void CDM_FEA::CalcA() //populate "a" matrix!
{
for(int b=0; b<NumBonds; b++){ //for each bond!
MakeBond(a, b);
}
}
void CDM_FEA::CalcForces() //fills in forces, reaction forces, and strains!!!
{
for (int i=0; i<DOF; i++){ //set all to zero force
F[i] = 0;
e[i] = 0; //internal strains
b[i] = 0; //do reactions here.... (if we want)
}
for (int i=0; i<pObj->GetNumVox(); i++){
MaxSE[i] = 0;
}
//set up a smaller F = Kx matrix involving just the two blocks involved in each bond (to calculate "F")
double* TmpK = new double[4*DOFperBlock*DOFperBlock]; //technically only need the upper diagonal
double* TmpX = new double[2*DOFperBlock];
double* TmpF = new double[2*DOFperBlock];
float* FBig = new float [DOF*3]; //one for each dimension, so we can keep track of multiple bonds getting added up & average
for (int i=0; i<3*DOF; i++){FBig[i] = 0;} //initialize to zeros
for(int bond=0; bond<NumBonds; bond++){ //for each bond!
int BondDirec = BondDir[bond]; //which direction is this?
int El1 = IndextoDOF[Indi[bond]];
int El2 = IndextoDOF[Indj[bond]];
for (int i=0; i<4*DOFperBlock*DOFperBlock; i++) //zero out them all
TmpK[i] = 0;
for (int i=0; i<2*DOFperBlock; i++){
TmpX[i] = 0;
TmpF[i] = 0;
}
MakeBond(TmpK, bond);
for (int i=0; i<DOFperBlock; i++){ //set up our little displacement vector
TmpX[i] = x[El1*DOFperBlock+i];
TmpX[DOFperBlock + i] = x[El2*DOFperBlock+i];
}
//multiply out!
for (int i=0; i<2*DOFperBlock; i++){ //cycle through each row
for (int j=i; j<2*DOFperBlock; j++){ //cycle through each column (only for upper diag)
TmpF[i] += (TmpK[i*2*DOFperBlock+j]*TmpX[j]);
if (i != j)
TmpF[j] += (TmpK[i*2*DOFperBlock+j]*TmpX[i]);
}
}
float StrainEnergy = 0;
for (int i=0; i<2*DOFperBlock; i++){ //cycle through each row
StrainEnergy += (float)(TmpX[i]*TmpF[i]); //abs value already
}
//StrainEnergy = abs(StrainEnergy); //only care about magnitude!
//check against both bonds!
if (StrainEnergy > MaxSE[El1])
MaxSE[El1] = StrainEnergy;
if (StrainEnergy > MaxSE[El2])
MaxSE[El2] = StrainEnergy;
for (int i=0; i<DOFperBlock; i++) { //local forces to universal coordinates
int CurIndex = DOF*BondDirec + El1*DOFperBlock+i; //first element
if (FBig[CurIndex] == 0)
FBig[CurIndex] = (float)abs(TmpF[i]);
else
FBig[CurIndex] = (float)(FBig[CurIndex] + abs(TmpF[i]))/2;
CurIndex = DOF*BondDirec + El2*DOFperBlock+i;
if (FBig[CurIndex] == 0)
FBig[CurIndex] = (float)abs(TmpF[DOFperBlock + i]);
else
FBig[CurIndex] = (float)(FBig[CurIndex] + abs(TmpF[DOFperBlock + i]))/2;
b[El1*DOFperBlock+i] += TmpF[i];
b[El2*DOFperBlock+i] += TmpF[DOFperBlock + i];
}
double LinearStrain = abs(x[El1*DOFperBlock + BondDirec] - x[El2*DOFperBlock + BondDirec])/pObj->GetLatticeDim(); //simple volumetric strain (no shear...)
if (LinearStrain > e[El1*DOFperBlock + BondDirec]) e[El1*DOFperBlock + BondDirec] = LinearStrain;
if (LinearStrain > e[El2*DOFperBlock + BondDirec]) e[El2*DOFperBlock + BondDirec] = LinearStrain;
}
//render FBig to F!
for (int i=0; i<DOF; i++){ //each element
for (int j=0; j<3; j++){ //each direction of possible bond
F[i] += FBig[DOF*j + i];
}
}
delete[]TmpK;
TmpK = NULL;
delete[]TmpX;
TmpX = NULL;
delete[]TmpF;
TmpF = NULL;
delete[]FBig;
FBig = NULL;
FindMaxOverall(&Reaction, b, MaxReactions);
FindMaxOverall(&Force, F, MaxForces);
FindMaxOverall(&Strain, e, MaxStrains);
}
Residue::Residue(StructureBase *parent,
const CResidue& residue, int moleculeID,
const ResidueGraphList& standardDictionary,
const ResidueGraphList& localDictionary,
int nResidues, int moleculeType) :
StructureBase(parent), code(NO_CODE), alphaID(NO_ALPHA_ID), type(eOther)
{
// get ID
id = residue.GetId().Get();
// get Residue name
if (residue.IsSetName()) namePDB = residue.GetName();
// get CResidue_graph*
// standard (of correct type) or local dictionary?
