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Commit 79903792 authored by Studer Gabriel's avatar Studer Gabriel
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delete dead code

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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
// ------------------------------------------------------------------------------
#include <ost/mol/mol.hh>
#include <ost/conop/heuristic_builder.hh>
#define BOOST_TEST_DYN_LINK
#include <boost/test/unit_test.hpp>
#include <ost/log.hh>
using boost::unit_test_framework::test_suite;
using namespace ost;
using namespace ost::conop;
using namespace ost::mol;
namespace {
} // anon ns
ResidueHandle make_arg(ChainHandle chain)
{
XCSEditor e=chain.GetEntity().EditXCS();
ResidueHandle res = e.AppendResidue(chain, "ARG");
e.InsertAtom(res, "N",geom::Vec3(20.202,33.112,58.011));
e.InsertAtom(res, "CA",geom::Vec3(19.396,31.903,58.033));
e.InsertAtom(res, "C",geom::Vec3(18.608,31.739,59.328));
e.InsertAtom(res, "O",geom::Vec3(17.651,30.965,59.381));
e.InsertAtom(res, "CB",geom::Vec3(20.284,30.681,57.801));
e.InsertAtom(res, "CG",geom::Vec3(20.665,30.488,56.342));
e.InsertAtom(res, "CD",geom::Vec3(21.557,29.281,56.154));
e.InsertAtom(res, "NE",geom::Vec3(22.931,29.557,56.551));
e.InsertAtom(res, "CZ",geom::Vec3(23.901,28.653,56.528));
e.InsertAtom(res, "NH1",geom::Vec3(23.640,27.417,56.130));
e.InsertAtom(res, "NH2",geom::Vec3(25.132,28.980,56.893));
return res;
}
ResidueHandle make_leu(ChainHandle chain)
{
XCSEditor e=chain.GetEntity().EditXCS();
ResidueHandle res=e.AppendResidue(chain, "LEU");
e.InsertAtom(res, "N", geom::Vec3(19.003,32.473,60.366));
e.InsertAtom(res, "CA", geom::Vec3(18.330,32.402,61.664));
e.InsertAtom(res, "C", geom::Vec3(17.884,33.787,62.117));
e.InsertAtom(res, "O", geom::Vec3(17.853,34.091,63.308));
e.InsertAtom(res, "CB", geom::Vec3(19.269,31.793,62.710));
e.InsertAtom(res, "CG", geom::Vec3(19.695,30.340,62.501));
e.InsertAtom(res, "CD1", geom::Vec3(20.585,29.897,63.648));
e.InsertAtom(res, "CD2", geom::Vec3(18.461,29.459,62.420));
return res;
}
ResidueHandle make_defective_leu(ChainHandle chain)
{
XCSEditor e=chain.GetEntity().EditXCS();
ResidueHandle res=e.AppendResidue(chain, "LEU");
e.InsertAtom(res, "N", geom::Vec3(19.003,32.473,60.366));
e.InsertAtom(res, "CA", geom::Vec3(18.330,32.402,61.664));
e.InsertAtom(res, "C", geom::Vec3(17.884,33.787,62.117));
e.InsertAtom(res, "O", geom::Vec3(17.853,34.091,63.308));
e.InsertAtom(res, "CB", geom::Vec3(19.269,31.793,102.710));
e.InsertAtom(res, "CG", geom::Vec3(19.695,30.340,62.501));
e.InsertAtom(res, "CD1", geom::Vec3(20.585,29.897,63.648));
e.InsertAtom(res, "CD2", geom::Vec3(18.461,29.459,62.420));
return res;
}
void verify_connectivity_x(const ResidueHandle& res)
{
BOOST_CHECK(BondExists(res.FindAtom("XN"),
res.FindAtom("XCA")));
BOOST_CHECK(BondExists(res.FindAtom("XCA"),
res.FindAtom("XC")));
BOOST_CHECK(BondExists(res.FindAtom("XC"),
res.FindAtom("XO")));
BOOST_CHECK(BondExists(res.FindAtom("XCA"),
res.FindAtom("XCB")));
BOOST_CHECK(BondExists(res.FindAtom("XCB"),
res.FindAtom("XCG")));
if (res.GetKey()=="ARG") {
BOOST_CHECK(BondExists(res.FindAtom("XCB"),
res.FindAtom("XCG")));
BOOST_CHECK(BondExists(res.FindAtom("XCG"),
res.FindAtom("XCD")));
BOOST_CHECK(BondExists(res.FindAtom("XCD"),
res.FindAtom("XNE")));
BOOST_CHECK(BondExists(res.FindAtom("XNE"),
res.FindAtom("XCZ")));
BOOST_CHECK(BondExists(res.FindAtom("XCZ"),
res.FindAtom("XNH1")));
BOOST_CHECK(BondExists(res.FindAtom("XCZ"),
res.FindAtom("XNH2")));
// TODO: Check that no other atoms are connected!
