def setHetero(self, data):
"""Deprecated for removal in v1.3, use ``setFlag('hetatm', data)``
instead."""
from prody import deprecate
deprecate('setHerero', "setFlag('hetatm', data)", '1.3')
return self.setFlag('hetatm', data)
def getMappedFlags(self):
"""Deprecated for removal in v1.3, use :meth:`getFlags` instead
(``getFlags('mapped')``)."""
from prody import deprecate
deprecate('getMappedFlags', "getFlags('mapped')")
return self.getFlags('mapped')
def getHeteros(self):
"""Deprecated for removal in v1.3, use ``getFlags('hetatm')`` instead.
"""
from prody import deprecate
deprecate('getHereros', "getFlags('hetatm')", '1.3')
return self.getFlags('hetatm')
def getNonstdProperties(resname):
"""Deprecated for removal in v1.4, use :func:`listNonstdAAProps` instead.
"""
from prody import deprecate
deprecate('getNonstdProperties', 'listNonstdAAProps')
return listNonstdAAProps(resname)
def getNonstdProperties(resname):
"""Deprecated for removal in v1.4, use :func:`listNonstdAAProps` instead.
"""
from prody import deprecate
deprecate('getNonstdProperties', 'listNonstdAAProps')
return listNonstdAAProps(resname)
def getModes(self):
"""Deprecated for removal in v1.3, use ``list(nma)`` instead."""
from prody import deprecate
deprecate('getModes', 'list(nma)')
return list(self)
def isData(self, label):
"""Deprecated, use :meth:`isDataLabel` instead."""
from prody import deprecate
deprecate('isData', 'isDataLabel', 'v1.3')
return self.isDataLabel(label)
def getMode(self, index):
"""Deprecated for removal in v1.3, use indexing instead."""
from prody import deprecate
deprecate('getMode', 'nma[index]')
return self[index]
def setVerbosity(self, level):
"""Deprecated for removal in v1.3, set :attr:`verbosity` directly."""
from prody import deprecate
deprecate('setVerbosity', 'verbosity')
self._setverbosity(level)
def getCovariance(self):
"""Deprecated, use :func:`~.calcCovariance` instead."""
prody.deprecate('getCovariance', 'calcCovariance')
return prody.calcCovariance(self)
def getEigenvectors(self):
"""Deprecated, use :meth:`getEigvecs` instead."""
prody.deprecate('getEigenvector', 'getEigvecs')
return self.getEigvecs()
def getEigenvalues(self):
"""Deprecated, use :meth:`getEigvals` instead."""
prody.deprecate('getEigenvalue', 'getEigvals')
return self.getEigvals()
def getVerbosity(self):
"""Deprecated for removal in v1.3, get :attr:`verbosity` directly."""
from prody import deprecate
deprecate('getVerbosity', 'verbosity')
return self._getverbosity()
def closeLogfile(self, filename):
"""Deprecated, use :meth:`close` instead."""
from prody import deprecate
deprecate('closeLogfile', 'close')
self.start(filename)
def startLogfile(self, filename, **kwargs):
"""Deprecated, use :meth:`start` instead."""
from prody import deprecate
deprecate('startLogfile', 'start')
self.start(filename, **kwargs)
def getPrefix(self):
"""Deprecated for removal in v1.3, get :attr:`prefix` directly."""
from prody import deprecate
deprecate('getPrefix', 'prefix')
return self._prefix
def get4x4Matrix(self):
"""Deprecated for removal in v1.1, use :meth:`getMatrix` instead."""
deprecate('get4x4Matrix', 'getMatrix')
return self.getMatrix()
# ProDy: A Python Package for Protein Dynamics Analysis
#
# Copyright (C) 2010-2012 Ahmet Bakan
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>
"""Deprecated for removal in v1.2, use :mod:`.utilities` instead."""
__author__ = "Ahmet Bakan"
__copyright__ = "Copyright (C) 2010-2012 Ahmet Bakan"
from prody import deprecate
deprecate("prody.tools", "prody.utilities", ver="1.2")
from prody import utilities
from prody.utilities import *
__all__ = list(utilities.__all__)