set_structure
#
- biotite.structure.io.pdbqt.set_structure(pdbqt_file, atoms, charges=None, atom_types=None, rotatable_bonds=None, root=None, include_torsdof=True)[source]#
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
andENDBRANCH
lines.None
- The molecule is handled as rigid receptor: NoROOT
,BRANCH
andENDBRANCH
lines will be written.'rigid'
- The molecule is handled as rigid ligand: Only aROOT
line will be written.'all'
- The molecule is handled as flexible ligand: AROOT
line will be written and all rotatable bonds are included usingBRANCH
andENDBRANCH
lines.BondList
- The molecule is handled as flexible ligand: AROOT
line will be written and all bonds in the givenBondList
are considered flexible viaBRANCH
andENDBRANCH
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 isNone
. 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 inputatoms
, that was removed due to being a nonpolar hydrogen.