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()
if len(np.unique(mol.insertion)) > 1:
mol.renumberResidues()
ca_indices, nco_indices, proline_indices, chain_ids = self._getSelections(
mol)
mol.filter(self.sel, _logger=False)
xyz = np.swapaxes(np.swapaxes(np.atleast_3d(mol.coords), 1, 2), 0, 1)
xyz = np.array(xyz.copy(), dtype=np.float32) / 10 # converting to nm
from mdtraj.geometry._geometry import _dssp as dssp
natoms = np.unique((nco_indices.shape[0], ca_indices.shape[0],
proline_indices.shape[0], chain_ids.shape[0]))
if len(natoms) != 1:
raise AssertionError(
'Wrong dimensions in SS data arrays. Report this bug on the issue tracker.'
)
data = dssp(xyz, nco_indices, ca_indices, proline_indices, chain_ids)
if self.simplified:
trans = str.maketrans('HGIEBTS ', 'HHHEECCC')
data = data.translate(trans)
data = np.fromiter(data, dtype=np.dtype('U2'))
data = data.reshape(mol.numFrames, len(chain_ids))
if self.integer:
if self.simplified:
data[data == 'H'] = 2
data[data == 'E'] = 1
data[data == 'C'] = 0
else:
data[data == 'H'] = 3
data[data == 'B'] = 4
data[data == 'E'] = 5
data[data == 'G'] = 6
data[data == 'I'] = 7
data[data == 'T'] = 8
data[data == 'S'] = 9
data[data == ' '] = 10
data = np.array(data, dtype=np.int32)
#data[:, np.logical_not(protein_indices)] = 'NA'
return data
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()
if len(np.unique(mol.insertion)) > 1:
mol.renumberResidues()
ca_indices, nco_indices, proline_indices, chain_ids = self._getSelections(mol)
mol.filter(self.sel, _logger=False)
xyz = np.swapaxes(np.swapaxes(np.atleast_3d(mol.coords), 1, 2), 0, 1)
xyz = np.array(xyz.copy(), dtype=np.float32) / 10 # converting to nm
from mdtraj.geometry._geometry import _dssp as dssp
natoms = np.unique((nco_indices.shape[0], ca_indices.shape[0], proline_indices.shape[0], chain_ids.shape[0]))
if len(natoms) != 1:
raise AssertionError('Wrong dimensions in SS data arrays. Report this bug on the issue tracker.')
data = dssp(xyz, nco_indices, ca_indices, proline_indices, chain_ids)
if self.simplified:
trans = str.maketrans('HGIEBTS ', 'HHHEECCC')
data = data.translate(trans)
data = np.fromiter(data, dtype=np.dtype('U2'))
data = data.reshape(mol.numFrames, len(chain_ids))
if self.integer:
if self.simplified:
data[data == 'H'] = 2
data[data == 'E'] = 1
data[data == 'C'] = 0
else:
data[data == 'H'] = 3
data[data == 'B'] = 4
data[data == 'E'] = 5
data[data == 'G'] = 6
data[data == 'I'] = 7
data[data == 'T'] = 8
data[data == 'S'] = 9
data[data == ' '] = 10
data = np.array(data, dtype=np.int32)
#data[:, np.logical_not(protein_indices)] = 'NA'
return data
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.
"""
mol = args[0]
ca_indices, nco_indices, proline_indices, chain_ids = self._getSelections(
mol)
#print(nco_indices)
#print(ca_indices)
#print(proline_indices)
#print(chain_ids)
xyz = np.swapaxes(np.swapaxes(np.atleast_3d(mol.coords), 1, 2), 0, 1)
xyz = np.array(xyz.copy(), dtype=np.float32) / 10 # converting to nm
from mdtraj.geometry._geometry import _dssp as dssp
data = dssp(xyz, nco_indices, ca_indices, proline_indices, chain_ids)
if self.simplified:
trans = str.maketrans('HGIEBTS ', 'HHHEECCC')
data = data.translate(trans)
data = np.fromiter(data, dtype=np.dtype('U2'))
data = data.reshape(mol.numFrames, len(chain_ids))
if self.integer:
data[data == 'H'] = 2
data[data == 'E'] = 1
data[data == 'C'] = 0
data = np.array(data, dtype=np.int32)
#data[:, np.logical_not(protein_indices)] = 'NA'
return data
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.
"""
mol = mol.copy()
molprops = self._getMolProp(mol, "all")
ca_indices = molprops["ca_indices"]
nco_indices = molprops["nco_indices"]
proline_indices = molprops["proline_indices"]
chain_ids = molprops["chain_ids"]
mol.filter(self.sel, _logger=False)
xyz = np.swapaxes(np.swapaxes(np.atleast_3d(mol.coords), 1, 2), 0, 1)
xyz = np.array(xyz.copy(), dtype=np.float32) / 10 # converting to nm
try:
from mdtraj.geometry._geometry import _dssp as dssp
except ImportError:
raise ImportError(
"To calculate secondary structure you need to install mdtraj with `conda install mdtraj -c conda-forge`"
)
natoms = np.unique((
nco_indices.shape[0],
ca_indices.shape[0],
proline_indices.shape[0],
chain_ids.shape[0],
))
if len(natoms) != 1:
raise AssertionError(
"Wrong dimensions in SS data arrays. Report this bug on the issue tracker."
)
data = dssp(xyz, nco_indices, ca_indices, proline_indices, chain_ids)
if self.simplified:
trans = str.maketrans("HGIEBTS ", "HHHEECCC")
data = data.translate(trans)
data = np.fromiter(data, dtype=np.dtype("U2"))
data = data.reshape(mol.numFrames, len(chain_ids))
if self.integer:
if self.simplified:
data[data == "H"] = 2
data[data == "E"] = 1
data[data == "C"] = 0
else:
data[data == "H"] = 3
data[data == "B"] = 4
data[data == "E"] = 5
data[data == "G"] = 6
data[data == "I"] = 7
data[data == "T"] = 8
data[data == "S"] = 9
data[data == " "] = 10
data = np.array(data, dtype=np.int32)
# data[:, np.logical_not(protein_indices)] = 'NA'
return data