def calc_hbonds():
# variables
A = []
D = []
hbonds = []
d_crit = 3.5
a_crit = 30.0
for atom in mybgf.a:
if selection:
if "O" in atom.ffType and eval(selection):
A.append(atom)
if "O" in atom.ffType and eval(selection):
D.append(atom)
else:
if "O" in atom.ffType:
A.append(atom)
if "O" in atom.ffType:
D.append(atom)
if not len(A) or not len(D):
nu.die(
"There are no atoms which can make H_bond (O atoms so far)!"
)
# calculate hbonds
for d_atom in D:
d = np.array([d_atom.x, d_atom.y, d_atom.z])
neigh_anos = bt.get_neighbors_aNo(A,
d,
r=d_crit,
pbc=mytrj.pbc[t])
for ano in neigh_anos:
a_atom = mybgf.getAtom(ano)
h = bt.is_hbonded2(mybgf, d_atom,
a_atom) # returns hbonded H coord
if len(h) != 0:
a = np.array([a_atom.x, a_atom.y, a_atom.z])
dist = nu.pbc_dist(a, d, mytrj.pbc[t])
u = h - d
v = a - d
theta = np.dot(u, v) / norm(u) / norm(v)
theta = np.degrees(arccos(theta))
hbonds.append(
[d_atom.aNo, a_atom.aNo, d, a, dist, theta])
return hbonds
def calc_hbonds():
# variables
A = []
D = []
hbond_angles = []
d_crit = 3.5
a_crit = 30.0
for atom in mybgf.a:
if selection:
if "O" in atom.ffType and eval(selection):
A.append(atom)
if "O" in atom.ffType and eval(selection):
D.append(atom)
else:
if "O" in atom.ffType:
A.append(atom)
if "O" in atom.ffType:
D.append(atom)
if not len(A) or not len(D):
nu.die(
"There are no atoms which can make H_bond (O atoms so far)!"
)
# calculate hbonds
for d_atom in D:
d = np.array([d_atom.x, d_atom.y, d_atom.z]) # donor coord
neigh_anos = bt.get_neighbors_aNo(A, d, r=d_crit, k=6)
neigh_hbonded_coord = []
for ano in neigh_anos:
a_atom = mybgf.getAtom(ano)
a = np.array([a_atom.x, a_atom.y,
a_atom.z]) # acceptor coord
if bt.is_hbonded(mybgf, d_atom, a_atom):
neigh_hbonded_coord.append(a)
for i, j in itertools.combinations(neigh_hbonded_coord, 2):
angle = nu.angle(i, d, j, radians=False)
hbond_angles.append(angle)
return hbond_angles
def calc_hbonds():
hbonds = []
d_crit = 3.6
if selection:
for atom in mybgf.a:
if "O" in atom.ffType and eval(selection):
A.append(atom)
if "O" in atom.ffType and eval(selection):
D.append(atom)
# calculate hbonds
for d_atom in D:
d = np.array([d_atom.x, d_atom.y, d_atom.z]) # donor coord
neigh_anos = bt.get_neighbors_aNo(A,
d,
r=d_crit,
pbc=mytrj.pbc[t],
k=6)
for ano in neigh_anos:
a_atom = mybgf.getAtom(ano)
a = np.array([a_atom.x, a_atom.y,
a_atom.z]) # acceptor coord
dist = nu.pbc_dist(a, d, mytrj.pbc[t])
if dist > 2.0:
for ano in d_atom.CONECT:
h_atom = mybgf.getAtom(ano)
h = np.array([h_atom.x, h_atom.y, h_atom.z])
u = h - d
v = a - d
theta = np.dot(u, v) / norm(u) / norm(v)
#theta = np.degrees(arccos(theta))
if -0.17364817766693034885171662676931 < theta < 1.0:
hbonds.append([dist, np.degrees(theta)])
return hbonds
def calc_hbonds(mybgf, selection=""):
# variables
A = []
D = []
hbonds = []
d_crit = 3.5
a_crit = 30.0
for atom in mybgf.a:
if selection:
if "O" in atom.ffType and eval(selection):
A.append(atom)
if "O" in atom.ffType and eval(selection):
D.append(atom)
else:
if "O" in atom.ffType:
A.append(atom)
if "O" in atom.ffType:
D.append(atom)
if not len(A) or not len(D):
nu.die("There are no atoms which can make H_bond (O atoms so far)!")