}
if (res.GetKey()=="ILE") {
BOOST_CHECK(BondExists(res.FindAtom("XCG"),
res.FindAtom("XCD1")));
BOOST_CHECK(BondExists(res.FindAtom("XCG"),
res.FindAtom("XCD2")));
// TODO: Check that no other atoms are connected!
}
}
void verify_connectivity(const ResidueHandle& res)
{
BOOST_CHECK(BondExists(res.FindAtom("N"),
res.FindAtom("CA")));
BOOST_CHECK(BondExists(res.FindAtom("CA"),
res.FindAtom("C")));
BOOST_CHECK(BondExists(res.FindAtom("C"),
res.FindAtom("O")));
BOOST_CHECK(BondExists(res.FindAtom("CA"),
res.FindAtom("CB")));
BOOST_CHECK(BondExists(res.FindAtom("CB"),
res.FindAtom("CG")));
if (res.GetKey()=="ARG") {
BOOST_CHECK(BondExists(res.FindAtom("CB"),
res.FindAtom("CG")));
BOOST_CHECK(BondExists(res.FindAtom("CG"),
res.FindAtom("CD")));
BOOST_CHECK(BondExists(res.FindAtom("CD"),
res.FindAtom("NE")));
BOOST_CHECK(BondExists(res.FindAtom("NE"),
res.FindAtom("CZ")));
BOOST_CHECK(BondExists(res.FindAtom("CZ"),
res.FindAtom("NH1")));
BOOST_CHECK(BondExists(res.FindAtom("CZ"),
res.FindAtom("NH2")));
// TODO: Check that no other atoms are connected!
}
if (res.GetKey()=="ILE") {
BOOST_CHECK(BondExists(res.FindAtom("CG"),
res.FindAtom("CD1")));
BOOST_CHECK(BondExists(res.FindAtom("CG"),
res.FindAtom("CD2")));
// TODO: Check that no other atoms are connected!
}
}
BOOST_AUTO_TEST_SUITE( conop );
BOOST_AUTO_TEST_CASE(name_based_connect)
{
EntityHandle e=CreateEntity();
ChainHandle c=e.EditXCS().InsertChain("A");
ResidueHandle ile=make_leu(c);
ResidueHandle arg=make_arg(c);
HeuristicBuilder heuristic_builder;
AtomHandleList atoms =e .GetAtomList();
for (AtomHandleList::const_iterator i = atoms.begin(), e = atoms.end(); i!=e; ++i ){
heuristic_builder.FillAtomProps(*i);
}
EntityHandle de=CreateEntity();
ChainHandle dc=de.EditXCS().InsertChain("A");
ResidueHandle dile=make_defective_leu(dc);
HeuristicBuilder dheuristic_builder;
dheuristic_builder.SetBondFeasibilityCheck(false);
atoms = de.GetAtomList();
for (AtomHandleList::const_iterator i = atoms.begin(), e = atoms.end(); i!=e; ++i ){
dheuristic_builder.FillAtomProps(*i);
}
BOOST_TEST_MESSAGE("running distance based checks on arginine");
heuristic_builder.ConnectAtomsOfResidue(arg);
verify_connectivity(arg);
BOOST_TEST_MESSAGE("running distance based checks on leu");
heuristic_builder.ConnectAtomsOfResidue(ile);
verify_connectivity(ile);
BOOST_TEST_MESSAGE("running distance based checks on defective leu");
dheuristic_builder.ConnectAtomsOfResidue(dile);
verify_connectivity(dile);
}
BOOST_AUTO_TEST_CASE(test_assign_torsions){
EntityHandle e=CreateEntity();
ChainHandle c=e.EditXCS().InsertChain("A");
ResidueHandle l1=make_leu(c);
ResidueHandle a2=make_arg(c);
ResidueHandle l3=make_leu(c);
l1.SetChemClass(ChemClass(ChemClass::L_PEPTIDE_LINKING));
a2.SetChemClass(ChemClass(ChemClass::L_PEPTIDE_LINKING));
l3.SetChemClass(ChemClass(ChemClass::L_PEPTIDE_LINKING));
HeuristicBuilder heuristic_builder;
AtomHandleList atoms = e.GetAtomList();
for (AtomHandleList::const_iterator i = atoms.begin(), e = atoms.end(); i!=e; ++i ){
heuristic_builder.FillAtomProps(*i);
}
heuristic_builder.ConnectAtomsOfResidue(l1);
heuristic_builder.ConnectAtomsOfResidue(a2);
heuristic_builder.ConnectAtomsOfResidue(l3);
XCSEditor edi=e.EditXCS();
edi.Connect(l1.FindAtom("C"), a2.FindAtom("N"));
edi.Connect(a2.FindAtom("C"), l3.FindAtom("N"));
heuristic_builder.AssignTorsions(c);
BOOST_CHECK(a2.GetPhiTorsion().IsValid());
BOOST_CHECK(l3.GetPhiTorsion().IsValid());
BOOST_CHECK(l1.GetPsiTorsion().IsValid());
BOOST_CHECK(a2.GetPsiTorsion().IsValid());
}
BOOST_AUTO_TEST_SUITE_END( );
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