def validate_gro_file(self, filename):
""" Validate gro file, this is the first step and we save the molecule object """
os.chdir(self._folder)
self.gro_filename = filename
try:
m = Molecule(self.gro_filename)
pdb_string = '\n'.join(m.write_pdb(range(m.na)))
ret = {
'success': True,
'n_shots': len(m),
'n_atoms': m.na,
'pdbString': pdb_string,
}
except Exception as e:
print(e)
ret = {'success': False, 'error': str(e)}
return ret
def get_target_objective_data(self, target_name, opt_iter):
""" Read objective data for a target and an optimization iteration from the tmp folder """
res = {}
target_options = self.input_options['tgt_opts'].get(target_name, None)
if target_options is None:
res['error'] = f"target {target_name} not found"
print(f"get_target_objective_data: {res['error']}")
return res
# check the tmp folder for this target
folder = os.path.join(self.tmp_folder, target_name,
f'iter_{opt_iter:04d}')
if not os.path.isdir(folder):
res['error'] = f"tmp folder {folder} not found"
print(f"get_target_objective_data: {res['error']}")
return res
# get target type specific objective information
target_type = target_options['type']
if target_type.lower().startswith('abinitio'):
# read energy compare data
energy_compare_file = os.path.join(folder, 'EnergyCompare.txt')
if not os.path.isfile(energy_compare_file):
res['error'] = f"file {energy_compare_file} not found"
print(f"get_target_objective_data: {res['error']}")
return res
energy_compare_data = np.loadtxt(energy_compare_file)
res['qm_energies'] = energy_compare_data[:, 0].tolist()
res['mm_energies'] = energy_compare_data[:, 1].tolist()
res['diff'] = energy_compare_data[:, 2].tolist()
res['weights'] = energy_compare_data[:, 3].tolist()
# read molecule geometry
mol_file = os.path.join(folder, 'coords.xyz')
m = Molecule(mol_file)
# generate pdb string
if 'resname' not in m.Data:
m.Data['resname'] = ['MOL'] * m.na
m.Data['resid'] = [1] * m.na
res['pdbString'] = '\n'.join(m.write_pdb(range(m.na)))
else:
res['error'] = f"get objective data for target type {target_type} not implemented"
print(f"get_target_objective_data: {res['error']}")
return res
return res
def validate_coords_file(self, filename):
""" Validate coords xyz file, this is the first step and we save the molecule object """
os.chdir(self._folder)
self.coords_filename = filename
try:
m = Molecule(self.coords_filename)
# generate pdb string
if 'resname' not in m.Data:
m.Data['resname'] = ['MOL'] * m.na
m.Data['resid'] = [1] * m.na
pdb_string = '\n'.join(m.write_pdb(range(m.na)))
ret = {
'success': True,
'n_shots': len(m),
'n_atoms': m.na,
'pdbString': pdb_string,
}
except Exception as e:
print(e)
ret = {'success': False, 'error': str(e)}
return ret