elements.check_atom(atom[i])
if (21 <= number <= 30 or 39 <= number <= 48 or 57 <= number <= 80
or 89 <= number <= 109):
total_metal += 1
atom_metal.append(atom[i])
coord_metal.append(coord[i])
coord_metal = np.asarray(coord_metal, dtype=np.float64)
return total_metal, atom_metal, coord_metal
def plot_fit_plane(self):
"""
Display complex and two fit planes of two sets of ligand in molecule.
"""
###############
# Clear boxes #
###############
self.box_angle1.delete(0, tk.END)
self.box_angle2.delete(0, tk.END)
self.box_eq1.delete(0, tk.END)
self.box_eq2.delete(0, tk.END)
########################
# Find eq of the plane #
########################
xx, yy, z, abcd = plane.find_fit_plane(self.coord_A)
plane_a = (xx, yy, z)
a1, b1, c1, d1 = abcd
self.box_eq1.insert(
tk.INSERT, f"{a1:8.5f}x {b1:+8.5f}y {c1:+8.5f}z {d1:+8.5f} = 0")
xx, yy, z, abcd = plane.find_fit_plane(self.coord_B)
plane_b = (xx, yy, z)
a2, b2, c2, d2 = abcd
self.box_eq2.insert(
tk.INSERT, f"{a2:8.5f}x {b2:+8.5f}y {c2:+8.5f}z {d2:+8.5f} = 0")
####################################
# Calculate angle between 2 planes #
####################################
angle = linear.angle_btw_planes(a1, b1, c1, a2, b2, c2)
self.box_angle1.insert(tk.INSERT, f"{angle:10.6f}") # insert to box
sup_angle = abs(180 - angle) # supplementary angle
self.box_angle2.insert(tk.INSERT,
f"{sup_angle:10.6f}") # insert to box
###############
# Plot planes #
###############
fig = plt.figure()
# fig = plt.figure(figsize=(5, 4), dpi=100)
ax = Axes3D(fig)
# ax = fig.add_subplot(111, projection='3d')
# Plot all atoms
for i in range(len(self.coord)):
# Determine atomic number
n = elements.check_atom(self.atom[i])
ax.scatter(
self.coord[i][0],
self.coord[i][1],
self.coord[i][2],
marker="o",
linewidths=0.5,
edgecolors="black",
picker=5,
color=elements.check_color(n),
label=f"{self.atom[i]}",
s=elements.check_radii(n) * 300,
)
atoms_pair = []
for i in range(len(self.bond_list)):
get_atoms = self.bond_list[i]
x, y, z = zip(*get_atoms)
atoms = list(zip(x, y, z))
atoms_pair.append(atoms)
# Draw line
for i in range(len(atoms_pair)):
merge = list(zip(atoms_pair[i][0], atoms_pair[i][1]))
x, y, z = merge
ax.plot(x, y, z, "k-", color="black", linewidth=2)
# Set legend
# Remove duplicate labels in legend.
# Ref.https://stackoverflow.com/a/26550501/6596684
handles, labels = ax.get_legend_handles_labels()
handle_list, label_list = [], []
for handle, label in zip(handles, labels):
if label not in label_list:
handle_list.append(handle)
label_list.append(label)
leg = fig.legend(handle_list,
label_list,
loc="lower left",
scatterpoints=1,
fontsize=12)
# Fixed size of point in legend
# Ref. https://stackoverflow.com/a/24707567/6596684
for i in range(len(leg.legendHandles)):
leg.legendHandles[i]._sizes = [90]
# Set axis
ax.set_xlabel(r"X", fontsize=15)
ax.set_ylabel(r"Y", fontsize=15)
ax.set_zlabel(r"Z", fontsize=15)
ax.set_title("Full complex", fontsize="12")
ax.grid(True)
# Plot plane A
xx, yy, z = plane_a
ax.plot_surface(xx, yy, z, alpha=0.2, color="green")
# Plot plane B
xx, yy, z = plane_b
ax.plot_surface(xx, yy, z, alpha=0.2, color="red")
# ax.set_xlim(-10, 10)
# ax.set_ylim(-10, 10)
# ax.set_zlim(0, 10)
# plt.axis('equal')
# plt.axis('off')
plt.show()
def pick_atom(self, group):
"""
On-mouse pick atom and get XYZ coordinate.
Parameters
----------
group : str
Group A or B.
"""
fig = plt.figure()
# fig = plt.figure(figsize=(5, 4), dpi=100)
ax = Axes3D(fig)
# ax = fig.add_subplot(111, projection='3d')
# Plot all atoms
for i in range(len(self.coord)):
# Determine atomic number
n = elements.check_atom(self.atom[i])
ax.scatter(
self.coord[i][0],
self.coord[i][1],
self.coord[i][2],
marker="o",
linewidths=0.5,
edgecolors="black",
picker=5,
color=elements.check_color(n),
label=f"{self.atom[i]}",
s=elements.check_radii(n) * 300,
)
atoms_pair = []
for i in range(len(self.bond_list)):
get_atoms = self.bond_list[i]
x, y, z = zip(*get_atoms)
atoms = list(zip(x, y, z))
atoms_pair.append(atoms)
# Draw line
for i in range(len(atoms_pair)):
merge = list(zip(atoms_pair[i][0], atoms_pair[i][1]))
x, y, z = merge
ax.plot(x, y, z, "k-", color="black", linewidth=2)
# Set legend
# Remove duplicate labels in legend.
# Ref.https://stackoverflow.com/a/26550501/6596684
handles, labels = ax.get_legend_handles_labels()
handle_list, label_list = [], []
for handle, label in zip(handles, labels):
if label not in label_list:
handle_list.append(handle)
label_list.append(label)
leg = fig.legend(handle_list,
label_list,
loc="lower left",
scatterpoints=1,
fontsize=12)
# Fixed size of point in legend
# Ref. https://stackoverflow.com/a/24707567/6596684
for i in range(len(leg.legendHandles)):
leg.legendHandles[i]._sizes = [90]
# Set axis
ax.set_xlabel(r"X", fontsize=15)
ax.set_ylabel(r"Y", fontsize=15)
ax.set_zlabel(r"Z", fontsize=15)
ax.set_title("Full complex", fontsize="12")
ax.grid(True)
def insert_text(text, coord, group):
"""
Insert text in boxes.
