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Merged
Bike merged 2 commits into from
Feb 10, 2026
Merged

Use allocate() instead of allocate_with_default_constructor() #76

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8cc553b
Use allocate() instead of allocate_with_default_constructor()
Bike Feb 10, 2026
6432d3c
Merge branch 'main' into allocate_without_default_constructor
Bike Feb 10, 2026
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2 changes: 1 addition & 1 deletion include/cando/adapt/iterateCons.h
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Expand Up @@ -56,7 +56,7 @@ SMART(IterateCons );
public:
static IterateCons_sp create(core::List_sp beg)
{
auto r = gctools::GC<IterateCons_O>::allocate_with_default_constructor();
auto r = gctools::GC<IterateCons_O>::allocate();
r->init(beg);
return r;
};
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2 changes: 1 addition & 1 deletion include/cando/chem/alias.h
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Expand Up @@ -63,7 +63,7 @@ namespace chem
public:
static Alias_sp create(core::Symbol_sp monomerAlias, core::Symbol_sp atomAlias )
{
auto a = gctools::GC<Alias_O>::allocate_with_default_constructor();
auto a = gctools::GC<Alias_O>::allocate();
a->setMonomerAlias(monomerAlias);
a->setAtomAlias(atomAlias);
return a;
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34 changes: 12 additions & 22 deletions include/cando/chem/chemInfo.h
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Expand Up @@ -351,7 +351,7 @@ class Logical_O : public AtomOrBondMatchNode_O
core::T_sp a1,
core::T_sp a2)
{ _G();
auto obj = gctools::GC<Logical_O>::allocate_with_default_constructor();
auto obj = gctools::GC<Logical_O>::allocate();
obj->_Operator = op;
if (a1.nilp()) {
obj->_Left = nil<core::T_O>();
Expand Down Expand Up @@ -415,7 +415,7 @@ class ResidueTest_O : public AtomOrBondMatchNode_O
{
_G();
LOG(("ResidueTest_sp create: ringTag = (%s)") , _rep_(ri));
auto obj = gctools::GC<ResidueTest_O>::allocate_with_default_constructor();
auto obj = gctools::GC<ResidueTest_O>::allocate();
obj->_Bond = b;
obj->_AtomTest = at;
obj->_RingTag = ri;
Expand Down Expand Up @@ -457,7 +457,7 @@ class BondLogical_O : public BondMatcher_O {
BondMatcher_sp a1,
BondMatcher_sp a2)
{ _G();
auto obj = gctools::GC<BondLogical_O>::allocate_with_default_constructor();
auto obj = gctools::GC<BondLogical_O>::allocate();
obj->_Operator = op;
obj->_Left = a1;
obj->_Right = a2;
Expand All @@ -468,7 +468,7 @@ class BondLogical_O : public BondMatcher_O {
// gc::Nilable<AtomOrBondMatchNode_sp> a2 )
BondMatcher_sp a)
{ _G();
auto obj = gctools::GC<BondLogical_O>::allocate_with_default_constructor();
auto obj = gctools::GC<BondLogical_O>::allocate();
obj->_Operator = op;
obj->_Left = a;
obj->_Right = unbound<BondMatcher_O>();
Expand Down Expand Up @@ -531,7 +531,7 @@ class BondToAtomTest_O : public BondMatchNode_O
#if 0
static BondToAtomTest_sp create(BondEnum b, core::T_sp nilOrNode )
{_G();
auto obj = gctools::GC<BondToAtomTest_O>::allocate_with_default_constructor();
auto obj = gctools::GC<BondToAtomTest_O>::allocate();
obj->_Bond = b;
if (nilOrNode.nilp()) {
obj->_AtomTest = _Nil<core::T_O>();
Expand Down Expand Up @@ -666,7 +666,7 @@ class AtomTest_O : public AtomOrBondMatchNode_O
static AtomTest_sp create( AtomTestEnum t, int iArg, int num, const char* el, core::Symbol_sp sym)
{_G();
LOG(("Creating an AtomTest"));
auto obj = gctools::GC<AtomTest_O>::allocate_with_default_constructor();
auto obj = gctools::GC<AtomTest_O>::allocate();
obj->_Test = t;
obj->_IntArg = iArg;
obj->_NumArg = num;
Expand Down Expand Up @@ -829,7 +829,7 @@ class AntechamberFocusAtomMatch_O : public AtomOrBondMatchNode_O
int numberOfElectronWithdrawingGroups,
gc::Nilable<AtomOrBondMatchNode_sp> atomicProperty )
{_G();
auto obj = gctools::GC<AntechamberFocusAtomMatch_O>::allocate_with_default_constructor();
