def defaultEquilRestraints(self, decay, mol=None):
"""Get the default equilibration restraints
Parameters
----------
decay : str
The restrains will get scaled to 0 over this much time.
Returns
-------
restraints : list
A list of default protein restraints
Examples
--------
>>> md = Equilibration()
>>> res = md.defaultEquilRestraints('20ns')
"""
caatoms = AtomRestraint("protein and name CA", 0, [(1, 0), (0, decay)])
notcaatoms = AtomRestraint("protein and noh and not name CA", 0,
[(0.1, 0), (0, decay)])
nucleic = AtomRestraint("nucleic and backbone", 0, [(1, 0),
(0, decay)])
nucleicside = AtomRestraint("nucleic and not backbone and noh", 0,
[(0.1, 0), (0, decay)])
restraints = [caatoms, notcaatoms, nucleic, nucleicside]
if mol is not None:
restraints = [
r for r in restraints if mol.atomselect(r.selection).sum()
]
return restraints
def _constraints2restraints(self):
restraints = list()
for constr in sorted(self.constraints):
restraints.append(AtomRestraint(constr, 0, [(self.constraints[constr], 0)]))
return restraints
def defaultEquilRestraints(self, decay):
""" Get the default protein restraints
Parameters
----------
decay : str
The restrains will get scaled to 0 over this much time.
Returns
-------
restraints : list
A list of default protein restraints
Examples
--------
>>> md = Equilibration()
>>> res = md.defaultEquilRestraints('20ns')
"""
caatoms = AtomRestraint("protein and name CA", 0, [(1, 0), (0, decay)])
notcaatoms = AtomRestraint(
"protein and noh and not name CA", 0, [(0.1, 0), (0, decay)]
)
return [caatoms, notcaatoms]