def project(self, mol):
""" Project molecule.
Parameters
----------
mol : :class:`Molecule <moleculekit.molecule.Molecule>`
A :class:`Molecule <moleculekit.molecule.Molecule>` object to project.
Returns
-------
data : np.ndarray
An array containing the projected data.
"""
getMolProp = lambda prop: self._getMolProp(mol, prop)
radii = getMolProp('radii')
atom_mapping = getMolProp('atom_mapping')
sel = getMolProp('sel')
xyz = np.swapaxes(
np.swapaxes(np.atleast_3d(mol.coords[sel, :, :]), 1, 2), 0, 1)
xyz = np.array(xyz.copy(), dtype=np.float32) / 10 # converting to nm
try:
from mdtraj.geometry._geometry import _sasa as sasa
except ImportError:
raise ImportError(
'To calculate SASA you need to install mdtraj with `conda install mdtraj -c omnia`'
)
out = np.zeros((mol.numFrames, atom_mapping.max() + 1),
dtype=np.float32)
sasa(xyz, radii / 10, int(self._numSpherePoints), atom_mapping,
out) # Divide radii by 10 for nm
return out
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.
"""
radii, atom_mapping, sel = self._getRadiiMapping(mol)
xyz = np.swapaxes(
np.swapaxes(np.atleast_3d(mol.coords[sel, :, :]), 1, 2), 0, 1)
xyz = np.array(xyz.copy(), dtype=np.float32) / 10 # converting to nm
from mdtraj.geometry._geometry import _sasa as sasa
out = np.zeros((mol.numFrames, atom_mapping.max() + 1),
dtype=np.float32)
sasa(xyz, radii / 10, int(self._numSpherePoints), atom_mapping,
out) # Divide radii by 10 for nm
return out
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.
"""
radii, atom_mapping, sel = self._getRadiiMapping(mol)
xyz = np.swapaxes(np.swapaxes(np.atleast_3d(mol.coords[sel, :, :]), 1, 2), 0, 1)
xyz = np.array(xyz.copy(), dtype=np.float32) / 10 # converting to nm
from mdtraj.geometry._geometry import _sasa as sasa
out = np.zeros((mol.numFrames, atom_mapping.max() + 1), dtype=np.float32)
sasa(xyz, radii / 10, int(self._numSpherePoints), atom_mapping, out) # Divide radii by 10 for nm
return out