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, "1fdn")
sel = Selection(mdl)
rsr = mdl.restraints
at = mdl.atoms
rsr.add(forms.Gaussian(group=physical.bond,
                       feature=MyDist(at['CA:1:A'], at['C:1:A']),
                       mean=1.5380, stdev=0.0364))
sel.energy()