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, position)[source]¶
Add a proton to an atom at a specific position.
- Parameters
atom – atom to protonate
position – position for proton
- protonate(molecules)[source]¶
Protonate all atoms in the molecular container.
- Parameters
molecules – molecular containers
- static remove_all_hydrogen_atoms(molecular_container)[source]¶
Remove all hydrogen atoms from molecule.
- Parameters
molecular_container – molecule to remove hydrogens from
- set_bond_distance(bvec, element)[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)[source]¶
Set the number of protons to add to this atom.
- Parameters
atom – atom for calculation
- static set_proton_names(heavy_atoms)[source]¶
Set names for protons.
- Parameters
heavy_atoms – list of heavy atoms with protons to be named
- set_steric_number_and_lone_pairs(atom)[source]¶
Set steric number and lone pairs for atom.
- Parameters
atom – atom for calculation