Révision f3004731 modules/formats.py

b/modules/formats.py
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"""Module for the conversion of coordinate files to library-workable 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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"""


  		





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import logging


  		





  
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import rdkit.Chem.AllChem as Chem


  		





  
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logger = logging.getLogger('DockOnSurf')


  		





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def confs_to_mol_list(mol: Chem.rdchem.Mol, idx_lst=None):


  		





  
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    """Converts the conformers inside a rdkit mol object to a list of


  		





  
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    separate mol objects.


  		





  
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    @param mol: rdkit mol object containing at least one conformer.


  		





  
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    @param idx_lst:


  		





  
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    @return: list of separate mol objects.


  		





  
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    """


  		





  
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    if idx_lst is None:


  		





  
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        idx_lst = list(range(mol.GetNumConformers()))


  		





  
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    return [Chem.MolFromMolBlock(Chem.MolToMolBlock(mol, confId=int(idx)),


  		





  
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                                 removeHs=False) for idx in idx_lst]


  		





  
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def rdkit_mol_to_ase_atoms(mol: Chem.rdchem.Mol):


  		





  
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    """Converts a rdkit mol object into ase Atoms object.


  		





  
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    @param mol: rdkit mol object containing only one conformer.


  		





  
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    @return ase.Atoms: ase Atoms object with the same coordinates.


  		





  
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    """


  		





  
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    from ase import Atoms


  		





  
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    symbols = [atm.GetSymbol() for atm in mol.GetAtoms()]


  		





  
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    positions = mol.GetConformer(0).GetPositions()


  		





  
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    return Atoms(symbols=symbols, positions=positions)


  		





  
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def adapt_format(requirement, coord_file):


  		





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    """Converts the coordinate files into a required 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 formnat 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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