/*!
The constructor
*/
ACoreDistObj::ACoreDistObj(Conf const & theConf, B const NeedHint) :
Function(theConf.SysHdl(), NeedHint)
{
WatchError
//Alert(Energy::e().ModelId() != EnergyCls<HpEnergy>::ModelId, eEnergyMismatch);
Dim tDimen = Space::Dimen();
Hdl tSysHdl = theConf.SysHdl();
Dim tSpan = Protein::p().Span();
Dim tLength = Protein::p().Length();
block1<Prm,nmm> tResult(tSpan * tLength / 2);
block1<Prm,nmm> hCore(tDimen);
for(Cmp tCmp = 0; tCmp < tDimen; ++tCmp)
{
block1<Prm,xmm> corePrms;
for(Pos tPos = 0; tPos < tSpan; ++tPos)
{
Typ tTyp = Protein::p().Type(tPos);
if (toHp[tTyp]==0) continue;
corePrms.insertMem(Prm(TermVar,tPos * tDimen + tCmp));
}
// now sum all the points
Prm SumComp = Prm(TermFunc,SumXiFeVi::def(Xv, tSysHdl, corePrms.items(), corePrms.itemCount()));
Prm CompVal = Prm(TermFunc,UdivXiFeVi::def(Xv,tSysHdl, SumComp,UdivXiFeVi::bind(corePrms.itemCount())));
hCore.insert(CompVal);
}
for(Pos tPos = 0; tPos < tSpan; ++tPos)
{
Typ tTyp = Protein::p().Type(tPos);
if (toHp[tTyp]==0) continue;
Prm tDiff[tDimen], tSqrd[tDimen];
for(Cmp tCmp = 0; tCmp < tDimen; ++tCmp)
{
Prm tVar1 = Prm(TermVar,tPos * tDimen + tCmp);
Prm tVar2 = Prm(hCore[tCmp]);
tDiff[tCmp] = Prm(TermFunc,BsubXiFeVi::def(Xv, tSysHdl, tVar1, tVar2));
tSqrd[tCmp] = Prm(TermFunc,UsqrXiFeVi::def(Xv, tSysHdl, tDiff[tCmp]));
}
tResult.insert(Prm(TermFunc,SumXiFeVi::def(Xv, tSysHdl, tSqrd, tDimen),ValueAsEvalMin));
}
//mFuncHdl = SumXiFcMi::def(Xv, tSysHdl, tResult.items(), tResult.size());
//mMetricRec = &SumXiFcMi::ref(tSysHdl, mFuncHdl).MetricRec();
if (NeedHint)
{
mFuncHdl = SumXiEFcMiHn::def(Xv | EvalMin, tSysHdl, tResult.items(), tResult.itemCount());
mMetricRec = &SumXiEFcMiHn::refc(tSysHdl, mFuncHdl).MetricRec();
}
else
{
mFuncHdl = SumXiFcMi::def(Xv, tSysHdl, tResult.items(), tResult.itemCount());
mMetricRec = &SumXiFcMi::refc(tSysHdl, mFuncHdl).MetricRec();
}
CatchError
}
openPlatypusSpace
/*!
The constructor
*/
PlusDistObj::PlusDistObj(Conf const & theConf, B const NeedHint) :
Function(theConf.SysHdl(), NeedHint)
{
WatchError
Warn(!(Energy::e().ModelId() != EnergyCls<MjEnergy>::ModelId ||
Energy::e().ModelId() != EnergyCls<BarerraEnergy>::ModelId), eEnergyMismatch);
Z modelCutoff=(Energy::e().ModelId() == EnergyCls<MjEnergy>::ModelId)?0:-1000;
Dim tDimen = Space::Dimen();
Hdl tSysHdl = theConf.SysHdl();
Dim tSpan = Protein::p().Span();
Dim tLength = Protein::p().Length();
block1<Prm,nmm> tResult(tSpan * tLength / 2);
for(Pos tPos1 = 0; tPos1 < tSpan; ++tPos1)
{
Typ tTyp1 = Protein::p().Type(tPos1);
//if (tTyp1 != Energy::e().Type(2, 'H')) continue;
for(Pos tPos2 = tPos1 + 2; tPos2 < tLength; ++tPos2)
{
Typ tTyp2 = Protein::p().Type(tPos2);
//if (tTyp2 != Energy::e().Type(2, 'H')) continue;
if(Energy::e().Level(tTyp1,tTyp2)<=modelCutoff) continue;
Prm tDiff[tDimen], tSqrd[tDimen];
for(Cmp tCmp = 0; tCmp < tDimen; ++tCmp)
{
Prm tVar1 = Prm(TermVar,tPos1 * tDimen + tCmp);
Prm tVar2 = Prm(TermVar,tPos2 * tDimen + tCmp);
tDiff[tCmp] = Prm(TermFunc,BsubXiFeVi::def(Xv, tSysHdl, tVar1, tVar2));
tSqrd[tCmp] = Prm(TermFunc,UsqrXiFeVi::def(Xv, tSysHdl, tDiff[tCmp]));
}
tResult.insert(Prm(TermFunc,SumXiFeVi::def(Xv, tSysHdl, tSqrd, tDimen),ValueAsEvalMin));
}
}
//mFuncHdl = SumXiFcMi::def(Xv, tSysHdl, tResult.items(), tResult.size());
//mMetricRec = &SumXiFcMi::ref(tSysHdl, mFuncHdl).MetricRec();
if (NeedHint)
{
mFuncHdl = SumXiEFcMiHn::def(Xv | EvalMin, tSysHdl, tResult.items(), tResult.itemCount());
mMetricRec = &SumXiEFcMiHn::refc(tSysHdl, mFuncHdl).MetricRec();
}
else
{
mFuncHdl = SumXiFcMi::def(Xv, tSysHdl, tResult.items(), tResult.itemCount());
mMetricRec = &SumXiFcMi::refc(tSysHdl, mFuncHdl).MetricRec();
}
CatchError
}
openPlatypusSpace
/*!
