4.3.2. propka.hydrogens¶
4.3.2.1. Hydrogens¶
Calculations related to hydrogen placement.
Functions
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Adds Gln & Asn hydrogen atoms to residues according to the ‘old way’. |
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Adds Arg hydrogen atoms to residues according to the ‘old way’. |
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Adds hydrogen backbone atoms to residues according to the old way. |
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Adds His hydrogen atoms to residues according to the ‘old way’. |
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Adds Trp hydrogen atoms to residues according to the ‘old way’. |
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Add a new hydrogen to an atom at the specified position. |
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Protonate the molecule. |
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Protonates an atom, x1_atom, given a direction. |
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Protonates an atom, x1_atom, given a direction. |
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Protonates a SP2 atom, given a list of atoms |
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Set names for ligands in molecular container. |
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Set up bonding for a molecular container. |
Set up bonding and protonation for a molecule. |
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Set up bonding for a molecular container. |
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propka.hydrogens.
add_amd_hydrogen
(residue)[source]¶ Adds Gln & Asn hydrogen atoms to residues according to the ‘old way’.
- Parameters
residue – glutamine or asparagine residue to protonate
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propka.hydrogens.
add_arg_hydrogen
(residue)[source]¶ Adds Arg hydrogen atoms to residues according to the ‘old way’.
- Parameters
residue – arginine residue to protonate
- Returns
list of hydrogen atoms
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propka.hydrogens.
add_backbone_hydrogen
(residue, o_atom, c_atom)[source]¶ 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]
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propka.hydrogens.
add_his_hydrogen
(residue)[source]¶ Adds His hydrogen atoms to residues according to the ‘old way’.
- Parameters
residue – histidine residue to protonate
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propka.hydrogens.
add_trp_hydrogen
(residue)[source]¶ Adds Trp hydrogen atoms to residues according to the ‘old way’.
- Parameters
residue – tryptophan residue to protonate
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propka.hydrogens.
make_new_h
(atom, x, y, z)[source]¶ 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
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propka.hydrogens.
protonate_30_style
(molecular_container)[source]¶ Protonate the molecule.
- Parameters
molecular_container – molecule
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propka.hydrogens.
protonate_average_direction
(x1_atom, x2_atom, x3_atom)[source]¶ 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
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propka.hydrogens.
protonate_direction
(x1_atom, x2_atom, x3_atom)[source]¶ 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
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propka.hydrogens.
protonate_sp2
(x1_atom, x2_atom, x3_atom)[source]¶ 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
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propka.hydrogens.
set_ligand_atom_names
(molecular_container)[source]¶ Set names for ligands in molecular container.
- Parameters
molecular_container – molecular container for ligand names
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propka.hydrogens.
setup_bonding
(molecular_container)[source]¶ Set up bonding for a molecular container.
- Parameters
molecular_container – the molecular container in question
- Returns
BondMaker object