dockonsurf / modules / read_coords.py @ 8ab593ee
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| 1 | 8ab593ee | Carles | def read_coords(requirement, coord_file): |
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| 2 | 8ab593ee | Carles | from ase.io.formats import filetype |
| 3 | 8ab593ee | Carles | |
| 4 | 8ab593ee | Carles | req_vals = ['rdkit', 'ase'] |
| 5 | 8ab593ee | Carles | file_type_vals = ['xyz', 'mol'] |
| 6 | 8ab593ee | Carles | assert requirement in req_vals, ValueError('Not an adequate requirement.\n' |
| 7 | 8ab593ee | Carles | f'adequate requirements: {req_vals}')
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| 8 | 8ab593ee | Carles | assert filetype(coord_file) in file_type_vals, TypeError('The file formnat ' |
| 9 | 8ab593ee | Carles | 'is not supported')
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| 10 | 8ab593ee | Carles | |
| 11 | 8ab593ee | Carles | if requirement == 'rdkit': |
| 12 | 8ab593ee | Carles | if filetype(coord_file) == 'xyz': |
| 13 | 8ab593ee | Carles | from xyz2mol import xyz2mol, read_xyz_file |
| 14 | 8ab593ee | Carles | atoms, charge, xyz_coordinates = read_xyz_file(coord_file) |
| 15 | 8ab593ee | Carles | rd_mol_obj = xyz2mol(atoms, xyz_coordinates, charge=charge) |
| 16 | 8ab593ee | Carles | return rd_mol_obj
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| 17 | 8ab593ee | Carles | elif filetype(coord_file) == 'mol': |
| 18 | 8ab593ee | Carles | from rdkit.Chem import MolFromMolFile |
| 19 | 8ab593ee | Carles | return MolFromMolFile(coord_file)
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| 20 | 8ab593ee | Carles | |
| 21 | 8ab593ee | Carles | if requirement == 'ase': |
| 22 | 8ab593ee | Carles | import ase.io |
| 23 | 8ab593ee | Carles | return ase.io.read(coord_file) |