From 5c668e4ec5b82bc4a545c4b1409619556b1f8f1f Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@stud.unibas.ch>
Date: Fri, 7 Jun 2013 15:54:10 +0200
Subject: [PATCH] ost crashed, if not enough atoms fulfilled the distance
threshold to build superposable subsets. At least three atoms are required.
This scenario gets now checked and an error is thrown.
---
modules/mol/alg/src/svd_superpose.cc | 7 +++++++
modules/mol/alg/tests/test_superposition.cc | 23 ++++++++++++++++++++-
2 files changed, 29 insertions(+), 1 deletion(-)
diff --git a/modules/mol/alg/src/svd_superpose.cc b/modules/mol/alg/src/svd_superpose.cc
index a1181ba29..fbc69cd1d 100644
--- a/modules/mol/alg/src/svd_superpose.cc
+++ b/modules/mol/alg/src/svd_superpose.cc
@@ -289,6 +289,13 @@ SuperpositionResult MeanSquareMinimizerImpl::IterativeMinimize(int max_cycles, R
transformed_atoms = this->TransformEMatX(atoms1_, transformation_matrix);
matching_indices = this->CreateMatchingSubsets(transformed_atoms, atoms2_, distance_threshold);
+ if(matching_indices.size()<3){
+ std::stringstream ss;
+ ss<<"Failed to Converge, less than 3 superposable atoms in iteration ";
+ ss<<cycles<<"!";
+ throw Error(ss.str());
+ }
+
subset1 = EMatX::Zero(matching_indices.size(),3);
subset2 = EMatX::Zero(matching_indices.size(),3);
diff --git a/modules/mol/alg/tests/test_superposition.cc b/modules/mol/alg/tests/test_superposition.cc
index 3196c5d9f..e3c88d647 100644
--- a/modules/mol/alg/tests/test_superposition.cc
+++ b/modules/mol/alg/tests/test_superposition.cc
@@ -25,7 +25,8 @@
#include <boost/test/unit_test.hpp>
#include <boost/test/auto_unit_test.hpp>
#include <ost/mol/mol.hh>
- #include <ost/mol/builder.hh>
+#include <ost/mol/builder.hh>
+#include <ost/message.hh>
using namespace ost;
using namespace ost::mol;
@@ -96,6 +97,26 @@ BOOST_AUTO_TEST_CASE(iterative_superposition_svd)
BOOST_CHECK(res_1.fraction_superposed==1.0);
BOOST_CHECK(res_2.fraction_superposed==7.0/8.0);
BOOST_CHECK(res_3.ncycles==3);
+
+ EntityHandle eh_2_atoms = Builder()
+ .Chain("A")
+ .Residue("D")
+ .Atom("A",geom::Vec3(0,0,0))
+ .Atom("B",geom::Vec3(0,0,0));
+
+ //Error, that has to be thrown during initialization of superposition object
+ BOOST_CHECK_THROW(IterativeSuperposeSVD(eh_2_atoms.CreateFullView(),
+ eh_2_atoms.CreateFullView(),
+ 1,5.0,false), Error);
+
+ //forces an error, since there won't be enough atoms within the distance
+ //threshold after the first superposition.
+ ed.SetAtomPos(atoms[0],geom::Vec3(50,50,50));
+ ed.SetAtomPos(atoms[1],geom::Vec3(50,50,50));
+ ed.SetAtomPos(atoms[2],geom::Vec3(50,50,50));
+ ed.SetAtomPos(atoms[3],geom::Vec3(50,50,50));
+
+ BOOST_CHECK_THROW(IterativeSuperposeSVD(ev1, ev2, 5, 5.0, false), Error);
}
--
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