pyxtal.representation module

class pyxtal.representation.representation(x, smiles=None)

Bases: object

A class to handle the 1D representation of molecular crystal Works for Zprime > 1

Parameters:

• x – a list of [cell, site_1, site_2, …]

• smiles – a list of [smile_1, smile_2, …]

classmethod from_pyxtal(struc, standard=False)

Initialize 1D rep. from the pyxtal object

Parameters:

struc – pyxtal object

classmethod from_string(inputs, smiles, composition=None)

Initialize 1D rep. from the string

Parameters:

• inputs – input string

• smiles – list of smiles

get_dist(rep)

get distance with the other rep1 Now only supports Z’=1

same_smiles(smiles)

to_pyxtal(smiles=None, composition=None, molecules=None)

Export the pyxtal structure

Parameters:

• smiles – list of smiles

• composition – list of composition

• molecules – optional list of pyxtal_molecule objects aligned with smiles

to_standard_setting()

to_string(time=None, eng=None, tag=None)

Export string representation

Parameters:

• time – float

• eng – float

• tag – string

update_smiles(smiles)

Update the smiles of the representation

class pyxtal.representation.representation_atom(x)

Bases: object

A class to handle the 1D representation of atomic crystal Works for Zprime > 1

Parameters:

x – a list of [cell, site_1, site_2, …]

classmethod from_pyxtal(struc, standard=True)

Initialize 1D rep. from the pyxtal object

Parameters:

struc – pyxtal object

to_array()

Export only variables to a 1d numpy array

to_pyxtal()

Export the pyxtal structure

Parameters:

• smiles – list of smiles

• composition – list of composition

to_standard_setting()

to_string(time=None, eng=None, tag=None)

Export string representation

Parameters:

• time – float

• eng – float

• tag – string