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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/CONCEPT/textPersistenceManager.h>
#include <BALL/KERNEL/secondaryStructure.h>
#include <BALL/KERNEL/protein.h>
///////////////////////////
START_TEST(SecondaryStructure)
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
using namespace BALL;
String filename;
using std::ofstream;
using std::ios;
SecondaryStructure* s1;
CHECK(SecondaryStructure() throw())
s1 = new SecondaryStructure;
TEST_NOT_EQUAL(s1, 0)
RESULT
CHECK(~SecondaryStructure() throw())
delete s1;
RESULT
CHECK(SecondaryStructure(const SecondaryStructure& secondary_structure, bool deep = true) throw())
Residue r1;
SecondaryStructure s1("s1"), s2;
s1.append(r1);
s2 = SecondaryStructure(s1);
TEST_EQUAL(s2.getName(), "s1")
TEST_EQUAL(s2.countResidues(), 1)
RESULT
CHECK(SecondaryStructure(const String& name) throw())
SecondaryStructure s1("s1");
TEST_EQUAL(s1.getName(), "s1")
SecondaryStructure s2("");
TEST_EQUAL(s2.getName(), "")
RESULT
CHECK(void clear() throw())
Protein p1;
SecondaryStructure s1("s1");
Residue r1;
p1.append(s1);
s1.append(r1);
s1.clear();
TEST_EQUAL(s1.getName(), "")
TEST_EQUAL(s1.countResidues(), 0)
RESULT
CHECK(void destroy() throw())
Protein p1;
SecondaryStructure s1("s1");
Residue r1;
p1.append(s1);
s1.append(r1);
s1.destroy();
TEST_EQUAL(s1.getName(), "")
TEST_EQUAL(s1.countResidues(), 0)
RESULT
CHECK(void set(const SecondaryStructure& secondary_structure, bool deep = true) throw())
SecondaryStructure s1("s1"), s2;
Residue r1;
s1.append(r1);
s2.set(s1);
TEST_EQUAL(s2.getName(), "s1")
TEST_EQUAL(s2.countResidues(), 1)
RESULT
CHECK(SecondaryStructure& operator = (const SecondaryStructure& secondary_structure) throw())
SecondaryStructure s1("s1"), s2;
Residue r1;
s1.append(r1);
s2 = s1;
TEST_EQUAL(s2.getName(), "s1")
TEST_EQUAL(s2.countResidues(), 1)
RESULT
CHECK(void get(SecondaryStructure& secondary_structure, bool deep = true) const throw())
SecondaryStructure s1("s1"), s2;
Residue r1;
s1.append(r1);
s1.get(s2);
TEST_EQUAL(s2.getName(), "s1")
TEST_EQUAL(s2.countResidues(), 1)
RESULT
CHECK(void swap(SecondaryStructure& secondary_structure) throw())
SecondaryStructure s1("s1");
SecondaryStructure s2("s2");
Residue r1, r2, r3;
s1.append(r1);
s1.append(r2);
s2.append(r3);
s1.swap(s2);
TEST_EQUAL(s1.getName(), "s2")
TEST_EQUAL(s1.countResidues(), 1)
TEST_EQUAL(s2.getName(), "s1")
TEST_EQUAL(s2.countResidues(), 2)
RESULT
CHECK(Protein* getProtein() throw())
Protein p1;
SecondaryStructure s1("s1");
p1.append(s1);
s1.getProtein()->setName("X");
TEST_EQUAL(p1.getName(), "X")
RESULT
CHECK(const Protein* getProtein() const throw())
Protein p1("X");
SecondaryStructure s1("s1");
p1.append(s1);
const Protein p2(p1);
TEST_EQUAL(s1.getProtein()->getName(), "X")
RESULT
CHECK(Chain* getChain() throw())
Chain c1;
SecondaryStructure s1("s1");
c1.append(s1);
s1.getChain()->setName("X");
TEST_EQUAL(c1.getName(), "X")
RESULT
CHECK(const Chain* getChain() const throw())
Chain c1("X");
SecondaryStructure s1("s1");
c1.append(s1);
const Chain p2(c1);
TEST_EQUAL(s1.getChain()->getName(), "X")
