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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
#include <BALL/CONCEPT/classTest.h>
#include <BALLTestConfig.h>
///////////////////////////
#include <BALL/KERNEL/residue.h>
#include <BALL/KERNEL/chain.h>
#include <BALL/KERNEL/protein.h>
#include <BALL/KERNEL/system.h>
#include <BALL/KERNEL/PDBAtom.h>
#include <BALL/CONCEPT/textPersistenceManager.h>
#include <BALL/FORMAT/HINFile.h>
#include <BALL/MATHS/common.h>
///////////////////////////
START_TEST(Residue)
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
using namespace BALL;
using namespace std;
PRECISION(1E-5)
String filename;
NEW_TMP_FILE(filename)
CHECK(const PDBAtom* getPDBAtom(Position position) const throw())
Residue r1("r1");
TEST_EQUAL(r1.getPDBAtom(0), 0)
PDBAtom a1("a1");
r1.insert(a1);
TEST_EQUAL(r1.getPDBAtom(0), &a1)
RESULT
CHECK(void setID(const String& id) throw())
Residue r1("x");
TEST_EQUAL(r1.getID(), "")
r1.setID("");
TEST_EQUAL(r1.getID(), "")
r1.setID("r1");
TEST_EQUAL(r1.getID(), "r1")
RESULT
CHECK(const String& getID() const throw())
Residue r1("x");
TEST_EQUAL(r1.getID(), "")
r1.setID("");
TEST_EQUAL(r1.getID(), "")
r1.setID("r1");
TEST_EQUAL(r1.getID(), "r1")
RESULT
CHECK(void setInsertionCode(char insertion_code) throw())
Residue r1('x');
TEST_EQUAL(r1.getInsertionCode(), ' ')
r1.setInsertionCode('r');
TEST_EQUAL(r1.getInsertionCode(), 'r')
RESULT
CHECK(setInsertionCode invalid)
Residue r1('x');
TEST_EQUAL(r1.getInsertionCode(), ' ');
TEST_EXCEPTION(Exception::InvalidArgument, r1.setInsertionCode('\0'));
TEST_EQUAL(r1.getInsertionCode(), ' ');
RESULT
CHECK(void unsetInsertionCode())
Residue r1('x');
TEST_EQUAL(r1.getInsertionCode(), ' ');
r1.setInsertionCode('A');
TEST_EQUAL(r1.getInsertionCode(), 'A');
r1.unsetInsertionCode();
TEST_EQUAL(r1.getInsertionCode(), ' ');
RESULT
CHECK(char getInsertionCode() const throw())
Residue r1('x');
TEST_EQUAL(r1.getInsertionCode(), ' ')
r1.setInsertionCode('r');
TEST_EQUAL(r1.getInsertionCode(), 'r')
RESULT
CHECK(Size countPDBAtoms() const throw())
Residue r1('x');
PDBAtom a("a");
TEST_EQUAL(r1.countPDBAtoms(), 0)
r1.insert(a);
TEST_EQUAL(r1.countPDBAtoms(), 1)
RESULT
CHECK(void prepend(PDBAtom& atom) throw())
Residue r1('x');
PDBAtom a1("a1");
PDBAtom a2("a2");
r1.prepend(a1);
r1.prepend(a2);
TEST_EQUAL(r1.getPDBAtom(0), &a2)
TEST_EQUAL(r1.getPDBAtom(1), &a1)
RESULT
CHECK(void append(PDBAtom& atom) throw())
Residue r1('x');
PDBAtom a1("a1");
PDBAtom a2("a2");
r1.append(a1);
r1.append(a2);
TEST_EQUAL(r1.getPDBAtom(0), &a1)
TEST_EQUAL(r1.getPDBAtom(1), &a2)
RESULT
CHECK(void insert(PDBAtom& atom) throw())
Residue r1('x');
PDBAtom a1("a1");
PDBAtom a2("a2");
r1.insert(a1);
r1.insert(a2);
TEST_EQUAL(r1.getPDBAtom(0), &a1)
TEST_EQUAL(r1.getPDBAtom(1), &a2)
RESULT
CHECK(void insertBefore(PDBAtom& atom, Composite& before) throw())
Residue r1('x');
PDBAtom a1("a1");
PDBAtom a2("a2");
PDBAtom a3("a3");
r1.insert(a1);
r1.insert(a2);
r1.insertBefore(a3, a2);
TEST_EQUAL(r1.getPDBAtom(0), &a1)
TEST_EQUAL(r1.getPDBAtom(1), &a3)
TEST_EQUAL(r1.getPDBAtom(2), &a2)
RESULT
CHECK(void insertAfter(PDBAtom& atom, Composite& after) throw())
Residue r1('x');
PDBAtom a1("a1");
PDBAtom a2("a2");
PDBAtom a3("a3");
r1.insert(a1);
r1.insert(a2);