# calculate hbonds
for d_atom in D:
d = np.array([d_atom.x, d_atom.y, d_atom.z]) # donor coord
neigh_anos = bt.get_neighbors_aNo(A,
d,
r=d_crit,
pbc=mytrj.pbc[t],
k=6)
donors = [d_atom.aNo] + d_atom.CONECT
for ano in neigh_anos:
a_atom = mybgf.getAtom(ano)
a = np.array([a_atom.x, a_atom.y, a_atom.z]) # acceptor coord
acceptors = [a_atom.aNo] + a_atom.CONECT
for ano in d_atom.CONECT:
h_atom = mybgf.getAtom(ano)
h = np.array([h_atom.x, h_atom.y, h_atom.z])
u = h - d
v = a - d
theta = np.dot(u, v) / norm(u) / norm(v)
theta = np.degrees(arccos(theta))
if theta < a_crit: # HBond exists
dist = nu.pbc_dist(a, d, mytrj.pbc[t])
dist_ah = nu.pbc_dist(d, h, mytrj.pbc[t])
# E_vdw
sigma_r = O_sigma / dist
sigma_r_6 = sigma_r**6
sigma_r_12 = sigma_r**12
E_vdw = 4.0 * O_epsilon * (sigma_r_12 - sigma_r_6)
# E_vdw in kcal/mol
# E_coul
E_coul = 0.0
for i, j in itertools.product(donors, acceptors):
atom1 = mybgf.getAtom(i)
atom2 = mybgf.getAtom(j)
a1 = [atom1.x, atom1.y, atom1.z]
a2 = [atom2.x, atom2.y, atom2.z]
dist_ij = nu.pbc_dist(a1, a2, mytrj.pbc[t])
E_coul += 332.06371 * atom1.charge * atom2.charge / dist_ij # E_coul in kcal/mol
# E_hbond
E_hbond = E_coul + E_vdw # E_hbond = E_vdw + E_coul
# update for v4
# angle between H-O-H plane and O..O vector
H1 = mybgf.getAtom(d_atom.CONECT[0])
h1 = [H1.x, H1.y, H1.z] # H1
H2 = mybgf.getAtom(d_atom.CONECT[1])
h2 = [H2.x, H2.y, H2.z] # H2
p = d - h1
q = d - h2
n = np.cross(p, q) # normal vector of the H1-O-H2 plane
m = a - d
# O..O vector
alpha = np.dot(n, m) / norm(n) / norm(m)
alpha = np.degrees(arcsin(
alpha)) # angle between H-O-H plane and O..O vector
hbonds.append([
d_atom.aNo, a_atom.aNo, d, a, dist, theta,
[E_coul, E_vdw, E_hbond], dist_ah, alpha
]) # v4
return hbonds
def hbonds(mybgf, selection = ""):
'''
This function calculates Hydrogen bonds(hbonds) between O(donor) and O(acceptor), especially for water molecules.
Input:
- bgf.BgfFile mybgf
- string selection: a region to search donor and acceptor atoms in mybgf
Output:
- int n_sel_atoms: number of hbond-able atoms in the selection region
- list hbonds: self-descriptive
'''
# variables
pbc = mybgf.CRYSTX[:3]
d_crit = 3.5; a_crit = 30.0 # Chandler's criteria
if selection:
A = [atom for atom in mybgf.a if "O" in atom.ffType and eval(selection)]
D = [atom for atom in mybgf.a if "O" in atom.ffType and eval(selection)]
else:
A = [atom for atom in mybgf.a if "O" in atom.ffType]
D = [atom for atom in mybgf.a if "O" in atom.ffType]
if not len(A) or not len(D):
nu.warn("There are no atoms which can make hbonds (O atoms so far)!")
