def rot_mol_plane_3_1(frame1_cords,frame2_cords,part='ring',atom_list=[]):
part_rotation=0
if part=='ring':
_atom_list=range(config.ring_start_atom_no,config.ring_end_atom_no+1)
elif part=='track':
_atom_list=range(config.track_start_atom_no,config.track_end_atom_no+1)
else:
assert len(atom_list)!=0,'atoms_list should not be empty'
_atom_list=atom_list
if config.axis=='x':
axis=0
elif config.axis=='y':
axis=1
elif config.axis=='z':
axis=2
frame1_cords,frame2_cords=shift_origin.shiftOrigin(frame1_cords,frame2_cords,process='rotation')
frame1_part_cords_df=frame1_cords[frame1_cords['atom_no'].isin(_atom_list)]
frame2_part_cords_df=frame2_cords[frame2_cords['atom_no'].isin(_atom_list)]
coplanar_atom_no_list=findCoplanarAtoms(frame1_part_cords_df)
frame1_coplanar_atom_cords_list=frame1_part_cords_df[frame1_part_cords_df['atom_no'].isin(coplanar_atom_no_list)][['x','y','z']].values[:-1]
frame2_coplanar_atom_cords_list=frame2_part_cords_df[frame2_part_cords_df['atom_no'].isin(coplanar_atom_no_list)][['x','y','z']].values[:-1]
frame1_plane=vector.getPlaneNormal(frame1_coplanar_atom_cords_list)
frame2_plane=vector.getPlaneNormal(frame2_coplanar_atom_cords_list)
frame1_plane[axis]=0
frame2_plane[axis]=0
part_rotation=getRPYAngles(frame1_plane,frame2_plane,axis=config.axis)[axis]
return math.degrees(part_rotation)
def trans_atomic_r_t(frame1_cords, frame2_cords, part='ring', atom_list=[]):
part_translation = 0
avg_part_translation = 0
if part == 'ring':
_atom_list = range(config.ring_start_atom_no,
config.ring_end_atom_no + 1)
elif part == 'track':
_atom_list = range(config.track_start_atom_no,
config.track_end_atom_no + 1)
else:
assert len(atom_list) != 0, 'atoms_list should not be empty'
_atom_list = atom_list
if config.axis == 'x':
axis = 0
elif config.axis == 'y':
axis = 1
elif config.axis == 'z':
axis = 2
frame1_cords, frame2_cords = shift_origin.shiftOrigin(
frame1_cords, frame2_cords, process='translation')
for atom_no in _atom_list:
frame1_atom_cords = frame1_cords[frame1_cords['atom_no'] == atom_no][[
'x', 'y', 'z'
]].values[0]
frame2_atom_cords = frame2_cords[frame2_cords['atom_no'] == atom_no][[
'x', 'y', 'z'
]].values[0]
#getRPYAngles with new prev_frame_cords
#translate cords of prev_frame
trans_vec = getAtomicDisplacement(frame1_atom_cords, frame2_atom_cords)
part_translation += trans_vec[axis]
avg_part_translation = part_translation / len(_atom_list)
return avg_part_translation * constants.angstrom
def rot_mol_plane_3(frame1_cords,frame2_cords,part='ring',atom_list=[]):
part_rotation=0
if part=='ring':
_atom_list=range(config.ring_start_atom_no,config.ring_end_atom_no+1)
elif part=='track':
_atom_list=range(config.track_start_atom_no,config.track_end_atom_no+1)
else:
assert len(atom_list)!=0,'atoms_list should not be empty'
_atom_list=atom_list
if config.axis=='x':
axis=0
elif config.axis=='y':
axis=1
elif config.axis=='z':
axis=2
frame1_cords,frame2_cords=shift_origin.shiftOrigin(frame1_cords,frame2_cords,process='rotation')
frame1_part_cords_df=frame1_cords[frame1_cords['atom_no'].isin(_atom_list)]
frame2_part_cords_df=frame2_cords[frame2_cords['atom_no'].isin(_atom_list)]
coplanar_atom_no_list=findCoplanarAtoms(frame1_part_cords_df)
frame1_coplanar_atom_cords_list=frame1_part_cords_df[frame1_part_cords_df['atom_no'].isin(coplanar_atom_no_list)][['x','y','z']].values[:-1]
frame2_coplanar_atom_cords_list=frame2_part_cords_df[frame2_part_cords_df['atom_no'].isin(coplanar_atom_no_list)][['x','y','z']].values[:-1]
frame1_plane=vector.getPlaneNormal(frame1_coplanar_atom_cords_list)
frame2_plane=vector.getPlaneNormal(frame2_coplanar_atom_cords_list)
part_rotation=getRPYAngles(frame1_plane,frame2_plane,axis=config.axis)[axis]
'''
RPY gives accurate results when vector are perpendicular to the axis of rotation
RPY gives both positive and negative values
Following angle calulation will give only positive values
frame1_plane[axis]=0
frame2_plane[axis]=0
part_rotation=vector.getAngleR(frame1_plane,frame2_plane)
'''
return math.degrees(part_rotation)
def rot_atomic_r_t_3(frame1_cords,frame2_cords,part='ring',atom_list=[]):
part_rotation=0
if part=='ring':
_atom_list=config.ring_atom_no_list
elif part=='track':
_atom_list=config.track_atom_no_list
else:
assert len(atom_list)!=0,'atoms_list should not be empty'
_atom_list=atom_list
if config.axis=='x':
axis=0
elif config.axis=='y':
axis=1
elif config.axis=='z':
axis=2
