idpet.featurization package
Submodules
idpet.featurization.angles module
- idpet.featurization.angles.featurize_a_angle(traj, get_names=True, atom_selector='protein and name CA')[source]
Calculate Cα-based torsion angles angles from a given MD trajectory.
- Return type:
Union
[ndarray
,Tuple
[ndarray
,List
[str
]]]
Parameters
- traj: mdtraj.Trajectory
The MDTraj trajectory containing the protein structure.
- get_names: bool, optional
If True, returns feature names along with the alpha angles. Default is True.
- atom_selector: str, optional
The atom selection string for C-alpha atoms. Default is “protein and name CA”.
Returns
- Union[np.ndarray, Tuple[np.ndarray, List[str]]]
If get_names is True, returns a tuple with alpha angle values and feature names. If get_names is False, returns an array of alpha angle values.
Notes
This function calculates Cα-based torsion angles angles from a given MD trajectory.
- idpet.featurization.angles.featurize_phi_psi(traj, get_names=True, ravel=True)[source]
Calculate phi (ϕ) and psi (ψ) angles from a given MD trajectory.
- Return type:
Union
[ndarray
,Tuple
[ndarray
,List
[str
]]]
Parameters
- traj: mdtraj.Trajectory
The MDTraj trajectory containing the protein structure.
- get_names: bool, optional
If True, returns feature names along with the phi and psi angles. Default is True.
- ravel: bool, optional
If True, returns the angles in a flattened array. Default is True.
Returns
- Union[np.ndarray, Tuple[np.ndarray, List[str]]]
If get_names is True, returns a tuple with phi and psi angles along with feature names. If get_names is False, returns an array of phi and psi angles.
Notes
This function calculates phi (ϕ) and psi (ψ) angles from a given MD trajectory.
- idpet.featurization.angles.featurize_tr_angle(traj, type, min_sep=2, max_sep=None, ravel=True, get_names=True)[source]
Calculate trRosetta angles between pair of residues.
- Return type:
array
Parameters
- trajmdtraj.Trajectory
The MDtraj trajectory object.
- typestr
The type of angle to calculate. Supported options: ‘omega’ or ‘phi’.
- min_sepint, optional
The minimum sequence separation for angle calculations. Default is 2.
- max_sepUnion[None, int, float], optional
The maximum sequence separation for angle calculations. Default is None.
- ravelbool, optional
Whether to flatten the output array. Default is True.
- get_namesbool, optional
Whether to return the names of the calculated features. Default is True.
Returns
- anglesnumpy.ndarray
A numpy array storing the angle values.
Notes
This function calculates trRosetta angles between pairs of residues. For more information, refer to the original trRosetta paper (https://pubmed.ncbi.nlm.nih.gov/31896580/).
- idpet.featurization.angles.featurize_tr_omega(traj, min_sep=2, max_sep=None, ravel=True, get_names=True)[source]
Calculate omega angles from trRosetta. These angles are torsion angles defined between a pair of residues i and j and involving the following atoms:
Ca(i) – Cb(i) – Cb(j) – Ca(j)
If a residue does not have a Cb atom, a pseudo-Cb will be added automatically.
Parameters
- traj: mdtraj.Trajectory
The MDTraj trajectory containing the protein structure.
- min_sep: int, optional
The minimum separation between residues for computing omega angles. Default is 2.
- max_sep: int, optional
The maximum separation between residues for computing omega angles. Default is None.
- ravel: bool, optional
If True, returns a flattened array of omega angle values. Default is True.
- get_names: bool, optional
If True, returns feature names along with the omega angles. Default is True.
Returns
- Union[np.ndarray, Tuple[np.ndarray, List[str]]]
If ravel is True, returns a flattened array of omega angle values. If ravel is False, returns a 3D array of omega angle values. If get_names is True, returns a tuple with feature names along with the omega angles.
Notes
This function calculates omega angles from trRosetta for a given MD trajectory.
- rtype:
Union
[ndarray
,Tuple
[ndarray
,List
[str
]]]
- idpet.featurization.angles.featurize_tr_phi(traj, min_sep=2, max_sep=None, ravel=True, get_names=True)[source]
Calculate phi angles from trRosetta. These angles are defined between a pair of residues i and j and involve the following atoms:
Ca(i) – Cb(i) – Cb(j)
If a residue does not have a Cb atom, a pseudo-Cb will be added automatically.
Parameters
- traj: mdtraj.Trajectory
The MDTraj trajectory containing the protein structure.
- min_sep: int, optional
The minimum separation between residues for computing phi angles. Default is 2.
- max_sep: int, optional
The maximum separation between residues for computing phi angles. Default is None.
- ravel: bool, optional
If True, returns a flattened array of phi angle values. Default is True.
- get_names: bool, optional
If True, returns feature names along with the phi angles. Default is True.
Returns
- Union[np.ndarray, Tuple[np.ndarray, List[str]]]
If ravel is True, returns a flattened array of phi angle values. If ravel is False, returns a 3D array of phi angle values. If get_names is True, returns a tuple with feature names along with the phi angles.
Notes
This function calculates phi angles from trRosetta for a given MD trajectory.
- rtype:
Union
[ndarray
,Tuple
[ndarray
,List
[str
]]]
idpet.featurization.distances module
- idpet.featurization.distances.calc_ca_dmap(traj, min_sep=1, max_sep=None)[source]
Calculate the (N, L, L) distance maps between C-alpha atoms for visualization.
