diff --git a/chilife/RotamerEnsemble.py b/chilife/RotamerEnsemble.py index 741a3673..c8d465b3 100755 --- a/chilife/RotamerEnsemble.py +++ b/chilife/RotamerEnsemble.py @@ -33,11 +33,10 @@ class RotamerEnsemble: rotlib : str Rotamer library to use for constructing the RotamerEnsemble **kwargs : dict - minimize: bool - Switch to turn on/off minimization. During minimization each rotamer is optimized in dihedral space - with respect to both internal and external clashes, and deviation from the starting conformation in - dihedral space. + Switch to turn on/off minimization. During minimization each rotamer is optimized in dihedral space + with respect to both internal and external clashes, and deviation from the starting conformation in + dihedral space. min_method: str Name of the minimization algorithm to use. All ``scipy.optimize.minimize`` algorithms are available and include: ‘Nelder-Mead’, ‘Powell’, ‘CG’, ‘BFGS’, ‘Newton-CG’, ‘L-BFGS-B’, ‘TNC’, ‘COBYLA’, ‘SLSQP’, @@ -52,44 +51,6 @@ class RotamerEnsemble: Python function or callable object that takes a protein and a RotamerEnsemble object as input and returns an energy value (kcal/mol) for each atom of each rotamer in the ensemble. See also :mod:`Scoring ` . Defaults to :mod:`chiLife.get_lj_rep ` . - forgive : float - Softening factor to be passed to ``energy_func``. Only used if ``energy_func`` uses a softening factor. - Defaults to 1.0. See :mod:`Scoring ` . - temp : float - Temperature to use when running ``energy_func``. Only used if ``energy_func`` accepts a temperature - argument Defaults to 298 K. - clash_radius : float - Cutoff distance (angstroms) for inclusion of atoms in clash evaluations. This distance is measured from - ``clash_ori`` Defaults to the longest distance between any two atoms in the rotamer ensemble plus 5 - angstroms. - clash_ori : str - Atom selection to use as the origin when finding atoms within the ``clash_radius``. Defaults to 'cen', - the centroid of the rotamer ensemble heavy atoms. - protein_tree : Scipy.spatial.cKDTree - KDTree of atom positions for fast distance calculations and neighbor detection. Defaults to None - trim: bool - When true, the lowest `trim_tol` fraction of rotamers in the ensemble will be removed. - trim_tol: float - Tolerance for trimming rotamers from the ensemble. trim_tol=0.005 means the bottom 0.5% of rotamers - will be removed. - alignment_method : str - Method to use when attaching or aligning the rotamer ensemble backbone with the protein backbone. - Defaults to ``'bisect'`` which aligns the CA atom, the vectors bisecting the N-CA-C angle and the - N-CA-C plane. - dihedral_sigmas : float, numpy.ndarray - Standard deviations of dihedral angles (degrees) for off rotamer sampling. Can be a single number for - isotropic sampling, a vector to define each dihedral individually or a matrix to define a value for - each rotamer and each dihedral. Setting this value to np.inf will force uniform (accessible volume) - sampling. Defaults to 35 degrees. - weighted_sampling : bool - Determines whether the rotamer ensemble is sampled uniformly or based off of their intrinsic weights. - Defaults to False. - use_H : bool - Determines if hydrogen atoms are used or not. Defaults to False. - - - protein_tree : Scipy.spatial.cKDTree - KDTree of atom positions for fast distance calculations and neighbor detection. Defaults to None forgive : float Softening factor to be passed to ``energy_func``. Only used if ``energy_func`` uses a softening factor. Defaults to 1.0. See :mod:`Scoring ` . @@ -103,10 +64,20 @@ class RotamerEnsemble: clash_ori : str Atom selection to use as the origin when finding atoms within the ``clash_radius``. Defaults to 'cen', the centroid of the rotamer ensemble heavy atoms. + protein_tree : Scipy.spatial.cKDTree + KDTree of atom positions for fast distance calculations and neighbor detection. Defaults to None + trim: bool + When true, the lowest `trim_tol` fraction of rotamers in the ensemble will be removed. + trim_tol: float + Tolerance for trimming rotamers from the ensemble. trim_tol=0.005 means the bottom 0.5% of rotamers + will be removed. alignment_method : str Method to use when attaching or aligning the rotamer ensemble backbone with the protein backbone. Defaults to ``'bisect'`` which aligns the CA atom, the vectors bisecting the N-CA-C angle and the N-CA-C plane. + sample : int, bool + Argument to use the off-rotamer sampling method. If ``False`` or ``0`` the off-rotamer sampling method + will not be used. If ``int`` the ensemble will be generated with that many off-rotamer samples. dihedral_sigmas : float, numpy.ndarray Standard deviations of dihedral angles (degrees) for off rotamer sampling. Can be a single number for isotropic sampling, a vector to define each dihedral individually or a matrix to define a value for @@ -117,14 +88,6 @@ class RotamerEnsemble: Defaults to False. use_H : bool Determines if hydrogen atoms are used or not. Defaults to False. - - sample : int, bool - Argument to use the off-rotamer sampling method. If ``False`` or ``0`` the off-rotamer sampling method - will not be used. If ``int`` the ensemble will be generated with that many off-rotamer samples. - energy_func : callable - Python function or callable object that takes a protein and a RotamerEnsemble object as input and - returns an energy value (kcal/mol) for each atom of each rotamer in the ensemble. See also - :mod:`Scoring ` . Defaults to :mod:`chiLife.get_lj_rep ` . """