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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
#include <BALL/CONCEPT/classTest.h>
#include <BALLTestConfig.h>
#include <BALL/KERNEL/PTE.h>
#include <BALL/KERNEL/system.h>
#include <BALL/STRUCTURE/addHydrogenProcessor.h>
#include <BALL/STRUCTURE/fragmentDB.h>
#include <BALL/STRUCTURE/peptideBuilder.h>
START_TEST(class_name)
using namespace BALL;
FragmentDB db("");
CHECK(AddHydrogenProcessor::AddHydrogenProcessor())
AddHydrogenProcessor proc;
TEST_EQUAL(proc.getNumberOfAddedHydrogens(), 0);
RESULT
CHECK(AddHydrogenProcessor::start())
AddHydrogenProcessor proc;
System s;
Molecule m;
Atom a(PTE["C"], "C");
m.insert(a);
s.insert(m);
s.apply(proc);
TEST_EQUAL(proc.getNumberOfAddedHydrogens(), 4);
TEST_EQUAL(proc.start(), true);
TEST_EQUAL(proc.getNumberOfAddedHydrogens(), 0);
RESULT
CHECK(AddHydrogenProcessor::operator()(Atom&))
AddHydrogenProcessor proc;
Atom a(PTE[Element::C], "C");
proc(a);
TEST_EQUAL(a.countBonds(), 4);
// Proper cleanup
std::vector<Atom*> partners;
for(Atom::BondIterator it = a.beginBond(); +it; ++it) {
partners.push_back(it->getPartner(a));
}
for(std::vector<Atom*>::iterator it = partners.begin(); it != partners.end(); ++it) {
delete *it;
}
TEST_EQUAL(proc.getNumberOfAddedHydrogens(), 4);
RESULT
CHECK(AddHydrogenProcessor::operator()(Residue&))
AddHydrogenProcessor proc;
// Build a dipeptide
Peptides::PeptideBuilder builder("GG");
builder.setFragmentDB(&db);
Protein* prot = builder.construct();
// Delete the peptide bond H
Fragment* res = prot->getChain(0)->getResidue(1);
Atom* hatom = res->getAtom("H");
res->remove(*hatom);
delete hatom;
proc(*res);
TEST_EQUAL(proc.getNumberOfAddedHydrogens(), 1);
delete prot;
RESULT
CHECK(AddHydrogenProcessor::getConnectivity(const Atom&) const)
AddHydrogenProcessor proc;
Atom c(PTE[Element::C], "C");
Atom o(PTE[Element::O], "O");
Atom n(PTE[Element::N], "N");
Atom p(PTE[Element::P], "P");
Atom f(PTE[Element::F], "F");
TEST_EQUAL(proc.getConnectivity(c), 4);
TEST_EQUAL(proc.getConnectivity(o), 2);
TEST_EQUAL(proc.getConnectivity(n), 3);
TEST_EQUAL(proc.getConnectivity(p), 3);
TEST_EQUAL(proc.getConnectivity(f), 1);
RESULT
CHECK(Composite::apply(AddHydrogenProcessor&))
AddHydrogenProcessor proc;
// Build a dipeptide
Peptides::PeptideBuilder builder("GG");
builder.setFragmentDB(&db);
Protein* prot = builder.construct();
TEST_EQUAL(prot->countAtoms(), 17);
// Delete the peptide bond H
Fragment* res = prot->getChain(0)->getResidue(1);
Atom* hatom = res->getAtom("H");
res->remove(*hatom);
delete hatom;
TEST_EQUAL(prot->countAtoms(), 16);
TEST_EQUAL(proc.getNumberOfAddedHydrogens(), 0);
prot->apply(proc);
TEST_EQUAL(proc.getNumberOfAddedHydrogens(), 2);
TEST_EQUAL(prot->countAtoms(), 18);
delete prot;
RESULT
//getNumberOfAddedHydrogens() const is already implicitly checked
//setRings() is not really checkable
END_TEST
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