auto obj = gctools::GC<AntechamberFocusAtomMatch_O>::allocate();
obj->_ResidueNames = residueNames;
obj->_AtomicNumber = atomicNumber;
obj->_NumberOfAttachedAtoms = numberOfAttachedAtoms;
Expand Down Expand Up @@ -885,7 +885,7 @@ class Chain_O : public BondListMatchNode_O
CL_LISPIFY_NAME("make-chain.head.tail");
// CL_DEF_CLASS_METHOD static Chain_sp create_head_tail( BondMatchNode_sp head, BondListMatchNode_sp tail ) {
CL_DEF_CLASS_METHOD static Chain_sp create_head_tail( core::T_sp head, core::T_sp tail ) {
auto obj = gctools::GC<Chain_O>::allocate_with_default_constructor();
auto obj = gctools::GC<Chain_O>::allocate();
// obj->_Head = head;
// obj->_Tail = tail;
if (head.nilp()){
Expand All @@ -912,7 +912,7 @@ class Chain_O : public BondListMatchNode_O
}
}
CL_DEF_CLASS_METHOD static Chain_sp create_empty_chain() {
auto obj = gctools::GC<Chain_O>::allocate_with_default_constructor();
auto obj = gctools::GC<Chain_O>::allocate();
return obj;
}
public:
Expand Down Expand Up @@ -959,15 +959,15 @@ class Branch_O : public BondListMatchNode_O
// CL_DEF_CLASS_METHOD static Branch_sp create_left_right( BondListMatchNode_sp left, BondListMatchNode_sp right )
// {
// _G();
// auto obj = gctools::GC<Branch_O>::allocate_with_default_constructor();
// auto obj = gctools::GC<Branch_O>::allocate();
// obj->_Left = left;
// obj->_Right = right;
// return obj;
// }
CL_DEF_CLASS_METHOD static Branch_sp create_left_right( core::T_sp left, core::T_sp right )
{
_G();
auto obj = gctools::GC<Branch_O>::allocate_with_default_constructor();
auto obj = gctools::GC<Branch_O>::allocate();
if(left.nilp()){
obj->_Left = nil<core::T_O>();
} else {
Expand All @@ -985,7 +985,7 @@ class Branch_O : public BondListMatchNode_O
CL_LISPIFY_NAME("make-branch.left");
CL_DEF_CLASS_METHOD static Branch_sp create_left( BondListMatchNode_sp left ) {
_G();
auto obj = gctools::GC<Branch_O>::allocate_with_default_constructor();
auto obj = gctools::GC<Branch_O>::allocate();
obj->_Left = left;
obj->_Right = nil<core::T_O>();
return obj;
Expand Down Expand Up @@ -1019,16 +1019,6 @@ class AfterMatchBondToAtomTest_O : public RootMatchNode_O
core::Symbol_sp _AtomTag1;
core::Symbol_sp _AtomTag2;
BondEnum _Bond;
public:
static AfterMatchBondToAtomTest_sp create( core::Symbol_sp tag1, core::Symbol_sp tag2, BondEnum b)
{
_G();
auto obj = gctools::GC<AfterMatchBondToAtomTest_O>::allocate_with_default_constructor();
obj->_AtomTag1 = tag1;
obj->_AtomTag2 = tag2;
obj->_Bond = b;
return obj;
};
public:
// virtual adapt::QDomNode_sp asXml(string name=XmlTag_AfterMatchBondToAtomTest());
virtual ChemInfoType type() { return afterMatchBondToAtomTest; };
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2 changes: 1 addition & 1 deletion include/cando/chem/conformationCollection.h
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Expand Up @@ -96,7 +96,7 @@ class ConformationCollectionEntry_O : public core::CxxObject_O
#if 0
inline ConformationCollectionEntry_sp create_ConformationCollectionEntry(core::LispPtr e,ConformationCollection_sp s)
{
auto ee = gctools::GC<ConformationCollectionEntry_O>::allocate_with_default_constructor();
auto ee = gctools::GC<ConformationCollectionEntry_O>::allocate();
ee->setConformationCollection(s);
return ee;
};
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2 changes: 1 addition & 1 deletion include/cando/chem/energyRigidBodyStaple.h
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Expand Up @@ -124,7 +124,7 @@ class EnergyRigidBodyStaple_O : public EnergyRigidBodyComponent_O
public:
CL_LISPIFY_NAME("make-energy-rigid-body-staple");
CL_DEF_CLASS_METHOD static EnergyRigidBodyStaple_sp make() {
auto energy = gctools::GC<EnergyRigidBodyStaple_O>::allocate_with_default_constructor();
auto energy = gctools::GC<EnergyRigidBodyStaple_O>::allocate();
return energy;
}

