The atom class: a single atom in a model or structure
Keywords: manual

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The `atom` class: a single atom in a model or structure

The `atom` class holds information about a single atom, in a `model` (see model.atoms) or an alignment template structure. The `atom` class is derived from the `point` class, and thus all `point` methods (e.g., point.select_sphere()) can also be called on `atom` objects, and all `point` members (e.g. point.x) are available. See Section 6.18.

Example: examples/python/atoms.py

      # Example for 'atom' objects

      from modeller import *
      from modeller.scripts import complete_pdb

      env = environ()
      env.io.atom_files_directory = '../atom_files'
      env.libs.topology.read(file='$(LIB)/top_heav.lib')
      env.libs.parameters.read(file='$(LIB)/par.lib')

      mdl = complete_pdb(env, "1fas")

      # 'mdl.atoms' is a list of all atoms in the model
      print "Name of C-alpha atom in residue 4: ", mdl.atoms['CA:4'].name
      a = mdl.atoms[0]
      print "Coordinates of first atom: %.3f, %.3f, %.3f" % (a.x, a.y, a.z)

      # Each 'residue' object lists its own atoms, as does each chain
      a = mdl.residues['10'].atoms[0]
      print "Biso for first atom in residue 10: %.3f" % a.biso

      a = mdl.chains[0].residues[-1].atoms[-1]
      print "Biso for last atom in last residue in first chain: %.3f" % a.biso

Subsections

- atom.dvx -- objective function derivative
- atom.vx -- x component of velocity
- atom.biso -- isotropic temperature factor
- atom.occ -- occupancy
- atom.charge -- electrostatic charge
- atom.mass -- mass
- atom.name -- PDB name
- atom.residue -- residue object