return
# calculate hbonds
hbonds = [];
for d_atom in D:
d = np.array([d_atom.x, d_atom.y, d_atom.z]) # donor coord
neigh_anos = bt.get_neighbors_aNo(A, d, r=d_crit, pbc=pbc, k=7)
donors = [d_atom.aNo] + d_atom.CONECT
for ano in neigh_anos:
a_atom = mybgf.getAtom(ano)
a = np.array([a_atom.x, a_atom.y, a_atom.z]) # acceptor coord
acceptors = [a_atom.aNo] + a_atom.CONECT
for ano in d_atom.CONECT:
h_atom = mybgf.getAtom(ano)
h = np.array([h_atom.x, h_atom.y, h_atom.z])
u = h - d; v = a - d;
theta = np.dot(u, v) / norm(u) / norm(v); theta = np.degrees(arccos(theta))
if theta < a_crit: # HBond exists
dist = nu.pbc_dist(a, d, pbc)
dist_ah = nu.pbc_dist(d, h, pbc)
# E_vdw
sigma_r = O_sigma / dist; sigma_r_6 = sigma_r**6; sigma_r_12 = sigma_r**12
E_vdw = 4.0 * O_epsilon * (sigma_r_12 - sigma_r_6); # E_vdw in kcal/mol
# E_coul
E_coul = 0.0
for i, j in itertools.product(donors, acceptors):
atom1 = mybgf.getAtom(i)
atom2 = mybgf.getAtom(j)
a1 = [atom1.x, atom1.y, atom1.z]
a2 = [atom2.x, atom2.y, atom2.z]
dist_ij = nu.pbc_dist(a1, a2, pbc)
E_coul += 332.06371 * atom1.charge * atom2.charge / dist_ij # E_coul in kcal/mol
# E_hbond
E_hbond = E_coul + E_vdw # E_hbond = E_vdw + E_coul
# update for v4
# angle between H-O-H plane and O..O vector
#H1 = mybgf.getAtom(d_atom.CONECT[0]); h1 = [H1.x, H1.y, H1.z] # H1
#H2 = mybgf.getAtom(d_atom.CONECT[1]); h2 = [H2.x, H2.y, H2.z] # H2
#p = d - h1; q = d - h2; n = np.cross(p, q) # normal vector of the H1-O-H2 plane
#m = a - d; # O..O vector
#alpha = np.dot(n, m) / norm(n) / norm(m); alpha = np.degrees(arcsin(alpha)) # angle between H-O-H plane and O..O vector
#hbonds.append([d_atom.aNo, a_atom.aNo, d, a, dist, theta, [E_coul, E_vdw, E_hbond], dist_ah, alpha]) # v4
hbonds.append([d_atom.aNo, a_atom.aNo, dist, theta, E_hbond]) # v5
return hbonds
def calc_hbonds():
# variables
A = []
D = []
hbonds = []
d_crit = 3.5
a_crit = 30.0
for atom in mybgf.a:
if selection:
if "O" in atom.ffType and eval(selection):
A.append(atom)
if "O" in atom.ffType and eval(selection):
D.append(atom)
else:
if "O" in atom.ffType:
A.append(atom)
if "O" in atom.ffType:
D.append(atom)
if not len(A) or not len(D):
nu.die(
"There are no atoms which can make H_bond (O atoms so far)!"
