def getTranslation(file,
frame1_no,
frame2_no,
part1='ring',
part2='track',
type='absolute',
method='trans_com',
part1_atom_list=[],
part2_atom_list=[],
unit='m'):
assert frame2_no >= frame1_no, 'Invalid Frame Numbers'
frame1_cords = io.readFileMd(file,
frame1_no,
frame_no_pos=config.frame_no_pos)
frame2_cords = io.readFileMd(file,
frame2_no,
frame_no_pos=config.frame_no_pos)
return _getTranslation(frame1_cords,
frame2_cords,
part1=part1,
part2=part2,
type=type,
method=method,
part1_atom_list=part1_atom_list,
part2_atom_list=part2_atom_list,
unit=unit)
def getNetRotation(file,start_frame_no,end_frame_no,step_size=1,part1='ring',part2='track',type='absolute',method='rot_atomic_r_t_2',part1_atom_list=[],part2_atom_list=[]):
net_rotation=0
data={'frame_no':[],'rotation':[]}
assert end_frame_no>=start_frame_no,'Invalid Frame Numbers'
prev_frame_no=start_frame_no
prev_frame_cords=io.readFileMd(file,prev_frame_no,frame_no_pos=config.frame_no_pos)
for curr_frame_no in tqdm(range(start_frame_no+step_size,end_frame_no+1,step_size)):
curr_frame_cords=io.readFileMd(file,curr_frame_no,frame_no_pos=config.frame_no_pos)
rotation=_getRotation(prev_frame_cords,curr_frame_cords,part1=part1,part2=part2,type=type,method=method,part1_atom_list=part1_atom_list,part2_atom_list=part2_atom_list)
net_rotation+=rotation
prev_frame_no=curr_frame_no
prev_frame_cords=curr_frame_cords.copy()
data['frame_no'].append(curr_frame_no)
data['rotation'].append(rotation)
return (net_rotation,data)
def getAvgTKE(file,
start_frame_no,
end_frame_no,
step_size=1,
part1='ring',
part2='track',
type='absolute',
method='energy_trans_com',
part1_atom_list=[],
part2_atom_list=[]):
avg_TKE = 0
net_TKE = 0
data = {'frame_no': [], 'TKE': []}
assert end_frame_no >= start_frame_no, 'Invalid Frame Numbers'
prev_frame_no = start_frame_no
prev_frame_cords = io.readFileMd(file,
prev_frame_no,
frame_no_pos=config.frame_no_pos)
for curr_frame_no in tqdm(
range(start_frame_no + step_size, end_frame_no + 1, step_size)):
curr_frame_cords = io.readFileMd(file,
curr_frame_no,
frame_no_pos=config.frame_no_pos)
TKE = _getTKE(prev_frame_cords,
curr_frame_cords,
part1=part1,
part2=part2,
type=type,
method=method,
part1_atom_list=part1_atom_list,
part2_atom_list=part2_atom_list)
net_TKE += TKE
prev_frame_no = curr_frame_no
prev_frame_cords = curr_frame_cords.copy()
data['frame_no'].append(curr_frame_no)
data['TKE'].append(TKE)
avg_TKE = net_TKE / len(range(start_frame_no, end_frame_no + 1, step_size))
return (avg_TKE, data)
def getRKE(file,
frame1_no,
frame2_no,
part1='ring',
part2='track',
type='absolute',
method='energy_rot_atomic_r_t',
part1_atom_list=[],
part2_atom_list=[]):
assert frame2_no >= frame1_no, 'Invalid Frame Numbers'
frame1_cords = io.readFileMd(file,
frame1_no,
frame_no_pos=config.frame_no_pos)
frame2_cords = io.readFileMd(file,
frame2_no,
frame_no_pos=config.frame_no_pos)
return _getRKE(frame1_cords,
frame2_cords,
part1=part1,
part2=part2,
type=type,
method=method,
part1_atom_list=part1_atom_list,
part2_atom_list=part2_atom_list)
def extractMolecule(file_path,atom_no=0):
if isMd(file_path):
with open(file_path,'r') as file:
df_cords=io.readFileMd(file,config.start_frame_no,frame_no_pos=config.frame_no_pos)
else:
df_cords=io.readFile(file_path)
io.writeFile('ring_track_frame.tmp.xyz',df_cords)
subprocess.run(['babel','ring_track_frame.tmp.xyz','ring_track_frame.tmp.mol'])
G=io.readFile('ring_track_frame.tmp.mol',info='graph')
subprocess.run(['rm','ring_track_frame.tmp.xyz','ring_track_frame.tmp.mol'])
cc_list=list(nx.connected_component_subgraphs(G))
print(f'number of molecules found is {len(cc_list)}')
for cc in cc_list:
if atom_no in list(cc.nodes):
return sorted(list(cc.nodes))