def calc_pucker(self):
atom_pos = self.coords[self.pucker_idx]
angles = tools.dihedral(atom_pos)
angles = angles.reshape(-1,5)
# calculate pseudorotation parameters
x1 = angles[:,4]+angles[:,1]-angles[:,3]-angles[:,0]
#Pconst = 2.0*(np.sin(np.pi/5.) + np.sin(np.pi/2.5))
x2 = 3.0776835*angles[:,2]
# phase
p0 = np.arctan2(x1,x2)
p0[np.where( p0 < 0.0 )] += 2.0*np.pi
# amplitude
tm = angles[:,2]/np.cos(p0)
#print angles.shape,p0.shape,tm.shape
angles = np.concatenate((angles,tm[:,np.newaxis]),axis=1)
angles = np.concatenate((angles,p0[:,np.newaxis]),axis=1)
return np.degrees(angles)
# supone que las moléculas de H2O no están disociadas
#rmaxo = float(input("Distancia máxima O a Hg : "))
rmaxo = 2.53
out = tl.SM(NALA,MXYZ,rmaxo)
NAW = out[0]
if NAW < 1 :
print(f"No se calcula dihedro, ya que se necesita almenos una molécula de H2O")
else :
VR1 = out[1]
VR = np.zeros((NAW,4))
for i in range(NAW) :
for j in range(4) :
VR[i,j] = VR1[i,j]
RHg1 = out[2]
RHg = np.zeros((3))
for i in range(3) :
RHg[i] = RHg1[i]
# Función externa que calcula el angulo de torsión entre 2 planos,
# que son definidos por 2 puntos (Praxeolitic formule).
out = tl.dihedral(NAW,VR,RHg)
NO = int(NAW/3)
d1 = out
dihedros = np.zeros((NO))
print (f"Cantidad de dihedros : ",NO)
for i in range(NO):
dihedros[i] = d1[i]
print(f"dihedro : ",dihedros[i])
def calc_j3(self):
atom_pos = self.coords[self.j3_idx]
angles = tools.dihedral(atom_pos)
return np.degrees(angles)
def calc_bb_torsion(self):
atom_pos_bb = self.coords[self.bb_idx]
atom_pos_chi = self.coords[self.chi_idx]
bb_angles = np.degrees(tools.dihedral(atom_pos_bb))
chi_angles = np.degrees(tools.dihedral(atom_pos_chi))
return bb_angles,chi_angles
