diff --git a/modules/mol/alg/doc/molalg.rst b/modules/mol/alg/doc/molalg.rst index d4b71376c848fc14e9e0dcb1abecb7421e8debc1..237a5c3444d3ec8f1300e04477d9acc8c59c19d2 100644 --- a/modules/mol/alg/doc/molalg.rst +++ b/modules/mol/alg/doc/molalg.rst @@ -467,42 +467,18 @@ Local Distance Test scores (lDDT, DRMSD) :type cutoffs_length: int -.. class:: lDDTSettings(bond_tolerance=12, \ - angle_tolerance=12, \ - radius=15, \ +.. class:: lDDTSettings(radius=15, \ sequence_separation=0, \ - sel="", \ - parameter_file_path="", \ - structural_checks=True, \ - consistency_checks=True, \ cutoffs=(0.5, 1.0, 2.0, 4.0), \ label="locallddt") Object containing the settings used for lDDT calculations. - :param bond_tolerance: Sets :attr:`bond_tolerance`. - :param angle_tolerance: Sets :attr:`angle_tolerance`. :param radius: Sets :attr:`radius`. :param sequence_separation: Sets :attr:`sequence_separation`. - :param sel: Sets :attr:`sel`. - :param parameter_file_path: Sets :attr:`parameter_file_path`. - :param structural_checks: Sets :attr:`structural_checks`. - :param consistency_checks: Sets :attr:`consistency_checks`. :param cutoffs: Sets :attr:`cutoffs`. :param label: Sets :attr:`label`. - .. attribute:: bond_tolerance - - Tolerance in stddevs for bonds. - - :type: :class:`float` - - .. attribute:: angle_tolerance - - Tolerance in stddevs for angles. - - :type: :class:`float` - .. attribute:: radius Distance inclusion radius. @@ -515,32 +491,6 @@ Local Distance Test scores (lDDT, DRMSD) :type: :class:`int` - .. attribute:: sel - - Selection performed on reference(s). - - :type: :class:`str` - - .. attribute:: parameter_file_path - - Path to the stereochemical parameter file. If set to "", it the default file - shipped with OpenStructure is used (see - :class:`~ost.io.StereoChemicalParamsReader`). - - :type: :class:`str` - - .. attribute:: structural_checks - - Are structural checks and filter input data on? - - :type: :class:`bool` - - .. attribute:: consistency_checks - - Are consistency checks on? - - :type: :class:`bool` - .. attribute:: cutoffs List of thresholds used to determine distance conservation. @@ -553,13 +503,6 @@ Local Distance Test scores (lDDT, DRMSD) :type: :class:`str` - .. method:: SetStereoChemicalParamsPath(path) - - Set the path to the stereochemical parameter file. - - :param path: Path to stereochemical parameter file - :type path: str - .. method:: PrintParameters() Print settings. @@ -1840,4 +1783,4 @@ API :param ent: Structure to check :type ent: :class:`~ost.mol.EntityHandle` :param lib: Compound library - :type lib: :class:`~ost.conop.CompoundLib` \ No newline at end of file + :type lib: :class:`~ost.conop.CompoundLib`