set_structure

biotite.structure.io.pdbqt.set_structure(pdbqt_file, atoms, charges=None, atom_types=None, rotatable_bonds=None, root=None, include_torsdof=True)

Write an AtomArray into a PDBQT file.

EXPERIMENTAL: Future API changes are probable.

Parameters:

pdbqt_filePDBQTFile

The PDBQT file.

atomsAtomArray, shape=(n,)

The atoms to be written into this file. Must have an associated BondList.

chargesndarray, shape=(n,), dtype=float, optional

Partial charges for each atom in atoms. By default, the charges are calculated using the PEOE method (partial_charges()).

atom_typesndarray, shape=(n,), dtype=”U1”, optional

Custom AutoDock atom types for each atom in atoms.

rotatable_bondsNone or ‘rigid’ or ‘all’ or BondList, optional

This parameter describes, how rotatable bonds are handled, with respect to ROOT, BRANCH and ENDBRANCH lines.

• None - The molecule is handled as rigid receptor: No ROOT, BRANCH and ENDBRANCH lines will be written.

• 'rigid' - The molecule is handled as rigid ligand: Only a ROOT line will be written.

• 'all' - The molecule is handled as flexible ligand: A ROOT line will be written and all rotatable bonds are included using BRANCH and ENDBRANCH lines.

• BondList - The molecule is handled as flexible ligand: A ROOT line will be written and all bonds in the given BondList are considered flexible via BRANCH and ENDBRANCH lines.

rootint, optional

Specifies the index of the atom following the ROOT line. Setting the root atom is useful for specifying the anchor in flexible side chains. This parameter has no effect, if rotatable_bonds is None. By default, the first atom is also the root atom.

include_torsdofbool, optional

By default, a TORSDOF (torsional degrees of freedom) record is written at the end of the file. By setting this parameter to false, the record is omitted.

Returns:

maskndarray, shape=(n,), dtype=bool

A boolean mask, that is False for each atom of the input atoms, that was removed due to being a nonpolar hydrogen.