Int now valid for get_indices #38
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Added parsing for interger indexes to the get_indices function of the MDAnalysisParser class
arm61
commented
Oct 24, 2023
Added a new keyword to MDAnalysisParser: s_indices
Extended the s_indices keyword to ASEParser and PymatgenParser
arm61
commented
Oct 31, 2023
| @staticmethod | ||
| def get_molecules(structure: "ase.atoms.Atoms", coords: List[np.ndarray], | ||
| indices: List[int]) -> Tuple[np.ndarray, np.ndarray, Tuple[np.ndarray, np.ndarray]]: | ||
| """ |
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Looks like there is still a docstring missing here.
kinisi/parser.py
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| return structure, coords, (flat_indices, framework_indices) | ||
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| @staticmethod | ||
| def get_framework(structure: "ase.atoms.Atoms", indices: List[int]) -> Tuple[np.ndarray, np.ndarray]: |
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And here, I guess it is just about copy and pasting from the other parsers.
kinisi/parser.py
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| structure, coords, latt = self.get_structure_coords_latt(atoms, sub_sample_traj, progress) | ||
| progress: bool = True, | ||
| s_indices: List[int] = None): |
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This is short for specie_indices right? Perhaps just indices or the fully specie_indices is preferred?
This was referenced Nov 5, 2023
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Added parsing for interger indexes to the get_indices function of the MDAnalysisParser class