propka.bonds

Bonds

PROPKA representation of bonds.

Classes

BondMaker()

Makes bonds?

class propka.bonds.BondMaker

Makes bonds?

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

add_pi_electron_information(molecules)

Add pi electron information to a molecule.

Parameters:

molecules – list of molecules for adding pi electron information.

add_pi_electron_table_info(atoms)

Add table information on pi electrons

Parameters:

atoms – list of atoms for pi electron table information checking

check_distance(atom1, atom2)

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

connect_backbone(residue1, residue2)

Sets up bonds in the backbone

Parameters:

• residue1 – first residue to connect

• residue2 – second residue to connect

find_bonds_for_atoms(atoms)

Finds all bonds for a list of atoms

Parameters:

atoms – list of atoms in which to find bonds.

find_bonds_for_atoms_disjoint(atoms1, atoms2)

Finds all bonds between two disjoint sets of atoms.

Parameters:

• atoms1 – list of atoms

• atoms2 – list of atoms

find_bonds_for_atoms_using_boxes(atoms)

Finds all bonds for a list of atoms.

Parameters:

atoms – list of atoms for finding bonds

find_bonds_for_ligand(ligand)

Finds bonds for all atoms in the ligand molecule

Parameters:

ligand – ligand molecule to search for bonds

find_bonds_for_molecules_using_boxes(molecules: MolecularContainer)

Finds all bonds for a molecular container.

Parameters:

molecules – list of molecules for finding bonds.

find_bonds_for_protein_by_distance(molecule)

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)

Find bonds for this residue’s backbone.

Parameters:

residue – reside to search for backbone bonds.

find_bonds_for_side_chain(atoms)

Finds bonds for a side chain.

Parameters:

atoms – list of atoms to check for bonds

find_bonds_for_terminal_oxygen(residue)

Look for bonds for terminal oxygen.

Parameters:

residue (residue - test) –

static has_bond(atom1, atom2)

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)

Makes a bond between atom1 and atom2

Parameters:

• atom1 – first atom to bond

• atom2 – second atom to bond