//------------------------------------------------------------------------------ // This file is part of the OpenStructure project // // 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 #include #include using namespace ost; using namespace ost::mol; EntityHandle mk_test_ent() { EntityHandle ent=CreateEntity(); ent.SetName("TestEntity"); XCSEditor edi=ent.EditXCS(); ChainHandle chain_a=edi.InsertChain("A"); ResidueHandle res_a=edi.AppendResidue(chain_a, "A"); AtomHandle atom_a=edi.InsertAtom(res_a, "A", geom::Vec3()); AtomHandle atom_b=edi.InsertAtom(res_a, "B", geom::Vec3()); ResidueHandle res_b=edi.AppendResidue(chain_a, "B"); AtomHandle atom_c=edi.InsertAtom(res_b, "C", geom::Vec3()); AtomHandle atom_d=edi.InsertAtom(res_b, "D", geom::Vec3()); ChainHandle chain_b=edi.InsertChain("B"); ResidueHandle res_c=edi.AppendResidue(chain_b, "C"); AtomHandle atom_e=edi.InsertAtom(res_c, "E", geom::Vec3()); AtomHandle atom_f=edi.InsertAtom(res_c, "F", geom::Vec3()); ResidueHandle res_d=edi.AppendResidue(chain_b, "D"); AtomHandle atom_g=edi.InsertAtom(res_d, "G", geom::Vec3()); AtomHandle atom_h=edi.InsertAtom(res_d, "H", geom::Vec3()); edi.Connect(atom_a, atom_b); edi.Connect(atom_b, atom_c); edi.Connect(atom_c, atom_d); edi.Connect(atom_d, atom_e); edi.Connect(atom_e, atom_f); edi.Connect(atom_f, atom_g); edi.Connect(atom_g, atom_h); return ent; } bool find_bond(AtomHandle a, AtomHandle b, const BondHandleList& bonds) { return std::find(bonds.begin(), bonds.end(), a.FindBondToAtom(b))!=bonds.end(); } BOOST_AUTO_TEST_SUITE( mol_base ); BOOST_AUTO_TEST_CASE(test_difference) { EntityHandle ent=mk_test_ent(); EntityView full=ent.CreateFullView(); EntityView v1=ent.Select("aname=A,B,C"); EntityView diff_view=mol::Difference(full, v1); BOOST_CHECK_EQUAL(diff_view.GetBondCount(), 5); BOOST_CHECK_EQUAL(diff_view.GetAtomCount(), 5); BOOST_CHECK_EQUAL(diff_view.GetResidueCount(), 3); BOOST_CHECK_EQUAL(diff_view.GetChainCount(), 2); // check chains BOOST_CHECK(diff_view.FindChain("A")); BOOST_CHECK(diff_view.FindChain("B")); // check residues BOOST_CHECK(!diff_view.ViewForHandle(ent.FindResidue("A", mol::ResNum(1)))); BOOST_CHECK(diff_view.ViewForHandle(ent.FindResidue("A", mol::ResNum(2)))); BOOST_CHECK(diff_view.ViewForHandle(ent.FindResidue("B", mol::ResNum(1)))); BOOST_CHECK(diff_view.ViewForHandle(ent.FindResidue("B", mol::ResNum(2)))); // check atoms BOOST_CHECK(!diff_view.ViewForHandle(ent.FindAtom("A", mol::ResNum(1), "A"))); BOOST_CHECK(!diff_view.ViewForHandle(ent.FindAtom("A", mol::ResNum(1), "B"))); BOOST_CHECK(!diff_view.ViewForHandle(ent.FindAtom("A", mol::ResNum(2), "C"))); BOOST_CHECK(diff_view.ViewForHandle(ent.FindAtom("A", mol::ResNum(2), "D"))); BOOST_CHECK(diff_view.ViewForHandle(ent.FindAtom("B", mol::ResNum(1), "E"))); BOOST_CHECK(diff_view.ViewForHandle(ent.FindAtom("B", mol::ResNum(1), "F"))); BOOST_CHECK(diff_view.ViewForHandle(ent.FindAtom("B", mol::ResNum(2), "G"))); BOOST_CHECK(diff_view.ViewForHandle(ent.FindAtom("B", mol::ResNum(2), "H"))); // check