const ResidueGraphList *dictionary = NULL;
int graphID = 0;
if (residue.GetResidue_graph().IsStandard() &&
residue.GetResidue_graph().GetStandard().GetBiostruc_residue_graph_set_id().IsOther_database() &&
residue.GetResidue_graph().GetStandard().GetBiostruc_residue_graph_set_id().GetOther_database().GetDb() == "Standard residue dictionary" &&
residue.GetResidue_graph().GetStandard().GetBiostruc_residue_graph_set_id().GetOther_database().GetTag().IsId() &&
residue.GetResidue_graph().GetStandard().GetBiostruc_residue_graph_set_id().GetOther_database().GetTag().GetId() == 1) {
dictionary = &standardDictionary;
graphID = residue.GetResidue_graph().GetStandard().GetResidue_graph_id().Get();
} else if (residue.GetResidue_graph().IsLocal()) {
dictionary = &localDictionary;
graphID = residue.GetResidue_graph().GetLocal().Get();
} else
ERRORMSG("confused by Molecule #?, Residue #" << id << "; can't find appropriate dictionary");
// look up appropriate Residue_graph
const CResidue_graph *residueGraph = NULL;
ResidueGraphList::const_iterator i, ie=dictionary->end();
for (i=dictionary->begin(); i!=ie; ++i) {
if (i->GetObject().GetId().Get() == graphID) {
residueGraph = i->GetPointer();
break;
}
}
if (!residueGraph)
ERRORMSG("confused by Molecule #?, Residue #" << id << "; can't find Residue-graph ID #" << graphID);
// get iupac-code if present - assume it's the first character of the first VisibleString
if (residueGraph->IsSetIupac_code())
code = residueGraph->GetIupac_code().front()[0];
// get residue-graph name if present
if (residueGraph->IsSetDescr()) {
CResidue_graph::TDescr::const_iterator j, je = residueGraph->GetDescr().end();
for (j=residueGraph->GetDescr().begin(); j!=je; ++j) {
if (j->GetObject().IsName()) {
nameGraph = j->GetObject().GetName();
break;
}
}
}
// get type
if (residueGraph->IsSetResidue_type() &&
// handle special case of single-residue "heterogens" composed of a natural residue - leave as 'other'
!(nResidues == 1 &&
(moleculeType == Molecule::eSolvent || moleculeType == Molecule::eNonpolymer || moleculeType == Molecule::eOther)))
type = static_cast<eType>(residueGraph->GetResidue_type());
// get StructureObject* parent
const StructureObject *object;
if (!GetParentOfType(&object) || object->coordSets.size() == 0) {
ERRORMSG("Residue()::Residue() : parent doesn't have any CoordSets");
return;
}
// get atom info
nAtomsWithAnyCoords = 0;
CResidue_graph::TAtoms::const_iterator a, ae = residueGraph->GetAtoms().end();
for (a=residueGraph->GetAtoms().begin(); a!=ae; ++a) {
const CAtom& atom = a->GetObject();
int atomID = atom.GetId().Get();
AtomInfo *info = new AtomInfo;
AtomPntr ap(moleculeID, id, atomID);
// see if this atom is present in any CoordSet
StructureObject::CoordSetList::const_iterator c, ce=object->coordSets.end();
for (c=object->coordSets.begin(); c!=ce; ++c) {
if (((*c)->atomSet->GetAtom(ap, true, true))) {
++nAtomsWithAnyCoords;
break;
}
}
info->residue = this;
// get name if present
if (atom.IsSetName()) info->name = atom.GetName();
// get code if present - just use first one of the SEQUENCE
if (atom.IsSetIupac_code())
info->code = atom.GetIupac_code().front();
// get atomic number, assuming it's the integer value of the enumerated type
CAtom_Base::EElement atomicNumber = atom.GetElement();
info->atomicNumber = static_cast<int>(atomicNumber);
// get ionizable status
if (atom.IsSetIonizable_proton() &&
atom.GetIonizable_proton() == CAtom::eIonizable_proton_true)
info->isIonizableProton = true;
else
info->isIonizableProton = false;
// assign (unique) name
info->glName = parentSet->CreateName(this, atomID);
// classify atom
info->classification = ClassifyAtom(this, atom);
// store alphaID in residue
if (info->classification == eAlphaBackboneAtom) alphaID = atomID;
// add info to map
if (atomInfos.find(atom.GetId().Get()) != atomInfos.end())
ERRORMSG("Residue #" << id << ": confused by multiple atom IDs " << atom.GetId().Get());
atomInfos[atomID] = info;
}
// get bonds
CResidue_graph::TBonds::const_iterator b, be = residueGraph->GetBonds().end();
for (b=residueGraph->GetBonds().begin(); b!=be; ++b) {
int order = b->GetObject().IsSetBond_order() ?
b->GetObject().GetBond_order() : Bond::eUnknown;
const Bond *bond = MakeBond(this,
moleculeID, id, b->GetObject().GetAtom_id_1().Get(),
moleculeID, id, b->GetObject().GetAtom_id_2().Get(),
order);
if (bond) bonds.push_back(bond);
}
}
