model.md

class model.Model( Atomselection )

Some attributes:

• model.title ( name )
• model.atoms ( list of atoms)
• model.residues ( list of residues )
• model.chains ( list of chains )
• model.chdic ( dictionary to retrieve chains by id )
• model.box ( unit cell or simulation box )

Some methods:

see also Atomselection methods

• model.fetch_residues(["SER","TRP"]) ( return list of all serine and tryptophane residues )
• del model['A'] ( remove chain A )
• model.remove_residue( molecule ) ( remove a residue )
• model.remove_atom( atom ) ( remove atom )
• model.make_chains() ( make chain list )
• model.make_residues() ( make residue list )
• model.write("out.pdb") ( write structure file )

Construction methods:

>>> m = Model()                   # empty model
>>> m = Model("protein.pdb")  # create model from pdb or gro file
>>> m = Model( atoms = list_of_atoms )     # create model from list of atoms
>>> m = Model( residues = list_of_molecules )     # create model from list of residues
>>> m = Model( chains = list_of_chains )     # create model from list of chains
>>> m = Model( pdbline = line )                 # from pdbfile as single string ( m = Model( open('in.pdb').read() ) )