RESULT
CHECK(Residue* getResidue(Position position) throw())
SecondaryStructure s1("s1");
TEST_EQUAL(s1.getResidue(0), 0)
Residue r1("X");
s1.insert(r1);
s1.getResidue(0)->setName("r1");
TEST_EQUAL(r1.getName(), "r1")
RESULT
CHECK(const Residue* getResidue(Position position) const throw())
SecondaryStructure s1("s1");
TEST_EQUAL(s1.getResidue(0), 0)
Residue r1("r1");
s1.insert(r1);
TEST_EQUAL(s1.getResidue(0), &r1)
RESULT
CHECK(PDBAtom* getPDBAtom(Position position) throw())
SecondaryStructure s1("s1");
TEST_EQUAL(s1.getPDBAtom(0), 0)
PDBAtom a1("x");
Residue r1;
s1.insert(r1);
r1.insert(a1);
s1.getPDBAtom(0)->setName("a1");
TEST_EQUAL(a1.getName(), "a1")
RESULT
CHECK(const PDBAtom* getPDBAtom(Position position) const throw())
SecondaryStructure s1("s1");
TEST_EQUAL(s1.getPDBAtom(0), 0)
Residue r1;
s1.insert(r1);
PDBAtom a1("a1");
r1.insert(a1);
TEST_EQUAL(s1.getPDBAtom(0), &a1)
RESULT
CHECK(Residue* getNTerminal() throw())
SecondaryStructure s1;
Residue r1("X");
Residue r2("r2");
r1.setProperty(Residue::PROPERTY__AMINO_ACID);
r2.setProperty(Residue::PROPERTY__AMINO_ACID);
TEST_EQUAL(s1.getNTerminal(), 0)
s1.insert(r1);
s1.insert(r2);
TEST_NOT_EQUAL(s1.getNTerminal(), 0)
if (s1.getNTerminal() != 0)
{
s1.getNTerminal()->setName("r1");
}
TEST_EQUAL(r1.getName(), "r1")
RESULT
CHECK(const Residue* getNTerminal() const throw())
SecondaryStructure s1;
Residue r1("r1");
Residue r2("r2");
r1.setProperty(Residue::PROPERTY__AMINO_ACID);
r2.setProperty(Residue::PROPERTY__AMINO_ACID);
TEST_EQUAL(s1.getNTerminal(), 0)
s1.insert(r1);
s1.insert(r2);
TEST_NOT_EQUAL(s1.getNTerminal(), 0)
if (s1.getNTerminal() != 0)
{
TEST_EQUAL(s1.getNTerminal()->getName(), "r1")
}
RESULT
CHECK(Residue* getCTerminal() throw())
SecondaryStructure s1;
Residue r1("1");
Residue r2("2");
r1.setProperty(Residue::PROPERTY__AMINO_ACID);
r2.setProperty(Residue::PROPERTY__AMINO_ACID);
TEST_EQUAL(s1.getCTerminal(), 0)
s1.insert(r1);
s1.insert(r2);
TEST_NOT_EQUAL(s1.getCTerminal(), 0)
if (s1.getCTerminal() != 0)
{
s1.getCTerminal()->setName("r2");
}
TEST_EQUAL(r2.getName(), "r2")
RESULT
CHECK(const Residue* getCTerminal() const throw())
SecondaryStructure s1;
Residue r1("r1");
Residue r2("r2");
r1.setProperty(Residue::PROPERTY__AMINO_ACID);
r2.setProperty(Residue::PROPERTY__AMINO_ACID);
TEST_EQUAL(s1.getCTerminal(), 0)
s1.insert(r1);
s1.insert(r2);
TEST_NOT_EQUAL(s1.getCTerminal(), 0)
if (s1.getCTerminal() != 0)
{
TEST_EQUAL(s1.getCTerminal()->getName(), "r2")
}
RESULT
CHECK(Size countResidues() const throw())
SecondaryStructure s1;
Residue r1("r1");
TEST_EQUAL(s1.countResidues(), 0)
s1.insert(r1);
TEST_EQUAL(s1.countResidues(), 1)
RESULT
CHECK(Size countPDBAtoms() const throw())
SecondaryStructure s1;
Residue r1("r1");
PDBAtom a1("a1");
r1.insert(a1);
TEST_EQUAL(s1.countPDBAtoms(), 0)
s1.insert(r1);
TEST_EQUAL(s1.countPDBAtoms(), 1)
RESULT
CHECK(void prepend(Residue& residue) throw())
SecondaryStructure s1;
Residue r1;
Residue r2;
s1.insert(r1);
TEST_EQUAL(s1.getResidue(0), &r1)
s1.prepend(r2);
TEST_EQUAL(s1.getResidue(0), &r2)
TEST_EQUAL(s1.getResidue(1), &r1)
RESULT
CHECK(void append(Residue& residue) throw())
