From 4e4c273b8402280a15559cc675689e0332c75f19 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@stud.unibas.ch>
Date: Thu, 23 May 2013 15:32:56 +0200
Subject: [PATCH] added possibility to superpose two vectors of Vec3
---
modules/mol/alg/pymod/export_svd_superpose.cc | 5 ++++-
modules/mol/alg/src/svd_superpose.cc | 11 +++++++++++
modules/mol/alg/src/svd_superpose.hh | 8 ++++++++
3 files changed, 23 insertions(+), 1 deletion(-)
diff --git a/modules/mol/alg/pymod/export_svd_superpose.cc b/modules/mol/alg/pymod/export_svd_superpose.cc
index 9c4087021..d5f942fe7 100644
--- a/modules/mol/alg/pymod/export_svd_superpose.cc
+++ b/modules/mol/alg/pymod/export_svd_superpose.cc
@@ -36,6 +36,8 @@ void export_svdSuperPose()
{
SuperpositionResult (*sup1)(const mol::EntityView&,const mol::EntityView&,bool) = SuperposeSVD;
SuperpositionResult (*sup2)(const std::vector<geom::Vec3>&,const std::vector<geom::Vec3>& ) = SuperposeSVD;
+ SuperpositionResult (*sup3)(const mol::EntityView&,const mol::EntityView&, int, Real, bool) = IterativeSuperposeSVD;
+ SuperpositionResult (*sup4)(const std::vector<geom::Vec3>&,const std::vector<geom::Vec3>&, int, Real) = IterativeSuperposeSVD;
class_<SuperpositionResult>("SuperpositionResult", init<>())
.def_readwrite("ncycles", &SuperpositionResult::ncycles)
.def_readwrite("rmsd", &SuperpositionResult::rmsd)
@@ -51,7 +53,8 @@ void export_svdSuperPose()
def("SuperposeAtoms", &SuperposeAtoms,(arg("apply_transform")=true));
def("SuperposeSVD", sup1, (arg("apply_transform")=true));
def("SuperposeSVD", sup2, (arg("apply_transform")=true));
- def("IterativeSuperposeSVD", &IterativeSuperposeSVD,(arg("max_iterations")=5, arg("distance_threshold")=3.0,arg("apply_transform")=true));
+ def("IterativeSuperposeSVD", sup3,(arg("max_iterations")=5, arg("distance_threshold")=3.0,arg("apply_transform")=true));
+ def("IterativeSuperposeSVD", sup4,(arg("max_iterations")=5, arg("distance_threshold")=3.0));
def("CalculateRMSD", &CalculateRMSD, (arg("transformation")=geom::Mat4()));
}
diff --git a/modules/mol/alg/src/svd_superpose.cc b/modules/mol/alg/src/svd_superpose.cc
index 38dd51202..c5279eb35 100644
--- a/modules/mol/alg/src/svd_superpose.cc
+++ b/modules/mol/alg/src/svd_superpose.cc
@@ -498,5 +498,16 @@ SuperpositionResult IterativeSuperposeSVD(const mol::EntityView& ev,
return result;
}
+SuperpositionResult DLLEXPORT_OST_MOL_ALG IterativeSuperposeSVD(const std::vector<geom::Vec3>& pl1,
+ const std::vector<geom::Vec3>& pl2,
+ int max_cycles,
+ Real distance_threshold){
+
+ MeanSquareMinimizer msm = MeanSquareMinimizer::FromPointLists(pl1, pl2);
+ SuperpositionResult result = msm.IterativeMinimize(max_cycles, distance_threshold);
+ result.rmsd = calc_rmsd_for_point_lists(pl1, pl2, result.transformation);
+ return result;
+}
+
}}} //ns
diff --git a/modules/mol/alg/src/svd_superpose.hh b/modules/mol/alg/src/svd_superpose.hh
index bdbaf505d..28ee7a0d4 100644
--- a/modules/mol/alg/src/svd_superpose.hh
+++ b/modules/mol/alg/src/svd_superpose.hh
@@ -102,6 +102,14 @@ SuperpositionResult DLLEXPORT_OST_MOL_ALG IterativeSuperposeSVD(const mol::Entit
Real distance_threshold,
bool apply_transform);
+/// \brief iterative superposition of two point lists
+SuperpositionResult DLLEXPORT_OST_MOL_ALG IterativeSuperposeSVD(const std::vector<geom::Vec3>& pl1,
+ const std::vector<geom::Vec3>& pl2,
+ int max_cycles,
+ Real distance_threshold);
+
+
+
/// \brief calculates RMSD for two entity view
Real DLLEXPORT_OST_MOL_ALG CalculateRMSD(const mol::EntityView& ev1,
const mol::EntityView& ev2,
--
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