From a0cf7b5945134e7ed41467ba1a6744263407865e Mon Sep 17 00:00:00 2001 From: Rafal Gumienny <r.gumienny@unibas.ch> Date: Thu, 26 Apr 2018 15:24:29 +0200 Subject: [PATCH] docs: SCHWED-3132 Update function documentation that do not use lDDTSettings anymore --- modules/mol/alg/doc/molalg.rst | 25 ++++++++++++--------- modules/mol/alg/src/local_dist_diff_test.hh | 2 +- 2 files changed, 16 insertions(+), 11 deletions(-) diff --git a/modules/mol/alg/doc/molalg.rst b/modules/mol/alg/doc/molalg.rst index dfa77bc36..fd9490a52 100644 --- a/modules/mol/alg/doc/molalg.rst +++ b/modules/mol/alg/doc/molalg.rst @@ -306,7 +306,7 @@ Local Distance Test scores (lDDT, DRMSD) :returns: :class:`~ost.mol.alg.GlobalRDMap` -.. function:: PreparelDDTGlobalRDMap(reference_list, settings) +.. function:: PreparelDDTGlobalRDMap(reference_list, cutoff_list, sequence_separation, max_dist) A wrapper around :func:`CreateDistanceList` and :func:`CreateDistanceListFromMultipleReferences`. Depending on the length of @@ -315,9 +315,12 @@ Local Distance Test scores (lDDT, DRMSD) :param reference_list: a list of reference structures from which distances are derived :type reference_list: list of :class:`~ost.mol.EntityView` - :param settings: lDDT settings - :type settings: :class:`~ost.mol.alg.lDDTSettings` - + :param max_dist: the inclusion radius in Angstroms (to determine which + distances are checked for conservation) + :type max_dist: :class:`float` + :param sequence_separation: sequence separation parameter ie. maximum distance + between two sequences. + :type sequence_separation: :class:`int` :returns: :class:`~ost.mol.alg.GlobalRDMap` @@ -361,7 +364,7 @@ Local Distance Test scores (lDDT, DRMSD) :type angle_tolerance: float -.. function:: GetlDDTPerResidueStats(model, distance_list, settings) +.. function:: GetlDDTPerResidueStats(model, distance_list, structural_checks, label) Get the per-residue statistics from the lDDT calculation. @@ -369,20 +372,22 @@ Local Distance Test scores (lDDT, DRMSD) :type model: :class:`~ost.mol.EntityHandle` :param distance_list: The list of distances to check for conservation :type distance_list: :class:`~ost.mol.alg.GlobalRDMap` - :param settings: lDDT settings - :type settings: :class:`~ost.mol.alg.lDDTSettings` + :param structural_checks: Where structural checks performed on the model? + :type structural_checks: bool :returns: Per-residue local lDDT scores :rtype: :class:`list` of :class:`~ost.mol.alg.lDDTLocalScore` -.. function:: PrintlDDTPerResidueStats(scores, settings) +.. function:: PrintlDDTPerResidueStats(scores, structural_checks, cutoffs_length) Print per-residue statistics from lDDT calculation. :param scores: Local lDDT scores :type scores: :class:`list` of :class:`~ost.mol.alg.lDDTLocalScore` - :param settings: lDDT settings - :type settings: :class:`~ost.mol.alg.lDDTSettings` + :param structural_checks: Where structural checks performed on the model? + :type structural_checks: bool + :param cutoffs_length: Length of the cutoffs list used to calculate lDDT + :type cutoffs_length: int .. class:: lDDTLocalScore(cname, rname, rnum, is_assessed, quality_problems, \ diff --git a/modules/mol/alg/src/local_dist_diff_test.hh b/modules/mol/alg/src/local_dist_diff_test.hh index b32d66301..916fe4fac 100644 --- a/modules/mol/alg/src/local_dist_diff_test.hh +++ b/modules/mol/alg/src/local_dist_diff_test.hh @@ -168,7 +168,7 @@ Real DLLEXPORT_OST_MOL_ALG LocalDistDiffTest(const EntityView& mdl, Real cutoff, Real max_dist, const String& local_ldt_property_string=""); -/// TODO document me +/// \brief Wrapper around LocalDistDiffTest Real DLLEXPORT_OST_MOL_ALG LocalDistDiffTest(const EntityView& v, std::vector<EntityView>& ref_list, const GlobalRDMap& glob_dist_list, -- GitLab