propka.protonate
Protonate a structure
The Protonate
processes a
propka.molecular_container.MolecularContainer
and adds
protons.
Classes
|
Protonates atoms using VSEPR theory |
- class propka.protonate.Protonate(verbose=False)[source]
Protonates atoms using VSEPR theory
- static add_proton(atom: Atom, position: Vector)[source]
Add a proton to an atom at a specific position.
- Parameters:
atom – atom to protonate
position – position for proton
- protonate(molecules: MolecularContainer)[source]
Protonate all atoms in the molecular container.
- Parameters:
molecules – molecular containers
- static remove_all_hydrogen_atoms(molecular_container: MolecularContainer)[source]
Remove all hydrogen atoms from molecule.
- Parameters:
molecular_container – molecule to remove hydrogens from
- set_bond_distance(bvec: Vector, element: str) Vector [source]
Set bond distance between atom and element.
- Parameters:
bvec – bond vector
element – bonded element
- Returns:
scaled bond vector
- set_number_of_protons_to_add(atom: Atom)[source]
Set the number of protons to add to this atom.
- Parameters:
atom – atom for calculation
- static set_proton_names(heavy_atoms: Iterable[Atom])[source]
Set names for protons.
- Parameters:
heavy_atoms – list of heavy atoms with protons to be named
- set_steric_number_and_lone_pairs(atom: Atom)[source]
Set steric number and lone pairs for atom.
- Parameters:
atom – atom for calculation