pmx_molecule.md

molecule.Molecule()

class molecule.Molecule(Atomselection)

Some attributes:

• molecule.id ( molecule or residue id)
• molecule.resname ( name )
• molecule.atoms ( list of atoms )

Some methods:

see also Atomselection methods

There are a couple of methods that are protein specific

• molecule.get_phi( degree = True) ( return phi angle )
• molecule.get_psi()
• molecule.get_omega()
• molecule.get_chi( 1 )
• molecule.set_phi( new_phi, propagate = True ) ( set new phi angle and propagate change through the chain )
• molecule.set_psi(new_psi,...)
• molecule.set_omega( new_omega )
• molecule.set_chi(1, new_chi ) ( new value for chi 1 )

Other methods:

• molecule.set_resname( new_resname ) ( new residue name, atom residue names are renamed, too )
• molecule.insert_atom( position, Atom) ( insert a new atom at a certain position)
• molecule.append( Atom ) ( append new atom at the end of the atom list )
• molecule.remove(Atom) ( remove this atom )
• del molecule['CA'] ( remove atom with name CA )
• molecule.write( "out.pdb") ( write molecule as pdb )
• molecule.copy() ( make a hard copy of this molecule)
• molecule.new_aa( "A") ( create new alanine residue )

Construction options:

>>> mol = Molecule()                                       # empty molecule
>>> mol = Molecule( atoms = list_of_atoms )     # create molecule from a list of atoms
>>> mol = Molecule().new_aa( "SER")               # create serine