pmx_chain.md

class chain.Chain(Atomselection)

Some arttributes:

• chain.id ( chain identifier )
• chain.atoms ( list of atoms )
• chain.residues ( list of residues )

Protein specific methods:

• chain.sequence() ( return peptide sequence as string )
• chain.get_sequence() ( return sequence in fasta format )
• chain.create( "AFGCFRT") ( create chain instance from sequence )
• chain.nbuild("R") ( attach arginine at the n-terminus )
• chain.cbuild("R") ( attach arginine at the c-terminus )
• chain.fuse( other_chain ) ( attach a second chain at the c-terminus )
• chain.add_nterm_cap() ( attach an ACE molecule at the n-terminus )
• chain.add_cterm_cap() ( attach NME molecule at the c-terminus )

Other methods:

• chain.fetch_residues(["ALA","GLY","TRP"]) ( return all ALA, GLY and TRP residues)
• del chain5 ( remove residue 5 from the chain )
• chain.insert_residue(pos, mol ) ( insert a new residue into the chain )
• chain.renumber_residues()
• chain.set_chain_id("Z") ( set new chain id, change is propagated to all atoms in the chain )
• chain.copy() ( hard copy of the chain )

Construction options:

>>> c = Chain()                                      # empty chain
>>> c = Chain().create("AFGTRL")           # create peptide chain
>>> c = Chain( atoms = list_of_atoms )    # create a chain from a list of atoms
>>> c = Chain( residues = list_of_molecules )   # create a chain from a list of molecules