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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 <boost/test/unit_test.hpp>
#include <ost/mol/mm/interaction.hh>
#include <ost/mol/mol.hh>
#include <ost/mol/builder.hh>
#include <ost/message.hh>
using namespace ost::mol::mm;
BOOST_AUTO_TEST_SUITE( mol_mm );
BOOST_AUTO_TEST_CASE(test_set_stuff)
{
Interaction harmonic_bond = Interaction(HarmonicBond);
Interaction harmonic_angle = Interaction(HarmonicAngle);
Interaction urey_bradley = Interaction(UreyBradleyAngle);
Interaction periodic_dihedral = Interaction(PeriodicDihedral);
Interaction periodic_improper = Interaction(PeriodicImproper);
Interaction harmonic_improper = Interaction(HarmonicImproper);
Interaction cmap = Interaction(CMap);
Interaction lj = Interaction(LJ);
Interaction lj_pair = Interaction(LJPair);
Interaction gbsa = Interaction(GBSA);
Interaction distance_constraint = Interaction(DistanceConstraint);
Interaction exclusion = Interaction(Exclusion);
Interaction harmonic_distance_restraint = Interaction(HarmonicDistanceRestraint);
Interaction harmonic_position_restraint = Interaction(HarmonicPositionRestraint);
//std::vector<String> one_string, two_string, three_string, four_string, five_string;
//std::vector<Real> one_real, two_real, three_real, four_real, five_real, zero_real;
std::vector<Real> one_real(1);
std::vector<Real> two_real(2);
std::vector<Real> three_real(3);
std::vector<Real> four_real(4);
std::vector<Real> five_real(5);
std::vector<Real> seven_real(7);
std::vector<Real> zero_real(0);
std::vector<String> one_string(1);
std::vector<String> two_string(2);
std::vector<String> three_string(3);
std::vector<String> four_string(4);
std::vector<String> five_string(5);
BOOST_CHECK(!harmonic_bond.IsParametrized());
BOOST_CHECK_THROW(harmonic_bond.SetNames(one_string),ost::Error);
BOOST_CHECK_THROW(harmonic_angle.SetNames(one_string),ost::Error);
BOOST_CHECK_THROW(urey_bradley.SetNames(one_string),ost::Error);
BOOST_CHECK_THROW(periodic_dihedral.SetNames(one_string),ost::Error);
BOOST_CHECK_THROW(periodic_improper.SetNames(one_string),ost::Error);
BOOST_CHECK_THROW(harmonic_improper.SetNames(one_string),ost::Error);
BOOST_CHECK_THROW(cmap.SetNames(one_string),ost::Error);
BOOST_CHECK_THROW(lj.SetNames(two_string),ost::Error);
BOOST_CHECK_THROW(lj_pair.SetNames(one_string),ost::Error);
BOOST_CHECK_THROW(gbsa.SetNames(two_string),ost::Error);
BOOST_CHECK_THROW(distance_constraint.SetNames(one_string),ost::Error);
BOOST_CHECK_THROW(exclusion.SetNames(one_string),ost::Error);
BOOST_CHECK_THROW(harmonic_distance_restraint.SetNames(one_string),ost::Error);
BOOST_CHECK_THROW(harmonic_position_restraint.SetNames(two_string),ost::Error);
BOOST_CHECK_THROW(harmonic_bond.SetTypes(one_string),ost::Error);
BOOST_CHECK_THROW(harmonic_angle.SetTypes(one_string),ost::Error);
BOOST_CHECK_THROW(urey_bradley.SetTypes(one_string),ost::Error);
BOOST_CHECK_THROW(periodic_dihedral.SetTypes(one_string),ost::Error);
BOOST_CHECK_THROW(periodic_improper.SetTypes(one_string),ost::Error);
BOOST_CHECK_THROW(harmonic_improper.SetTypes(one_string),ost::Error);
BOOST_CHECK_THROW(cmap.SetTypes(one_string),ost::Error);
BOOST_CHECK_THROW(lj.SetTypes(two_string),ost::Error);
BOOST_CHECK_THROW(lj_pair.SetTypes(one_string),ost::Error);
BOOST_CHECK_THROW(gbsa.SetTypes(two_string),ost::Error);
BOOST_CHECK_THROW(distance_constraint.SetTypes(one_string),ost::Error);
BOOST_CHECK_THROW(exclusion.SetTypes(one_string),ost::Error);
BOOST_CHECK_THROW(harmonic_distance_restraint.SetTypes(one_string),ost::Error);
BOOST_CHECK_THROW(harmonic_position_restraint.SetTypes(two_string),ost::Error);
BOOST_CHECK_THROW(harmonic_bond.SetParam(one_real),ost::Error);
