Révision b6f47f2d modules/formats.py
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"""Module for the conversion of coordinate files to library-workable objects
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"""Module for the conversion between atomic coordinates files and objects
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functions: |
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confs_to_mol_list: Converts the conformers inside a rdkit mol object to a list |
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of separate mol objects. |
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rdkit_mol_to_ase_atoms: Converts a rdkit mol object into ase Atoms object. |
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adapt_format: Converts the coordinate files into a required library object type |
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adapt_format: Converts the coordinate files into a required library object type. |
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read_coords: Reads the atomic coordinates resulting from finished calculations. |
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""" |
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import logging |
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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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# TODO Add routine to read charge |
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rd_mol_obj = xyz2mol(atomic_nums, xyz_coordinates, charge=0) |
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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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if requirement == 'ase': |
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logger.debug(conv_info) |
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return ase.io.read(coord_file) |
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def read_coords(code, run_type, req): |
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"""Reads the atomic coordinates resulting from finished calculations. |
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Given a run_type ('isolated', 'screening' or 'refinement') directory
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containing different subdirectories with finished calculations in every |
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subdirectory, it reads the coordinates inside each subdirectory according to |
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the specified code and returns a list of objects required. |
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@param code: the code that produced the coordinates out of a calculation. |
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@param run_type: the type of calculation (and also the name of the folder) |
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containing the calculation subdirectories. |
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@param req: The required object type to make the list of. |
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@return: list of collection-of-atoms objects. (rdkit.Mol, ase.Atoms, etc.) |
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""" |
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import os |
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if code == 'cp2k': |
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pattern = '-pos-1.xyz' |
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else: |
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pattern = '' |
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return [adapt_format(req, f'{run_type}/{conf}/{fil}')
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for conf in os.listdir(run_type) |
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for fil in os.listdir(f"{run_type}/{conf}") if pattern in fil]
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