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Parameters

​
residues
List[Residue]
required
List of Residue objects

​
Methods

​
chain_ID

ID of the monomer chain.

​
mutability

List of mutability of each Residue in Chain.

​
sequence

String (one-letter) representation of amino acids in Chain.

​
mutable_residues

List of mutable Residues in Chain

​
mutable_residue_indexes

List of the indexes of mutable Residues in Chain

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length

Number of amino acids in Chain.

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from_pdb

Create Chain object from a PDB file string. Residue indices are 0-indexed. Parameters
​
file_path
str
required
​
chain_id
str
required

​
from_cif

Create Chain object from a CIF file string. Parameters
​
cif_data
str
required

​
remove_residue

Remove the Residue at the given index (0-indexed). Parameters
​
index
int
required

​
add_residue

Add a Residue of type amino_acid at the position specified by index (0-indexed). Parameters
​
amino_acid
str
required
​
index
int
required

​
mutate_residue

Change identity of Residue at position specified by index to ‘amino_acid’ Parameters
​
index
int
required
​
amino_acid
str
required

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Example

import bagel as bg

residues = [
    bg.Residue(name='A', chain_ID='A', index=0, mutable=True),
    bg.Residue(name='G', chain_ID='A', index=1, mutable=True),
]
chain = bg.Chain(residues=residues)
chain.mutate_residue(index=1, amino_acid='V')