- Return type:
ndarray
Parameters
- trajmdtraj.Trajectory
The MDtraj trajectory object.
Returns
- dmapnumpy.ndarray
The distance maps of shape (N, L, L), where N is the number of frames and L is the number of C-alpha atoms.
Notes
This function calculates the distance maps between C-alpha atoms for visualization purposes.
- idpet.featurization.distances.calc_com_dmap(traj, min_sep=1, max_sep=None)[source]
Calculate the (N, L, L) distance maps between center of mass (COM) atoms for visualization.
- Return type:
ndarray
Parameters
- trajmdtraj.Trajectory
The MDtraj trajectory object.
Returns
- dmapnumpy.ndarray
The distance maps of shape (N, L, L), where N is the number of frames and L is the number of center of mass (COM) atoms.
Notes
This function calculates the distance maps between center of mass (COM) atoms for visualization purposes.
- idpet.featurization.distances.featurize_ca_dist(traj, get_names=True, atom_selector='name CA', *args, **kwargs)[source]
Calculate C-alpha distances between pairs of residues.
- Return type:
Union
[ndarray
,Tuple
[ndarray
,List
[str
]]]
Parameters
- trajmdtraj.Trajectory
The MDtraj trajectory object.
- min_sepint, optional
The minimum sequence separation for distance calculations. Default is 2.
- max_sepint or None, optional
The maximum sequence separation for distance calculations. Default is None.
- inversebool, optional
Whether to calculate inverse distances. Default is False.
- get_namesbool, optional
Whether to return the names of the calculated features. Default is True.
- atom_selectorstr, optional
The atom selection string. Default is “name CA”.
Returns
- distancesnumpy.ndarray or Tuple
The calculated C-alpha distances. If get_names is True, returns a tuple containing distances and corresponding feature names.
Notes
This function calculates C-alpha distances between pairs of residues.
- idpet.featurization.distances.featurize_com_dist(traj, min_sep=2, max_sep=None, inverse=False, get_names=True, atom_selector='name == CA')[source]
Calculate center of mass (COM) distances between pairs of residues.
- Return type:
Union
[ndarray
,Tuple
[ndarray
,List
[str
]]]
Parameters
- trajmdtraj.Trajectory
The MDtraj trajectory object.
- min_sepint, optional
The minimum sequence separation for distance calculations. Default is 2.
- max_sepint or None, optional
The maximum sequence separation for distance calculations. Default is None.
- inversebool, optional
Whether to calculate inverse distances. Default is False.
- get_namesbool, optional
Whether to return the names of the calculated features. Default is True.
- atom_selectorstr, optional
The atom selection string. Default is “name == CA”.
Returns
- distancesnumpy.ndarray or Tuple
The calculated center of mass (COM) distances. If get_names is True, returns a tuple containing distances and corresponding feature names.
Notes
This function calculates center of mass (COM) distances between pairs of residues.
idpet.featurization.ensemble_level module
Calculate features at the ensemble level.
- idpet.featurization.ensemble_level.calc_flory_scaling_exponent(traj)[source]
- Return type:
Tuple
[float
]
Calculate the apparent Flory scaling exponent in an ensemble. Code adapted from:
Arguments
- trajmdtraj.Trajectory
Input trajectory object.
Returns
- resuts: tuple
Tuple containing the nu (Flory scaling exponent), error on nu, R0 and error on R0. All values are calculated by fitting the internal scaling profiles. For more information see https://pubmed.ncbi.nlm.nih.gov/38297118/ and https://pubs.acs.org/doi/full/10.1021/acs.jpcb.3c01619.
- idpet.featurization.ensemble_level.calc_flory_scaling_exponent_cg(traj)[source]
- Return type:
Tuple
[float
]
Calculate the apparent Flory scaling exponent in an ensemble. Code adapted from:
Arguments
- trajmdtraj.Trajectory
Input trajectory object.
Returns
- resuts: tuple
Tuple containing the nu (Flory scaling exponent), error on nu, R0 and error on R0. All values are calculated by fitting the internal scaling profiles. For more information see https://pubmed.ncbi.nlm.nih.gov/38297118/ and https://pubs.acs.org/doi/full/10.1021/acs.jpcb.3c01619.
idpet.featurization.glob module
idpet.featurization.utils module
- idpet.featurization.utils.get_max_sep(L, max_sep)[source]
Get the maximum separation between indices.
- Return type:
int
Parameters
- Lint
The size of the matrix.
- max_sepUnion[None, int, float]
The maximum separation between indices.
Returns
- int
The maximum separation between indices.
Notes
This function calculates the maximum separation between indices based on the size of the matrix and the provided maximum separation value.
- idpet.featurization.utils.get_triu_indices(L, min_sep=1, max_sep=None)[source]
Get the upper triangle indices of a square matrix with specified minimum and maximum separations.
- Return type:
List
[list
]
Parameters
- Lint
The size of the square matrix.
- min_sepint, optional
The minimum separation between indices. Default is 1.
- max_sepUnion[None, int, float], optional
The maximum separation between indices. Default is None.
Returns
- List[list]
A list of lists containing the upper triangle indices of the square matrix.
Notes
This function returns the upper triangle indices of a square matrix with the specified minimum and maximum separations.