biotite.structure.connect_via_residue_names

biotite.structure.connect_via_residue_names(atoms, atom_mask=None, inter_residue=True)

Create a BondList for a given atom array (stack), based on the deposited bonds for each residue in the RCSB components.cif dataset.

Bonds between two adjacent residues are created for the atoms expected to connect these residues, i.e. 'C' and 'N' for peptides and "O3'" and 'P' for nucleotides.

Parameters:

atomsAtomArray, shape=(n,) or AtomArrayStack, shape=(m,n)

The structure to create the BondList for.

atom_maskndarray, dtype=bool, shape=(n,), optional

DEPRECATED: This option has no effect.

inter_residuebool, optional

If true, connections between consecutive amino acids and nucleotides are also added.

Returns:

BondList

The created bond list. No bonds are added for residues that are not found in components.cif.

See also

connect_via_distances

Notes

If obtaining the bonds from an MMTF file is not possible, this is the recommended way to obtain BondList for a structure. However, this method can only find bonds for residues in the RCSB components.cif dataset. Although this includes most molecules one encounters, this will fail for exotic molecules, e.g. specialized inhibitors.