static
bool reduceGraphEquivalences(NGHolder &g, EquivalenceType eq_type) {
// create a list of equivalence classes to check
WorkQueue work_queue(num_vertices(g));
// get information on every vertex in the graph
// new vertices are allocated here, and stored in infos
ptr_vector<VertexInfo> infos = getVertexInfos(g);
// partition the graph
auto classes = partitionGraph(infos, work_queue, g, eq_type);
// do equivalence processing
equivalence(classes, work_queue, eq_type);
// replace equivalent classes with single vertices
// new vertices are (possibly) allocated here, and stored in infos
return mergeEquivalentClasses(classes, infos, g);
}
int CXXSurface::upLoadSphere(CXXSphereElement &theSphere, double probeRadius, const int sense){
int oldVertexCount;
CXXCoord theCentre = theSphere.centre();
vector<int, CXX::CXXAlloc<int> > equivalence(theSphere.nVertices());
vector<int, CXX::CXXAlloc<int> > uniqueAndDrawn(theSphere.nVertices());
int nDrawn = 0;
for (unsigned i=0; i< theSphere.nVertices(); i++){
CXXCoord comp1(theSphere.vertex(i).vertex());
uniqueAndDrawn[i] = 0;
if (theSphere.vertex(i).doDraw()){
uniqueAndDrawn[i] = 1;
if (uniqueAndDrawn[i]){
equivalence[i] = nDrawn++;
}
}
}
static const std::string vertexName("vertices");
static const std::string accessiblesName("accessibles");
static const std::string normalsName("normals");
{
oldVertexCount = numberOfVertices();
vertices.resize(oldVertexCount+nDrawn);
int verticesHandle = getVectorHandle(vertexName);
int accessiblesHandle = getVectorHandle(accessiblesName);
int normalsHandle = getVectorHandle(normalsName);
int iDraw = 0;
for (unsigned int i=0; i< theSphere.nVertices(); i++){
if (uniqueAndDrawn[i]){
CXXCoord vertexCoord = theSphere.vertex(i).vertex();
if (sense == CXXSphereElement::Contact){
vertices[oldVertexCount+iDraw].setCoord(accessiblesHandle, vertexCoord);
CXXCoord normal = vertexCoord - theCentre;
CXXCoord diff(normal);
diff *= (theSphere.radius() - probeRadius) / theSphere.radius();
normal.normalise();
vertices[oldVertexCount+iDraw].setCoord(normalsHandle, normal);
CXXCoord vertex = theCentre + diff;
vertices[oldVertexCount+iDraw].setCoord(verticesHandle, vertex);
}
else if (sense == CXXSphereElement::Reentrant) {
vertices[oldVertexCount+iDraw].setCoord(verticesHandle, vertexCoord);
CXXCoord normal = theCentre - vertexCoord;
normal.normalise();
vertices[oldVertexCount+iDraw].setCoord(normalsHandle, normal);
vertices[oldVertexCount+iDraw].setCoord(accessiblesHandle, theCentre);
}
else if (sense == CXXSphereElement::VDW) {
vertices[oldVertexCount+iDraw].setCoord(verticesHandle, vertexCoord);
CXXCoord normal = vertexCoord - theCentre;
normal.normalise();
vertices[oldVertexCount+iDraw].setCoord(normalsHandle, normal);
vertices[oldVertexCount+iDraw].setCoord(accessiblesHandle, vertexCoord+normal);
}
else if (sense == CXXSphereElement::Accessible) {
vertices[oldVertexCount+iDraw].setCoord(verticesHandle, vertexCoord);
CXXCoord normal = vertexCoord - theCentre;
normal.normalise();
vertices[oldVertexCount+iDraw].setCoord(normalsHandle, normal);
vertices[oldVertexCount+iDraw].setCoord(accessiblesHandle, vertexCoord);
}
iDraw++;
}
}
}
//Add atom pointers to the surface
{
void *atomBuffer[nDrawn];// = new void*[nDrawn];
int iDraw = 0;
for (unsigned int i=0; i< theSphere.nVertices(); i++){
if (uniqueAndDrawn[i]){
mmdb::PAtom anAtom;
if ((anAtom = theSphere.vertex(i).getAtom())!=0 ){
atomBuffer[iDraw] = (void *) anAtom;
}
else atomBuffer[iDraw] = (void *) theSphere.getAtom();
iDraw++;
}
}
updateWithPointerData(nDrawn, "atom", oldVertexCount, atomBuffer);
//delete [] atomBuffer;
}
// Add triangles to surface
{
int triangleBuffer[theSphere.nFlatTriangles()*3];// = new int[theSphere.nFlatTriangles()*3];
int drawCount = 0;
std::list<CXXSphereFlatTriangle, CXX::CXXAlloc<CXXSphereFlatTriangle> >::const_iterator trianglesEnd =
theSphere.getFlatTriangles().end();
for (std::list<CXXSphereFlatTriangle, CXX::CXXAlloc<CXXSphereFlatTriangle> >::const_iterator triangle =
theSphere.getFlatTriangles().begin();
triangle != trianglesEnd;
++triangle){
const CXXSphereFlatTriangle &theTriangle(*triangle);
if (theTriangle.doDraw()){
if (sense == CXXSphereElement::Contact ||
sense == CXXSphereElement::VDW ||
sense == CXXSphereElement::Accessible){
for (unsigned int j=0; j<3; j++){
int index = equivalence[theTriangle[2-j]];
triangleBuffer[3*drawCount+j] = index + oldVertexCount;
}
}
else {
for (unsigned int j=0; j<3; j++){
int index = equivalence[theTriangle[j]];
triangleBuffer[3*drawCount+j] = index + oldVertexCount;
}
}
drawCount++;
}
}
extendTriangles(triangleBuffer, drawCount);
//delete [] triangleBuffer;
}
return 0;
}