The constructor
*/
SideChainCns::SideChainCns(Conf const & theConf, B const NeedHint) :
Function(theConf.SysHdl(), NeedHint)
{
WatchError
Dim tDimen = Space::Dimen();
Hdl tSysHdl = theConf.SysHdl();
Dim tSpan = Protein::p().Span();
Dim tLength = Protein::p().Length();
block1<Prm,nmm> tResult(tSpan * tLength / 2);
Int tSqrNeighDist = Lattice::l().SqrNeighDist();
for(Pos tPos1 = 0; tPos1 < tLength; ++tPos1)
{
Pos tPos2;
if(tPos1<tLength/2)
tPos2 = tPos1 + 1;
else
tPos2 = tPos1 - tLength/2;
Prm tDiff[tDimen], tSqrd[tDimen];
for(Cmp tCmp = 0; tCmp < tDimen; ++tCmp)
{
Prm tVar1 = Prm(TermVar,tPos1 * tDimen + tCmp);
Prm tVar2 = Prm(TermVar,tPos2 * tDimen + tCmp);
tDiff[tCmp] = Prm(TermFunc,BsubXiFeVi::def(Xv, tSysHdl, tVar1, tVar2));
tSqrd[tCmp] = Prm(TermFunc,UsqrXiFeVi::def(Xv, tSysHdl, tDiff[tCmp]));
}
Prm tDist = Prm(TermFunc,SumXiFeVi::def(Xv, tSysHdl, tSqrd, tDimen));
tResult.insert(Prm(TermFunc,UequXiFcMi::def(Xv, tSysHdl, tDist, UequXiFcMi::bind(tSqrNeighDist)), MetricAsEvalMin));
}
cout << tResult.itemCount() <<endl;
if (NeedHint)
{
mFuncHdl = SumXiEFcMiHn::def(Xm | EvalMin, tSysHdl, tResult.items(), tResult.itemCount());
mMetricRec = &SumXiEFcMiHn::refc(tSysHdl, mFuncHdl).MetricRec();
}
else
{
mFuncHdl = SumXiFcMi::def(Xm, tSysHdl, tResult.items(), tResult.itemCount());
mMetricRec = &SumXiFcMi::refc(tSysHdl, mFuncHdl).MetricRec();
}
CatchError
}
Foam::tmp<Foam::scalarField> Foam::waveSuperposition::scale
(
const vector2DField& xy
) const
{
tmp<scalarField> tResult(new scalarField(xy.size(), 1));
scalarField& result = tResult.ref();
if (scale_.valid())
{
const scalarField x(xy.component(0));
forAll(result, i)
{
result[i] *= scale_->value(x[i]);
}
}
Foam::tmp<Foam::DimensionedField<Type, Foam::volMesh>> Foam::levelSetAverage
(
const fvMesh& mesh,
const scalarField& levelC,
const scalarField& levelP,
const DimensionedField<Type, volMesh>& positiveC,
const DimensionedField<Type, pointMesh>& positiveP,
const DimensionedField<Type, volMesh>& negativeC,
const DimensionedField<Type, pointMesh>& negativeP
)
{
tmp<DimensionedField<Type, volMesh>> tResult
(
new DimensionedField<Type, volMesh>
(
IOobject
(
positiveC.name() + ":levelSetAverage",
mesh.time().timeName(),
mesh
),
mesh,
dimensioned<Type>("0", positiveC.dimensions(), Zero)
)
);
DimensionedField<Type, volMesh>& result = tResult.ref();
forAll(result, cI)
{
const List<tetIndices> cellTetIs =
polyMeshTetDecomposition::cellTetIndices(mesh, cI);
scalar v = 0;
Type r = Zero;
forAll(cellTetIs, cellTetI)
{
const triFace triIs = cellTetIs[cellTetI].faceTriIs(mesh);
const FixedList<point, 4>
tet =
{
mesh.cellCentres()[cI],
mesh.points()[triIs[0]],
mesh.points()[triIs[1]],
mesh.points()[triIs[2]]
};
const FixedList<scalar, 4>
level =
{
levelC[cI],
levelP[triIs[0]],
levelP[triIs[1]],
levelP[triIs[2]]
};
const cut::volumeIntegrateOp<Type>
positive = FixedList<Type, 4>
({
positiveC[cI],
positiveP[triIs[0]],
positiveP[triIs[1]],
positiveP[triIs[2]]
});
const cut::volumeIntegrateOp<Type>
negative = FixedList<Type, 4>
({
negativeC[cI],
negativeP[triIs[0]],
negativeP[triIs[1]],
negativeP[triIs[2]]
