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## User-defined restraint forms

To create a new restraint form, derive a new class from the base `forms.restraint_form`. You should then override the following functions: `__init__`, `eval`, `vmin`, `rvmin`, `min_mean`, `vheavy`, `rvheavy`, and `heavy_mean`. Note that presently you can only derive from this base class, not from MODELLER built-in forms.

Restraint forms can act on one or more features (each of which has an accompanying integer modality, which you can use for any purpose), and can take any number of floating-point parameters as input. The features and parameters are stored in `self._features` and `self._parameters` respectively, but for convenience the base constructor `restraint_form.__init__` can set initial values for these.

The `eval` function is called from MODELLER with the current feature values, their types and modalities, and the parameter vector. You should return the objective function contribution and, if requested, the derivatives with respect to each feature. The feature types are required by the `deltaf` function, which returns the difference between the current feature value and the mean (a simple subtraction is not sufficient, as some feature types are periodic). Note that you must use the passed parameter vector, as the class is not persistent, and as such the `self._parameters` variable (or any other object variable you may have set) is not available to this function.

The other functions are used to return the minimal and heavy restraint violations (both absolute and relative; see Section 5.3.1) and the means. The heavy and minimal means correspond to the global and local minima.

Example: examples/python/user_form.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 mygauss(forms.restraint_form):
          """An implementation of Modeller's harmonic/Gaussian restraint (type 3)
             in pure Python"""

          rt = 0.5900991    # RT at 297.15K, in kcal/mol

          def __init__(self, group, feature, mean, stdev):
              forms.restraint_form.__init__(self, group, feature, 0, (mean, stdev))

          def eval(self, feats, iftyp, modal, param, deriv):
              (mean, stdev) = param
              delt = self.deltaf(feats[0], mean, iftyp[0])
              val = self.rt * 0.5 * delt**2  / stdev**2
              if deriv:
                  fderv = self.rt * delt / stdev**2
                  return val, [fderv]
              else:
                  return val

          def vmin(self, feats, iftyp, modal, param):
              (mean, stdev) = param
              return self.deltaf(feats[0], mean, iftyp[0])

          def rvmin(self, feats, iftyp, modal, param):
              (mean, stdev) = param
              return self.deltaf(feats[0], mean, iftyp[0]) / stdev

          def min_mean(self, feats, iftyp, modal, param):
              (mean, stdev) = param
              return [mean]

          # There is only one minimum, so the 'heavy' mean is the same as the 'min'
          vheavy = vmin
          rvheavy = rvmin
          heavy_mean = min_mean

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

Next: User-defined energy terms Up: User-defined features and restraint Previous: User-defined feature types Contents Index