Parameters
----------
text : str
Text.
coord : list or array
Coordinates.
group : str
Group A or B.
"""
if group == "A":
self.box_1.insert(tk.INSERT, text + "\n")
self.box_1.see(tk.END)
self.coord_A.append(coord)
elif group == "B":
self.box_2.insert(tk.INSERT, text + "\n")
self.box_2.see(tk.END)
self.coord_B.append(coord)
def on_pick(event):
"""
Pick point and get XYZ data
Parameters
----------
event : object
Event object for on-pick function.
Examples
--------
>>> def on_pick(event):
>>> ... ind = event.ind
>>> ... print("on_pick scatter:", ind, np.take(x, ind), np.take(y, ind))
"""
ind = event.ind[0]
x, y, z = event.artist._offsets3d
for i in range(len(self.atom)):
if x[ind] == self.coord[i][0]:
if y[ind] == self.coord[i][1]:
if z[ind] == self.coord[i][2]:
atom = self.atom[i]
break
results = f"{i + 1} {atom} : {x[ind]} {y[ind]} {z[ind]}"
coord = [x[ind], y[ind], z[ind]]
insert_text(results, coord, group)
# Highlight selected atom
index = elements.check_atom(atom)
ax.scatter(
x[ind],
y[ind],
z[ind],
marker="o",
linewidths=0.5,
edgecolors="orange",
picker=5,
alpha=0.5,
color="yellow",
s=elements.check_radii(index) * 400,
)
# print(i+1, atom, x[ind], y[ind], z[ind])
fig.canvas.mpl_connect("pick_event", on_pick)
# plt.axis('equal')
# plt.axis('off')
plt.show()
def plot_fit_plane(acf, coord_A, coord_B):
"""
Display complex and two fit planes of two sets of ligand in molecule.
Parameters
----------
acf : list
Atomic labels and coordinates of full complex.
coord_A : list
List of chunk of atoms, set A.
coord_B : list
List of chunk of atoms, set B.
Returns
-------
None : None
"""
########################
# Find eq of the plane #
########################
xx, yy, z, abcd = calc_fit_plane(coord_A)
plane_A = (xx, yy, z)
a1, b1, c1, d1 = abcd
xx, yy, z, abcd = calc_fit_plane(coord_B)
plane_B = (xx, yy, z)
a2, b2, c2, d2 = abcd
####################################
# Calculate angle between 2 planes #
####################################
angle = linear.angle_btw_planes(a1, b1, c1, a2, b2, c2)
sup_angle = abs(180 - angle) # supplementary angle
###############
# Plot planes #
###############
fal, fcl = acf[0]
fig = plt.figure()
# fig = plt.figure(figsize=(5, 4), dpi=100)
ax = Axes3D(fig)
# ax = fig.add_subplot(111, projection='3d')
# Plot all atoms
for i in range(len(fcl)):
# Determine atomic number
n = elements.check_atom(fal[i])
ax.scatter(fcl[i][0], fcl[i][1], fcl[i][2],
marker='o', linewidths=0.5, edgecolors='black', picker=5,
color=elements.check_color(n), label=f"{fal[i]}",
s=elements.check_radii(n) * 300)
# Calculate distance
bond_list = tools.find_bonds(fal, fcl)
atoms_pair = []
for i in range(len(bond_list)):
get_atoms = bond_list[i]
x, y, z = zip(*get_atoms)
atoms = list(zip(x, y, z))
atoms_pair.append(atoms)
# Draw line
for i in range(len(atoms_pair)):
merge = list(zip(atoms_pair[i][0], atoms_pair[i][1]))
x, y, z = merge
ax.plot(x, y, z, 'k-', color="black", linewidth=2)
# Set legend
# Remove duplicate labels in legend.
# Ref.https://stackoverflow.com/a/26550501/6596684
handles, labels = ax.get_legend_handles_labels()
handle_list, label_list = [], []
for handle, label in zip(handles, labels):
if label not in label_list:
handle_list.append(handle)
label_list.append(label)
leg = fig.legend(handle_list, label_list,
loc="lower left", scatterpoints=1, fontsize=12)
# Fixed size of point in legend
# Ref. https://stackoverflow.com/a/24707567/6596684
for i in range(len(leg.legendHandles)):
leg.legendHandles[i]._sizes = [90]
# Set axis
ax.set_xlabel(r'X', fontsize=15)
ax.set_ylabel(r'Y', fontsize=15)
ax.set_zlabel(r'Z', fontsize=15)
ax.set_title('Full complex', fontsize="12")
ax.grid(True)
# Plot plane A
xx, yy, z = plane_A
ax.plot_surface(xx, yy, z, alpha=0.2, color='green')
# Plot plane B
xx, yy, z = plane_B
ax.plot_surface(xx, yy, z, alpha=0.2, color='red')
# ax.set_xlim(-10, 10)
# ax.set_ylim(-10, 10)
# ax.set_zlim(0, 10)
# plt.axis('equal')
# plt.axis('off')
plt.show()