From 240d5fb6b44b8fa3ea554ad47e6fc9e711cb42be Mon Sep 17 00:00:00 2001 From: Pat Riley Date: Mon, 25 Aug 2025 10:56:59 -0400 Subject: [PATCH] Update documentation for rdShapeAlign.AlignMol opt_param (#8724) * Update documentation for opt_param * Revert default to 1.0 * revert all 0.5 default changes --- External/pubchem_shape/Wrap/cshapealign.cpp | 19 +++++++++++++++++-- 1 file changed, 17 insertions(+), 2 deletions(-) diff --git a/External/pubchem_shape/Wrap/cshapealign.cpp b/External/pubchem_shape/Wrap/cshapealign.cpp index e84380308..3e8a7d0c5 100644 --- a/External/pubchem_shape/Wrap/cshapealign.cpp +++ b/External/pubchem_shape/Wrap/cshapealign.cpp @@ -197,8 +197,13 @@ probeConfId : int, optional useColors : bool, optional Whether or not to use colors in the scoring (default is True) opt_param : float, optional + Balance of shape and color for optimization. + 0 is only color, 0.5 is equal weight, and 1.0 is only shape max_preiters : int, optional + In the two phase optimization, the maximum iterations done on all poses. max_postiters : int, optional + In the two phase optimization, the maximum iterations during the second phase on + only the best poses from the first phase Returns @@ -226,9 +231,14 @@ probeConfId : int, optional Probe conformer ID (default is -1) useColors : bool, optional Whether or not to use colors in the scoring (default is True) -optParam : float, optional +opt_param : float, optional + Balance of shape and color for optimization. + 0 is only color, 0.5 is equal weight, and 1.0 is only shape max_preiters : int, optional + In the two phase optimization, the maximum iterations done on all poses. max_postiters : int, optional + In the two phase optimization, the maximum iterations during the second phase on + only the best poses from the first phase applyRefShift : bool, optional If True, apply the reference shape's shift translation to the final coordinates. @@ -254,8 +264,13 @@ refShape : ShapeInput probeShape : ShapeInput Probe shape opt_param : float, optional + Balance of shape and color for optimization. + 0 is only color, 0.5 is equal weight, and 1.0 is only shape max_preiters : int, optional + In the two phase optimization, the maximum iterations done on all poses. max_postiters : int, optional + In the two phase optimization, the maximum iterations during the second phase on + only the best poses from the first phase Returns @@ -315,4 +330,4 @@ Returns .def_readwrite("sof", &ShapeInput::sof); } -BOOST_PYTHON_MODULE(rdShapeAlign) { wrap_pubchemshape(); } \ No newline at end of file +BOOST_PYTHON_MODULE(rdShapeAlign) { wrap_pubchemshape(); }