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## User-defined feature types

To create a new feature type, derive a new class from the base `features.feature`. You should then set the `numatoms` member to the number of atoms your feature acts on, and also override the following functions: `eval`, `deriv`, and `is_angle`. You can also derive your class from any of the built-in MODELLER features (e.g., `features.angle`) if you desire.

The `eval` function is called from MODELLER with a `model` object and the indices of the atoms defining the feature. Your function should return the value of the feature. The `deriv` function is similar, but is also passed the current feature value; you should return the derivatives of the feature with respect to x, y and z of each defining atom. The `is_angle` function should return `True` if your feature is an angle, in which case MODELLER will automatically deal with periodicity for you, and convert any feature values to degrees for the user. (Your `eval` and `deriv` functions should, however, return angle values in radians.)

Example: examples/python/user_feat.py

      from modeller import *
      from modeller.scripts import complete_pdb

      env = environ()

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

      class mydist(features.feature):
          """An implementation of Modeller's distance feature (type 1) in
             pure Python. For improved performance, see cuser_feat.py, which
             implements the feature in C."""

          numatoms = 2

          def eval(self, mdl, atom_indices):
              (a1, a2) = self.indices_to_atoms(mdl, atom_indices)
              dist = ((a1.x - a2.x) ** 2 + (a1.y - a2.y) ** 2
                      + (a1.z - a2.z) ** 2) ** 0.5
              return dist

          def deriv(self, mdl, atom_indices, feat):
              (a1, a2) = self.indices_to_atoms(mdl, atom_indices)
              dx1 = (a1.x - a2.x) / feat
              dy1 = (a1.y - a2.y) / feat
              dz1 = (a1.z - a2.z) / feat
              dx2 = -dx1
              dy2 = -dy1
              dz2 = -dz1
              return ((dx1, dx2), (dy1, dy2), (dz1, dz2))

          def is_angle(self):
              return False

      mdl = complete_pdb(env, "1fdx")
      sel = selection(mdl)
      rsr = mdl.restraints
      at = mdl.atoms
      rsr.add(forms.gaussian(group=physical.bond,
                             feature=mydist(at['CA:1'], at['C:1']),
                             mean=1.5380, stdev=0.0364))
      sel.energy()

Next: User-defined restraint forms Up: User-defined features and restraint Previous: User-defined features and restraint Contents Index