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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
#include <BALL/CONCEPT/classTest.h>
#include <BALLTestConfig.h>
///////////////////////////
#include <BALL/STRUCTURE/fragmentDB.h>
#include <BALL/FORMAT/HINFile.h>
#include <BALL/FORMAT/PDBFile.h>
#include <BALL/KERNEL/system.h>
#include <BALL/KERNEL/residue.h>
#include <BALL/KERNEL/PTE.h>
#include <BALL/KERNEL/forEach.h>
#include <BALL/KERNEL/bond.h>
#include <BALL/KERNEL/atom.h>
using namespace BALL;
///////////////////////////
START_TEST(Fragment)
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
FragmentDB db("fragments/Fragments.db");
CHECK(getResidue(const String&))
const Residue* res = db.getResidue("GLY");
TEST_NOT_EQUAL(res, 0)
if (res != 0)
{
TEST_EQUAL(res->isNTerminal(), false)
TEST_EQUAL(res->isCTerminal(), false)
}
ABORT_IF(res == 0)
// check the atoms
AtomConstIterator atom_it = res->beginAtom();
Position i = 0;
for (; +atom_it; ++atom_it, ++i)
{
switch (i)
{
case 5:
TEST_EQUAL(atom_it->getName(), "N")
TEST_EQUAL(atom_it->getElement().getSymbol(), "N")
TEST_EQUAL(atom_it->countBonds(), 2)
break;
case 2:
TEST_EQUAL(atom_it->getName(), "H")
TEST_EQUAL(atom_it->getElement().getSymbol(), "H")
TEST_EQUAL(atom_it->countBonds(), 1)
break;
case 4:
TEST_EQUAL(atom_it->getName(), "CA")
TEST_EQUAL(atom_it->getElement().getSymbol(), "C")
TEST_EQUAL(atom_it->countBonds(), 4)
break;
case 0:
TEST_EQUAL(atom_it->getName(), "1HA")
TEST_EQUAL(atom_it->getElement().getSymbol(), "H")
TEST_EQUAL(atom_it->countBonds(), 1)
break;
case 1:
TEST_EQUAL(atom_it->getName(), "2HA")
TEST_EQUAL(atom_it->getElement().getSymbol(), "H")
TEST_EQUAL(atom_it->countBonds(), 1)
break;
case 3:
TEST_EQUAL(atom_it->getName(), "C")
TEST_EQUAL(atom_it->getElement().getSymbol(), "C")
TEST_EQUAL(atom_it->countBonds(), 2)
break;
case 6:
TEST_EQUAL(atom_it->getName(), "O")
TEST_EQUAL(atom_it->getElement().getSymbol(), "O")
TEST_EQUAL(atom_it->countBonds(), 1)
break;
default:
STATUS("Too many atoms")
TEST_EQUAL(0, 1)
}
}
// check the bonds
Atom::BondConstIterator bond_it;
i =0;
BALL_FOREACH_BOND(*res, atom_it, bond_it)
{
switch (i)
{
case 0: TEST_EQUAL(bond_it->getOrder(), Bond::ORDER__SINGLE) break;
case 1: TEST_EQUAL(bond_it->getOrder(), Bond::ORDER__SINGLE) break;
case 2: TEST_EQUAL(bond_it->getOrder(), Bond::ORDER__SINGLE) break;
case 3: TEST_EQUAL(bond_it->getOrder(), Bond::ORDER__SINGLE) break;
case 4: TEST_EQUAL(bond_it->getOrder(), Bond::ORDER__DOUBLE) break;
case 5: TEST_EQUAL(bond_it->getOrder(), Bond::ORDER__SINGLE) break;
default:
STATUS("Too many bonds")
TEST_EQUAL(0, 1)
}
i++;
}
RESULT
CHECK(FragmentDB::BuildBondsProcessor::operator () )
ABORT_IF(db.getResidue("GLY") == 0)
Residue res(*db.getResidue("GLY"));
AtomIterator atom_it = res.beginAtom();
for (; +atom_it; ++atom_it)
{
atom_it->destroyBonds();
}
// build the bonds
res.apply(db.build_bonds);
// check the bonds
Atom::BondIterator bond_it;
Position i = 0;
BALL_FOREACH_BOND(res, atom_it, bond_it)
{
switch (i)
{