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2 changes: 1 addition & 1 deletion include/cando/chem/forceField.h
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Expand Up @@ -121,7 +121,7 @@ class ForceField_O : public core::CxxObject_O
// static ForceField_sp open_ForceField(const string& fn);
CL_LISPIFY_NAME("ForceField/make");
CL_DEF_CLASS_METHOD static ForceField_sp make() {
auto ff = gctools::GC<ForceField_O>::allocate_with_default_constructor();
auto ff = gctools::GC<ForceField_O>::allocate();
return ff;
};
public:
Expand Down
2 changes: 1 addition & 1 deletion include/cando/chem/numericalFunction.h
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Expand Up @@ -152,7 +152,7 @@ inline NumericalFunction_sp NumericalFunction_O::create(core::T_sp xaxis,
core::T_sp yaxis,
double xstart, double xinc)
{
auto f = gctools::GC<NumericalFunction_O>::allocate_with_default_constructor();
auto f = gctools::GC<NumericalFunction_O>::allocate();
f->setXAxisName(xaxis);
f->setYAxisName(yaxis);
f->setXStart(xstart);
Expand Down
2 changes: 1 addition & 1 deletion include/cando/chem/spanningLoop.h
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Expand Up @@ -124,7 +124,7 @@ namespace chem {

public:
static SpanningLoop_sp create(Atom_sp t) {
auto s = gctools::GC<SpanningLoop_O>::allocate_with_default_constructor();
auto s = gctools::GC<SpanningLoop_O>::allocate();
s->setTop(t);
return s;
};
Expand Down
2 changes: 1 addition & 1 deletion include/cando/chem/write_mmcif.h
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Expand Up @@ -55,7 +55,7 @@ namespace chem
/*! factory */
static MmcifWriter_sp make(core::T_sp pathDesignator)
{
auto me = gctools::GC<MmcifWriter_O>::allocate_with_default_constructor();
auto me = gctools::GC<MmcifWriter_O>::allocate();
me->open(pathDesignator);
return me;
}
Expand Down
6 changes: 3 additions & 3 deletions include/cando/chem/zMatrix.h
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Expand Up @@ -120,7 +120,7 @@ CL_DEFMETHOD int getBondAtomIndex() const { return this->_AtomBond;};
inline ZMatrixBondInternal_sp ZMatrixBondInternal_O::create(Atom_sp newAtom, Atom_sp bondToAtom,
ZMatrixInternal_O::atomMap atomIndexes, ZMatrix_sp zMatrix )
{_G();
auto zz = gctools::GC<ZMatrixBondInternal_O>::allocate_with_default_constructor();
auto zz = gctools::GC<ZMatrixBondInternal_O>::allocate();
zz->setZMatrix(zMatrix);
zz->setup(newAtom,bondToAtom,atomIndexes);
return zz;
Expand Down Expand Up @@ -169,7 +169,7 @@ CL_DEFMETHOD int getAngleAtomIndex() const { return this->_AtomAngle;}
Atom_sp angleToAtom,
ZMatrixInternal_O::atomMap atomIndexes, ZMatrix_sp zMatrix)
{_G();
auto zz = gctools::GC<ZMatrixAngleInternal_O>::allocate_with_default_constructor();
auto zz = gctools::GC<ZMatrixAngleInternal_O>::allocate();
zz->setZMatrix(zMatrix);
zz->setup(newAtom,bondToAtom,angleToAtom,atomIndexes);
return zz;
Expand Down Expand Up @@ -221,7 +221,7 @@ CL_DEFMETHOD int getDihedralAtomIndex() const { return this->_AtomDihedral;}
Atom_sp angleToAtom, Atom_sp dihedralToAtom,
ZMatrixInternal_O::atomMap atomIndexes, ZMatrix_sp zMatrix)
{_G();
auto zz = gctools::GC<ZMatrixDihedralInternal_O>::allocate_with_default_constructor();
auto zz = gctools::GC<ZMatrixDihedralInternal_O>::allocate();
zz->setZMatrix(zMatrix);
zz->setup(newAtom,bondToAtom,angleToAtom,dihedralToAtom,atomIndexes);
return zz;
Expand Down
2 changes: 1 addition & 1 deletion include/cando/geom/archive/coloredVertexList.h
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Expand Up @@ -91,7 +91,7 @@ namespace geom
public:
static ColoredVertexList_sp create(uint size)
{
auto a = gctools::GC<ColoredVertexList_O>::allocate_with_default_constructor();
auto a = gctools::GC<ColoredVertexList_O>::allocate();
a->resize(size);
return a;
}
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2 changes: 1 addition & 1 deletion include/cando/geom/ovector2.h
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Expand Up @@ -76,7 +76,7 @@ CL_DEFMETHOD double getY() { return this->_Value.getY(); };

