# Deformation force field
#
# Written by Konrad Hinsen
#
"""
Deformation force field (elastic network model)
For proteins, CalphaForceField is usually a better choice.
"""
__docformat__ = 'restructuredtext'
from MMTK.ForceFields.ForceField import ForceField, ForceFieldData
from MMTK import Utility
from MMTK_forcefield import NonbondedList, NonbondedListTerm
from MMTK_deformation import DeformationTerm
from Scientific import N
#
# The deformation force field class
#
[docs]class DeformationForceField(ForceField):
"""
Deformation force field for protein normal mode calculations
The pair interaction force constant has the form
k(r)=factor*exp(-(r**2-0.01)/range**2). The default value
for range is appropriate for a C-alpha model of a protein.
The offset of 0.01 is a convenience for defining factor;
with this definition, factor is the force constant for a
distance of 0.1nm.
"""
def __init__(self, fc_length = 0.7, cutoff = 1.2, factor = 46402.):
"""
:param fc_length: a range parameter
:type fc_length: float
: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 factor: a global scaling factor
:type factor: float
"""
self.arguments = (fc_length, cutoff, factor)
ForceField.__init__(self, 'deformation')
self.arguments = (fc_length, cutoff, factor)
self.fc_length = fc_length
self.cutoff = cutoff
self.factor = factor
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 = DeformationTerm(universe._spec, nbl, self.fc_length,
self.cutoff, self.factor, 1.)
return [update, ev]