def find_bonds(fal, fcl, cutoff_global=2.0, cutoff_hydrogen=1.2):
"""
Find all bond distance and filter the possible bonds.
- Compute distance of all bonds
- Screen bonds out based on global cutoff distance
- Screen H bonds out based on local cutoff distance
Parameters
----------
fal : list
List of atomic labels of full complex.
fcl : list
List of atomic coordinates of full complex.
cutoff_global : float
Global cutoff for screening bonds
Default value is 2.0 Angstroms.
cutoff_hydrogen : float
Cutoff for screening bonds between hydrogen and other atoms.
Default value is 1.2 Angstroms.
Returns
-------
check_2_bond_list : list
Selected bonds.
"""
pair_list = []
bond_list = []
for i in range(len(fcl)):
for j in range(i + 1, len(fcl)):
if i == 0:
distance = linear.euclidean_dist(fcl[i], fcl[j])
else:
distance = linear.euclidean_dist(fcl[i], fcl[j])
pair_list.append([fal[i], fal[j]])
bond_list.append([fcl[i], fcl[j], distance])
check_1_bond_list = []
screen_1_pair_list = []
for i in range(len(bond_list)):
if bond_list[i][2] <= cutoff_global:
check_1_bond_list.append(
[bond_list[i][0], bond_list[i][1], bond_list[i][2]])
screen_1_pair_list.append([pair_list[i][0], pair_list[i][1]])
check_2_bond_list = []
for i in range(len(check_1_bond_list)):
if screen_1_pair_list[i][0] == "H" or screen_1_pair_list[i][1] == "H":
if check_1_bond_list[i][2] <= cutoff_hydrogen:
check_2_bond_list.append(
[check_1_bond_list[i][0], check_1_bond_list[i][1]])
else:
check_2_bond_list.append(
[check_1_bond_list[i][0], check_1_bond_list[i][1]])
return check_2_bond_list
def calc_d_bond(c_octa):
"""
Calculate metal-ligand bond distance and return value in Angstrom.
Parameters
----------
c_octa : array
Atomic coordinates of octahedral structure.
Returns
-------
bond_dist : list
Individual metal-ligand bond distance.
Examples
--------
>>> coord
[[2.298354000, 5.161785000, 7.971898000], # <- Metal atom
[1.885657000, 4.804777000, 6.183726000],
[1.747515000, 6.960963000, 7.932784000],
[4.094380000, 5.807257000, 7.588689000],
[0.539005000, 4.482809000, 8.460004000],
[2.812425000, 3.266553000, 8.131637000],
[2.886404000, 5.392925000, 9.848966000]]
>>> calc_d_bond(coord)
[1.869580869461656,
1.8820188587261812,
1.9465848640994314,
1.9479642654866642,
1.9702004656851546,
1.9805587036803534]
"""
bond_dist = [
linear.euclidean_dist(c_octa[0], c_octa[i]) for i in range(1, 7)
]
return bond_dist
def find_faces_octa(c_octa):
"""
Find the eight faces of octahedral structure.
1) Choose 3 atoms out of 6 ligand atoms.
The total number of combination is 20.
2) Orthogonally project metal center atom onto the face:
m ----> m'
3) Calculate the shortest distance between original metal center to its projected point.
4) Sort the 20 faces in ascending order of the shortest distance.
5) Delete 12 faces that closest to metal center atom (first 12 faces).
6) The remaining 8 faces are the (reference) face of octahedral structure.
7) Find 8 opposite faces.
Parameters
----------
c_octa : array
Atomic coordinates of octahedral structure.
Returns
-------
a_ref_f : list
Atomic labels of reference face.
c_ref_f : array
Atomic coordinates of reference face.
a_oppo_f : list
Atomic labels of opposite face.
c_oppo_f : array
Atomic coordinates of opposite face.
Examples
--------
Reference plane Opposite plane
[[1 2 3] [[4 5 6]
[1 2 4] ---> [3 5 6]
... ...