BOOST_CHECK_THROW(harmonic_angle.SetParam(one_real),ost::Error);
BOOST_CHECK_THROW(urey_bradley.SetParam(one_real),ost::Error);
BOOST_CHECK_THROW(periodic_dihedral.SetParam(one_real),ost::Error);
BOOST_CHECK_THROW(periodic_improper.SetParam(one_real),ost::Error);
BOOST_CHECK_THROW(harmonic_improper.SetParam(one_real),ost::Error);
BOOST_CHECK_THROW(cmap.SetParam(two_real),ost::Error);
BOOST_CHECK_THROW(lj.SetParam(one_real),ost::Error);
BOOST_CHECK_THROW(lj_pair.SetParam(one_real),ost::Error);
BOOST_CHECK_THROW(gbsa.SetParam(one_real),ost::Error);
BOOST_CHECK_THROW(distance_constraint.SetParam(two_real),ost::Error);
BOOST_CHECK_THROW(exclusion.SetParam(one_real),ost::Error);
BOOST_CHECK_THROW(harmonic_distance_restraint.SetParam(one_real),ost::Error);
BOOST_CHECK_THROW(harmonic_position_restraint.SetParam(one_real),ost::Error);
BOOST_CHECK_NO_THROW(harmonic_bond.SetNames(two_string));
BOOST_CHECK_NO_THROW(harmonic_angle.SetNames(three_string));
BOOST_CHECK_NO_THROW(urey_bradley.SetNames(three_string));
BOOST_CHECK_NO_THROW(periodic_dihedral.SetNames(four_string));
BOOST_CHECK_NO_THROW(periodic_improper.SetNames(four_string));
BOOST_CHECK_NO_THROW(harmonic_improper.SetNames(four_string));
BOOST_CHECK_NO_THROW(cmap.SetNames(five_string));
BOOST_CHECK_NO_THROW(lj.SetNames(one_string));
BOOST_CHECK_NO_THROW(lj_pair.SetNames(two_string));
BOOST_CHECK_NO_THROW(gbsa.SetNames(one_string));
BOOST_CHECK_NO_THROW(distance_constraint.SetNames(two_string));
BOOST_CHECK_NO_THROW(exclusion.SetNames(two_string));
BOOST_CHECK_NO_THROW(harmonic_distance_restraint.SetNames(two_string));
BOOST_CHECK_NO_THROW(harmonic_position_restraint.SetNames(one_string));
BOOST_CHECK_NO_THROW(harmonic_bond.SetTypes(two_string));
BOOST_CHECK_NO_THROW(harmonic_angle.SetTypes(three_string));
BOOST_CHECK_NO_THROW(urey_bradley.SetTypes(three_string));
BOOST_CHECK_NO_THROW(periodic_dihedral.SetTypes(four_string));
BOOST_CHECK_NO_THROW(periodic_improper.SetTypes(four_string));
BOOST_CHECK_NO_THROW(harmonic_improper.SetTypes(four_string));
BOOST_CHECK_NO_THROW(cmap.SetTypes(five_string));
BOOST_CHECK_NO_THROW(lj.SetTypes(one_string));
BOOST_CHECK_NO_THROW(lj_pair.SetTypes(two_string));
BOOST_CHECK_NO_THROW(gbsa.SetTypes(one_string));
BOOST_CHECK_NO_THROW(distance_constraint.SetTypes(two_string));
BOOST_CHECK_NO_THROW(exclusion.SetTypes(two_string));
BOOST_CHECK_NO_THROW(harmonic_distance_restraint.SetTypes(two_string));
BOOST_CHECK_NO_THROW(harmonic_position_restraint.SetTypes(one_string));
BOOST_CHECK_NO_THROW(harmonic_bond.SetParam(two_real));
BOOST_CHECK_NO_THROW(harmonic_angle.SetParam(two_real));
BOOST_CHECK_NO_THROW(urey_bradley.SetParam(four_real));
BOOST_CHECK_NO_THROW(periodic_dihedral.SetParam(three_real));
BOOST_CHECK_NO_THROW(periodic_improper.SetParam(three_real));
BOOST_CHECK_NO_THROW(harmonic_improper.SetParam(two_real));
BOOST_CHECK_NO_THROW(lj.SetParam(two_real));
BOOST_CHECK_NO_THROW(lj_pair.SetParam(two_real));
BOOST_CHECK_NO_THROW(gbsa.SetParam(two_real));
BOOST_CHECK_NO_THROW(distance_constraint.SetParam(one_real));
BOOST_CHECK_NO_THROW(exclusion.SetParam(zero_real));
BOOST_CHECK_NO_THROW(harmonic_distance_restraint.SetParam(two_real));
BOOST_CHECK_NO_THROW(harmonic_position_restraint.SetParam(seven_real));
std::vector<Real> valid_cmap_parameters;
valid_cmap_parameters.push_back(2.0);
valid_cmap_parameters.push_back(0.0);
valid_cmap_parameters.push_back(0.0);
valid_cmap_parameters.push_back(0.0);
valid_cmap_parameters.push_back(0.0);
BOOST_CHECK_NO_THROW(cmap.SetParam(valid_cmap_parameters));
BOOST_CHECK(harmonic_bond.IsParametrized());
Interaction new_bond = Interaction(HarmonicBond);
std::vector<String> with_wildcard, without_wildcard;
with_wildcard.push_back("A");
