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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
#include <BALL/CONCEPT/classTest.h>
#include <BALLTestConfig.h>
///////////////////////////
#include <BALL/FORMAT/MOL2File.h>
#include <BALL/KERNEL/forEach.h>
#include <BALL/KERNEL/PTE.h>
#include <BALL/KERNEL/atom.h>
#include <BALL/KERNEL/bond.h>
#include <BALL/KERNEL/system.h>
#include <BALL/KERNEL/molecule.h>
#include <BALL/MATHS/vector3.h>
///////////////////////////
START_TEST(MOL2File)
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
using namespace BALL;
MOL2File* mf = 0;
CHECK(MOL2File::MOL2File())
mf = new MOL2File;
TEST_NOT_EQUAL(mf, 0)
RESULT
CHECK(MOL2File::~MOL2File())
delete mf;
RESULT
CHECK(MOL2File::read(System& system))
MOL2File f(BALL_TEST_DATA_PATH(AAG.mol2));
System system;
f.read(system);
TEST_EQUAL(system.countAtoms(), 30)
TEST_EQUAL(system.countResidues(), 3)
TEST_EQUAL(system.countBonds(), 29)
RESULT
CHECK(MOL2File::MOL2File(const String& filename, File::OpenMode open_mode))
MOL2File f(BALL_TEST_DATA_PATH(AAG.mol2), std::ios::in);
System system;
f.read(system);
TEST_EQUAL(system.countAtoms(), 30)
TEST_EQUAL(system.countResidues(), 3)
TEST_EQUAL(system.countBonds(), 29)
MOL2File f2(BALL_TEST_DATA_PATH(chimera-test.mol2));
System s2;
f2.read(s2);
TEST_EQUAL(s2.countAtoms(), 3);
TEST_EQUAL(s2.countBonds(), 2);
// writing is tested below...
RESULT
CHECK(MOL2File::write(const System& system))
Molecule* m = new Molecule;
m->setName("MOL");
System S;
S.setName("SYSTEM");
S.insert(*m);
Atom* a1 = new Atom();
Atom* a2 = new Atom();
m->insert(*a1);
m->insert(*a2);
a1->setName("A1");
a1->setElement(PTE[Element::N]);
a1->setCharge(0.5);
a1->setPosition(Vector3(0.1, 0.2, 0.3));
a2->setName("A2");
a2->setElement(PTE[Element::O]);
a2->setCharge(-0.5);
a2->setPosition(Vector3(0.5, 0.6, 0.7));
a1->createBond(*a2);
a1->getBond(*a2)->setOrder(Bond::ORDER__DOUBLE);
String filename;
NEW_TMP_FILE(filename)
MOL2File f(filename, std::ios::out);
f.write(S);
f.close();
TEST_FILE_REGEXP(filename.c_str(), BALL_TEST_DATA_PATH(MOL2File_test.mol2))
RESULT
CHECK(MOL2File::MOL2File& operator >> (System& system))
MOL2File f(BALL_TEST_DATA_PATH(AAG.mol2));
System S;
f >> S;
f.close();
TEST_EQUAL(S.countAtoms(), 30)
RESULT
CHECK(MOL2File::MOL2File& operator << (const System& system))
Molecule* m = new Molecule;
m->setName("MOL");
System S;
S.setName("SYSTEM");
S.insert(*m);
Atom* a1 = new Atom();
Atom* a2 = new Atom();
m->insert(*a1);
m->insert(*a2);
a1->setName("A1");
a1->setElement(PTE[Element::N]);
a1->setCharge(0.5);
a1->setPosition(Vector3(0.1, 0.2, 0.3));
a2->setName("A2");
a2->setElement(PTE[Element::O]);
a2->setCharge(-0.5);
a2->setPosition(Vector3(0.5, 0.6, 0.7));
a1->createBond(*a2);
a1->getBond(*a2)->setOrder(Bond::ORDER__DOUBLE);
String filename;
NEW_TMP_FILE(filename)
MOL2File f(filename, std::ios::out);
f << S;
f.close();
TEST_FILE_REGEXP(filename.c_str(), BALL_TEST_DATA_PATH(MOL2File_test.mol2))
RESULT
CHECK([Extra]Reading of triple bonds)
MOL2File f(BALL_TEST_DATA_PATH(MOL2File_test2.mol2));
System S;
CAPTURE_OUTPUT_LEVEL(2000)
f >> S;
COMPARE_OUTPUT("")
f.close();
TEST_EQUAL(S.countAtoms(), 21)
TEST_EQUAL(S.countResidues(), 0)
TEST_EQUAL(S.countBonds(), 23)
RESULT
CHECK([Extra]Handling of subfragments)
MOL2File f(BALL_TEST_DATA_PATH(MOL2File_test3.mol2));
System S;
CAPTURE_OUTPUT_LEVEL(2000)
f >> S;
COMPARE_OUTPUT("")
f.close();
TEST_EQUAL(S.countAtoms(), 47)
TEST_EQUAL(S.countFragments(), 3)
TEST_EQUAL(S.countBonds(), 51)
Size n = 1;
for (FragmentIterator fi(S.beginFragment()); +fi; ++fi, ++n)
{
Size na = 0;
Size nb = 0;
switch (n)
{
case 1: na = 43; nb = 49; break;
case 2:
case 3: na = 2; nb = 1; break;
default: break;
}
TEST_EQUAL(fi->countAtoms(), na)
TEST_EQUAL(fi->countBonds(), nb)
}
RESULT
CHECK([Extra]Handling of static sets)
MOL2File f(BALL_TEST_DATA_PATH(MOL2File_test4.mol2));
System S;
CAPTURE_OUTPUT_LEVEL(2000)
f >> S;
COMPARE_OUTPUT("");
f.close();
TEST_EQUAL(f.getNumberOfSets(), 1)
MOL2File::SetStruct& set = f.getSet(0);
TEST_EQUAL(set.number_of_members, 16)
for (Position i=0; i<set.number_of_members; i++)
TEST_EQUAL((Position)set.static_members[i], i+1)
RESULT
CHECK([Extra]Handling of linebreaks in static sets)
MOL2File f(BALL_TEST_DATA_PATH(MOL2File_test_set_linebreak.mol2));
System S;
f >> S;
TEST_EQUAL(f.getNumberOfSets(), 1)
MOL2File::SetStruct& set = f.getSet(0);
TEST_EQUAL(set.number_of_members, 20)
for (Position i=0; i<set.number_of_members; i++)
TEST_EQUAL((Position)set.static_members[i], i+1)
RESULT
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
END_TEST
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