// === MmffVanDerWaalsCalculation ========================================== //
MmffVanDerWaalsCalculation::MmffVanDerWaalsCalculation(const MmffAtom *a,
const MmffAtom *b)
: MmffCalculation(VanDerWaals, 2, 2)
{
setAtom(0, a);
setAtom(1, b);
}
// === OplsAngleBendCalculation ============================================ //
OplsAngleBendCalculation::OplsAngleBendCalculation(const chemkit::ForceFieldAtom *a, const chemkit::ForceFieldAtom *b, const chemkit::ForceFieldAtom *c)
: OplsCalculation(AngleBend, 3, 2)
{
setAtom(0, a);
setAtom(1, b);
setAtom(2, c);
}
// === MmffBondStrechCalculation =========================================== //
MmffBondStrechCalculation::MmffBondStrechCalculation(const MmffAtom *a,
const MmffAtom *b)
: MmffCalculation(BondStrech, 2, 2)
{
setAtom(0, a);
setAtom(1, b);
}
// === UffElectrostaticCalculation ========================================= //
UffElectrostaticCalculation::UffElectrostaticCalculation(const chemkit::ForceFieldAtom *a,
const chemkit::ForceFieldAtom *b)
: UffCalculation(Electrostatic, 2, 2)
{
setAtom(0, a);
setAtom(1, b);
}
// === UffVanDerWaalsCalculation =========================================== //
UffVanDerWaalsCalculation::UffVanDerWaalsCalculation(const chemkit::ForceFieldAtom *a,
const chemkit::ForceFieldAtom *b)
: UffCalculation(VanDerWaals, 2, 2)
{
setAtom(0, a);
setAtom(1, b);
}
// === MmffElectrostaticCalculation ======================================== //
MmffElectrostaticCalculation::MmffElectrostaticCalculation(const MmffAtom *a,
const MmffAtom *b)
: MmffCalculation(Electrostatic, 2, 3)
{
setAtom(0, a);
setAtom(1, b);
}
// === OplsTorsionCalculation ============================================== //
OplsTorsionCalculation::OplsTorsionCalculation(const chemkit::ForceFieldAtom *a, const chemkit::ForceFieldAtom *b, const chemkit::ForceFieldAtom *c, const chemkit::ForceFieldAtom *d)
: OplsCalculation(Torsion, 4, 3)
{
setAtom(0, a);
setAtom(1, b);
setAtom(2, c);
setAtom(3, d);
}
// === MmffStrechBendCalculation =========================================== //
MmffStrechBendCalculation::MmffStrechBendCalculation(const MmffAtom *a,
const MmffAtom *b,
const MmffAtom *c)
: MmffCalculation(BondStrech | AngleBend, 3, 5)
{
setAtom(0, a);
setAtom(1, b);
setAtom(2, c);
}
// === MmffAngleBendCalculation ============================================ //
MmffAngleBendCalculation::MmffAngleBendCalculation(const MmffAtom *a,
const MmffAtom *b,
const MmffAtom *c)
: MmffCalculation(AngleBend, 3, 2)
{
setAtom(0, a);
setAtom(1, b);
setAtom(2, c);
}
// === UffAngleBendCalculation ============================================= //
UffAngleBendCalculation::UffAngleBendCalculation(const chemkit::ForceFieldAtom *a,
const chemkit::ForceFieldAtom *b,
const chemkit::ForceFieldAtom *c)
: UffCalculation(AngleBend, 3, 4)
{
setAtom(0, a);
setAtom(1, b);
setAtom(2, c);
}
// === MmffTorsionCalculation ============================================== //
MmffTorsionCalculation::MmffTorsionCalculation(const MmffAtom *a,
const MmffAtom *b,
const MmffAtom *c,
const MmffAtom *d)
: MmffCalculation(Torsion, 4, 3)
{
setAtom(0, a);
setAtom(1, b);
setAtom(2, c);
setAtom(3, d);
}
// === UffInversionCalculation ============================================= //
UffInversionCalculation::UffInversionCalculation(const chemkit::ForceFieldAtom *a,
const chemkit::ForceFieldAtom *b,
const chemkit::ForceFieldAtom *c,
const chemkit::ForceFieldAtom *d)
: UffCalculation(Inversion, 4, 4)
{
setAtom(0, a);
setAtom(1, b);
setAtom(2, c);
setAtom(3, d);
}
// === MmffOutOfPlaneBendingCalculation ==================================== //
MmffOutOfPlaneBendingCalculation::MmffOutOfPlaneBendingCalculation(const MmffAtom *a,
const MmffAtom *b,
const MmffAtom *c,
const MmffAtom *d)
: MmffCalculation(Inversion, 4, 1)
{
setAtom(0, a);
setAtom(1, b);
setAtom(2, c);
setAtom(3, d);
}
Residue::~Residue()
{
int i;
if (name != NULL)
{
delete [] name;
name = NULL;
}
if (resID != NULL)
{
delete [] resID;
resID = NULL;
}
if (insertionName != NULL)
{
delete [] insertionName;
insertionName = NULL;
}
// Delete the atom pointers, since that is the contract when they get passed in.