[2 3 5]] [1 4 6]]
"""
########################
# Find reference faces #
########################
# Find the shortest distance from metal center to each triangle
distance = []
a_ref_f = []
c_ref_f = []
for i in range(1, 5):
for j in range(i + 1, 6):
for k in range(j + 1, 7):
a, b, c, d = octadist.src.plane.find_eq_of_plane(
c_octa[i], c_octa[j], c_octa[k])
m = projection.project_atom_onto_plane(c_octa[0], a, b, c, d)
d_btw = linear.euclidean_dist(m, c_octa[0])
distance.append(d_btw)
a_ref_f.append([i, j, k])
c_ref_f.append([c_octa[i], c_octa[j], c_octa[k]])
# Sort faces by distance in ascending order
dist_a_c = list(zip(distance, a_ref_f, c_ref_f))
dist_a_c.sort()
distance, a_ref_f, c_ref_f = list(zip(*dist_a_c))
c_ref_f = np.asarray(c_ref_f)
# Remove first 12 triangles, the rest of triangles is 8 faces of octahedron
a_ref_f = a_ref_f[12:]
c_ref_f = c_ref_f[12:]
#######################
# Find opposite faces #
#######################
all_atom = [1, 2, 3, 4, 5, 6]
a_oppo_f = []
for i in range(len(a_ref_f)):
new_a_ref_f = []
for j in all_atom:
if j not in (a_ref_f[i][0], a_ref_f[i][1], a_ref_f[i][2]):
new_a_ref_f.append(j)
a_oppo_f.append(new_a_ref_f)
v = np.array(c_octa)
c_oppo_f = []
for i in range(len(a_oppo_f)):
coord_oppo = []
for j in range(3):
coord_oppo.append([
v[int(a_oppo_f[i][j])][0], v[int(a_oppo_f[i][j])][1],
v[int(a_oppo_f[i][j])]
][2])
c_oppo_f.append(coord_oppo)
return a_ref_f, c_ref_f, a_oppo_f, c_oppo_f
def param_octa(aco):
"""
Show structural parameters of selected octahedral structure.
Parameters
----------
aco : list
Atomic labels and coordinates of octahedral structure.
Returns
-------
None : None
"""
master = tk.Tk()
master.title("Results")
master.geometry("380x530")
master.option_add("*Font", "Arial 10")
frame = tk.Frame(master)
frame.grid()
lbl = tk.Label(frame, text="Structural parameters of octahedral structure")
lbl.grid(row=0, pady="5", padx="5", sticky=tk.W)
box = tkscrolled.ScrolledText(frame,
wrap="word",
width="50",
height="30",
undo="True")
box.grid(row=1, pady="5", padx="5")
for n in range(len(aco)):
if n > 0: # separator between files
box.insert(tk.END, "\n\n=================================\n\n")
box.insert(tk.INSERT, f"File : {aco[n][0]}\n")
box.insert(tk.END, f"Metal: {aco[n][1]}\n")
box.insert(tk.END, "Bond distance (Å)")
for i in range(7):
for j in range(i + 1, 7):
distance = linear.euclidean_dist(aco[n][3][i], aco[n][3][j])
if i == 0:
texts = f"{aco[n][2][i]}-{aco[n][2][j]}{j} {distance:10.6f}"
else:
texts = f"{aco[n][2][i]}{i}-{aco[n][2][j]}{j} {distance:10.6f}"
box.insert(tk.END, "\n" + texts)
box.insert(tk.END, "\n\nBond angle (°)")
for i in range(7):
for j in range(i + 1, 7):
for k in range(j + 1, 7):
vec1 = aco[n][3][i] - aco[n][3][j]
vec2 = aco[n][3][k] - aco[n][3][j]
angle = linear.angle_btw_vectors(vec1, vec2)
if i == 0:
texts = f"{aco[n][2][k]}{k}-{aco[n][2][i]}-{aco[n][2][j]}{j} {angle:10.6f}"
else:
texts = f"{aco[n][2][k]}{k}-{aco[n][2][i]}{i}-{aco[n][2][j]}{j} {angle:10.6f}"
box.insert(tk.END, "\n" + texts)
box.insert(tk.END, "\n")
def param_complex(acf):
"""
Show structural parameters of the complex.
Parameters
----------
acf : list
Atomic labels and coordinates of full complex.
Returns
-------
None : None
"""
master = tk.Tk()
master.title("Results")
master.geometry("380x530")
master.option_add("*Font", "Arial 10")
frame = tk.Frame(master)
frame.grid()
lbl = tk.Label(frame, text="Structural parameters of octahedral structure")
lbl.grid(row=0, pady="5", padx="5", sticky=tk.W)
box = tkscrolled.ScrolledText(frame,
wrap="word",
width="50",
height="30",
undo="True")
box.grid(row=1, pady="5", padx="5")
box.insert(tk.INSERT, "Bond distance (Å)")
fal, fcl = acf[0]
for i in range(len(fcl)):
for j in range(i + 1, len(fcl)):
distance = linear.euclidean_dist(fcl[i], fcl[j])
if i == 0:
texts = f"{fal[i]}-{fal[j]}{j} {distance:10.6f}"
else:
texts = f"{fal[i]}{i}-{fal[j]}{j} {distance:10.6f}"
box.insert(tk.END, "\n" + texts)
box.insert(tk.END, "\n\nBond angle (°)")
for i in range(len(fcl)):
for j in range(i + 1, len(fcl)):
for k in range(j + 1, len(fcl)):
vec1 = fcl[i] - fcl[j]
vec2 = fcl[k] - fcl[j]
angle = linear.angle_btw_vectors(vec1, vec2)
if i == 0:
texts = f"{fal[k]}{k}-{fal[i]}-{fal[j]}{j} {angle:10.6f}"
else:
texts = f"{fal[k]}{k}-{fal[i]}{i}-{fal[j]}{j} {angle:10.6f}"
box.insert(tk.END, "\n" + texts)
box.insert(tk.END, "\n")