void MeshGeometry::addTriangles(const Core::Array<unsigned int>& indiceArray)
{
m_indices.reserve(m_indices.size() + indiceArray.size());
std::copy(indiceArray.begin(), indiceArray.end(),
std::back_inserter(m_indices));
m_dirty = true;
}
void Spectra::setMode(int mode)
{
if (mode >= 0
&& mode < static_cast<int>(m_molecule->vibrationFrequencies().size())) {
m_mode = mode;
// Now calculate the frames and set them on the molecule.
m_molecule->setCoordinate3d(0);
Core::Array<Vector3> atomPositions = m_molecule->atomPositions3d();
Core::Array<Vector3> atomDisplacements = m_molecule->vibrationLx(mode);
int frames = 5;
int frameCounter = 0;
m_molecule->setCoordinate3d(atomPositions, frameCounter++);
double factor = 0.01 * m_amplitude;
// Current coords + displacement.
for (int i = 1; i <= frames; ++i) {
Core::Array<Vector3> framePositions;
for (Index atom = 0; atom < m_molecule->atomCount(); ++atom) {
framePositions.push_back(atomPositions[atom] + atomDisplacements[atom]
* factor * (double(i) / frames));
}
m_molecule->setCoordinate3d(framePositions, frameCounter++);
}
// + displacement back to original.
for (int i = frames - 1; i >=0; --i) {
Core::Array<Vector3> framePositions;
for (Index atom = 0; atom < m_molecule->atomCount(); ++atom) {
framePositions.push_back(atomPositions[atom] + atomDisplacements[atom]
* factor *(double(i) / frames));
}
m_molecule->setCoordinate3d(framePositions, frameCounter++);
}
// Current coords - displacement.
for (int i = 1; i <= frames; ++i) {
Core::Array<Vector3> framePositions;
for (Index atom = 0; atom < m_molecule->atomCount(); ++atom) {
framePositions.push_back(atomPositions[atom] - atomDisplacements[atom]
* factor *(double(i) / frames));
}
m_molecule->setCoordinate3d(framePositions, frameCounter++);
}
// - displacement back to original.
for (int i = frames - 1; i >=0; --i) {
Core::Array<Vector3> framePositions;
for (Index atom = 0; atom < m_molecule->atomCount(); ++atom) {
framePositions.push_back(atomPositions[atom] - atomDisplacements[atom]
* factor *(double(i) / frames));
}
m_molecule->setCoordinate3d(framePositions, frameCounter++);
}
}
}
size_t LineStripGeometry::addLineStrip(const Core::Array<Vector3f> &vertices,
const Core::Array<Vector3ub> &rgb,
float lineWidth)
{
if (vertices.empty() || vertices.size() != rgb.size())
return InvalidIndex;
size_t result = m_lineStarts.size();
m_lineStarts.push_back(static_cast<unsigned int>(m_vertices.size()));
m_lineWidths.push_back(lineWidth);
Array<Vector3ub>::const_iterator colorIter(rgb.begin());
Array<Vector3f>::const_iterator vertIter(vertices.begin());
Array<Vector3f>::const_iterator vertEnd(vertices.end());
m_vertices.reserve(m_vertices.size() + vertices.size());
Vector4ub tmpColor(0, 0, 0, m_opacity);
while (vertIter != vertEnd) {
tmpColor.head<3>() = *(colorIter++);
m_vertices.push_back(PackedVertex(*(vertIter++), tmpColor));
}
m_dirty = true;
return result;
}
//
// Info::putChunk
//
void Info::putChunk(char const *name, Core::Array<Core::String> const &strs, bool junk)
{
std::size_t base;
std::size_t off;
// Calculate base offset.
base = strs.size() * 4 + 4;
if(junk) base += 8;
// Calculate size of chunk.
off = base;
for(auto const &s : strs)
off += lenString(s);
// Write chunk header.
putData(name, 4);
putWord(off);
// Write string count.
if(junk) putWord(0);
putWord(strs.size());
if(junk) putWord(0);
// Write string offsets.
off = base;
for(auto const &s : strs)
{
putWord(off);
off += lenString(s);
}
// Write strings.
