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//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library is free software; you can redistribute it and/or modify it under
// the terms of the GNU Lesser General Public License as published by the Free
// Software Foundation; either version 3.0 of the License, or (at your option)
// any later version.
// This library is distributed in the hope that it will be useful, but WITHOUT
// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
// details.
//
// You should have received a copy of the GNU Lesser General Public License
// along with this library; if not, write to the Free Software Foundation, Inc.,
// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
//------------------------------------------------------------------------------
/*
* Author Juergen Haas
*/
#include <ost/mol/alg/svd_superpose.hh>
#define BOOST_TEST_DYN_LINK
#include <boost/test/unit_test.hpp>
#include <ost/mol/mol.hh>
#include <ost/mol/builder.hh>
#include <ost/message.hh>
using namespace ost;
using namespace ost::mol;
using namespace ost::mol::alg;
struct Fixture {
Fixture() {
e = Builder()
.Chain("A")
.Residue("DUM")
.Atom("A",geom::Vec3(-5,-5,-5))
.Atom("B",geom::Vec3(-5, 5,-5))
.Atom("C",geom::Vec3(-5, 5, 5))
.Atom("D",geom::Vec3(-5,-5, 5))
.Atom("E",geom::Vec3(5,-5, 5))
.Atom("F",geom::Vec3(5,-5,-5))
.Atom("G",geom::Vec3(5, 5,-5))
.Atom("H",geom::Vec3(5, 5, 5));
}
EntityHandle e;
};
BOOST_AUTO_TEST_SUITE( mol_alg );
BOOST_AUTO_TEST_CASE(superposition_svd)
{
Fixture f1, f2;
EntityView ev1 = f1.e.CreateFullView();
XCSEditor ed=f1.e.EditXCS();
EntityView ev2 = f2.e.CreateFullView();
AtomHandleList atoms = f1.e.GetAtomList();
for (AtomHandleList::const_iterator i = atoms.begin(), e = atoms.end(); i !=e ; ++i) {
AtomHandle atom=*i;
ed.SetAtomPos(atom, geom::EulerTransformation(0.1, 0, 0)*atom.GetPos()
+geom::Vec3(0, 5, 0));
}
SuperpositionResult res;
res=SuperposeSVD(ev1, ev2, true);
BOOST_CHECK(res.rmsd<0.0001);
}
BOOST_AUTO_TEST_CASE(iterative_superposition_svd)
{
Fixture f1, f2;
EntityView ev1 = f1.e.CreateFullView();
EntityView ev2 = f2.e.CreateFullView();
XCSEditor ed=f1.e.EditXCS();
AtomHandleList atoms = f1.e.GetAtomList();
ed.SetAtomPos(atoms[0],geom::Vec3(-10,-10,-10));
for (AtomHandleList::const_iterator i = atoms.begin(), e = atoms.end(); i !=e ; ++i) {
AtomHandle atom=*i;
ed.SetAtomPos(atom, geom::EulerTransformation(0.1, 0, 0)*atom.GetPos()
+geom::Vec3(0, 5, 0));
}
SuperpositionResult res_classic, res_1, res_2, res_3;
res_1=IterativeSuperposeSVD(ev1, ev2, 1, 5.0, false);
res_2=IterativeSuperposeSVD(ev1, ev2, 2, 5.0, false);
res_3=IterativeSuperposeSVD(ev1, ev2, 10, 5.0, false);
res_classic=SuperposeSVD(ev1,ev2, false);
BOOST_CHECK(res_2.rmsd_superposed_atoms<0.0001);
BOOST_CHECK(res_2.rmsd>1.0);
BOOST_CHECK(res_1.rmsd==res_classic.rmsd);
BOOST_CHECK(res_1.ncycles==1);
BOOST_CHECK(res_2.ncycles==2);
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);
}
BOOST_AUTO_TEST_SUITE_END();
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