def project(self, *args, **kwargs):
""" Project molecule.
Parameters
----------
mol : :class:`Molecule <htmd.molecule.molecule.Molecule>`
A :class:`Molecule <htmd.molecule.molecule.Molecule>` object to project.
Returns
-------
data : np.ndarray
An array containing the projected data.
"""
# -------------- DEPRECATION PATCH --------------
if isinstance(self, np.ndarray) or isinstance(self, Molecule):
from warnings import warn
warn('Static use of the project method will be deprecated in the next version of HTMD. '
'Please change your projection code according to the tutorials on www.htmd.org')
data = _MetricRmsdOld.project(self, *args, **kwargs)
logger.warning('Static use of the project method will be deprecated in the next version of HTMD. '
'Please change your projection code according to the tutorials on www.htmd.org')
return data
# ------------------ CUT HERE -------------------
mol = args[0]
mol = mol.copy()
(trajalnsel, trajrmsdsel, centersel) = self._getSelections(mol)
if self._pbc:
mol.wrap()
#mol.coords = self._wrapPositions(mol.box, mol.coords, centersel)
mol.align(sel=trajalnsel, refmol=self._refmol, refsel=self._refalnsel)
return molRMSD(mol, self._refmol, trajrmsdsel, self._refrmsdsel)
def project(self, *args, **kwargs):
""" Project molecule.
Parameters
----------
mol : :class:`Molecule <htmd.molecule.molecule.Molecule>`
A :class:`Molecule <htmd.molecule.molecule.Molecule>` object to project.
Returns
-------
data : np.ndarray
An array containing the projected data.
"""
# -------------- DEPRECATION PATCH --------------
if isinstance(self, np.ndarray) or isinstance(self, Molecule):
from warnings import warn
warn('Static use of the project method will be deprecated in the next version of HTMD. '
'Please change your projection code according to the tutorials on www.htmd.org')
data = _MetricRmsdOld.project(self, *args, **kwargs)
logger.warning('Static use of the project method will be deprecated in the next version of HTMD. '
'Please change your projection code according to the tutorials on www.htmd.org')
return data
# ------------------ CUT HERE -------------------
mol = args[0]
mol = mol.copy()
(trajalnsel, trajrmsdsel, centersel) = self._getSelections(mol)
if self._pbc:
mol.wrap(centersel)
#mol.coords = self._wrapPositions(mol.box, mol.coords, centersel)
mol.align(sel=trajalnsel, refmol=self._refmol, refsel=self._refalnsel)
return molRMSD(mol, self._refmol, trajrmsdsel, self._refrmsdsel)
def _processTraj(self, mol):
(trajalnsel, trajrmsdsel, centersel) = self._getSelections(mol)
mol = mol.copy()
if self._pbc:
mol.wrap()
#mol.coords = self._wrapPositions(mol.box, mol.coords, centersel)
mol.align(sel=trajalnsel, refmol=self._refmol, refsel=self._refalnsel)
return molRMSD(mol, self._refmol, trajrmsdsel, self._refrmsdsel)
def _processTraj(self, mol):
(trajalnsel, trajrmsdsel, centersel) = self._getSelections(mol)
mol = mol.copy()
if self._pbc:
mol.wrap()
#mol.coords = self._wrapPositions(mol.box, mol.coords, centersel)
mol.align(sel=trajalnsel, refmol=self._refmol, refsel=self._refalnsel)
return molRMSD(mol, self._refmol, trajrmsdsel, self._refrmsdsel)
def project(self, mol):
""" Project molecule.
Parameters
----------
mol : :class:`Molecule <htmd.molecule.molecule.Molecule>`
A :class:`Molecule <htmd.molecule.molecule.Molecule>` object to project.
Returns
-------
data : np.ndarray
An array containing the projected data.
"""
mol = mol.copy()
(trajalnsel, trajrmsdsel, centersel) = self._getSelections(mol)
if self._pbc:
mol.wrap(centersel)
#mol.coords = self._wrapPositions(mol.box, mol.coords, centersel)
mol.align(sel=trajalnsel, refmol=self._refmol, refsel=self._refalnsel)
return molRMSD(mol, self._refmol, trajrmsdsel, self._refrmsdsel)
def project(self, mol):
""" Project molecule.
Parameters
----------
mol : :class:`Molecule <htmd.molecule.molecule.Molecule>`
A :class:`Molecule <htmd.molecule.molecule.Molecule>` object to project.
Returns
-------
data : np.ndarray
An array containing the projected data.
"""
mol = mol.copy()
(trajalnsel, trajrmsdsel, centersel) = self._getSelections(mol)
if self._pbc:
mol.wrap(centersel)
#mol.coords = self._wrapPositions(mol.box, mol.coords, centersel)
mol.align(sel=trajalnsel, refmol=self._refmol, refsel=self._refalnsel)
return molRMSD(mol, self._refmol, trajrmsdsel, self._refrmsdsel)
def foo(mol, ref):
from htmd.molecule.util import molRMSD
mol.wrap('protein')
mol.align('protein and name CA', refmol=ref)
return molRMSD(mol, ref, mol.atomselect('protein and name CA'), ref.atomselect('protein and name CA'))
def foo(mol, ref):
from htmd.molecule.util import molRMSD
mol.wrap('protein')
mol.align('protein and name CA', refmol=ref)
return molRMSD(mol, ref, mol.atomselect('protein and name CA'),
ref.atomselect('protein and name CA'))
