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]