propka.hydrogens

Hydrogens

Calculations related to hydrogen placement.

Functions

add_amd_hydrogen(residue)	Adds Gln & Asn hydrogen atoms to residues according to the 'old way'.
add_arg_hydrogen(residue)	Adds Arg hydrogen atoms to residues according to the 'old way'.
add_backbone_hydrogen(residue, o_atom, c_atom)	Adds hydrogen backbone atoms to residues according to the old way.
add_his_hydrogen(residue)	Adds His hydrogen atoms to residues according to the 'old way'.
add_trp_hydrogen(residue)	Adds Trp hydrogen atoms to residues according to the 'old way'.
make_new_h(atom, x, y, z)	Add a new hydrogen to an atom at the specified position.
protonate_30_style(molecular_container)	Protonate the molecule.
protonate_average_direction(x1_atom, ...)	Protonates an atom, x1_atom, given a direction.
protonate_direction(x1_atom, x2_atom, x3_atom)	Protonates an atom, x1_atom, given a direction.
protonate_sp2(x1_atom, x2_atom, x3_atom)	Protonates a SP2 atom, given a list of atoms
set_ligand_atom_names(molecular_container)	Set names for ligands in molecular container.
setup_bonding(molecular_container)	Set up bonding for a molecular container.
setup_bonding_and_protonation(...)	Set up bonding and protonation for a molecule.
setup_bonding_and_protonation_30_style(...)	Set up bonding for a molecular container.

propka.hydrogens.add_amd_hydrogen(residue: List[Atom]) → None

Adds Gln & Asn hydrogen atoms to residues according to the ‘old way’.

Parameters:

residue – glutamine or asparagine residue to protonate

propka.hydrogens.add_arg_hydrogen(residue: List[Atom]) → List[Atom]

Adds Arg hydrogen atoms to residues according to the ‘old way’.

Parameters:

residue – arginine residue to protonate

Returns:

list of hydrogen atoms

propka.hydrogens.add_backbone_hydrogen(residue: List[Atom], o_atom: Atom | None, c_atom: Atom | None) → Tuple[Atom | None, Atom | None]

Adds hydrogen backbone atoms to residues according to the old way.

dR is wrong for the N-terminus (i.e. first residue) but it doesn’t affect anything at the moment. Could be improved, but works for now.

Parameters:

• residue – residue to protonate

• o_atom – backbone oxygen atom

• c_atom – backbone carbon atom

Returns:

[new backbone oxygen atom, new backbone carbon atom]

propka.hydrogens.add_his_hydrogen(residue: List[Atom]) → None

Adds His hydrogen atoms to residues according to the ‘old way’.

Parameters:

residue – histidine residue to protonate

propka.hydrogens.add_trp_hydrogen(residue: List[Atom]) → None

Adds Trp hydrogen atoms to residues according to the ‘old way’.

Parameters:

residue – tryptophan residue to protonate

propka.hydrogens.make_new_h(atom: Atom, x: float, y: float, z: float) → Atom

Add a new hydrogen to an atom at the specified position.

Parameters:

• atom – atom to protonate

• x – x position of hydrogen

• y – y position of hydrogen

• z – z position of hydrogen

Returns:

new hydrogen atom

propka.hydrogens.protonate_30_style(molecular_container: MolecularContainer) → None

Protonate the molecule.

Parameters:

molecular_container – molecule

propka.hydrogens.protonate_average_direction(x1_atom: Atom, x2_atom: Atom, x3_atom: Atom) → Atom

Protonates an atom, x1_atom, given a direction.

New direction for x1_atom is (x1_atom/x2_atom -> x3_atom). Note, this one uses the average of x1_atom & x2_atom (N & O) unlike the previous N - C = O

Parameters:

• x1_atom – atom to be protonated

• x2_atom – atom for direction

• x3_atom – other atom for direction

Returns:

new hydrogen atom

propka.hydrogens.protonate_direction(x1_atom: Atom, x2_atom: Atom, x3_atom: Atom) → Atom

Protonates an atom, x1_atom, given a direction.

New direction for x1_atom proton is (x2_atom -> x3_atom).

Parameters:

• x1_atom – atom to be protonated

• x2_atom – atom for direction

• x3_atom – other atom for direction

Returns:

new hydrogen atom

propka.hydrogens.protonate_sp2(x1_atom: Atom, x2_atom: Atom, x3_atom: Atom) → Atom

Protonates a SP2 atom, given a list of atoms

Parameters:

• x1_atom – atom to set direction

• x2_atom – atom to be protonated

• x3_atom – other atom to set direction

Returns:

new hydrogen atom

propka.hydrogens.set_ligand_atom_names(molecular_container: MolecularContainer) → None

Set names for ligands in molecular container.

Parameters:

molecular_container – molecular container for ligand names

propka.hydrogens.setup_bonding(molecular_container: MolecularContainer) → BondMaker

Set up bonding for a molecular container.

Parameters:

molecular_container – the molecular container in question

Returns:

BondMaker object

propka.hydrogens.setup_bonding_and_protonation(molecular_container: MolecularContainer) → None

Set up bonding and protonation for a molecule.

Parameters:

• parameters – not used

• molecular_container – molecule container.

propka.hydrogens.setup_bonding_and_protonation_30_style(molecular_container: MolecularContainer) → BondMaker

Set up bonding for a molecular container.

Parameters:

molecular_container – the molecular container in question

Returns:

BondMaker object