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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
//------------------------------------------------------------------------------
/*
* Authors: Marco Biasini, Juergen Haas
*/
#define BOOST_TEST_DYN_LINK
#include <boost/test/unit_test.hpp>
#include <ost/mol/mol.hh>
#include <ost/message.hh>
using namespace ost;
using namespace ost::mol;
BOOST_AUTO_TEST_SUITE( mol_base );
BOOST_AUTO_TEST_CASE(test_in_sequence)
{
EntityHandle eh=CreateEntity();
XCSEditor e=eh.EditXCS();
ChainHandle ch1=e.InsertChain("A");
ResidueHandle rA = e.AppendResidue(ch1, "A");
ResidueHandle rB = e.AppendResidue(ch1, "B");
ResidueHandle rC = e.AppendResidue(ch1, "C");
BOOST_CHECK(!InSequence(rA,rB));
BOOST_CHECK(!InSequence(rB,rC));
BOOST_CHECK(!InSequence(rA,rC));
}
BOOST_AUTO_TEST_CASE(test_res_index_bzdng227)
{
EntityHandle eh=CreateEntity();
XCSEditor e=eh.EditXCS();
ChainHandle ch1=e.InsertChain("A");
ResidueHandle ra = e.AppendResidue(ch1, "A", 1);
ResidueHandle rb = e.AppendResidue(ch1, "B", 2);
ResidueHandle rc = e.AppendResidue(ch1, "C", 1);
BOOST_CHECK_EQUAL(ra.GetIndex(), 0);
BOOST_CHECK_EQUAL(rb.GetIndex(), 1);
BOOST_CHECK_EQUAL(rc.GetIndex(), 2);
}
BOOST_AUTO_TEST_CASE(throw_invalid_res_handle)
{
ChainHandle chain;
EntityHandle ent=CreateEntity();
XCSEditor edi=ent.EditXCS();
chain=edi.InsertChain("A");
ResidueHandle res=chain.FindResidue(ResNum(1));
BOOST_CHECK_THROW(CheckHandleValidity(res), InvalidHandle);
edi.AppendResidue(chain, "GLY");
res=chain.FindResidue(ResNum(1));
BOOST_CHECK_NO_THROW(CheckHandleValidity(res));
}
BOOST_AUTO_TEST_CASE(throw_invalid_res_view)
{
ChainHandle chain;
EntityHandle ent=CreateEntity();
XCSEditor edi=ent.EditXCS();
chain=edi.InsertChain("A");
ResidueView res;
BOOST_CHECK_THROW(CheckHandleValidity(res), InvalidHandle);
edi.AppendResidue(chain, "GLY");
EntityView ent_view=ent.CreateFullView();
res=ent_view.FindChain("A").FindResidue(1);
BOOST_CHECK_NO_THROW(CheckHandleValidity(res));
}
// Test that .GetHashCode() throws on invalid residue handle
BOOST_AUTO_TEST_CASE(throw_hash_code_invalid_res_handle)
{
ChainHandle chain;
EntityHandle ent=CreateEntity();
XCSEditor edi=ent.EditXCS();
chain=edi.InsertChain("A");
ResidueHandle res=chain.FindResidue(ResNum(1));
BOOST_CHECK_THROW(res.GetHashCode(), InvalidHandle);
edi.AppendResidue(chain, "GLY");
res=chain.FindResidue(ResNum(1));
BOOST_CHECK_NO_THROW(res.GetHashCode());
}
// Test that .GetHashCode() throws on invalid residue views
BOOST_AUTO_TEST_CASE(throw_hash_code_invalid_res_view)
{
ChainHandle chain;
EntityHandle ent=CreateEntity();
XCSEditor edi=ent.EditXCS();
chain=edi.InsertChain("A");
ResidueView res;
BOOST_CHECK_THROW(res.GetHashCode(), InvalidHandle);
