From b394465770740840decf1a0080d3b2bb61ac77a2 Mon Sep 17 00:00:00 2001
From: ansgar <ansgar@5a81b35b-ba03-0410-adc8-b2c5c5119f08>
Date: Wed, 28 Apr 2010 02:31:31 +0000
Subject: [PATCH] added generic pointlist -> pointlist superposition
git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2123 5a81b35b-ba03-0410-adc8-b2c5c5119f08
---
modules/mol/alg/pymod/export_svd_superpose.cc | 5 ++-
modules/mol/alg/src/svd_superpose.cc | 35 +++++++++++++++++++
modules/mol/alg/src/svd_superpose.hh | 7 ++++
3 files changed, 46 insertions(+), 1 deletion(-)
diff --git a/modules/mol/alg/pymod/export_svd_superpose.cc b/modules/mol/alg/pymod/export_svd_superpose.cc
index 435744e52..3acdc6f6b 100644
--- a/modules/mol/alg/pymod/export_svd_superpose.cc
+++ b/modules/mol/alg/pymod/export_svd_superpose.cc
@@ -30,6 +30,8 @@ using namespace ost::mol::alg;
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;
class_<SuperpositionResult>("SuperpositionResult", init<>())
.def_readwrite("ncycles", &SuperpositionResult::ncycles)
.def_readwrite("rmsd", &SuperpositionResult::rmsd)
@@ -41,7 +43,8 @@ void export_svdSuperPose()
&SuperpositionResult::entity_view2)
;
def("SuperposeAtoms", &SuperposeAtoms,(arg("apply_transform")=true));
- def("SuperposeSVD", &SuperposeSVD, (arg("apply_transform")=true));
+ def("SuperposeSVD", sup1);
+ def("SuperposeSVD", sup2);
def("CalculateRMSD", &CalculateRMSD, (arg("transformation")=geom::Mat4()));
def("IterativeSuperposition", &IterativeSuperposition, (arg("ncycles")=200,
arg("dist_thres")=4.0,
diff --git a/modules/mol/alg/src/svd_superpose.cc b/modules/mol/alg/src/svd_superpose.cc
index 2f770167f..191871a9c 100644
--- a/modules/mol/alg/src/svd_superpose.cc
+++ b/modules/mol/alg/src/svd_superpose.cc
@@ -131,6 +131,8 @@ public:
ERVecX Vec);
SuperpositionResult Run(const mol::AtomViewList& atoms1,
const mol::AtomViewList& atoms2);
+ SuperpositionResult Run(const std::vector<geom::Vec3>& pl1,
+ const std::vector<geom::Vec3>& pl2);
SuperpositionResult DoSuperposition();
EIGEN_MAKE_ALIGNED_OPERATOR_NEW //needed only if *fixed* sized matrices are
//members of classes
@@ -295,6 +297,12 @@ SuperpositionResult SuperposerSVD::Run(const mol::AtomViewList& atoms1,
return impl_->Run(atoms1, atoms2);
}
+SuperpositionResult SuperposerSVD::Run(const std::vector<geom::Vec3>& pl1,
+ const std::vector<geom::Vec3>& pl2)
+{
+ return impl_->Run(pl1,pl2);
+}
+
SuperpositionResult SuperposerSVDImpl::Run(const mol::AtomViewList& atoms1,
const mol::AtomViewList& atoms2)
{
@@ -315,6 +323,15 @@ SuperpositionResult SuperposerSVDImpl::Run(const mol::AtomViewList& atoms1,
return this->DoSuperposition();
}
+SuperpositionResult SuperposerSVDImpl::Run(const std::vector<geom::Vec3>& pl1,
+ const std::vector<geom::Vec3>& pl2)
+{
+ for (unsigned int counter=0; counter<pl1.size();++counter) {
+ atoms1_.row(counter)=ERVec3(SuperposerSVDImpl::Vec3ToEigenVec(pl1[counter]));
+ atoms2_.row(counter)=ERVec3(SuperposerSVDImpl::Vec3ToEigenVec(pl2[counter]));
+ }
+ return this->DoSuperposition();
+}
SuperpositionResult SuperposeAtoms(const mol::AtomViewList& atoms1,
@@ -370,6 +387,24 @@ SuperpositionResult SuperposeSVD(const mol::EntityView& ev1,
return res;
}
+SuperpositionResult SuperposeSVD(const std::vector<geom::Vec3>& pl1,
+ const std::vector<geom::Vec3>& pl2)
+{
+ if (pl1.size()!=pl2.size()){
+ throw std::runtime_error("pointlist lengths not equal");
+ }
+ if ((pl1.size()<3)){
+ throw std::runtime_error("three or more points required");
+ }
+ SuperposerSVD sp(pl1.size(), true);
+ SuperpositionResult res=sp.Run(pl1, pl2);
+ res.entity_view1=EntityView();
+ res.entity_view2=EntityView();
+ res.ncycles=1;
+ res.rmsd=0.0;
+ return res;
+}
+
SuperpositionResult IterativeSuperposition(mol::EntityView& ev1,
mol::EntityView& ev2,
int ncycles,
diff --git a/modules/mol/alg/src/svd_superpose.hh b/modules/mol/alg/src/svd_superpose.hh
index 80f076278..1b3f5e29a 100644
--- a/modules/mol/alg/src/svd_superpose.hh
+++ b/modules/mol/alg/src/svd_superpose.hh
@@ -59,6 +59,9 @@ public:
SuperpositionResult Run(const mol::AtomViewList& atoms1,
const mol::AtomViewList& atoms2);
+ SuperpositionResult Run(const std::vector<geom::Vec3>& pl1,
+ const std::vector<geom::Vec3>& pl2);
+
private:
SuperposerSVDImpl* impl_;
};
@@ -72,6 +75,10 @@ SuperpositionResult DLLEXPORT_OST_MOL_ALG SuperposeSVD(const mol::EntityView& ev
const mol::EntityView& ev2,
bool apply_transform);
+/// \brief superposes two pointlists
+SuperpositionResult DLLEXPORT_OST_MOL_ALG SuperposeSVD(const std::vector<geom::Vec3>& pl1,
+ const std::vector<geom::Vec3>& pl2);
+
/// \brief iterative superposition
SuperpositionResult DLLEXPORT_OST_MOL_ALG IterativeSuperposition(mol::EntityView& ev1,
mol::EntityView& ev2,
--
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