r1.insertAfter(a3, a2);
TEST_EQUAL(r1.getPDBAtom(0), &a1)
TEST_EQUAL(r1.getPDBAtom(1), &a2)
TEST_EQUAL(r1.getPDBAtom(2), &a3)
RESULT
CHECK(bool remove(PDBAtom& atom) throw())
Residue r1('x');
PDBAtom a1("a1");
PDBAtom a2("a2");
PDBAtom a3("a3");
r1.insert(a1);
r1.insert(a2);
r1.insertAfter(a3, a2);
r1.remove(a2);
TEST_EQUAL(r1.getPDBAtom(0), &a1)
TEST_EQUAL(r1.getPDBAtom(1), &a3)
RESULT
CHECK(void spliceBefore(Residue& residue) throw())
Residue r1('x');
Residue r2('x');
PDBAtom a1("a1");
PDBAtom a2("a2");
r1.insert(a1);
r2.insert(a2);
r1.spliceBefore(r2);
TEST_EQUAL(r1.getPDBAtom(0), &a2)
TEST_EQUAL(r1.getPDBAtom(1), &a1)
RESULT
CHECK(void spliceAfter(Residue& residue) throw())
Residue r1('x');
Residue r2('x');
PDBAtom a1("a1");
PDBAtom a2("a2");
r1.insert(a1);
r2.insert(a2);
r1.spliceAfter(r2);
TEST_EQUAL(r1.getPDBAtom(0), &a1)
TEST_EQUAL(r1.getPDBAtom(1), &a2)
RESULT
CHECK(void splice(Residue& residue) throw())
Residue r1('x');
Residue r2('x');
PDBAtom a1("a1");
PDBAtom a2("a2");
r1.insert(a1);
r2.insert(a2);
r1.splice(r2);
TEST_EQUAL(r1.getPDBAtom(0), &a2)
TEST_EQUAL(r1.getPDBAtom(1), &a1)
RESULT
CHECK(bool isAminoAcid() const throw())
Residue r1('x');
TEST_EQUAL(r1.isAminoAcid(), false)
r1.setProperty(Residue::PROPERTY__AMINO_ACID);
TEST_EQUAL(r1.isAminoAcid(), true)
RESULT
CHECK(bool isTerminal() const throw())
Residue r1('x');
r1.setProperty(Residue::PROPERTY__AMINO_ACID);
TEST_EQUAL(r1.isTerminal(), false)
Chain c1;
c1.insert(r1);
TEST_EQUAL(r1.isTerminal(), true)
Residue r2('x');
Residue r3('x');
r2.setProperty(Residue::PROPERTY__AMINO_ACID);
r3.setProperty(Residue::PROPERTY__AMINO_ACID);
c1.append(r2);
TEST_EQUAL(r1.isTerminal(), true)
c1.prepend(r3);
TEST_EQUAL(r1.isTerminal(), false)
RESULT
CHECK(bool isNTerminal() const throw())
Residue r1('x');
r1.setProperty(Residue::PROPERTY__AMINO_ACID);
TEST_EQUAL(r1.isNTerminal(), false)
Chain c1;
c1.insert(r1);
TEST_EQUAL(r1.isNTerminal(), true)
Residue r2('x');
Residue r3('x');
r2.setProperty(Residue::PROPERTY__AMINO_ACID);
r3.setProperty(Residue::PROPERTY__AMINO_ACID);
c1.append(r2);
TEST_EQUAL(r1.isNTerminal(), true)
c1.prepend(r3);
TEST_EQUAL(r1.isNTerminal(), false)
RESULT
CHECK(bool isCTerminal() const throw())
Residue r1('x');
r1.setProperty(Residue::PROPERTY__AMINO_ACID);
TEST_EQUAL(r1.isCTerminal(), false)
Chain c1;
c1.insert(r1);
TEST_EQUAL(r1.isCTerminal(), true)
Residue r2('x');
Residue r3('x');
r2.setProperty(Residue::PROPERTY__AMINO_ACID);
r3.setProperty(Residue::PROPERTY__AMINO_ACID);
c1.prepend(r3);
TEST_EQUAL(r1.isCTerminal(), true)
c1.append(r2);
TEST_EQUAL(r1.isCTerminal(), false)
RESULT
CHECK(bool isValid() const throw())
Residue r("r1", "id", 'i');
TEST_EQUAL(r.isValid(), true)
r.setName("");
TEST_EQUAL(r.isValid(), true)
RESULT
CHECK(void dump(std::ostream& s = std::cout, Size depth = 0) const throw())
Residue r1("r1", "test", 'X');
PDBAtom a1("a1");
r1.insert(a1);
std::ofstream outfile(filename.c_str(), std::ios::out);
r1.dump(outfile);
outfile.close();
TEST_FILE_REGEXP(filename.c_str(), BALL_TEST_DATA_PATH(Residue_test.txt))
RESULT
TextPersistenceManager pm;
using namespace RTTI;
pm.registerClass(getStreamName<Atom>(), Atom::createDefault);
pm.registerClass(getStreamName<Molecule>(), Molecule::createDefault);