bonds BondHandleList bonds=diff_view.GetBondList(); BOOST_CHECK(!find_bond(ent.FindAtom("A", mol::ResNum(1), "A"), ent.FindAtom("A", mol::ResNum(1), "B"), bonds)); BOOST_CHECK(!find_bond(ent.FindAtom("A", mol::ResNum(1), "B"), ent.FindAtom("A", mol::ResNum(2), "C"), bonds)); BOOST_CHECK(find_bond(ent.FindAtom("A", mol::ResNum(2), "C"), ent.FindAtom("A", mol::ResNum(2), "D"), bonds)); BOOST_CHECK(find_bond(ent.FindAtom("B", mol::ResNum(1), "E"), ent.FindAtom("B", mol::ResNum(1), "F"), bonds)); BOOST_CHECK(find_bond(ent.FindAtom("B", mol::ResNum(1), "F"), ent.FindAtom("B", mol::ResNum(2), "G"), bonds)); BOOST_CHECK(find_bond(ent.FindAtom("B", mol::ResNum(2), "G"), ent.FindAtom("B", mol::ResNum(2), "H"), bonds)); } BOOST_AUTO_TEST_CASE(test_union_a) { EntityHandle ent=mk_test_ent(); EntityView v1=ent.Select("aname=B,C"); EntityView v2=ent.Select("aname=F,G"); EntityView un=mol::Union(v1, v2); BOOST_CHECK_EQUAL(un.GetAtomCount(), 4); BOOST_CHECK_EQUAL(un.GetResidueCount(), 4); BOOST_CHECK_EQUAL(un.GetChainCount(), 2); // test chains BOOST_CHECK(un.FindChain("A")); BOOST_CHECK(un.FindChain("B")); // test residues BOOST_CHECK(un.ViewForHandle(ent.FindResidue("A", mol::ResNum(1)))); BOOST_CHECK(un.ViewForHandle(ent.FindResidue("A", mol::ResNum(2)))); BOOST_CHECK(un.ViewForHandle(ent.FindResidue("B", mol::ResNum(1)))); BOOST_CHECK(un.ViewForHandle(ent.FindResidue("B", mol::ResNum(2)))); // test atoms BOOST_CHECK(!un.ViewForHandle(ent.FindAtom("A", mol::ResNum(1), "A"))); BOOST_CHECK(un.ViewForHandle(ent.FindAtom("A", mol::ResNum(1), "B"))); BOOST_CHECK(un.ViewForHandle(ent.FindAtom("A", mol::ResNum(2), "C"))); BOOST_CHECK(!un.ViewForHandle(ent.FindAtom("A", mol::ResNum(2), "D"))); BOOST_CHECK(!un.ViewForHandle(ent.FindAtom("B", mol::ResNum(1), "E"))); BOOST_CHECK(un.ViewForHandle(ent.FindAtom("B", mol::ResNum(1), "F"))); BOOST_CHECK(un.ViewForHandle(ent.FindAtom("B", mol::ResNum(2), "G"))); BOOST_CHECK(!un.ViewForHandle(ent.FindAtom("B", mol::ResNum(2), "H"))); // bonds BondHandleList bonds=un.GetBondList(); BOOST_CHECK(!find_bond(ent.FindAtom("A", mol::ResNum(1), "A"), ent.FindAtom("A", mol::ResNum(1), "B"), bonds)); BOOST_CHECK(find_bond(ent.FindAtom("A", mol::ResNum(1), "B"), ent.FindAtom("A", mol::ResNum(2), "C"), bonds)); BOOST_CHECK(!find_bond(ent.FindAtom("A", mol::ResNum(2), "C"), ent.FindAtom("A", mol::ResNum(2), "D"), bonds)); BOOST_CHECK(!find_bond(ent.FindAtom("B", mol::ResNum(1), "E"), ent.FindAtom("B", mol::ResNum(1), "F"), bonds)); BOOST_CHECK(find_bond(ent.FindAtom("B", mol::ResNum(1), "F"), ent.FindAtom("B", mol::ResNum(2), "G"), bonds)); BOOST_CHECK(!find_bond(ent.FindAtom("B", mol::ResNum(2), "G"), ent.FindAtom("B", mol::ResNum(2), "H"), bonds)); } BOOST_AUTO_TEST_CASE(test_union_b) { EntityHandle