pmx_atomselection.md

class atomselection.Atomselection()

This class is a base class for other classes that contain lists of atoms (Molecule, Chain, Model). These classes inherit a bunch of methods from the Atomselection class.

Inherited methods:

• atomselection.write("out.pdb") ( write atoms in pdb format )
• atomselection.com() ( put atoms to center of mass )
• atomselection.a2nm() ( convert from Angstroem to nm )
• atomselection.nm2a() ( convert from nm to Angstroem )
• atomselection.get_symbol() ( determine element type for each atom )
• atomselection.make_long_name() ( make 4 charactor atom name )
• atomselection.coords() ( return coordinates of all atoms as matrix )
• atomselection.fetch_atoms(["CA","C","N"]) ( return atoms with these names )
• atomselection.translate( [1,2,3] ) ( move all atoms by this vector )
• atomselection.rotate( axis, degree ) ( rotate all atoms around axis by this angle )
• atomselection.random_rotation() ( rotate all atoms around a random vector )
• atomselection.search_neighbors() ( do grid based neighbor search )
• atomselection.get_by_id( list_of_atom_ids ) ( return list of atoms )