def translateAlongAxis(cords, axis, distance):
new_cords = cords.copy()
_axis = vector.getUnitVec(axis)
translation_vector = [0, 0, 0]
translation_vector[0] = distance * _axis[0]
translation_vector[1] = distance * _axis[1]
translation_vector[2] = distance * _axis[2]
new_cords['x'] = new_cords['x'] + translation_vector[0]
new_cords['y'] = new_cords['y'] + translation_vector[1]
new_cords['z'] = new_cords['z'] + translation_vector[2]
return new_cords
def getRotMat(axis, theta):
R = np.zeros((3, 3))
s = vector.getUnitVec(axis)
t = theta
vv = (1 - cos(t))
R[0][0] = s[0] * s[0] * vv + cos(t)
R[0][1] = s[0] * s[1] * vv - s[2] * sin(t)
R[0][2] = s[0] * s[2] * vv + s[1] * sin(t)
R[1][0] = s[0] * s[1] * vv + s[2] * sin(t)
R[1][1] = s[1] * s[1] * vv + cos(t)
R[1][2] = s[1] * s[2] * vv - s[0] * sin(t)
R[2][0] = s[0] * s[2] * vv - s[1] * sin(t)
R[2][1] = s[1] * s[2] * vv + s[0] * sin(t)
R[2][2] = s[2] * s[2] * vv + cos(t)
return R
def getNearestAtomList(df,point,direction,distance):
atom_list=[]
direction=vector.getUnitVec(direction)
for index,row in df.iterrows():
p=[0,0,0]
atom_cords=row[['x','y','z']].values
p[0]=atom_cords[0]-point[0]
p[1]=atom_cords[1]-point[1]
p[2]=atom_cords[2]-point[2]
projection=vector.getDotProduct(direction,p)
if isZero(p):
continue
if np.abs(round(projection,6))<=distance:
atom_list.append(row['atom_no'])
return atom_list
def getRPYAngles(v1,v2,axis='x',unit='radians'):
rpy=np.zeros(3)
s=vector.getCrossProduct(v1,v2)
s=vector.getUnitVec(s)
theta=vector.getAngleR(v1,v2)
R=getRotMat(s,theta)
if axis=='x':
rpy[1]=asin(fixArcDomain(-1*R[2][0]))
rpy[0]=asin(fixArcDomain(R[2][1]/cos(rpy[1])))
rpy[2]=asin(fixArcDomain(R[1][0]/cos(rpy[1])))
elif axis=='y':
rpy[2]=asin(-1*R[0][1])
rpy[1]=asin(R[0][2]/cos(rpy[2]))
rpy[0]=asin(R[2][1]/cos(rpy[2]))
elif axis=='z':
rpy[0]=asin(-1*R[1][2])
rpy[1]=asin(R[0][2]/cos(rpy[0]))
rpy[2]=asin(R[1][0]/cos(rpy[0]))
else:
print('To be implemented')
if unit=='radians':
return rpy
elif unit=='degrees':
return list(map(math.degrees,rpy))
def getAtomicDisplacement(v1, v2):
mag1 = vector.getMag(v1)
mag2 = vector.getMag(v2)
trans_vec = (mag2 - mag1) * vector.getUnitVec(v2)
return trans_vec