Source code for MMTK.ForceFields.CalphaFF

# C-alpha force field
#
# Written by Konrad Hinsen
#

"""
C-alpha force field for protein normal mode analysis
(Elastic Network Model)
"""

__docformat__ = 'restructuredtext'

from MMTK.ForceFields.ForceField import ForceField, ForceFieldData
from MMTK import Utility
from MMTK_forcefield import NonbondedList, NonbondedListTerm
from MMTK_deformation import CalphaTerm
from Scientific import N

#
# The deformation force field class
#
[docs]class CalphaForceField(ForceField): """ Effective harmonic force field for a C-alpha protein model """ def __init__(self, cutoff = None, scale_factor = 1., version=1): """ :param cutoff: the cutoff for pair interactions, should be at least 2.5 nm. Pair interactions in periodic systems are calculated using the minimum-image convention; the cutoff should therefore never be larger than half the smallest edge length of the elementary cell. :type cutoff: float :param scale_factor: a global scaling factor :type scale_factor: float """ ForceField.__init__(self, 'calpha') self.arguments = (cutoff,) self.cutoff = cutoff self.scale_factor = scale_factor self.version = version def ready(self, global_data): return True def evaluatorTerms(self, universe, subset1, subset2, global_data): nothing = N.zeros((0, 2), N.Int) if subset1 is not None: set1 = set(a.index for a in subset1.atomList()) set2 = set(a.index for a in subset2.atomList()) excluded_pairs = set(Utility.orderedPairs(list(set1-set2))) \ | set(Utility.orderedPairs(list(set2-set1))) excluded_pairs = N.array(list(excluded_pairs)) atom_subset = list(set1 | set2) atom_subset.sort() atom_subset = N.array(atom_subset) else: atom_subset = N.array([], N.Int) excluded_pairs = nothing nbl = NonbondedList(excluded_pairs, nothing, atom_subset, universe._spec, self.cutoff) update = NonbondedListTerm(nbl) cutoff = self.cutoff if cutoff is None: cutoff = 0. ev = CalphaTerm(universe._spec, nbl, cutoff, self.scale_factor, self.version) return [update, ev]