4.1.2. propka.bonds

4.1.2.1. Bonds

PROPKA representation of bonds.

Classes

BondMaker()

Makes bonds?

class propka.bonds.BondMaker[source]

Makes bonds?

TODO - the documentation for this class needs to be improved.

add_pi_electron_information(molecules)[source]

Add pi electron information to a molecule.

Parameters

molecules – list of molecules for adding pi electron information.

add_pi_electron_table_info(atoms)[source]

Add table information on pi electrons

Parameters

atoms – list of atoms for pi electron table information checking

check_distance(atom1, atom2)[source]

Check distance between two atoms

Parameters
  • atom1 – first atom for distance check

  • atom2 – second atom for distance check

Returns

True if within distance, False otherwise

check_for_cysteine_bonds(cys1, cys2)[source]

Looks for potential bonds between two cysteines.

Parameters
  • cys1 – one of the cysteines to check

  • cys1 – one of the cysteines to check

connect_backbone(residue1, residue2)[source]

Sets up bonds in the backbone

Parameters
  • residue1 – first residue to connect

  • residue2 – second residue to connect

find_bonds_for_atoms(atoms)[source]

Finds all bonds for a list of atoms

Parameters

atoms – list of atoms in which to find bonds.

find_bonds_for_atoms_using_boxes(atoms)[source]

Finds all bonds for a list of atoms.

Parameters

atoms – list of atoms for finding bonds

find_bonds_for_ligand(ligand)[source]

Finds bonds for all atoms in the ligand molecule

Parameters

ligand – ligand molecule to search for bonds

find_bonds_for_molecules_using_boxes(molecules)[source]

Finds all bonds for a molecular container.

Parameters

molecules – list of molecules for finding bonds.

find_bonds_for_protein(protein)[source]

Bonds proteins based on the way atoms normally bond.

Parameters

protein – the protein to search for bonds

find_bonds_for_protein_by_distance(molecule)[source]

Finds bonds for all atoms in the molecule.

Parameters

molecule – molecule in which to find bonds.

Returns

list of atoms

find_bonds_for_residue_backbone(residue)[source]

Find bonds for this residue’s backbone.

Parameters

residue – reside to search for backbone bonds.

find_bonds_for_side_chain(atoms)[source]

Finds bonds for a side chain.

Parameters

atoms – list of atoms to check for bonds

find_bonds_for_terminal_oxygen(residue)[source]

Look for bonds for terminal oxygen.

Parameters

- test residue (residue) –

generate_protein_bond_dictionary(atoms)[source]

Generate dictionary of protein bonds.

Parameters

atoms – list of atoms for bonding

static has_bond(atom1, atom2)[source]

Look for bond between two atoms.

Parameters
  • atom1 – first atom to check

  • atom2 – second atom to check

Returns

True if there is a bond between atoms

static make_bond(atom1, atom2)[source]

Makes a bond between atom1 and atom2

Parameters
  • atom1 – first atom to bond

  • atom2 – second atom to bond

put_atom_in_box(x, y, z, atom)[source]

Put an atom in a box.

Parameters
  • x – box x-coordinates

  • y – box y-coordinates

  • z – box z-coordinates

  • atom – the atom to place in a box