)
# calculate hbonds
for d_atom in D:
d = np.array([d_atom.x, d_atom.y, d_atom.z]) # donor coord
neigh_anos = bt.get_neighbors_aNo(A,
d,
r=d_crit,
pbc=mytrj.pbc[t],
k=6)
donors = [d_atom.aNo] + d_atom.CONECT
for ano in neigh_anos:
a_atom = mybgf.getAtom(ano)
a = np.array([a_atom.x, a_atom.y,
a_atom.z]) # acceptor coord
acceptors = [a_atom.aNo] + a_atom.CONECT
for ano in d_atom.CONECT:
h_atom = mybgf.getAtom(ano)
h = np.array([h_atom.x, h_atom.y, h_atom.z])
u = h - d
v = a - d
theta = np.dot(u, v) / norm(u) / norm(v)
theta = np.degrees(arccos(theta))
if theta < a_crit:
dist = nu.pbc_dist(a, d, mytrj.pbc[t])
dist_dh = nu.pbc_dist(d, h, mytrj.pbc[t])
# E_vdw
sigma_r = O_sigma / dist
sigma_r_6 = sigma_r**6
sigma_r_12 = sigma_r**12
E_vdw = 4.0 * O_epsilon * (sigma_r_12 - sigma_r_6)
# Evdw in kcal/mol
# E_coul
E_coul = 0.0
for i, j in itertools.product(donors, acceptors):
atom1 = mybgf.getAtom(i)
atom2 = mybgf.getAtom(j)
a1 = [atom1.x, atom1.y, atom1.z]
a2 = [atom2.x, atom2.y, atom2.z]
dist_ij = nu.pbc_dist(a1, a2, mytrj.pbc[t])
E_coul += 332.06371 * atom1.charge * atom2.charge / dist_ij
#E_coul /= 2.0
E_hbond = E_coul + E_vdw # E_hbond = E_vdw + E_coul
#print("e_coul: %f, e_coul2: %f, E_coul: %f, E_vdw: %f, E_hbond: %f, O-O dist: %f, O-H dist: %f" % (e_coul, e_coul2, E_coul, E_vdw, E_hbond, dist, dist_a_dh))
#print("E_coul: %f, E_vdw: %f, E_hbond: %f, O-O dist: %f" % (E_coul, E_vdw, E_hbond, dist))
#hbonds.append([d_atom.aNo, a_atom.aNo, d, a, dist, theta, [E_coul, E_vdw, E_hbond]])
hbonds.append([
d_atom.aNo, a_atom.aNo, d, a, dist, theta,
[E_coul, E_vdw, E_hbond], dist_dh
])
return hbonds
def hbonds(mybgf, selection = ""):
'''
This function calculates Hydrogen bonds(hbonds) between O(donor) and O(acceptor), especially for water molecules.
Input:
- bgf.BgfFile mybgf
- string selection: a region to search donor and acceptor atoms in mybgf
Output:
- int n_sel_atoms: number of hbond-able atoms in the selection region
- list hbonds: self-descriptive
'''
# variables
pbc = mybgf.CRYSTX[:3]
d_crit = 3.5; a_crit = 30.0 # Chandler's criteria
if selection:
A = [atom for atom in mybgf.a if "O" in atom.ffType and eval(selection)]
D = [atom for atom in mybgf.a if "O" in atom.ffType and eval(selection)]
else:
A = [atom for atom in mybgf.a if "O" in atom.ffType]
D = [atom for atom in mybgf.a if "O" in atom.ffType]
if not len(A) or not len(D):
nu.warn("There are no atoms which can make hbonds (O atoms so far)!")
return
# calculate hbonds
hbonds = [];
for d_atom in D:
d = np.array([d_atom.x, d_atom.y, d_atom.z]) # donor coord
neigh_anos = bt.get_neighbors_aNo(A, d, r=d_crit, pbc=pbc, k=5)
donors = [d_atom.aNo] + d_atom.CONECT
for ano in neigh_anos:
a_atom = mybgf.getAtom(ano)
a = np.array([a_atom.x, a_atom.y, a_atom.z]) # acceptor coord
acceptors = [a_atom.aNo] + a_atom.CONECT
for ano in d_atom.CONECT:
h_atom = mybgf.getAtom(ano)
h = np.array([h_atom.x, h_atom.y, h_atom.z])
u = h - d; v = a - d;
theta = np.dot(u, v) / norm(u) / norm(v); theta = np.degrees(arccos(theta))
if theta < a_crit: # HBond exists
# calculate pair energy as Hbond energy
dist = nu.pbc_dist(a, d, pbc)
dist_ah = nu.pbc_dist(d, h, pbc)
# E_vdw
sigma_r = O_sigma / dist; sigma_r_6 = sigma_r**6; sigma_r_12 = sigma_r**12
