How to use the spektral.chem.get_atomic_num function in spektral

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github danielegrattarola / spektral / spektral / utils / io.py View on Github external
# position in the X, Y, and Z dimensions.
    # After that there is a space, and three characters for an atomic symbol.
    # After the symbol, there are two characters for the mass difference from
    # the monoisotope.
    # Next you have three characters for the charge.
    # There are ten more fields with three characters each, but these are all
    # rarely used.

    start = HEADER_SIZE + 1  # Add 1 for counts line
    stop = start + n_atoms
    values = sdf[start:stop]

    atoms = []
    for i, v in enumerate(values):
        coords = np.array([float(v[pos:pos+10]) for pos in range(0, 30, 10)])
        atomic_num = get_atomic_num(v[31:34].strip())
        iso = int(v[34:36])
        charge = int(v[36:39])
        info = np.array([int(v[pos:pos+3]) for pos in range(39, len(v), 3)])
        atoms.append({'index': i,
                      'coords': coords,
                      'atomic_num': atomic_num,
                      'iso': iso,
                      'charge': charge,
                      'info': info})
    return atoms
github danielegrattarola / spektral / docs / autogen.py View on Github external
brain.get_fc_graphs
        ],
        'methods': [],
        'classes': []
    },
    {
        'page': 'chem.md',
        'functions': [
            chem.numpy_to_rdkit,
            chem.numpy_to_smiles,
            chem.rdkit_to_smiles,
            chem.sdf_to_nx,
            chem.nx_to_sdf,
            chem.validate_rdkit,
            chem.get_atomic_symbol,
            chem.get_atomic_num,
            chem.valid_score,
            chem.novel_score,
            chem.unique_score,
            chem.enable_rdkit_log,
            chem.plot_rdkit,
            chem.plot_rdkit_svg_grid
        ],
        'methods': [],
        'classes': []
    },
    {
        'page': 'utils/data.md',
        'classes': [
            utils.data.Batch
        ],
        'methods': [