SecondaryStructure s1;
Residue r1;
Residue r2;
s1.insert(r1);
s1.append(r2);
TEST_EQUAL(s1.getResidue(0), &r1)
TEST_EQUAL(s1.getResidue(1), &r2)
RESULT
CHECK(void insert(Residue& residue) throw())
SecondaryStructure s1;
Residue r1;
Residue r2;
s1.insert(r1);
s1.insert(r2);
TEST_EQUAL(s1.getResidue(0), &r1)
TEST_EQUAL(s1.getResidue(1), &r2)
RESULT
CHECK(void insertBefore(Residue& residue, Composite& before) throw())
SecondaryStructure s1;
Residue r1;
Residue r2;
Residue r3;
s1.insert(r1);
s1.append(r2);
s1.insertBefore(r3, r2);
TEST_EQUAL(s1.getResidue(0), &r1)
TEST_EQUAL(s1.getResidue(1), &r3)
TEST_EQUAL(s1.getResidue(2), &r2)
RESULT
CHECK(void insertAfter(Residue& residue, Composite& after) throw())
SecondaryStructure s1;
Residue r1;
Residue r2;
Residue r3;
s1.insert(r1);
s1.append(r2);
s1.insertAfter(r3, r1);
TEST_EQUAL(s1.getResidue(0), &r1)
TEST_EQUAL(s1.getResidue(1), &r3)
TEST_EQUAL(s1.getResidue(2), &r2)
RESULT
CHECK(bool remove(Residue& residue) throw())
SecondaryStructure s1("s1");
Residue r1;
Residue r2;
s1.append(r1);
s1.append(r2);
s1.remove(r1);
TEST_EQUAL(s1.countResidues(), 1)
TEST_EQUAL(s1.getResidue(0), &r2)
RESULT
CHECK(void spliceBefore(SecondaryStructure& secondary_structure) throw())
SecondaryStructure s1('x');
SecondaryStructure s2('x');
Residue r1("r1");
Residue r2("r2");
s1.insert(r1);
s2.insert(r2);
s1.spliceBefore(s2);
TEST_EQUAL(s1.getResidue(0), &r2)
TEST_EQUAL(s1.getResidue(1), &r1)
RESULT
CHECK(void spliceAfter(SecondaryStructure& secondary_structure) throw())
SecondaryStructure s1('x');
SecondaryStructure s2('x');
Residue r1("r1");
Residue r2("r2");
s1.insert(r1);
s2.insert(r2);
s1.spliceAfter(s2);
TEST_EQUAL(s1.getResidue(0), &r1)
TEST_EQUAL(s1.getResidue(1), &r2)
RESULT
CHECK(void splice(SecondaryStructure& secondary_structure) throw())
SecondaryStructure s1('x');
SecondaryStructure s2('x');
Residue r1("r1");
Residue r2("r2");
s1.insert(r1);
s2.insert(r2);
s1.splice(s2);
TEST_EQUAL(s1.getResidue(0), &r2)
TEST_EQUAL(s1.getResidue(1), &r1)
RESULT
CHECK(bool isValid() const throw())
SecondaryStructure s1("s1");
Residue r1;
s1.append(r1);
TEST_EQUAL(s1.isValid(), true)
RESULT
CHECK(void dump(std::ostream& s = std::cout, Size depth = 0) const throw())
SecondaryStructure s1("SecondaryStructure1");
Residue r1, r2;
r1.setName("Residue1");
r2.setName("Residue2");
s1.append(r1);
s1.append(r2);
NEW_TMP_FILE(filename)
std::ofstream outfile(filename.c_str(), std::ios::out);
s1.dump(outfile);
outfile.close();
TEST_FILE_REGEXP(filename.c_str(), BALL_TEST_DATA_PATH(SecondaryStructure_test.txt))
RESULT
TextPersistenceManager pm;
using namespace RTTI;
pm.registerClass(getStreamName<SecondaryStructure>(), SecondaryStructure::createDefault);
pm.registerClass(getStreamName<Residue>(), Residue::createDefault);
NEW_TMP_FILE(filename)
CHECK(void persistentWrite(PersistenceManager& pm, const char* name = 0) const)
std::ofstream ofile(filename.c_str(), std::ios::out);
SecondaryStructure* f1= new SecondaryStructure("name1");
Residue* f2 = new Residue("name2");
Residue* f3 = new Residue("name3");