inline OVector2_sp OVector2_O::createFromVector2(const Vector2& pnt)
{
auto ov = gctools::GC<OVector2_O>::allocate_with_default_constructor();
auto ov = gctools::GC<OVector2_O>::allocate();
ov->setAll(pnt.getX(),pnt.getY());
return ov;
}
Expand Down
4 changes: 2 additions & 2 deletions include/cando/kinematics/old/retired/atomo.h
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Expand Up @@ -60,14 +60,14 @@ namespace kinematics
public:
static Point_sp create(Point_sp handle)
{
auto atom = gctools::GC<Point_O>::allocate_with_default_constructor();
auto atom = gctools::GC<Point_O>::allocate();
atom->_PointTree = handle.pointTree();
atom->_Handle = handle;
return atom;
}
static Point_sp create(const PointTree_sp& tree, uint handleIndex)
{
auto atom = gctools::GC<Point_O>::allocate_with_default_constructor();
auto atom = gctools::GC<Point_O>::allocate();
atom->_PointTree = tree;
RefCountedAtomHandle handle(tree.get(),handleIndex);
try
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2 changes: 1 addition & 1 deletion src/adapt/retired/objRef.cc
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Expand Up @@ -79,7 +79,7 @@ string ObjRef_O::asString() {
*/
ObjRef_sp ObjRef_O::create(LispPtr e, const string &asString) {
string head, tail, orSelector, orName;
auto ref = gctools::GC<ObjRef_O>::allocate_with_default_constructor();
auto ref = gctools::GC<ObjRef_O>::allocate();
VectorStrings parts;
size_t split = asString.find("/");
if (split != string::npos) {
Expand Down
2 changes: 1 addition & 1 deletion src/chem/aggregate.cc
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Expand Up @@ -892,7 +892,7 @@ CL_LISPIFY_NAME(make-aggregate);
DOCGROUP(cando);
CL_DEFUN Aggregate_sp Aggregate_O::make(core::Symbol_sp name, core::List_sp molecules)
{
auto me = gctools::GC<Aggregate_O>::allocate_with_default_constructor();
auto me = gctools::GC<Aggregate_O>::allocate();
me->setName(name);
if (molecules.notnilp()) {
for ( auto cur : molecules ) {
Expand Down
2 changes: 1 addition & 1 deletion src/chem/alias.cc
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Expand Up @@ -82,7 +82,7 @@ CL_DEFUN core::T_sp chem__alias(core::Symbol_sp monAlias, core::Symbol_sp atomAl
#define DOCS_Alias_O_make "make AtomId args: monomer_sym atom_sym"
Alias_sp Alias_O::make(core::Symbol_sp monomerSym, core::Symbol_sp atomSym)
{
auto me = gctools::GC<Alias_O>::allocate_with_default_constructor();
auto me = gctools::GC<Alias_O>::allocate();
me->_MonomerAlias = monomerSym;
me->_AtomAlias = atomSym;
return me;
Expand Down
2 changes: 1 addition & 1 deletion src/chem/angle.cc
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Expand Up @@ -44,7 +44,7 @@ namespace chem

