stko.MAEExtractor

class stko.MAEExtractor(run_name, n=1)[source]

Bases: object

Extracts the lowest energy conformer from a .maegz file.

Macromodel conformer searches produce -out.maegz files containing all of the conformers found during the search and their energies and other data.

Initializing this class with a ConstructedMolecule finds the -out.maegz file of that ConstructedMolecule and converts it to a .mae file. It then creates and additional .mae file holding only the lowest energy conformer found.

Attributes

`maegz_path`	`-out.maegz` file generated by the conformer search.
`mae_path`	`.mae` file holding the conformers from the conformer search.
`content`	The content of the `.mae` file holding all the conformers.
`energies`	Energies of the lowest energy confromers and their id.
`min_energy`	The minimum energy found in the `.mae` file.
`path`	`.mae` file holding the extracted lowest energy conformer.

Methods

`extract_conformers`	Creates `.mae` files holding the lowest energy conformers.
`extract_energy`	Extracts the energy value from a `.mae` energy data block.
`lowest_energy_conformers`	Returns the id and energy of the lowest energy conformers.
`maegz_to_mae`	Converts the .maegz file to a .mae file.

Parameters:

run_name (str)
n (int)

extract_conformers(n)[source]

Creates .mae files holding the lowest energy conformers.

Parameters:: n (int) – The number of conformers to extract.
Return type:: None

extract_energy(block)[source]

Extracts the energy value from a .mae energy data block.

Parameters:: block (str) – An .mae energy data block.
Returns:: The energy value extracted from block or None if one is not found.
Return type:: float | None

lowest_energy_conformers(n)[source]

Returns the id and energy of the lowest energy conformers.

Parameters:

n (int) – The number of lowest energy conformers to return.

Returns:

A list of the form

returned = [(123.3, 23), (143.89, 1), (150.6, 12), ...]

Where each tuple holds the energy of the n lowest energy conformers and the id, respectively.

Return type:

list[tuple[float | None, int]]

maegz_to_mae()[source]

Converts the .maegz file to a .mae file.

Return type:: None

content: str

The content of the .mae file holding all the conformers.

This holds other data such as their energies too.

energies: list[tuple[float | None, int]]: Energies of the lowest energy confromers and their id.

mae_path: Path: .mae file holding the conformers from the conformer search.

maegz_path: Path: -out.maegz file generated by the conformer search.

min_energy: float | None: The minimum energy found in the .mae file.

path: Path: .mae file holding the extracted lowest energy conformer.