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

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.

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

The structure to create the BondList for.

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

If set, only the atoms, where this mask is True, are connected.

inter_residuebool, optional

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


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


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.