ent=mk_test_ent(); EntityView v1=ent.Select("aname=B,C"); EntityView v2=ent.Select("aname=A,B,C,F,G"); EntityView un=mol::Union(v1, v2); BOOST_CHECK_EQUAL(un.GetAtomCount(), 5); BOOST_CHECK_EQUAL(un.GetResidueCount(), 4); BOOST_CHECK_EQUAL(un.GetChainCount(), 2); // test chains BOOST_CHECK(un.FindChain("A")); BOOST_CHECK(un.FindChain("B")); // test residues BOOST_CHECK(un.ViewForHandle(ent.FindResidue("A", mol::ResNum(1)))); BOOST_CHECK(un.ViewForHandle(ent.FindResidue("A", mol::ResNum(2)))); BOOST_CHECK(un.ViewForHandle(ent.FindResidue("B", mol::ResNum(1)))); BOOST_CHECK(un.ViewForHandle(ent.FindResidue("B", mol::ResNum(2)))); // test atoms BOOST_CHECK(un.ViewForHandle(ent.FindAtom("A", mol::ResNum(1), "A"))); BOOST_CHECK(un.ViewForHandle(ent.FindAtom("A", mol::ResNum(1), "B"))); BOOST_CHECK(un.ViewForHandle(ent.FindAtom("A", mol::ResNum(2), "C"))); BOOST_CHECK(!un.ViewForHandle(ent.FindAtom("A", mol::ResNum(2), "D"))); BOOST_CHECK(!un.ViewForHandle(ent.FindAtom("B", mol::ResNum(1), "E"))); BOOST_CHECK(un.ViewForHandle(ent.FindAtom("B", mol::ResNum(1), "F"))); BOOST_CHECK(un.ViewForHandle(ent.FindAtom("B", mol::ResNum(2), "G"))); BOOST_CHECK(!un.ViewForHandle(ent.FindAtom("B", mol::ResNum(2), "H"))); // bonds BondHandleList bonds=un.GetBondList(); BOOST_CHECK(find_bond(ent.FindAtom("A", mol::ResNum(1), "A"), ent.FindAtom("A", mol::ResNum(1), "B"), bonds)); BOOST_CHECK(find_bond(ent.FindAtom("A", mol::ResNum(1), "B"), ent.FindAtom("A", mol::ResNum(2), "C"), bonds)); BOOST_CHECK(!find_bond(ent.FindAtom("A", mol::ResNum(2), "C"), ent.FindAtom("A", mol::ResNum(2), "D"), bonds)); BOOST_CHECK(!find_bond(ent.FindAtom("B", mol::ResNum(1), "E"), ent.FindAtom("B", mol::ResNum(1), "F"), bonds)); BOOST_CHECK(find_bond(ent.FindAtom("B", mol::ResNum(1), "F"), ent.FindAtom("B", mol::ResNum(2), "G"), bonds)); BOOST_CHECK(!find_bond(ent.FindAtom("B", mol::ResNum(2), "G"), ent.FindAtom("B", mol::ResNum(2), "H"), bonds)); } BOOST_AUTO_TEST_CASE(test_intersection_a) { EntityHandle ent=mk_test_ent(); EntityView v1=ent.Select("aname=B,C,F,G"); EntityView v2=ent.Select("aname=C,F,G"); EntityView is=mol::Intersection(v1, v2); BOOST_CHECK_EQUAL(is.GetBondCount(), 1); BOOST_CHECK_EQUAL(is.GetAtomCount(), 3); BOOST_CHECK_EQUAL(is.GetResidueCount(), 3); BOOST_CHECK_EQUAL(is.GetChainCount(), 2); // test chains BOOST_CHECK(is.FindChain("A")); BOOST_CHECK(is.FindChain("B")); // test residues BOOST_CHECK(!is.ViewForHandle(ent.FindResidue("A", mol::ResNum(1)))); BOOST_CHECK(is.ViewForHandle(ent.FindResidue("A", mol::ResNum(2)))); BOOST_CHECK(is.ViewForHandle(ent.FindResidue("B", mol::ResNum(1)))); BOOST_CHECK(is.ViewForHandle(ent.FindResidue("B", mol::ResNum(2)))); // test