Révision 748a6036 modules/formats.py
| b/modules/formats.py | ||
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@param spec_atms: List of tuples containing pairs of new/traditional |
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chemical symbols. |
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@return: an object the required library can work with. |
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""" # TODO POSCAR/CONTCAR files
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""" |
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import ase.io |
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from ase.io.formats import filetype |
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from modules.utilities import try_command |
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req_vals = ['rdkit', 'ase'] |
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file_type_vals = ['xyz', 'mol'] |
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lib_err = f"The conversion to the '{requirement}' library object type" \
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f" has not yet been implemented" |
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conv_info = f"Converted {coord_file} to {requirement} object type"
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fil_type_err = f'The {filetype(coord_file)} file formnat is not supported'
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fil_type_err = f'The {filetype(coord_file)} file format is not supported'
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if requirement not in req_vals: |
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logger.error(lib_err) |
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raise NotImplementedError(lib_err) |
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if filetype(coord_file) not in file_type_vals: |
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logger.error(fil_type_err) |
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raise NotImplementedError(fil_type_err) |
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if requirement == 'rdkit': |
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if filetype(coord_file) == 'xyz':
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from modules.xyz2mol import xyz2mol
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from modules.xyz2mol import xyz2mol
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if filetype(coord_file) == 'xyz': # TODO Include detection of charges.
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ase_atms = ase.io.read(coord_file) |
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atomic_nums = ase_atms.get_atomic_numbers().tolist() |
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xyz_coordinates = ase_atms.positions.tolist() |
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rd_mol_obj = xyz2mol(atomic_nums, xyz_coordinates, charge=0)
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rd_mol_obj = xyz2mol(atomic_nums, xyz_coordinates) |
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logger.debug(conv_info) |
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return Chem.AddHs(rd_mol_obj) |
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elif filetype(coord_file) == 'mol': |
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logger.debug(conv_info) |
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return Chem.AddHs(Chem.MolFromMolFile(coord_file, removeHs=False)) |
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else: |
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ase_atms = try_command(ase.io.read, |
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[(ase.io.formats.UnknownFileTypeError, |
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fil_type_err)], |
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coord_file) |
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atomic_nums = ase_atms.get_atomic_numbers().tolist() |
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xyz_coordinates = ase_atms.positions.tolist() |
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return xyz2mol(atomic_nums, xyz_coordinates) |
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if requirement == 'ase': |
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add_special_atoms(spec_atms) |
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logger.debug(conv_info) |
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rd_mol = Chem.AddHs(Chem.MolFromMolFile(coord_file, removeHs=False)) |
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return rdkit_mol_to_ase_atoms(rd_mol) |
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else: |
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return try_command(ase.io.read, |
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[(ase.io.formats.UnknownFileTypeError, |
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fil_type_err)], |
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coord_file) |
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def read_coords_cp2k(file, spec_atoms=tuple()): |
Formats disponibles : Unified diff