NEW_TMP_FILE(filename)
CHECK(void persistentWrite(PersistenceManager& pm, const char* name = 0) const)
std::ofstream ofile(filename.c_str(), std::ios::out);
Atom* f2= new Atom();
f2->setName("name2");
Atom* f3= new Atom();
f3->setName("name3");
Molecule* f1 = new Molecule("name1");
f1->insert(*f2);
f1->insert(*f3);
pm.setOstream(ofile);
*f1 >> pm;
ofile.close();
delete f1;
RESULT
CHECK(void persistentRead(PersistenceManager& pm))
std::ifstream ifile(filename.c_str());
pm.setIstream(ifile);
PersistentObject* ptr = pm.readObject();
TEST_NOT_EQUAL(ptr, 0)
if (ptr != 0)
{
TEST_EQUAL(isKindOf<Molecule>(ptr), true)
Molecule* f1 = castTo<Molecule>(*ptr);
TEST_EQUAL(f1->getName(), "name1")
TEST_EQUAL(f1->countAtoms(), 2)
TEST_EQUAL(f1->getAtom(0)->getName(), "name2")
TEST_EQUAL(f1->getAtom(1)->getName(), "name3")
delete f1;
}
else
{
throw Exception::NullPointer(__FILE__, __LINE__);
}
RESULT
CHECK(bool operator == (const Residue& residue) const throw())
Residue b1;
Residue b2;
TEST_EQUAL(b1 == b2, false)
b1 = b2;
TEST_EQUAL(b1 == b1, true)
RESULT
CHECK(bool operator != (const Residue& residue) const throw())
Residue b1;
Residue b2;
TEST_EQUAL(b1 != b2, true)
b1 = b2;
TEST_EQUAL(b1 != b1, false)
RESULT
CHECK(BALL_CREATE_DEEP(Residue))
Residue r1('x');
PDBAtom a1("a1");
r1.insert(a1);
Residue* test = (Residue*) r1.create(false, true);
TEST_EQUAL(test->getName(), "")
TEST_EQUAL(test->countPDBAtoms(), 0)
delete test;
test = (Residue*) r1.create(true, false);
TEST_EQUAL(test->getName(), "x")
TEST_EQUAL(test->countPDBAtoms(), 1)
delete test;
RESULT
CHECK(BALL_KERNEL_DEFINE_ITERATOR_CREATORS(PDBAtom))
Residue c;
PDBAtom p1,p2,p3;
c.insert(p1);
c.insert(p2);
c.insert(p3);
TEST_EQUAL(&*c.beginPDBAtom(), &p1)
TEST_EQUAL(&*++c.beginPDBAtom(), &p2)
TEST_EQUAL(&*--c.endPDBAtom(), &p3)
TEST_EQUAL(&*c.rbeginPDBAtom(), &p3)
RESULT
// ============================================================
// not to be tested:
// ============================================================
CHECK(BALL_KERNEL_DEFINE_ITERATOR_CREATORS(AtomContainer))
// not to be tested
RESULT
CHECK(Size countAtomContainers() const throw())
// not to be tested
RESULT
CHECK(bool isSuperAtomContainerOf(const AtomContainer& atom_container) const throw())
// not to be tested
RESULT
CHECK(bool remove(AtomContainer& AtomContainer) throw())
// not to be tested
RESULT
CHECK(const AtomContainer* getAtomContainer(Position position) const throw())
// not to be tested
RESULT
CHECK(void append(AtomContainer& atom_container) throw())
// not to be tested
RESULT
CHECK(void insert(AtomContainer& atom_container) throw())
// not to be tested
RESULT
CHECK(void insertAfter(AtomContainer& atom_container, Composite& composite) throw())
// not to be tested
RESULT
CHECK(void insertBefore(AtomContainer& atom_container, Composite& composite) throw())
// not to be tested
RESULT
CHECK(void prepend(AtomContainer& atom_container) throw())
// not to be tested
RESULT
CHECK(void splice(AtomContainer& AtomContainer) throw())
// not to be tested
RESULT
CHECK(void spliceAfter(AtomContainer& base_ragment) throw())
// not to be tested
RESULT
CHECK(void spliceBefore(AtomContainer& atom_container) throw())
// not to be tested
RESULT
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
END_TEST
|