edi.AppendResidue(chain, "GLY");
EntityView ent_view=ent.CreateFullView();
res=ent_view.FindChain("A").FindResidue(1);
BOOST_CHECK_NO_THROW(res.GetHashCode());
}
BOOST_AUTO_TEST_CASE(test_res_index)
{
EntityHandle eh=CreateEntity();
XCSEditor e=eh.EditXCS();
ChainHandle ch1=e.InsertChain("A");
ResidueHandle rA = e.AppendResidue(ch1, "A");
ResidueHandle rB = e.AppendResidue(ch1, "B");
ResidueHandle rC = e.AppendResidue(ch1, "C");
EntityView v(eh);
ChainView cv1(v, ch1);
ResidueView rvA = cv1.AddResidue(rA);
ResidueView rvB = cv1.AddResidue(rB);
ResidueView rvC = cv1.AddResidue(rC);
BOOST_CHECK_EQUAL(rvA.GetIndex(),0);
BOOST_CHECK_EQUAL(rvA.GetIndex(),cv1.GetResidueIndex(rvA.GetNumber()));
BOOST_CHECK_EQUAL(rvB.GetIndex(),1);
BOOST_CHECK_EQUAL(rvB.GetIndex(),cv1.GetResidueIndex(rvB.GetNumber()));
BOOST_CHECK_EQUAL(rvC.GetIndex(),2);
BOOST_CHECK_EQUAL(rvC.GetIndex(),cv1.GetResidueIndex(rvC.GetNumber()));
cv1.RemoveResidue(rvB);
BOOST_CHECK_EQUAL(rvA.GetIndex(),0);
BOOST_CHECK_EQUAL(rvA.GetIndex(),cv1.GetResidueIndex(rvA.GetNumber()));
BOOST_CHECK_EQUAL(rvC.GetIndex(),1);
BOOST_CHECK_EQUAL(rvC.GetIndex(),cv1.GetResidueIndex(rvC.GetNumber()));
}
BOOST_AUTO_TEST_CASE(rename_res)
{
EntityHandle eh=CreateEntity();
XCSEditor e=eh.EditXCS();
ChainHandle ch1=e.InsertChain("A");
ResidueHandle rA2B = e.AppendResidue(ch1, "A");
e.RenameResidue(rA2B, "B");
BOOST_CHECK_EQUAL(rA2B.GetName(), "B");
}
BOOST_AUTO_TEST_CASE(test_centralatom)
{
// COOK UP ENTITY FOR TEST
EntityHandle eh = CreateEntity();
XCSEditor e = eh.EditXCS();
ChainHandle ch = e.InsertChain("A");
// decent peptide with all entries
ResidueHandle rp1 = e.AppendResidue(ch, "A");
e.InsertAtom(rp1, "CA", geom::Vec3(2, 0, 0));
e.InsertAtom(rp1, "CB", geom::Vec3(1, 0, 0));
e.InsertAtom(rp1, "C", geom::Vec3(0, 0, 0));
e.InsertAtom(rp1, "O", geom::Vec3(0, 1, 0));
rp1.SetChemClass(ChemClass(ChemClass::PEPTIDE_LINKING));
// weird peptide with only CA and CB
ResidueHandle rp2 = e.AppendResidue(ch, "B");
e.InsertAtom(rp2, "CA", geom::Vec3(3, 0, 0));
e.InsertAtom(rp2, "CB", geom::Vec3(3, 1, 0));
rp2.SetChemClass(ChemClass(ChemClass::PEPTIDE_LINKING));
// CA-only peptide
ResidueHandle rp3 = e.AppendResidue(ch, "C");
e.InsertAtom(rp3, "CA", geom::Vec3(4, 0, 0));
rp3.SetChemClass(ChemClass(ChemClass::PEPTIDE_LINKING));
// peptide with custom atoms
ResidueHandle rp4 = e.AppendResidue(ch, "D");
AtomHandle rp4_ax = e.InsertAtom(rp4, "XX", geom::Vec3(5, 0, 0));
rp4.SetChemClass(ChemClass(ChemClass::PEPTIDE_LINKING));
// nucleotide with all needed entries
ResidueHandle rn1 = e.AppendResidue(ch, "E");
e.InsertAtom(rn1, "P", geom::Vec3(6, 0, 0));
e.InsertAtom(rn1, "OP1", geom::Vec3(6, 0.5, 0));
e.InsertAtom(rn1, "OP2", geom::Vec3(6, 1.5, 0));