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<SecondaryStructure>(ptr), true)
SecondaryStructure* f1 = castTo<SecondaryStructure>(*ptr);
TEST_EQUAL(f1->getName(), "name1")
TEST_EQUAL(f1->countResidues(), 2)
TEST_EQUAL(f1->getResidue(0)->getName(), "name2")
TEST_EQUAL(f1->getResidue(1)->getName(), "name3")
delete f1;
}
else
{
throw Exception::NullPointer(__FILE__, __LINE__);
}
RESULT
CHECK(bool operator == (const SecondaryStructure& secondary_structure) const throw())
SecondaryStructure b1;
SecondaryStructure b2;
TEST_EQUAL(b1 == b2, false)
b1 = b2;
TEST_EQUAL(b1 == b1, true)
RESULT
CHECK(bool operator != (const SecondaryStructure& secondary_structure) const throw())
SecondaryStructure b1;
SecondaryStructure b2;
TEST_EQUAL(b1 != b2, true)
b1 = b2;
TEST_EQUAL(b1 != b1, false)
RESULT
CHECK(BALL_CREATE_DEEP(SecondaryStructure))
SecondaryStructure s1("s1");
Residue r1('x');
s1.insert(r1);
SecondaryStructure* test = (SecondaryStructure*) s1.create(false, true);
TEST_EQUAL(test->getName(), "")
TEST_EQUAL(test->countResidues(), 0)
delete test;
test = (SecondaryStructure*) s1.create(true, false);
TEST_EQUAL(test->getName(), "s1")
TEST_EQUAL(test->countResidues(), 1)
delete test;
RESULT
CHECK(BALL_KERNEL_DEFINE_ITERATOR_CREATORS (Residue)(PDBAtom))
SecondaryStructure c;
Residue r1, r2;
c.insert(r1);
c.insert(r2);
PDBAtom p1,p2,p3;
r1.insert(p1);
r2.insert(p2);
r2.insert(p3);
TEST_EQUAL(&*c.beginResidue(), &r1)
TEST_EQUAL(&*--c.endResidue(), &r2)
TEST_EQUAL(&*c.rbeginResidue(), &r2)
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(Atom* getAtom(Position position) throw())
// not to be tested
RESULT
CHECK(bool remove(Atom &atom) throw())
// not to be tested
RESULT
CHECK(bool remove(AtomContainer &atom_container) throw())
// not to be tested
RESULT
CHECK(const Atom* getAtom(Position position) const throw())
// not to be tested
RESULT
CHECK(const Fragment* getFragment(Position position) const throw())
// not to be tested
RESULT
CHECK(void append(Atom &atom) throw())
// not to be tested
RESULT
CHECK(void append(AtomContainer &atom_container) throw())
// not to be tested
RESULT
CHECK(void insert(Atom &atom) throw())
// not to be tested
RESULT
CHECK(void insert(AtomContainer &atom_container) throw())
// not to be tested
RESULT
CHECK(void insertAfter(Atom &atom, Composite &after) throw())
// not to be tested
RESULT
CHECK(void insertAfter(AtomContainer &atom_container, Composite &after) throw())
// not to be tested
RESULT
CHECK(void insertBefore(Atom &atom, Composite &before) throw())
// not to be tested
RESULT
CHECK(void insertBefore(AtomContainer &atom_container, Composite &before) throw())
// not to be tested
RESULT
CHECK(void prepend(Atom &atom) throw())
// not to be tested
RESULT
CHECK(void prepend(AtomContainer &atom_container) throw())
// not to be tested
RESULT
CHECK(void splice(AtomContainer &atom_container) throw())
// not to be tested
RESULT
CHECK(void spliceAfter(AtomContainer &atom_container) throw())
// not to be tested
RESULT
CHECK(void spliceBefore(AtomContainer &atom_container) throw())
// not to be tested
RESULT
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
END_TEST
|
