biotite.structure.connect_via_residue_names¶
- 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 RCSBcomponents.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
Notes
This method can only find bonds for residues in the RCSB Chemical Component Dictionary. Although this includes most molecules one encounters, this will fail for exotic molecules, e.g. specialized inhibitors.