A module for multiple compound attachment and export of the .xyz files.

Index

add_ligands(core_dir, ligand_dir[, ...])	Add ligand(s) to one core.
export_dyes(mol_list[, new_dir, err_dir, ...])	Exports molecular coordinates to .xyz files.
sa_scores(mols[, filename])	Calculate the synthetic accessibility score for all molecules in mols.

API

CAT.dye.addlig.add_ligands(core_dir, ligand_dir, min_dist=1.2, n=1, symmetry=())

Add ligand(s) to one core.

Parameters:

• core_dir (str) – Name of directory where core coordinates are located

• ligand_dir (str) – Name of directory where ligands coordinates are located

• min_dist (float) – Criterion for the minimal interatomic distances

• n (int) – Number of substitutions

• symmetry (tuple[str]) – Keywords for substitution symmetry for deleting equivalent molecules

Returns:

New structures that are containg core and lingad fragments

Return type:

Iterator[Molecule]

CAT.dye.addlig.export_dyes(mol_list, new_dir='new_molecules', err_dir='err_molecules', min_dist=1.2)

Exports molecular coordinates to .xyz files.

Parameters:

• mol_list (Iterable[Molecule]) – List of molecules

• new_dir (str) – Name of the durectory to place new structures

• err_dir (str) – Name of the directory for molecules that do not fullfill min_dist criterion

• min_dist (float) – Criterion for the minimal interatomic distances

CAT.dye.addlig.sa_scores(mols, filename=None)

Calculate the synthetic accessibility score for all molecules in mols.