pmx_atom.md

pmx.atom

class atom.Atom()

This class stores all properties (attributes) related to an atom. E.g., when pmx reads a pdb file, each line starting with "ATOM" or "HETATM" is converted to an Atom instance. Hence, and atom object constructed from a pdb line contains:

• atom id (atom.id)
• atom name (atom.name)
• residue name (atom.resname)
• residue id (atom.resnr)
• chain id (atom.chain_id)
• coordinates (atom.x)
• occupancy (atom.occ)
• b-factor (atom.bfac)

In addition to storage properties, the atom class also has a number of methods:

• atom.dist( atom2 ) ( distance between two atoms)
• atom - atom2 ( same as above with overloaded "-" operator )
• atom.dist2( atom2) (squared distance, faster than distance)
• atom.angle( atom2, atom3, degree=True) angle calculation, returns rad by default )
• atom.dihedral( atom2, atom2, atom4, degree=True) (dihedral calculation)
• print atom ( writes atom as pdb line)

for full documentation use help(Atom) from the interpreter.