atoms BOOST_CHECK(!is.ViewForHandle(ent.FindAtom("A", mol::ResNum(1), "A"))); BOOST_CHECK(!is.ViewForHandle(ent.FindAtom("A", mol::ResNum(1), "B"))); BOOST_CHECK(is.ViewForHandle(ent.FindAtom("A", mol::ResNum(2), "C"))); BOOST_CHECK(!is.ViewForHandle(ent.FindAtom("A", mol::ResNum(2), "D"))); BOOST_CHECK(!is.ViewForHandle(ent.FindAtom("B", mol::ResNum(1), "E"))); BOOST_CHECK(is.ViewForHandle(ent.FindAtom("B", mol::ResNum(1), "F"))); BOOST_CHECK(is.ViewForHandle(ent.FindAtom("B", mol::ResNum(2), "G"))); BOOST_CHECK(!is.ViewForHandle(ent.FindAtom("B", mol::ResNum(2), "H"))); // bonds BondHandleList bonds=is.GetBondList(); BOOST_CHECK(!find_bond(ent.FindAtom("A", mol::ResNum(1), "A"), ent.FindAtom("A", mol::ResNum(1), "B"), bonds)); BOOST_CHECK(!find_bond(ent.FindAtom("A", mol::ResNum(1), "B"), ent.FindAtom("A", mol::ResNum(2), "C"), bonds)); BOOST_CHECK(!find_bond(ent.FindAtom("A", mol::ResNum(2), "C"), ent.FindAtom("A", mol::ResNum(2), "D"), bonds)); BOOST_CHECK(!find_bond(ent.FindAtom("B", mol::ResNum(1), "E"), ent.FindAtom("B", mol::ResNum(1), "F"), bonds)); BOOST_CHECK(find_bond(ent.FindAtom("B", mol::ResNum(1), "F"), ent.FindAtom("B", mol::ResNum(2), "G"), bonds)); BOOST_CHECK(!find_bond(ent.FindAtom("B", mol::ResNum(2), "G"), ent.FindAtom("B", mol::ResNum(2), "H"), bonds)); } BOOST_AUTO_TEST_CASE(test_intersection_b) { EntityHandle ent=mk_test_ent(); EntityView v1=ent.Select("aname=B,C,F,G"); EntityView v2=ent.Select("aname=F,G"); EntityView is=mol::Intersection(v1, v2); BOOST_CHECK_EQUAL(is.GetBondCount(), 1); BOOST_CHECK_EQUAL(is.GetAtomCount(), 2); BOOST_CHECK_EQUAL(is.GetResidueCount(), 2); BOOST_CHECK_EQUAL(is.GetChainCount(), 1); // test chains BOOST_CHECK(!is.FindChain("A")); BOOST_CHECK(is.FindChain("B")); // test residues BOOST_CHECK(!is.ViewForHandle(ent.FindResidue("A", mol::ResNum(1)))); BOOST_CHECK(!is.ViewForHandle(ent.FindResidue("A", mol::ResNum(2)))); BOOST_CHECK(is.ViewForHandle(ent.FindResidue("B", mol::ResNum(1)))); BOOST_CHECK(is.ViewForHandle(ent.FindResidue("B", mol::ResNum(2)))); // test atoms BOOST_CHECK(!is.ViewForHandle(ent.FindAtom("A", mol::ResNum(1), "A"))); BOOST_CHECK(!is.ViewForHandle(ent.FindAtom("A", mol::ResNum(1), "B"))); BOOST_CHECK(!is.ViewForHandle(ent.FindAtom("A", mol::ResNum(2), "C"))); BOOST_CHECK(!is.ViewForHandle(ent.FindAtom("A", mol::ResNum(2), "D"))); BOOST_CHECK(!is.ViewForHandle(ent.FindAtom("B", mol::ResNum(1), "E"))); BOOST_CHECK(is.ViewForHandle(ent.FindAtom("B", mol::ResNum(1), "F"))); BOOST_CHECK(is.ViewForHandle(ent.FindAtom("B", mol::ResNum(2), "G"))); BOOST_CHECK(!is.ViewForHandle(ent.FindAtom("B", mol::ResNum(2), "H"))); // bonds BondHandleList