if(junk && UseChunkSTRE)
{
off = base;
for(auto const &s : strs)
{
putString(s, off * 157135);
off += lenString(s);
}
}
else for(auto const &s : strs)
putString(s);
}
unsigned int MeshGeometry::addVertices(const Core::Array<Vector3f>& v,
const Core::Array<Vector3f>& n)
{
if (v.size() != n.size())
return InvalidIndex;
size_t result = m_vertices.size();
Core::Array<Vector3f>::const_iterator vIter = v.begin();
Core::Array<Vector3f>::const_iterator vEnd = v.end();
Core::Array<Vector3f>::const_iterator nIter = n.begin();
const Vector4ub tmpColor(m_color[0], m_color[1], m_color[2], m_opacity);
while (vIter != vEnd)
m_vertices.push_back(PackedVertex(tmpColor, *(nIter++), *(vIter++)));
m_dirty = true;
return static_cast<unsigned int>(result);
}
bool Molecule::removeAtom(Index index)
{
if (index >= atomCount())
return false;
Index uniqueId = findAtomUniqueId(index);
if (uniqueId == MaxIndex)
return false;
// Unique ID of an atom that was removed:
m_atomUniqueIds[uniqueId] = MaxIndex;
// Before removing the atom we must first remove any bonds to it.
Core::Array<BondType> atomBonds = Core::Molecule::bonds(atom(index));
while (atomBonds.size()) {
removeBond(atomBonds.back());
atomBonds = Core::Molecule::bonds(atom(index));
}
Index newSize = static_cast<Index>(m_atomicNumbers.size() - 1);
if (index != newSize) {
// We need to move the last atom to this position, and update its unique ID.
m_atomicNumbers[index] = m_atomicNumbers.back();
if (m_positions2d.size() == m_atomicNumbers.size())
m_positions2d[index] = m_positions2d.back();
if (m_positions3d.size() == m_atomicNumbers.size())
m_positions3d[index] = m_positions3d.back();
// Find any bonds to the moved atom and update their index.
atomBonds = Core::Molecule::bonds(atom(newSize));
foreach (const BondType& currentBond, atomBonds) {
std::pair<Index, Index> pair = m_bondPairs[currentBond.index()];
if (pair.first == newSize)
pair.first = index;
else if (pair.second == newSize)
pair.second = index;
m_bondPairs[currentBond.index()] = pair;
}
unsigned int MeshGeometry::addVertices(const Core::Array<Vector3f>& v,
const Core::Array<Vector3f>& n,
const Core::Array<Vector4ub>& c)
{
if (v.size() != n.size() || n.size() != c.size())
return InvalidIndex;
size_t result = m_vertices.size();
Core::Array<Vector3f>::const_iterator vIter = v.begin();
Core::Array<Vector3f>::const_iterator vEnd = v.end();
Core::Array<Vector3f>::const_iterator nIter = n.begin();
Core::Array<Vector4ub>::const_iterator cIter = c.begin();
while (vIter != vEnd)
m_vertices.push_back(PackedVertex(*(cIter++), *(nIter++), *(vIter++)));
m_dirty = true;
return static_cast<unsigned int>(result);
}
Bool FileSystem::Find( const Char * searchStr, Core::Array< PathString >& fileNames, Bool absolute )
{
WIN32_FIND_DATA ffd;
HANDLE hFind;
hFind = FindFirstFile( searchStr, &ffd );
if ( hFind == INVALID_HANDLE_VALUE )
{
return false;
}
Char dir[ 256 ];
Char * fileStart = dir;
if ( absolute )
{
if ( GetFullPathName( searchStr, 256, dir, &fileStart ) == 0 )
{
return false;
}
}
do
{
if ( ! ( ffd.dwFileAttributes & FILE_ATTRIBUTE_DIRECTORY ) )
{
PathString f( dir, fileStart - dir );
f += ffd.cFileName;
fileNames.PushBack( f );
}
}
while ( FindNextFile( hFind, &ffd ) != 0 );
FindClose( hFind );
return true;
}
