ties.Ligand

class ties.Ligand(ligand, config=None, save=True)[source]

The ligand helper class. Helps to load and manage the different copies of the ligand file. Specifically, it tracks the different copies of the original input files as it is transformed (e.g. charge assignment).

Parameters:

  • ligand (string) – ligand filepath

  • config (Config) – Optional configuration from which the relevant ligand settings can be used

  • save (bool) – write a file with unique atom names for further inspection

__init__(ligand, config=None, save=True)[source]

Constructor method

Methods

__init__(ligand[, config, save])

Constructor method

antechamber_prepare_mol2(**kwargs)

Converts the ligand into a .mol2 format.

are_atom_names_correct()

Checks if atom names:

convert_acprep_to_mol2()

If the file is not a prep/ac file, this function does not do anything.

correct_atom_names()

Ensure that each atom name:

generate_frcmod(**kwargs)

params

overwrite_coordinates_with(file, output_file)

Load coordinates from another file and overwrite the coordinates in the current file.

removeDU_atoms()

Ambertools antechamber creates sometimes DU dummy atoms.

suffix()

Attributes

LIG_COUNTER

renaming_map

Otherwise, key: newName, value: oldName.

rev_renaming_map