rn1.SetChemClass(ChemClass(ChemClass::DNA_LINKING));
// nucleotide with only P
ResidueHandle rn2 = e.AppendResidue(ch, "F");
e.InsertAtom(rn2, "P", geom::Vec3(7, 0, 0));
rn2.SetChemClass(ChemClass(ChemClass::DNA_LINKING));
// nucleotide with custom atoms
ResidueHandle rn3 = e.AppendResidue(ch, "G");
AtomHandle rn3_ax = e.InsertAtom(rn3, "XX", geom::Vec3(8, 0, 0));
rn3.SetChemClass(ChemClass(ChemClass::DNA_LINKING));
// unknown chem class
ResidueHandle ru = e.AppendResidue(ch, "H");
e.InsertAtom(ru, "P", geom::Vec3(9, 0, 0));
e.InsertAtom(ru, "CA", geom::Vec3(9, 1, 0));
AtomHandle ru_ax = e.InsertAtom(ru, "XX", geom::Vec3(9, 2, 0));
ru.SetChemClass(ChemClass(ChemClass::UNKNOWN));
// CHECK CENTRAL ATOMS
BOOST_CHECK(rp1.GetCentralAtom().IsValid());
BOOST_CHECK_EQUAL(rp1.GetCentralAtom().GetQualifiedName(), "A.A1.CA");
BOOST_CHECK(rp2.GetCentralAtom().IsValid());
BOOST_CHECK_EQUAL(rp2.GetCentralAtom().GetQualifiedName(), "A.B2.CA");
BOOST_CHECK(rp3.GetCentralAtom().IsValid());
BOOST_CHECK_EQUAL(rp3.GetCentralAtom().GetQualifiedName(), "A.C3.CA");
BOOST_CHECK(!rp4.GetCentralAtom().IsValid());
BOOST_CHECK(rn1.GetCentralAtom().IsValid());
BOOST_CHECK_EQUAL(rn1.GetCentralAtom().GetQualifiedName(), "A.E5.P");
BOOST_CHECK(rn2.GetCentralAtom().IsValid());
BOOST_CHECK_EQUAL(rn2.GetCentralAtom().GetQualifiedName(), "A.F6.P");
BOOST_CHECK(!rn3.GetCentralAtom().IsValid());
BOOST_CHECK(!ru.GetCentralAtom().IsValid());
// CHECK NORMALS
BOOST_CHECK_EQUAL(rp1.GetCentralNormal(), geom::Vec3(0, 1, 0));
BOOST_CHECK_EQUAL(rp2.GetCentralNormal(), geom::Vec3(0, -1, 0));
BOOST_CHECK_EQUAL(rp3.GetCentralNormal(), geom::Vec3(0, 0, 1));
BOOST_CHECK_EQUAL(rp4.GetCentralNormal(), geom::Vec3(1, 0, 0));
BOOST_CHECK_EQUAL(rn1.GetCentralNormal(), geom::Vec3(0, -1, 0));
BOOST_CHECK_EQUAL(rn2.GetCentralNormal(), geom::Vec3(0, 0, 1));
BOOST_CHECK_EQUAL(rn3.GetCentralNormal(), geom::Vec3(1, 0, 0));
BOOST_CHECK_EQUAL(ru.GetCentralNormal(), geom::Vec3(1, 0, 0));
// CHECK SETTING CENTRAL ATOMS
rp4.SetCentralAtom(rp4_ax);
BOOST_CHECK(rp4.GetCentralAtom().IsValid());
BOOST_CHECK_EQUAL(rp4.GetCentralAtom().GetQualifiedName(), "A.D4.XX");
BOOST_CHECK_EQUAL(rp4.GetCentralNormal(), geom::Vec3(0, 0, 1));
rn3.SetCentralAtom(rn3_ax);
BOOST_CHECK(rn3.GetCentralAtom().IsValid());
BOOST_CHECK_EQUAL(rn3.GetCentralAtom().GetQualifiedName(), "A.G7.XX");
BOOST_CHECK_EQUAL(rn3.GetCentralNormal(), geom::Vec3(0, 0, 1));
ru.SetCentralAtom(ru_ax);
BOOST_CHECK(ru.GetCentralAtom().IsValid());
BOOST_CHECK_EQUAL(ru.GetCentralAtom().GetQualifiedName(), "A.H8.XX");
// no normal for unknown residues
BOOST_CHECK_EQUAL(ru.GetCentralNormal(), geom::Vec3(1, 0, 0));
}
BOOST_AUTO_TEST_SUITE_END();
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