User-defined energy terms
Keywords: manual

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User-defined energy terms

To create a new energy term, derive a new class from the base `terms.energy_term`. You should then override the `eval` function. You can also override the `__init__` function if you want to define function parameters. Objects of this class can then be created and added to the energy_data.energy_terms list.

The `eval` function is called from MODELLER with a `model` object, and the indices of all selected atoms. You should return the objective function contribution and, if requested, the derivatives with respect to the Cartesian coordinates.

Example: examples/python/user_term.py

      from modeller import *
      from modeller.scripts import complete_pdb

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

      class myterm(terms.energy_term):
          """Custom energy term, which tries to force all atoms to one side of
             the x=10.0A plane"""

          _physical_type = physical.absposition

          # Override the __init__ function so that we can pass in a 'strength'
          # parameter
          def __init__(self, strength):
              self.strength = strength
              terms.energy_term.__init__(self)

          def eval(self, mdl, deriv, indats):
              atoms = self.indices_to_atoms(mdl, indats)
              e = 0.
              dvx = [0.] * len(indats)
              dvy = [0.] * len(indats)
              dvz = [0.] * len(indats)
              for (num, at) in enumerate(atoms):
                  # Enforce a linearly increasing potential in the x direction
                  if at.x > 10.0:
                      e += (at.x - 10.0) * self.strength
                      dvx[num] += self.strength
              if deriv:
                  return (e, dvx, dvy, dvz)
              else:
                  return e

      t = env.edat.energy_terms
      t.append(myterm(strength=1.0))

      mdl = complete_pdb(env, "1fdx")
      sel = selection(mdl)
      print sel.energy()