without_wildcard.push_back("A");
with_wildcard.push_back("X");
without_wildcard.push_back("A");
//should be initialized with false
BOOST_CHECK(!new_bond.HasNameWildcard());
BOOST_CHECK(!new_bond.HasTypeWildcard());
new_bond.SetNames(without_wildcard);
new_bond.SetTypes(without_wildcard);
BOOST_CHECK(!new_bond.HasNameWildcard());
BOOST_CHECK(!new_bond.HasTypeWildcard());
new_bond.SetNames(with_wildcard);
new_bond.SetTypes(with_wildcard);
BOOST_CHECK(new_bond.HasNameWildcard());
BOOST_CHECK(new_bond.HasTypeWildcard());
//Check hasname/hastype
BOOST_CHECK(new_bond.HasType("A"));
BOOST_CHECK(!new_bond.HasType("B"));
BOOST_CHECK(new_bond.HasName("A"));
BOOST_CHECK(!new_bond.HasType("B"));
}
BOOST_AUTO_TEST_CASE(test_match_stuff)
{
Interaction dihedral = Interaction(PeriodicDihedral);
std::vector<String> with_wildcard, without_wildcard;
with_wildcard.push_back("X");
with_wildcard.push_back("A");
with_wildcard.push_back("A");
with_wildcard.push_back("A");
without_wildcard.push_back("A");
without_wildcard.push_back("A");
without_wildcard.push_back("A");
without_wildcard.push_back("A");
dihedral.SetTypes(with_wildcard);
BOOST_CHECK(dihedral.MatchTypes(with_wildcard));
BOOST_CHECK(dihedral.MatchTypes(without_wildcard));
dihedral.SetTypes(without_wildcard);
BOOST_CHECK(dihedral.MatchTypes(without_wildcard));
BOOST_CHECK(!dihedral.MatchTypes(with_wildcard));
dihedral.SetNames(with_wildcard);
BOOST_CHECK(dihedral.MatchNames(with_wildcard));
BOOST_CHECK(dihedral.MatchNames(without_wildcard));
dihedral.SetNames(without_wildcard);
BOOST_CHECK(dihedral.MatchNames(without_wildcard));
BOOST_CHECK(!dihedral.MatchNames(with_wildcard));
}
BOOST_AUTO_TEST_CASE(test_replace_atom){
Interaction bond = Interaction(HarmonicBond);
std::vector<String> strings;
strings.push_back("A");
strings.push_back("B");
bond.SetNames(strings);
bond.ReplaceAtom("A","X","X");
std::vector<String> new_names = bond.GetNames();
BOOST_CHECK(new_names != strings);
bond.SetTypes(strings);
bond.ReplaceAtom("X","A","X");
std::vector<String> new_types = bond.GetTypes();
BOOST_CHECK(new_types == new_names);
}
BOOST_AUTO_TEST_CASE(test_getatoms){
ost::mol::EntityHandle e = ost::mol::Builder()
.Chain("A")
.Residue("ONE")
.Atom("A",geom::Vec3(-5,-5,-5))
.Atom("B",geom::Vec3(-5, 5,-5))
.Residue("TWO")
.Atom("A",geom::Vec3(1,1,1))
.Atom("B",geom::Vec3(2,2,2))
.Residue("THREE")
.Atom("A",geom::Vec3(3,3,3))
.Atom("B",geom::Vec3(4,4,4));
ost::mol::ResidueHandleList res_list = e.GetResidueList();
ost::mol::AtomHandleList atom_list_one = res_list[0].GetAtomList();
ost::mol::AtomHandleList atom_list_two = res_list[1].GetAtomList();
ost::mol::AtomHandleList atom_list_three = res_list[2].GetAtomList();
Interaction bond = Interaction(HarmonicBond);
std::vector<String> strings;
strings.push_back("A");
strings.push_back("B");
bond.SetNames(strings);
ost::mol::AtomHandleList bond_atom_list = bond.GetAtoms(res_list[0]);
BOOST_CHECK(atom_list_one[0] == bond_atom_list[0]);
BOOST_CHECK(atom_list_one[1] == bond_atom_list[1]);
strings[1] = "X";
bond.SetNames(strings);
BOOST_CHECK_THROW(bond.GetAtoms(res_list[0]),ost::Error);
strings[0] = "-A";
strings[1] = "B";
bond.SetNames(strings);
BOOST_CHECK_THROW(bond.GetAtoms(res_list[0]),ost::Error);
bond_atom_list = bond.GetAtoms(res_list[1]);
BOOST_CHECK(bond_atom_list[0] == atom_list_one[0]);
BOOST_CHECK(bond_atom_list[1] == atom_list_two[1]);
strings[1]="+B";
bond.SetNames(strings);
BOOST_CHECK_THROW(bond.GetAtoms(res_list[2]),ost::Error);
bond_atom_list = bond.GetAtoms(res_list[1]);
BOOST_CHECK(bond_atom_list[0] == atom_list_one[0]);
BOOST_CHECK(bond_atom_list[1] == atom_list_three[1]);
}
BOOST_AUTO_TEST_SUITE_END();
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