frame1_cords,frame2_cords=shift_origin.shiftOrigin(frame1_cords,frame2_cords,process='rotation')
frame1_cords[config.axis]=0
frame2_cords[config.axis]=0
for atom_no in _atom_list:
frame1_atom_cords=frame1_cords[frame1_cords['atom_no']==atom_no][['x','y','z']].values[0]
frame2_atom_cords=frame2_cords[frame2_cords['atom_no']==atom_no][['x','y','z']].values[0]
atom_rotation=getRPYAngles(frame1_atom_cords,frame2_atom_cords,axis=config.axis)
part_rotation+=atom_rotation[axis]
avg_part_rotation=part_rotation/len(_atom_list)
return math.degrees(avg_part_rotation)
def rot_atomic_r_t_2(frame1_cords,frame2_cords,part='ring',atom_list=[]):
if part=='ring':
_atom_list=range(config.ring_start_atom_no,config.ring_end_atom_no+1)
elif part=='track':
_atom_list=range(config.track_start_atom_no,config.track_end_atom_no+1)
else:
assert len(atom_list)!=0,'atoms_list should not be empty'
_atom_list=atom_list
if config.axis=='x':
axis=0
elif config.axis=='y':
axis=1
elif config.axis=='z':
axis=2
atom_rotation_list=[]
frame1_cords,frame2_cords=shift_origin.shiftOrigin(frame1_cords,frame2_cords,process='rotation')
frame1_cords[config.axis]=0
frame2_cords[config.axis]=0
for atom_no in _atom_list:
frame1_atom_cords=frame1_cords[frame1_cords['atom_no']==atom_no][['x','y','z']].values[0]
frame2_atom_cords=frame2_cords[frame2_cords['atom_no']==atom_no][['x','y','z']].values[0]
atom_rotation=vector.getAngleR(frame1_atom_cords,frame2_atom_cords)
sign=vector.getCrossProduct(frame1_atom_cords,frame2_atom_cords)[axis]
if sign<0:
sign=-1
else:
sign=1
#print(math.degrees(sign*atom_rotation))
atom_rotation_list.append(sign*atom_rotation)
#part_rotation=stats.mode(atom_rotation_list)[0]
part_rotation=np.average(atom_rotation_list)
return math.degrees(part_rotation)
def rot_atomic_r_t_1(frame1_cords,frame2_cords,part='ring',atom_list=[]):
part_rotation=0
if part=='ring':
_atom_list=range(config.ring_start_atom_no,config.ring_end_atom_no+1)
elif part=='track':
_atom_list=range(config.track_start_atom_no,config.track_end_atom_no+1)
else:
assert len(atom_list)!=0,'atoms_list should not be empty'
_atom_list=atom_list
if config.axis=='x':
axis=0
elif config.axis=='y':
axis=1
elif config.axis=='z':
axis=2
frame1_cords,frame2_cords=shift_origin.shiftOrigin(frame1_cords,frame2_cords,process='rotation')
for atom_no in _atom_list:
frame1_atom_cords=frame1_cords[frame1_cords['atom_no']==atom_no][['x','y','z']].values[0]
frame2_atom_cords=frame2_cords[frame2_cords['atom_no']==atom_no][['x','y','z']].values[0]
atom_rotation=getRPYAngles(frame1_atom_cords,frame2_atom_cords,axis=config.axis)
#getRPYAngles with new prev_frame_cords
#translate cords of prev_frame
part_rotation+=atom_rotation[axis]
avg_part_rotation=part_rotation/len(_atom_list)
return math.degrees(avg_part_rotation)
def rot_mol_plane_1(frame1_cords,frame2_cords,part='ring',atom_list=[]):
part_rotation=0
if part=='ring':
_atom_list=range(config.ring_start_atom_no,config.ring_end_atom_no+1)
elif part=='track':
_atom_list=range(config.track_start_atom_no,config.track_end_atom_no+1)
else:
assert len(atom_list)!=0,'atoms_list should not be empty'
_atom_list=atom_list
if config.axis=='x':
axis=0
elif config.axis=='y':
axis=1
elif config.axis=='z':
axis=2
frame1_cords,frame2_cords=shift_origin.shiftOrigin(frame1_cords,frame2_cords,process='rotation')
frame1_part_df=frame1_cords[frame1_cords['atom_no'].isin(_atom_list)]
frame2_part_df=frame2_cords[frame2_cords['atom_no'].isin(_atom_list)]
frame1_plane=findMolecularPlane(frame1_part_df)
frame2_plane=findMolecularPlane(frame2_part_df)
part_rotation=getRPYAngles(frame1_plane,frame2_plane,axis=config.axis)[axis]
return math.degrees(part_rotation)
def trans_com_1(frame1_cords, frame2_cords, part='ring', atom_list=[]):
if part == 'ring':
_atom_list = config.ring_atom_no_list
elif part == 'track':
_atom_list = config.track_atom_no_list
else:
assert len(atom_list) != 0, 'atoms_list should not be empty'
_atom_list = atom_list
frame1_cords, frame2_cords = shift_origin.shiftOrigin(
frame1_cords, frame2_cords, process='translation')
com1 = physics.getCom(frame1_cords, atom_list=_atom_list)
com2 = physics.getCom(frame2_cords, atom_list=_atom_list)
translation = [0.0, 0.0, 0.0]
translation[0] = com2[0] - com1[0]
translation[1] = com2[1] - com1[1]
translation[2] = com2[2] - com1[2]
if config.axis == 'x':
axis = 0
elif config.axis == 'y':
axis = 1
elif config.axis == 'z':
axis = 2
return translation[axis] * constants.angstrom