def calcGNM(self, n_modes=None):
"""Calculates GNM on the current Hi-C map."""
if self.useTrimmed:
gnm = TrimmedGNM(self._title, self.mask)
else:
gnm = GNM(self._title)
gnm.setKirchhoff(self.getKirchhoff())
gnm.calcModes(n_modes=n_modes)
return gnm
def calcGNM(self, n_modes=None, **kwargs):
"""Calculates GNM on the current Hi-C map."""
if 'hinges' in kwargs:
kwargs['hinges'] = False
if self.masked:
gnm = MaskedGNM(self._title, self.mask)
else:
gnm = GNM(self._title)
gnm.setKirchhoff(self.getKirchhoff())
gnm.calcModes(n_modes=n_modes, **kwargs)
return gnm
def calcGNM(self, n_modes=None, **kwargs):
"""Calculates GNM on the current Hi-C map. By default, ``n_modes`` is
set to **None** and ``zeros`` to **True**."""
if 'zeros' not in kwargs:
kwargs['zeros'] = True
if self.masked:
gnm = MaskedGNM(self._title, self.mask)
else:
gnm = GNM(self._title)
gnm.setKirchhoff(self.getKirchhoff())
gnm.calcModes(n_modes=n_modes, **kwargs)
return gnm