def sample_bb_angles(self, resnum):
""" Resamples phi and psi angles for a residue.
Returns the new [phi, psi] angles.
Arguments:
resnum -- number of the residue to resample
NB: This function sets the phi and psi angles to new values.
NOTE: Random seeds can be set via the set_seed() function:
fragbuilder.set_seed(some_number)
"""
if self._dbn is None:
self._dbn = basilisk_lib.basilisk_dbn()
aa_letter = self._sequence[resnum - 1]
aa = int(basilisk_lib.basilisk_utils.one_to_index(aa_letter))
chis, bb, ll = self._dbn.get_sample(aa)
angles_deg = [self._basilisk_to_deg(bb[0]),
self._basilisk_to_deg(bb[1])]
self.set_bb_angles(resnum, angles_deg)
return angles_deg
def __init__(self):
"""
Inititalize a DBN object from basilisk_lib.
"""
self.dbn = basilisk_lib.basilisk_dbn()
def __init__(self):
"""
Inititalize a DBN object from basilisk_lib.
"""
self.dbn = basilisk_lib.basilisk_dbn()
def sample_bb_angles(self, resnum):
""" Resamples phi and psi angles for a residue.
Returns the new [phi, psi] angles.
Arguments:
resnum -- number of the residue to resample
NB: This function sets the phi and psi angles to new values.
NOTE: Random seeds can be set via the set_seed() function:
fragbuilder.set_seed(some_number)
"""
if self._dbn is None:
self._dbn = basilisk_lib.basilisk_dbn()
aa_letter = self._sequence[resnum - 1]
aa = int(basilisk_lib.basilisk_utils.one_to_index(aa_letter))
chis, bb, ll = self._dbn.get_sample(aa)
angles_deg = [self._basilisk_to_deg(bb[0]),
self._basilisk_to_deg(bb[1])]
self.set_bb_angles(resnum, angles_deg)
return angles_deg
def sample_chi_angles(self, resnum, bb_dependency=True):
""" Resamples chi angles for a residue from BASILISK.
Returns the new chi angles.
Arguments:
resnum -- number of the residue to resample
Keyword arguments:
bb_dependency -- Whether to sample chi angles taking
phi/psi angles into account in BASILISK sampling. (default True)
NB: This function sets the chi angles to new values.
NOTE: Random seeds can be set via the set_seed() function:
fragbuilder.set_seed(some_number)
"""
if self._dbn is None:
self._dbn = basilisk_lib.basilisk_dbn()
angles = self._get_all_bb_angles()[resnum - 1]
phi = angles[1][0]/180.0*numpy.pi
psi = angles[1][1]/180.0*numpy.pi
aa_letter = self._sequence[resnum - 1]
aa = int(basilisk_lib.basilisk_utils.one_to_index(aa_letter))
if bb_dependency:
chis, bb, ll = self._dbn.get_sample(aa, phi, psi)
else:
chis, bb, ll = self._dbn.get_sample(aa)
chis_deg = []
for chi in chis:
chis_deg.append(self._basilisk_to_deg(chi))
self.set_chi_angles(resnum, chis_deg)
return chis_deg
def sample_chi_angles(self, resnum, bb_dependency=True):
""" Resamples chi angles for a residue from BASILISK.
Returns the new chi angles.
Arguments:
resnum -- number of the residue to resample
Keyword arguments:
bb_dependency -- Whether to sample chi angles taking
phi/psi angles into account in BASILISK sampling. (default True)
NB: This function sets the chi angles to new values.
NOTE: Random seeds can be set via the set_seed() function:
fragbuilder.set_seed(some_number)
"""
if self._dbn is None:
self._dbn = basilisk_lib.basilisk_dbn()
angles = self._get_all_bb_angles()[resnum - 1]
phi = angles[1][0]/180.0*numpy.pi
psi = angles[1][1]/180.0*numpy.pi
aa_letter = self._sequence[resnum - 1]
aa = int(basilisk_lib.basilisk_utils.one_to_index(aa_letter))
if bb_dependency:
chis, bb, ll = self._dbn.get_sample(aa, phi, psi)
else:
chis, bb, ll = self._dbn.get_sample(aa)
chis_deg = []
for chi in chis:
chis_deg.append(self._basilisk_to_deg(chi))
self.set_chi_angles(resnum, chis_deg)
return chis_deg
