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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
#include <BALL/CONCEPT/classTest.h>
#include <BALLTestConfig.h>
///////////////////////////
#include <BALL/STRUCTURE/reconstructFragmentProcessor.h>
#include <BALL/STRUCTURE/fragmentDB.h>
#include <BALL/STRUCTURE/structureMapper.h>
#include <BALL/STRUCTURE/residueChecker.h>
#include <BALL/KERNEL/PTE.h>
#include <BALL/KERNEL/atom.h>
#include <BALL/KERNEL/residue.h>
#include <BALL/KERNEL/system.h>
#include <BALL/FORMAT/HINFile.h>
///////////////////////////
START_TEST(ReconstructFragmentProcessor)
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
using namespace BALL;
ReconstructFragmentProcessor* ptr = 0;
CHECK(ReconstructFragmentProcessor::ReconstructFragmentProcessor())
ptr = new ReconstructFragmentProcessor;
TEST_NOT_EQUAL(ptr, 0)
RESULT
CHECK(ReconstructFragmentProcessor::~ReconstructFragmentProcessor())
delete ptr;
RESULT
CHECK(const FragmentDB* ReconstructFragmentProcessor::getFragmentDB() const)
ReconstructFragmentProcessor rfp;
TEST_EQUAL(rfp.getFragmentDB(), 0)
RESULT
FragmentDB frag_db("fragments/Fragments.db");
CHECK(void ReconstructFragmentProcessor::getFragmentDB(FragmentDB& frag_db))
ReconstructFragmentProcessor rfp;
TEST_EQUAL(rfp.getFragmentDB(), 0)
rfp.setFragmentDB(frag_db);
TEST_EQUAL(rfp.getFragmentDB(), &frag_db)
RESULT
CHECK(ReconstructFragmentProcessor::ReconstructFragmentProcessor(FragmentDB& frag_db))
ReconstructFragmentProcessor rfp(frag_db);
TEST_EQUAL(rfp.getFragmentDB(), &frag_db)
RESULT
CHECK(ReconstructFragmentProcessor::getNumberOfInsertedAtoms() const)
ReconstructFragmentProcessor rfp(frag_db);
TEST_EQUAL(rfp.getNumberOfInsertedAtoms(), 0)
RESULT
CHECK(ReconstructFragmentProcessor::reconstructFragment(Fragment& fragment, const Fragment& tplate))
Residue res;
PDBAtom& CA(*new PDBAtom);
CA.setName("CA");
CA.setElement(PTE[Element::C]);
res.insert(CA);
Residue res2(res);
const Fragment& ref = *frag_db.getFragment("LYS");
list<Atom*> reconstructed_atoms = ReconstructFragmentProcessor::reconstructFragment(res2, ref);
TEST_EQUAL(reconstructed_atoms.size(), ref.countAtoms() - 1)
TEST_EQUAL(res2.countAtoms(), ref.countAtoms())
RESULT
CHECK(ReconstructFragmentProcessor::operator ())
ReconstructFragmentProcessor rfp(frag_db);
// try to fix C and N-termini
System S;
HINFile f(BALL_TEST_DATA_PATH(ReconstructFragmentProcessor_test1.hin));
f >> S;
TEST_EQUAL(S.countAtoms(), 27)
ABORT_IF(S.countAtoms() != 27)
S.apply(rfp);
TEST_EQUAL(rfp.getNumberOfInsertedAtoms(), 4)
TEST_EQUAL(S.countAtoms(), 31)
RESULT
CHECK([EXTRA]Contents of FragmentDB -- proteinogenous amino acids)
ReconstructFragmentProcessor rfp(frag_db);
ResidueChecker rc(frag_db);
rc.disable(ResidueChecker::OVERLAPPING_ATOMS);
String aa_names[20] = {"ALA", "ARG", "ASN", "ASP", "CYS",
"GLN", "GLU", "GLY", "HIS", "ILE",
"LEU", "LYS", "MET", "PHE", "PRO",
"SER", "THR", "TRP", "TYR", "VAL"};
for (Position i = 0; i < 20; i++)
{
System S;
PDBAtom* atom = new PDBAtom;
atom->setName("CA");
atom->setElement(PTE[Element::C]);
Residue* res = new Residue;
res->setName(aa_names[i]);
res->insert(*atom);
Chain* chain = new Chain;
chain->insert(*res);
chain->setName("C");
Protein* protein = new Protein;
protein->insert(*chain);
protein->setName("P");
S.insert(*protein);
S.apply(frag_db.normalize_names);
S.apply(frag_db.build_bonds);
S.apply(rfp);
S.apply(frag_db.build_bonds);
S.apply(rc);
TEST_EQUAL(rc.getStatus(), true)
}
RESULT
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
END_TEST
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