cgexplore.molecular.Ensemble¶

class cgexplore.molecular.Ensemble(base_molecule, base_mol_path, conformer_xyz, data_json, overwrite)[source]¶

Class to contain ensemble information.

TODO: Rewrite into a .db.

Methods

`add_conformer`	Add a conformer to ensemble.
`get_base_molecule`	Get the base molecule defining the ensemble.
`get_conformer`	Get a specific conformer.
`get_lowest_e_conformer`	Get lowest energy conformer.
`get_molecule_num_atoms`	Get the number of atoms in the molecule in the ensemble.
`get_num_conformers`	Get number of conformers in ensemble.
`load_data`	Load ensemble data.
`load_trajectory`	Load trajectory.
`write_conformers_to_file`	Write conformers to xyz file.
`yield_conformers`	Yield conformers.

Parameters:

add_conformer(conformer, source)[source]¶

Add a conformer to ensemble.

Parameters:

Return type:

None

get_base_molecule()[source]¶

Get the base molecule defining the ensemble.

get_conformer(conf_id)[source]¶

Get a specific conformer.

get_lowest_e_conformer()[source]¶

Get lowest energy conformer.

get_molecule_num_atoms()[source]¶

Get the number of atoms in the molecule in the ensemble.

get_num_conformers()[source]¶

Get number of conformers in ensemble.

load_data()[source]¶

Load ensemble data.

load_trajectory()[source]¶

Load trajectory.

write_conformers_to_file()[source]¶

Write conformers to xyz file.

yield_conformers()[source]¶

Yield conformers.