- biotite.structure.connect_via_residue_names(atoms, atom_mask=None, inter_residue=True)[source]¶
BondListfor a given atom array (stack), based on the deposited bonds for each residue in the RCSB
Bonds between two adjacent residues are created for the atoms expected to connect these residues, i.e.
'N'for peptides and
- atomsAtomArray, shape=(n,) or AtomArrayStack, shape=(m,n)
The structure to create the
- 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.
The created bond list. No bonds are added for residues that are not found in
If obtaining the bonds from an MMTF file is not possible, this is the recommended way to obtain
BondListfor a structure. However, this method can only find bonds for residues in the RCSB
components.cifdataset. Although this includes most molecules one encounters, this will fail for exotic molecules, e.g. specialized inhibitors.