case 0: TEST_EQUAL(bond_it->getOrder(), Bond::ORDER__SINGLE) break;
case 1: TEST_EQUAL(bond_it->getOrder(), Bond::ORDER__SINGLE) break;
case 2: TEST_EQUAL(bond_it->getOrder(), Bond::ORDER__SINGLE) break;
case 3: TEST_EQUAL(bond_it->getOrder(), Bond::ORDER__SINGLE) break;
case 4: TEST_EQUAL(bond_it->getOrder(), Bond::ORDER__DOUBLE) break;
case 5: TEST_EQUAL(bond_it->getOrder(), Bond::ORDER__SINGLE) break;
default:
STATUS("Too many bonds")
TEST_EQUAL(0, 1)
}
i++;
}
RESULT
CHECK(FragmentDB::BuildBondsProcessor::operator () / Tripeptide)
HINFile infile(BALL_TEST_DATA_PATH(AlaGlySer.hin));
System S;
infile >> S;
TEST_EQUAL(S.countAtoms(), 31)
TEST_EQUAL(S.countResidues(), 3)
ABORT_IF(S.countResidues() != 3)
Atom::BondIterator bond_it;
AtomIterator atom_it;
ResidueIterator res_it = S.beginResidue();
for (; +res_it; ++res_it)
{
Size number_of_atoms = 0;;
BALL_FOREACH_BOND(*res_it, atom_it, bond_it)
{
number_of_atoms++;
STATUS(" " << bond_it->getFirstAtom()->getFullName() << "-" << bond_it->getSecondAtom()->getFullName())
}
STATUS("Number of bonds in residue " << res_it->getName() << ": " << number_of_atoms)
}
atom_it = S.beginAtom();
for (; +atom_it; ++atom_it)
{
atom_it->destroyBonds();
}
// build the bonds
S.apply(db.build_bonds);
// check the bonds
Position residue = 0;
for (res_it = S.beginResidue(); +res_it; ++res_it)
{
Position i = 0;
BALL_FOREACH_BOND(*res_it, atom_it, bond_it)
{
i++;
STATUS(" " << bond_it->getFirstAtom()->getFullName() << "-" << bond_it->getSecondAtom()->getFullName())
}
STATUS("Number of bonds in residue " << residue << " (" << res_it->getName() << "): " << i)
switch (residue)
{
case 0:
case 2:
TEST_EQUAL(i, 12)
break;
case 1:
TEST_EQUAL(i, 8);
break;
default:
STATUS("We should never have gotten here!")
TEST_EQUAL(1, 2)
}
residue++;
}
// Check the bonds within the whole protein
RESULT
CHECK(FragmentDB::BuildBondsProcessor::operator () / BPTI)
PDBFile infile(BALL_TEST_DATA_PATH(OoiEnergy_test.pdb));
System S;
infile >> S;
TEST_EQUAL(S.countAtoms(), 892)
TEST_EQUAL(S.countResidues(), 58)
ABORT_IF(S.countResidues() != 58)
// Delete all bonds
S.destroyBonds();
TEST_EQUAL(S.countBonds(), 0)
// build the bonds
S.apply(db.build_bonds);
TEST_EQUAL(S.countBonds(), 906)
RESULT
CHECK([EXTRA]DNA bond contruction)
PDBFile f(BALL_TEST_DATA_PATH(AG.pdb));
System S;
f.read(S);
f.close();
STATUS("number of atoms: " << S.countAtoms())
STATUS("number of bonds: " << S.countBonds())
TEST_EQUAL(S.countAtoms(), 34)
ABORT_IF(S.countAtoms() != 34)
FragmentDB db("");
STATUS("number of atoms: " << S.countAtoms())
STATUS("number of bonds: " << S.countBonds())
S.apply(db.build_bonds);
STATUS("number of atoms: " << S.countAtoms())
STATUS("number of bonds: " << S.countBonds())
S.apply(db.add_hydrogens);
STATUS("number of atoms: " << S.countAtoms())
STATUS("number of bonds: " << S.countBonds())
S.apply(db.build_bonds);
STATUS("number of atoms: " << S.countAtoms())
STATUS("number of bonds: " << S.countBonds())
RESULT
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
END_TEST
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