});
v += cut::volumeOp()(tet);
r += tetCut(tet, level, positive, negative);
}
result[cI] = r/v;
}
return tResult;
}
Foam::tmp<Foam::Field<Type>> Foam::levelSetAverage
(
const fvPatch& patch,
const scalarField& levelF,
const scalarField& levelP,
const Field<Type>& positiveF,
const Field<Type>& positiveP,
const Field<Type>& negativeF,
const Field<Type>& negativeP
)
{
typedef typename outerProduct<Type, vector>::type sumType;
tmp<Field<Type>> tResult(new Field<Type>(patch.size(), Zero));
Field<Type>& result = tResult.ref();
forAll(result, fI)
{
const face& f = patch.patch().localFaces()[fI];
vector a = vector::zero;
sumType r = Zero;
for(label eI = 0; eI < f.size(); ++ eI)
{
const edge e = f.faceEdge(eI);
const FixedList<point, 3>
tri =
{
patch.patch().faceCentres()[fI],
patch.patch().localPoints()[e[0]],
patch.patch().localPoints()[e[1]]
};
const FixedList<scalar, 3>
level =
{
levelF[fI],
levelP[e[0]],
levelP[e[1]]
};
const cut::areaIntegrateOp<Type>
positive = FixedList<Type, 3>
({
positiveF[fI],
positiveP[e[0]],
positiveP[e[1]]
});
const cut::areaIntegrateOp<Type>
negative = FixedList<Type, 3>
({
negativeF[fI],
negativeP[e[0]],
negativeP[e[1]]
});
a += cut::areaOp()(tri);
r += triCut(tri, level, positive, negative);
}
result[fI] = a/magSqr(a) & r;
}
return tResult;
}
openPlatypusSpace
/*!
The constructor
*/
ContactOrderObj::ContactOrderObj(Conf const & theConf, B const NeedHint) :
Function(theConf.SysHdl(), NeedHint)
{
WatchError
Warn(!(Energy::e().ModelId() != EnergyCls<HpEnergy>::ModelId ||
Energy::e().ModelId() != EnergyCls<MjEnergy>::ModelId ||
Energy::e().ModelId() != EnergyCls<BarerraEnergy>::ModelId), eEnergyMismatch);
Dim tDimen = Space::Dimen();
Hdl tSysHdl = theConf.SysHdl();
Dim tSpan = Protein::p().Span();
Dim tLength = Protein::p().Length();
block1<Prm,nmm> tResult(tSpan * tLength / 2);
Int tSqrNeighDist = Lattice::l().SqrNeighDist();
for(Pos tPos1 = 0; tPos1 < tSpan; ++tPos1)
{
//Typ tTyp1 = Protein::p().Type(tPos1);
for(Pos tPos2 = tPos1 + 2; tPos2 < tLength; ++tPos2)
{
//Typ tTyp2 = Protein::p().Type(tPos2);
//Eng tEng = Energy::e().Level(tTyp1, tTyp2);
Pos tEng=tPos2-tPos1;
//if(!tEng) continue;
Prm tDiff[tDimen], tSqrd[tDimen];
for(Cmp tCmp = 0; tCmp < tDimen; ++tCmp)
{
Prm tVar1 = Prm(TermVar,tPos1 * tDimen + tCmp);
Prm tVar2 = Prm(TermVar,tPos2 * tDimen + tCmp);
tDiff[tCmp] = Prm(TermFunc,BsubXiFeVi::def(Xv, tSysHdl, tVar1, tVar2));
tSqrd[tCmp] = Prm(TermFunc,UsqrXiFeVi::def(Xv, tSysHdl, tDiff[tCmp]));
}
Prm tDist = Prm(TermFunc,SumXiFeVi::def(Xv, tSysHdl, tSqrd, tDimen));
Prm tEqu = Prm(TermFunc,UequXiFcMi::def(Xv, tSysHdl, tDist, UequXiFcMi::bind(tSqrNeighDist)));
tResult.insert(Prm(TermFunc,UifXiKiFcMi::def(Xm, tSysHdl, tEqu,
UifXiKiFcMi::bind(castInt(0), tEng)),MetricAsEvalMin));
}
}
if(NeedHint)
{
mFuncHdl = SumXiEFcMiHn::def(Xm | EvalMin, tSysHdl, tResult.items(), tResult.itemCount());
mMetricRec = &SumXiEFcMiHn::refc(tSysHdl, mFuncHdl).MetricRec();
}
else
{
mFuncHdl = SumXiFcMi::def(Xm, tSysHdl, tResult.items(), tResult.itemCount());
mMetricRec = &SumXiFcMi::refc(tSysHdl, mFuncHdl).MetricRec();
}
CatchError
}
