Chain

This class stores arrays of residues/molecules. Thus, a Chain instance has residues and atoms attributes.

API Reference

class pmx.chain.Chain(seq=None, **kwargs)

Chain Class.

Parameters

seq (str, optional) – amino acid sequence. If Chain is initialised with a sequence, a peptide is built. By default seq=None.

residues

list of residues in Chain

Type

list

nres

number of residues in Chain

Type

int

atoms

list of atoms in Chain

Type

list

natoms

number of atoms in Chain

Type

int

id

atom id

Type

int

Methods

set_chain_id(chain_id)	Sets the chain ID.
get_sequence()	Returns the sequence of residues in FASTA format.
append(mol[, newResNum])	Appends a residue to the Chain.
insert_residue(pos, mol[, newResNum])	Inserts a residue at a specified position.
remove_residue(residue[, renumber_atoms, …])	Removes a residue.
replace_residue(residue, new[, bKeepResNum])	Replaces a residue.
nbuild(resn[, phi, psi])	Extend Chain at N-terminus.
cbuild(resn[, next_phi, psi])	Extend Chain at C-terminus.
add_nterm_cap()	Adds N-terminal cap (ACE).
add_cterm_cap()	Adds C-terminal cap (NME).
fetch_residues(key[, inv])	Fetch residues by residue names.
rename_atoms_to_gmx()	Renames atoms to comply with Gromacs syntax.