bonds=is.GetBondList(); BOOST_CHECK(!find_bond(ent.FindAtom("A", mol::ResNum(1), "A"), ent.FindAtom("A", mol::ResNum(1), "B"), bonds)); BOOST_CHECK(!find_bond(ent.FindAtom("A", mol::ResNum(1), "B"), ent.FindAtom("A", mol::ResNum(2), "C"), bonds)); BOOST_CHECK(!find_bond(ent.FindAtom("A", mol::ResNum(2), "C"), ent.FindAtom("A", mol::ResNum(2), "D"), bonds)); BOOST_CHECK(!find_bond(ent.FindAtom("B", mol::ResNum(1), "E"), ent.FindAtom("B", mol::ResNum(1), "F"), bonds)); BOOST_CHECK(find_bond(ent.FindAtom("B", mol::ResNum(1), "F"), ent.FindAtom("B", mol::ResNum(2), "G"), bonds)); BOOST_CHECK(!find_bond(ent.FindAtom("B", mol::ResNum(2), "G"), ent.FindAtom("B", mol::ResNum(2), "H"), bonds)); } BOOST_AUTO_TEST_CASE(entity_from_view) { EntityHandle ent=mk_test_ent(); EntityView v1=ent.Select("aname=B,C,F,G"); EntityHandle ent_fv=mol::CreateEntityFromView(v1, false); BOOST_CHECK_EQUAL(ent.GetName(), ent_fv.GetName()); BOOST_CHECK_EQUAL(ent_fv.GetBondCount(),2); BOOST_CHECK_EQUAL(ent_fv.GetAtomCount(), 4); BOOST_CHECK_EQUAL(ent_fv.GetResidueCount(), 4); BOOST_CHECK_EQUAL(ent_fv.GetChainCount(), 2); } BOOST_AUTO_TEST_CASE(ent_from_view_residue_props) { EntityHandle ent=mol::CreateEntity(); XCSEditor edi=ent.EditXCS(); ChainHandle ch=edi.InsertChain("A"); ResidueHandle res=edi.AppendResidue(ch, "DUMMY", mol::ResNum(666, '6')); res.SetOneLetterCode('X'); res.SetIsProtein(true); ChemClass cl(ChemClass::L_PEPTIDE_LINKING); res.SetSecStructure(SecStructure(SecStructure::ALPHA_HELIX)); res.SetChemClass(cl); EntityHandle copy=mol::CreateEntityFromView(ent.Select(""), false); ResidueHandle res2=copy.GetResidueList()[0]; BOOST_CHECK_EQUAL(res2.GetName(), String("DUMMY")); BOOST_CHECK_EQUAL(res2.GetOneLetterCode(), 'X'); BOOST_CHECK_EQUAL(res2.GetChemClass(), cl); BOOST_CHECK_EQUAL(res.GetSecStructure(), SecStructure::ALPHA_HELIX); BOOST_CHECK(res2.IsProtein()==true); BOOST_CHECK_EQUAL(res2.GetNumber(), ResNum(666, '6')); } BOOST_AUTO_TEST_CASE(ent_from_view_atom_props) { EntityHandle ent=mol::CreateEntity(); XCSEditor edi=ent.EditXCS(); ChainHandle ch=edi.InsertChain("A"); ResidueHandle res=edi.AppendResidue(ch, "DUMMY"); AtomHandle atom=edi.InsertAtom(res, "X", geom::Vec3(1,2,3), "C"); atom.SetMass(100.0); atom.SetBFactor(200.0); atom.SetOccupancy(300.0); atom.SetHetAtom(true); atom.SetRadius(500); atom.SetCharge(800); atom.SetAnisou(geom::Mat3(100,200,300)); EntityHandle copy=mol::CreateEntityFromView(ent.Select(""), false); AtomHandle atom2=copy.GetAtomList()[0]; BOOST_CHECK_EQUAL(atom2.GetPos(), geom::Vec3(1,2,3)); BOOST_CHECK_EQUAL(atom2.GetName(), String("X")); BOOST_CHECK_EQUAL(atom2.GetElement(), String("C")); BOOST_CHECK_EQUAL(atom2.GetMass(), Real(100.0)); BOOST_CHECK_EQUAL(atom2.GetCharge(), Real(800.0)); BOOST_CHECK_EQUAL(atom2.GetBFactor(), Real(200.0)); BOOST_CHECK_EQUAL(atom2.IsHetAtom(), true); BOOST_CHECK_EQUAL(atom2.GetAnisou(), geom::Mat3(100,200,300)); BOOST_CHECK_EQUAL(atom2.GetRadius(), Real(500.0)); } BOOST_AUTO_TEST_SUITE_END();