for (i=0; i<getNumberAtoms(); i++)
{
if (getAtom(i) != NULL)
{
delete getAtom(i);
setAtom(i, NULL);
}
}
}
static RSQueueRef __RSQueueCreateInstance(RSAllocatorRef allocator, RSIndex capacity, RSQueueAtomType atom)
{
RSQueueRef queue = (RSQueueRef)__RSRuntimeCreateInstance(allocator, _RSQueueTypeID, sizeof(struct __RSQueue) - sizeof(RSRuntimeBase));
queue->_lock = RSSpinLockInit;
if (atom == RSQueueAtom) setAtom(queue);
queue->_capacity = capacity;
queue->_queueCore = RSArrayCreateMutable(allocator, capacity);
return queue;
}
XPString::XPString(unsigned long index, const char* cp)
{
assert(m_XPRefCountedStringAtomArraySize != 0);
assert(m_XPRefCountedStringLastAtom != 0);
assert(index < m_XPRefCountedStringAtomArraySize);
m_str = setAtom(index, cp);
assert(m_str >= m_XPRefCountedStringAtomArray && m_str < m_XPRefCountedStringAtomArray + m_XPRefCountedStringAtomArraySize);
assert(m_str);
if (m_str)
m_str->AddRef();
assert(IsAtom());
}
// special constructors: first initializes array in addition to the string into the array
// second initializes string into atom array
// NOTE: cp MUST point to a permanently maintainted (i.e., static) string in memory
XPString::XPString(unsigned long totalNumberOfAtoms, unsigned long index, const char* cp)
{
//assert(m_XPRefCountedStringAtomArraySize == 0); // was firing on the Mac side on reload.
//assert(m_XPRefCountedStringLastAtom == 0); // was firing on the Mac side on reload.
//assert(m_XPRefCountedStringAtomArray == NULL); // was firing on the Mac side on reload.
initAtomArray(totalNumberOfAtoms); // *** initAtomArray is a class static function, but this is a constructor!
assert(index < m_XPRefCountedStringAtomArraySize);
m_str = setAtom(index, cp);
assert(m_str);
if (m_str)
m_str->AddRef();
assert(IsAtom());
}
// === OplsBondStrechCalculation =========================================== //
OplsBondStrechCalculation::OplsBondStrechCalculation(const chemkit::ForceFieldAtom *a, const chemkit::ForceFieldAtom *b)
: OplsCalculation(BondStrech, 2, 2)
{
setAtom(0, a);
setAtom(1, b);
}
// === OplsNonbondedCalculation ============================================ //
OplsNonbondedCalculation::OplsNonbondedCalculation(const chemkit::ForceFieldAtom *a, const chemkit::ForceFieldAtom *b)
: OplsCalculation(VanDerWaals | Electrostatic, 2, 5)
{
setAtom(0, a);
setAtom(1, b);
}
