nanoCAT.recipes.mol_filter

Recipes for filtering molecules.

Index

`get_mol_length`(mol, atom)	Return the distance between atom and the atom in mol which it is furthest removed from.
`filter_mol`(mol_list, data, filter)	Filter mol_list and data based on elements from mol_list.
`filter_data`(mol_list, data, filter)	Filter mol_list and data based on elements from data.

API

nanoCAT.recipes.get_mol_length(mol, atom)[source]

Return the distance between atom and the atom in mol which it is furthest removed from.

Examples

Use the a molecules length for filtering a list of molecules:

>>> from CAT.recipes import get_mol_length, filter_mol
>>> from scm.plams import Molecule

>>> mol_list = [Molecule(...), ...]
>>> data = [...]
>>> filter = lambda mol: get_mol_length(mol, mol.properties.get('anchor')) < 10

>>> mol_dict = filter_mol(mol_list, data, filter=filter)

Parameters

mol (Molecule or numpy.ndarray) – A PLAMS molecule or a 2D numpy array with a molecules Cartesian coordinates.
atom (Atom or numpy.ndarray) – A PLAMS atom or a 1D numpy array with an atoms Cartesian coordinates.

Returns

The largest distance between atom and all other atoms mol.

Return type

float

See also

filter_mol(): Filter mol_list and data based on elements from mol_list.

nanoCAT.recipes.filter_mol(mol_list, data, filter)[source]

Filter mol_list and data based on elements from mol_list.

Examples

>>> from scm.plams import Molecule
>>> from CAT.recipes import filter_mol

>>> mol_list = [Molecule(...), ...]
>>> data = [...]
>>> mol_dict1 = filter_mol(mol_list, data, filter=lambda n: n < 10)

>>> prop1 = [...]
>>> prop2 = [...]
>>> prop3 = [...]
>>> multi_data = zip([prop1, prop2, prop3])
>>> mol_dict2 = filter_mol(mol_list, multi_data, filter=lambda n: n < 10)

>>> keys = mol_dict1.keys()
>>> values = mol_dict1.values()
>>> mol_dict3 = filter_mol(keys, values, filter=lambda n: n < 5)

Parameters

mol_list (Iterable [Molecule]) – An iterable of the, to-be filtered, PLAMS molecules.
data (Iterable[T]) – An iterable which will be assigned as values to the to-be returned dict. These parameters will be filtered in conjunction with mol_list. Note that mol_list and data should be of the same length.
filter (Callable[[Molecule], bool]) – A callable for filtering the distance vector. An example would be lambda n: max(n) < 10.

Returns

A dictionary with all (filtered) molecules as keys and elements from data as values.

Return type

dict [Molecule, T]