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))
def stretchBond(infile_path,
outfile_path='',
atom0=0,
atom1=1,
moiety=list(range(56, 90)),
trans=0.1):
df = io.readFile(infile_path)
atom0_vec = df.iloc[atom0, :]
atom1_vec = df.iloc[atom1, :]
vec = np.zeros((3, ))
vec[0] = atom1_vec['x'] - atom0_vec['x']
vec[1] = atom1_vec['y'] - atom0_vec['y']
vec[2] = atom1_vec['z'] - atom0_vec['z']
mag = np.linalg.norm(vec)
uvec = vec / mag
trans_vec = trans * uvec
cords = df.loc[:, ['x', 'y', 'z']].values
cords[moiety] = cords[moiety] + trans_vec
new_df = df.copy()
new_df.loc[:, ['x', 'y', 'z']] = cords
io.writeFile(outfile_path, new_df)
validate(infile_path,
outfile_path,
atom0=atom0,
atom1=atom1,
moiety=moiety)
def fixAtoms(file_path, atoms_list):
df = io.readFile(file_path, file_type='opt')
print(df.head())
io.writeFile(file_path,
df,
file_type='opt',
info='fix_atoms',
atoms_list=atoms_list)
def init():
init_struct_file_path = os.path.join(config.proj_dir_abs_path,
config.init_job_dir_name,
config.init_job_dir_name + '.xyz')
print(f'optimizing intial structure file: {init_struct_file_path}')
df = io.readFile(init_struct_file_path)
job.runJob(config.init_job_dir_name,
config.init_job_dir_name,
steps=list(range(3, 10)))
def validate(infile_path,
outfile_path,
atom0=0,
atom1=1,
moiety=list(range(56, 90))):
prev_df = io.readFile(infile_path)
print(prev_df)
atom0_row = prev_df.iloc[atom0, :][['x', 'y', 'z']]
atom1_row = prev_df.iloc[atom1, :][['x', 'y', 'z']]
prev_dist=np.sqrt((atom0_row['x']-atom1_row['x'])**2 + \
(atom0_row['y']-atom1_row['y'])**2 + \
(atom0_row['z']-atom1_row['z'])**2)
nxt_df = io.readFile(outfile_path)
atom0_row = nxt_df.iloc[atom0, :][['x', 'y', 'z']]
atom1_row = nxt_df.iloc[atom1, :][['x', 'y', 'z']]
nxt_dist=np.sqrt((atom0_row['x']-atom1_row['x'])**2 + \
(atom0_row['y']-atom1_row['y'])**2 + \
(atom0_row['z']-atom1_row['z'])**2)
print('strech along {} , {}'.format(atom0, atom1))
print('moiety:' + str(moiety))
print('prev_dist: {} nxt_dist:{} difference:{}'.format(
prev_dist, nxt_dist, nxt_dist - prev_dist))
args_dict={'input_file_path':input_file_path,'output_dir_path':output_dir_path,'d_theta':d_theta,'ref_atom1_no':ref_atom1_no,'ref_atom2_no':ref_atom2_no,'atom_no_list':atom_no_list}
return args_dict
def getAxis(agrs_dict,cords_df):
axis=[0,0,0]
ref_atom1_no=args_dict['ref_atom1_no']
ref_atom2_no=args_dict['ref_atom2_no']
ref_atom1_cords=cords_df[cords_df['atom_no']==ref_atom1_no][['x','y','z']].values[0]
ref_atom2_cords=cords_df[cords_df['atom_no']==ref_atom2_no][['x','y','z']].values[0]
axis[0]=ref_atom2_cords[0]-ref_atom1_cords[0]
axis[1]=ref_atom2_cords[1]-ref_atom1_cords[1]
axis[2]=ref_atom2_cords[2]-ref_atom1_cords[2]
return axis
args_dict=get_sys_agrs()
output_file_name=args_dict['input_file_path'].split('/')[-1].split('.')[0]
output_file_md=open(os.path.join(args_dict['output_dir_path'],output_file_name+f'_md.xyz'),'w')
initial_cords_df=io.readFile(args_dict['input_file_path'])
ref_atom1_no=args_dict['ref_atom1_no']
ref_atom1_cords=initial_cords_df[initial_cords_df['atom_no']==ref_atom1_no][['x','y','z']].values[0]
shifted_initial_cords_df=rotation.shiftOrigin(initial_cords_df,ref_atom1_cords)
axis=getAxis(args_dict,initial_cords_df)
for key,value in args_dict.items():
print(f'{key} = {value}')
print(initial_cords_df.head())
print(f'rotation axis = {axis}')
for curr_frame_no,theta in enumerate(tqdm(range(0,360,args_dict['d_theta']))):
final_cords_df=rotation.rotateAlongAxis(shifted_initial_cords_df,axis,math.radians(theta),args_dict['atom_no_list'])
io.writeFile(os.path.join(args_dict['output_dir_path'],output_file_name+f'_{theta}.xyz'),final_cords_df)
io.writeFileMd(output_file_md,final_cords_df,curr_frame_no,frame_no_pos=2)