Révision 439ce5f7 modules/formats.py
| b/modules/formats.py | ||
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Accepted file tyoes: 'xyz', 'mol'. |
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@return: an object the required library can work with. |
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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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req_vals = ['rdkit', 'ase'] |
| ... | ... | |
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if requirement == 'rdkit': |
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if filetype(coord_file) == 'xyz': |
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from xyz2mol import read_xyz_file, xyz2mol |
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atoms, charge, xyz_coordinates = read_xyz_file(coord_file) |
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rd_mol_obj = xyz2mol(atoms, xyz_coordinates, charge=charge) |
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from xyz2mol import xyz2mol |
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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) # TODO Charge |
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logger.debug(conv_info) |
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return rd_mol_obj |
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elif filetype(coord_file) == 'mol': |
| ... | ... | |
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return MolFromMolFile(coord_file, removeHs=False) |
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|
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if requirement == 'ase': |
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import ase.io |
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logger.debug(conv_info) |
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return ase.io.read(coord_file) |
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