Angle_sp Angle_O::create(Atom_sp a1, Atom_sp a2, Atom_sp a3)
{
auto obj = gctools::GC<Angle_O>::allocate_with_default_constructor();
auto obj = gctools::GC<Angle_O>::allocate();
obj->setup(a1,a2,a3);
return obj;
}
Expand Down
6 changes: 3 additions & 3 deletions src/chem/atom.cc
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Expand Up @@ -108,7 +108,7 @@ CL_LISPIFY_NAME(make-atom);
DOCGROUP(cando);
CL_DEFUN Atom_sp Atom_O::make(core::Symbol_sp name, chem::Element element)
{
auto atom = gctools::GC<Atom_O>::allocate_with_default_constructor();
auto atom = gctools::GC<Atom_O>::allocate();
atom->setName(name);
atom->setElement(element);
return atom;
Expand Down Expand Up @@ -1279,7 +1279,7 @@ CL_LISPIFY_NAME("getBondList");
CL_DEFMETHOD BondList_sp Atom_O::getBondList()
{
VectorBond::const_iterator b;
auto bl = gctools::GC<BondList_O>::allocate_with_default_constructor();
auto bl = gctools::GC<BondList_O>::allocate();
for (b=this->_Bonds.begin();b!=this->_Bonds.end(); b++ )
{
bl->addBond(*b);
Expand Down Expand Up @@ -1364,7 +1364,7 @@ CL_LISPIFY_NAME("getHeavyAtomBondList");
CL_DEFMETHOD BondList_sp Atom_O::getHeavyAtomBondList()
{
VectorBond::const_iterator b;
auto bl = gctools::GC<BondList_O>::allocate_with_default_constructor();
auto bl = gctools::GC<BondList_O>::allocate();
Atom_sp me = this->sharedThis<Atom_O>();
for (b=this->_Bonds.begin();b!=this->_Bonds.end(); b++ )
{
Expand Down
2 changes: 1 addition & 1 deletion src/chem/atomGrid.cc
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Expand Up @@ -66,7 +66,7 @@ CL_DEF_CLASS_METHOD AtomGrid_sp AtomGrid_O::makeAtomGrid(NVector_sp positions,
double cellSize,
double padding )
{
auto me = gctools::GC<AtomGrid_O>::allocate_with_default_constructor();
auto me = gctools::GC<AtomGrid_O>::allocate();
me->buildAtomGrid( positions, effRadii, cellSize, padding );
return me;
}
Expand Down
2 changes: 1 addition & 1 deletion src/chem/atomId.cc
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Expand Up @@ -53,7 +53,7 @@ CL_LISPIFY_NAME(make-atom-id);
DOCGROUP(cando);
CL_DEFUN AtomId_sp AtomId_O::make(int mol, int res, int atom)
{
auto ai = gctools::GC<AtomId_O>::allocate_with_default_constructor();
auto ai = gctools::GC<AtomId_O>::allocate();
ai->_AtomId._Molecule = mol;
ai->_AtomId._Residue = res;
ai->_AtomId._Atom = atom;
Expand Down
2 changes: 1 addition & 1 deletion src/chem/atomIdMap.cc
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Expand Up @@ -89,7 +89,7 @@ void AtomIdMap_O::fields(core::Record_sp node)


CL_DEFUN chem::AtomIdMap_sp make_AtomIdMap() {
return gctools::GC<AtomIdMap_O>::allocate_with_default_constructor();
return gctools::GC<AtomIdMap_O>::allocate();
}


Expand Down
2 changes: 1 addition & 1 deletion src/chem/atomReference.cc
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Expand Up @@ -80,7 +80,7 @@ namespace chem
#define DOCS_AtomReference_O_make "make AtomReference args: alias"
AtomReference_sp AtomReference_O::make(core::T_sp alias)
{
auto me = gctools::GC<AtomReference_O>::allocate_with_default_constructor();
auto me = gctools::GC<AtomReference_O>::allocate();
me->_AtomAlias = alias;
return me;
};
Expand Down
4 changes: 2 additions & 2 deletions src/chem/bond.cc
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Expand Up @@ -74,7 +74,7 @@ CL_DEFUN bool chem__single_bond_p(chem::BondOrder o)

Bond_sp Bond_O::create(Atom_sp from, Atom_sp to, BondOrder o)
{
auto bond = gctools::GC<Bond_O>::allocate_with_default_constructor();
auto bond = gctools::GC<Bond_O>::allocate();
bond->_Atom1 = from;
bond->_Atom2 = to;
bond->setOrder(o);
Expand Down Expand Up @@ -623,7 +623,7 @@ use the same Bond_O's */
BondList_sp BondList_O::deepishCopy() const
{
BondList_O::const_iterator bi;
auto bl = gctools::GC<BondList_O>::allocate_with_default_constructor();
auto bl = gctools::GC<BondList_O>::allocate();
for ( bi=this->_Bonds.begin(); bi!=this->_Bonds.end(); bi++ ) bl->addBond(*bi);
return bl;
}
Expand Down
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