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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 (`Structure` class). 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 6.22.

Two `Atom` objects are considered equal if and only if they represent the same atom in the same structure.

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 in chain A: %s " \
            % mdl.atoms['CA:4:A'].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:A'].atoms[0]
      print("Biso for first atom in residue 10 in chain A %.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.accessibility — atomic accessibility
- Atom.occ — occupancy
- Atom.charge — electrostatic charge
- Atom.mass — mass
- Atom.name — PDB name
- Atom.type — CHARMM atom type
- Atom.residue — residue object
- Atom.get_equivalent_atom() — get equivalent atom in another residue