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Example structures

Small structures shipped with the package, used throughout the documentation: cage_isomer_builder.example_data.

Small example structures shipped with the package, so every example in the documentation runs the same from a clone or after pip install.

===================== ====================================================== name contents ===================== ====================================================== uio66_tri_node UiO-66 Zr6 node with three X connection points (tritopic, for Tri4Di6 cages) uio66_tetra_node UiO-66 Zr6 node with four X connection points uio66_sbu UiO-66 Zr6O8 cluster with 12 carboxylates bdc 1,4-phenylene linker with two X connection points biphenyl 4,4'-biphenylene linker with two X points NH2 NH2 fragment with one X attachment point methane methane (guest) ibuprofen ibuprofen (guest) RUBTAK01 UiO-66 crystal structure (CIF, Zr, one linker type) ABIXEQ Co MOF with two linker types (CIF) ABINOQ Zn MOF: bipyridine linker plus terminal thiolates (CIF) ===================== ======================================================

Examples:

>>> from cage_isomer_builder import example_data
>>> "bdc" in example_data.names()
True
>>> example_data.read("methane").get_chemical_formula()
'CH4'

names 

names()

Names of the shipped example structures, sorted.

Examples:

>>> from cage_isomer_builder import example_data
>>> example_data.names()[:3]
['ABINOQ', 'ABIXEQ', 'NH2']
Source code in cage_isomer_builder/example_data.py 
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def names():
    """
    Names of the shipped example structures, sorted.

    Examples
    --------
    >>> from cage_isomer_builder import example_data
    >>> example_data.names()[:3]
    ['ABINOQ', 'ABIXEQ', 'NH2']
    """
    return sorted(p.stem for p in _DIR.iterdir() if p.suffix in (".xyz", ".cif"))

path 

path(name)

Path of an example structure, given its name (with or without the file extension). Use it wherever a file path is accepted, e.g. Tri4Di6CageBuilder(node=example_data.path("uio66_tri_node"), ...).

Raises:

Type Description
KeyError

If there is no example of that name.

Examples:

>>> from cage_isomer_builder import example_data
>>> example_data.path("RUBTAK01").name
'RUBTAK01.cif'
Source code in cage_isomer_builder/example_data.py 
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def path(name):
    """
    Path of an example structure, given its name (with or without the file
    extension). Use it wherever a file path is accepted, e.g.
    ``Tri4Di6CageBuilder(node=example_data.path("uio66_tri_node"), ...)``.

    Raises
    ------
    KeyError
        If there is no example of that name.

    Examples
    --------
    >>> from cage_isomer_builder import example_data
    >>> example_data.path("RUBTAK01").name
    'RUBTAK01.cif'
    """
    stem = Path(name).stem
    for suffix in (".xyz", ".cif"):
        candidate = _DIR / f"{stem}{suffix}"
        if candidate.exists():
            return candidate
    raise KeyError(f"no example structure {name!r}; available: {names()}")

read 

read(name)

An example structure as ase.Atoms.

Examples:

>>> from cage_isomer_builder import example_data
>>> atoms = example_data.read("RUBTAK01")
>>> sorted(set(atoms.get_chemical_symbols()))
['C', 'H', 'O', 'Zr']
Source code in cage_isomer_builder/example_data.py 
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def read(name):
    """
    An example structure as ``ase.Atoms``.

    Examples
    --------
    >>> from cage_isomer_builder import example_data
    >>> atoms = example_data.read("RUBTAK01")
    >>> sorted(set(atoms.get_chemical_symbols()))
    ['C', 'H', 'O', 'Zr']
    """
    from ase.io import read as ase_read

    return ase_read(str(path(name)))