E_vdw = 4.0 * O_epsilon * (sigma_r_12 - sigma_r_6); # E_vdw in kcal/mol
# E_coul
E_coul = 0.0
for i, j in itertools.product(donors, acceptors):
atom1 = mybgf.getAtom(i)
atom2 = mybgf.getAtom(j)
a1 = [atom1.x, atom1.y, atom1.z]
a2 = [atom2.x, atom2.y, atom2.z]
dist_ij = nu.pbc_dist(a1, a2, pbc)
E_coul += 332.06371 * atom1.charge * atom2.charge / dist_ij # E_coul in kcal/mol
# E_hbond
E_hbond = E_coul + E_vdw # E_hbond = E_vdw + E_coul
'''
# calculate dreiding style hbond energy: http://lammps.sandia.gov/doc/pair_hbond_dreiding.html
# REMARK: tested on bulk water, ice, and confined water between MoS2 but achieved suspicious values:
# 6.0 $\AA$ maximum: -7.925 kcal/mol
# 8.0 $\AA$ maximum: -7.875 kcal/mol
# 11.0 $\AA$ maximum: -8.025 kcal/mol
# ice maximum: -8.325 kcal/mol
# water maximum: -7.775 kcal/mol
sigma = 2.75 # in A
epsilon = 9.0 # in kcal/mol
u = d - h; v = a - h; cos_theta = np.dot(u, v) / norm(u) / norm(v); #cos_theta = np.cos(theta)
sigma_r = sigma / dist; sigma_r_2 = sigma_r**2; sigma_r_12 = sigma_r_2**6; sigma_r_10 = sigma_r_2**5
E_hbond = epsilon * ( 5 * sigma_r_12 - 6 * sigma_r_10 ) * cos_theta**4
'''
hbonds.append([d_atom.aNo, a_atom.aNo, dist, theta, E_hbond]) # v5
return hbonds
def hbonds(mybgf, selection=""):
'''
This function calculates Hydrogen bonds(hbonds) between O(donor) and O(acceptor), especially for water molecules.
Input:
- bgf.BgfFile mybgf
- string selection: a region to search donor and acceptor atoms in mybgf
Output:
- int n_sel_atoms: number of hbond-able atoms in the selection region
- list hbonds: self-descriptive
'''
# variables
pbc = mybgf.CRYSTX[:3]
d_crit = 3.5
a_crit = 30.0 # Chandler's criteria
if selection:
D = [
atom for atom in mybgf.a
if ("O" in atom.ffType or "N" in atom.ffType or "F" in atom.ffType
or "S" in atom.ffType) and eval(selection)
]
A = [
atom for atom in mybgf.a
if ("O" in atom.ffType or "N" in atom.ffType or "F" in atom.ffType
or "S" in atom.ffType) and eval(selection)
]
else:
D = [
atom for atom in mybgf.a
if ("O" in atom.ffType or "N" in atom.ffType or "F" in atom.ffType
or "S" in atom.ffType)
]
A = [
atom for atom in mybgf.a
if ("O" in atom.ffType or "N" in atom.ffType or "F" in atom.ffType
or "S" in atom.ffType)
]
if not len(A) or not len(D):
nu.warn("There are no atoms which can make hbonds!")
return
# calculate hbonds
hbonds = []
for d_atom in tqdm.tqdm(D, ncols=120, desc='Iterating'):
d = np.array([d_atom.x, d_atom.y, d_atom.z]) # donor coord
donors_H = [
ano for ano in d_atom.CONECT if "H" in mybgf.getAtom(ano).ffType
]
neigh_anos, distances = bt.get_neighbors_aNo(
A, d, r=d_crit, pbc=pbc, k=5, return_distance=True
) # atoms within d_crit of donor will be acceptor candidates
for index, ano in enumerate(neigh_anos):
a_atom = mybgf.getAtom(ano)
a = np.array([a_atom.x, a_atom.y, a_atom.z]) # acceptor coord
for ano in donors_H:
h_atom = mybgf.getAtom(ano)
h = np.array([h_atom.x, h_atom.y, h_atom.z])
u = h - d
v = a - d
theta = np.dot(u, v) / norm(u) / norm(v)
theta = np.degrees(arccos(theta))
if theta < a_crit: # HBond exists
#dist = nu.pbc_dist(a, d, pbc)
#dist = distances[0][index]
#dist_ah = nu.pbc_dist(d, h, pbc)
hbonds.append([
d_atom.aNo, a_atom.aNo, distances[0][index + 1], theta
]) # v5.2
return hbonds