void RefinementState::calcEnergy ()
{
int i, j;
float r;
Vec2f d;
energy = 0;
for (i = _graph.vertexBegin(); i < _graph.vertexEnd(); i = _graph.vertexNext(i))
for (j = _graph.vertexBegin(); j < _graph.vertexEnd(); j = _graph.vertexNext(j))
{
if (i == j)
continue;
d.diff(layout[i], layout[j]);
r = d.lengthSqr();
if (r < 0.0001f)
r = 5000000.f;
else
r = 1 / r;
energy += r;
}
energy /= 2;
}
// Flip all verices from branch around (v1,v2)
void RefinementState::flipBranch (const Filter &branch, const RefinementState &state, int v1_idx, int v2_idx)
{
int i;
float r, t;
const Vec2f &v1 = state.layout[v1_idx];
const Vec2f &v2 = state.layout[v2_idx];
Vec2f d;
d.diff(v2, v1);
r = d.lengthSqr();
if (r < 0.000000001f)
throw Error("too small edge");
layout.clear_resize(state.layout.size());
for (i = _graph.vertexBegin(); i < _graph.vertexEnd(); i = _graph.vertexNext(i))
{
if (!branch.valid(i))
{
const Vec2f &vi = state.layout[i];
t = ((vi.x - v1.x) * d.x + (vi.y - v1.y) * d.y) / r;
layout[i].set(2 * d.x * t + 2 * v1.x - vi.x, 2 * d.y * t + 2 * v1.y - vi.y);
} else
layout[i] = state.layout[i];
}
}
bool Vec2f::normalization (const Vec2f &v)
{
float l = v.lengthSqr();
if (l < EPSILON * EPSILON)
return false;
l = (float)sqrt(l);
x = v.x / l;
y = v.y / l;
return true;
}
RefinementState::RefinementState (MoleculeLayoutGraph &graph) :
dist(0.f),
energy(0),
height(0.f),
CP_INIT,
TL_CP_GET(layout),
_graph(graph)
{
}
void RefinementState::calcDistance (int v1, int v2)
{
Vec2f d;
d.diff(layout[v1], layout[v2]);
dist = d.lengthSqr();
}
void MoleculeCleaner2d::_calcCoef(int to, int from0, int from1) {
Vec2f A0 = plane(_mol.getAtomXyz(from0));
Vec2f A1 = plane(_mol.getAtomXyz(from1));
Vec2f A2 = plane(_mol.getAtomXyz(to));
Vec2f vec = A1 - A0;
float dist2 = vec.lengthSqr();
float cross = Vec2f::cross(A1 - A0, A2 - A0); // c1
float dot = Vec2f::dot(A1 - A0, A2 - A0); // c2
Vec2f _coef = Vec2f(dot, cross) / dist2;
int len = std::max(coef[from0].size(), coef[from1].size());
_addCoef(from0, len - 1, ZERO);
_addCoef(from1, len - 1, ZERO);
for (int i = 0; i < len; i++) {
_addCoef(to, i, mult(_coef, coef[from1][i]));
Vec2f one_minus_coef = ONE - _coef;
_addCoef(to, i, mult(one_minus_coef, coef[from0][i]));
}
}
MoleculeLayoutSmoothingSegment::MoleculeLayoutSmoothingSegment(MoleculeLayoutGraphSmart& mol, Vec2f& start, Vec2f& finish) :
_graph(mol),
_start(start),
_finish(finish)
{
_center.zero();
Vec2f diameter = (_finish - _start);
_length = diameter.length();
Vec2f rotate_vector = diameter / diameter.lengthSqr();
rotate_vector.y *= -1;
_pos.clear_resize(_graph.vertexEnd());
bool is_line = false;
for (int v : _graph.vertices()) if (_graph.getVertex(v).degree() == 1) is_line = true;
if (!is_line) {
for (int v : _graph.vertices()) {
_pos[v].copy(_graph.getPos(v));
_pos[v] -= _start;
_pos[v].rotate(rotate_vector);
}
}
else {
// this is straight line
QS_DEF(Array<int>, vert);
vert.clear(); // list or vertices in order of connection
for (int v : _graph.vertices()) if (_graph.getVertex(v).degree() == 1) {
vert.push(v);
break;
}
vert.push(_graph.getVertex(vert[0]).neiVertex(_graph.getVertex(vert[0]).neiBegin()));
while (vert.size() < _graph.vertexCount()) {
for (int n = _graph.getVertex(vert.top()).neiBegin(); n != _graph.getVertex(vert.top()).neiEnd(); n = _graph.getVertex(vert.top()).neiNext(n))
if (_graph.getVertex(vert.top()).neiVertex(n) != vert[vert.size() - 2]) {
vert.push(_graph.getVertex(vert.top()).neiVertex(n));
}
}
for (int i = 0; i < vert.size(); i++) _pos[vert[i]].set(i * 1. / (vert.size() - 1), 0);
}
// double ternary search of center of component
float MLx = 0, Ly = 0, MRx = 0, Ry = 0, Lx, Rx;
for (int v : _graph.vertices()) {
MLx = __min(MLx, _pos[v].x);
MRx = __max(MRx, _pos[v].x);
Ly = __min(Ly, _pos[v].y);
Ry = __max(Ry, _pos[v].y);
}
while (Ry - Ly > EPSILON) {
float dy = (Ry - Ly) / 3;
float ry[2];
float My = Ly + dy;
for (int i = 0; i < 2; i++) {
Lx = MLx, Rx = MRx;
float rx[2];
while (Rx - Lx > EPSILON) {
float dx = (Rx - Lx) / 3;
float Mx = Lx + dx;
for (int j = 0; j < 2; j++) {
rx[j] = calc_radius(Vec2f(Mx, My));
Mx += dx;
}
if (rx[0] > rx[1]) Lx += dx; else Rx -= dx;
}
ry[i] = calc_radius(Vec2f(Rx, My));
My += dy;
}
if (ry[0] > ry[1]) Ly += dy; else Ry -= dy;
}
_center = Vec2f(Rx, Ry);
_radius = calc_radius(_center);
/*
_radius = 0;
Vec2f center(0.5, 0);
for (int v : _graph.vertices()) {
float dist = (center - _pos[v]).length();
if (dist > _radius) _radius = dist;
}
_center = center;*/
_square = 0;
}