SecondaryStructureResidue setup_coarse_secondary_structure_residue(
const Particles &ssr_ps, Model *mdl,
bool winner_takes_all_per_res) {
Floats scores;
scores.push_back(0.0);
scores.push_back(0.0);
scores.push_back(0.0);
int count = 0;
for (Particles::const_iterator p = ssr_ps.begin(); p != ssr_ps.end();
++p) {
IMP_USAGE_CHECK(SecondaryStructureResidue::get_is_setup(*p),
"all particles must be SecondaryStructureResidues");
SecondaryStructureResidue ssr(*p);
Floats tmp_scores;
tmp_scores.push_back(ssr.get_prob_helix());
tmp_scores.push_back(ssr.get_prob_strand());
tmp_scores.push_back(ssr.get_prob_coil());
int max_i = 0;
Float max = 0.0;
for (int i = 0; i < 3; i++) {
if (tmp_scores[i] > max) {
max = tmp_scores[i];
max_i = i;
}
if (!winner_takes_all_per_res) scores[i] += tmp_scores[i];
}
if (winner_takes_all_per_res) scores[max_i] += 1.0;
count++;
}
IMP_NEW(Particle, coarse_p, (mdl));
SecondaryStructureResidue ssres = SecondaryStructureResidue::setup_particle(
coarse_p, scores[0] / count, scores[1] / count, scores[2] / count);
return ssres;
}
core::MonteCarloMoverResult WeightMover::do_propose() {
IMP_OBJECT_LOG;
// store the old weights in case of reject
oldweights_ = w_.get_weights();
// Draw weights from a uniform distribution of variables that sum to one
// taken from http://stats.stackexchange.com/questions/14059/
// generate-uniformly-distributed-weights-that-sum-to-unity
// get the old x
Floats x;
x.push_back(oldweights_[0]);
for (unsigned i = 1; i < oldweights_.get_dimension() - 1; ++i) {
x.push_back(oldweights_[i] + x[i - 1]);
}
// zero vector in D dimension
algebra::VectorKD zero = algebra::get_zero_vector_kd(x.size());
// generate random perturbation of old components
algebra::VectorKD dX =
algebra::get_random_vector_in(algebra::SphereKD(zero, radius_));
// add perturbation to x and apply reflective boundaries
for (unsigned i = 0; i < x.size(); ++i) {
if (x[i] + dX[i] > 1.0)
x[i] = 2.0 - x[i] - dX[i];
else if (x[i] + dX[i] < 0.0)
x[i] = -x[i] - dX[i];
else
x[i] += dX[i];
}
// sort the new x here
std::sort(x.begin(), x.end(), std::less<double>());
// get the new weights
algebra::VectorKD newweights =
algebra::get_zero_vector_kd(oldweights_.get_dimension());
newweights[0] = x[0];
for (unsigned i = 1; i < newweights.get_dimension() - 1; ++i) {
newweights[i] = x[i] - x[i - 1];
}
newweights[newweights.get_dimension() - 1] = 1.0 - x[x.size() - 1];
// set the new weights
w_.set_weights(newweights);
return core::MonteCarloMoverResult(
ParticleIndexes(1, w_.get_particle()->get_index()), 1.0);
}
Floats CrossLinkData::get_nonmarginal_elements(double sigmai,
Floats dists) const {
Floats probs;
if (bias_) {
for (unsigned n = 0; n < dists.size(); n++) {
probs.push_back(get_biased_element(dists[n], sigmai));
}
}
if (!bias_) {
for (unsigned n = 0; n < dists.size(); n++) {
probs.push_back(get_unbiased_element(dists[n], sigmai));
}
}
return probs;
}
Floats GaussianProcessInterpolation::get_posterior_covariance_derivative(
Floats x, bool) const {
IMP_Eigen::VectorXd mat(get_posterior_covariance_derivative(x));
Floats tmp;
for (unsigned j = 0; j < mat.rows(); j++) tmp.push_back(mat(j));
return tmp;
}
TEST(Neighbors,CoverTreeDistanceNeighbors)
{
typedef std::vector<float> Floats;
const int N = 100;
const int k = 10;
Floats floats;
for (int i=0;i<N;i++)
floats.push_back(float(i));
float_distance_callback fdc;
tapkee::tapkee_internal::Neighbors neighbors =
tapkee::tapkee_internal::find_neighbors(tapkee::CoverTree, floats.begin(), floats.end(),
tapkee::tapkee_internal::PlainDistance<Floats::iterator,float_distance_callback>(fdc), k, true);
for (int i=0;i<N;i++)
{
// total number of found neighbors is k
ASSERT_EQ(neighbors[i].size(),k);
std::set<float> neighbors_set;
for (int j=0;j<k;j++)
neighbors_set.insert(neighbors[i][j]);
// there are no repeated values
ASSERT_EQ(neighbors_set.size(),k);
// the vector is not a neighbor of itself
ASSERT_EQ(neighbors_set.find(floats[i]),neighbors_set.end());
// check neighbors
int k_left = std::min(i,k/2);
int k_right = std::min(N-i-1,k/2);
for (int j=0; j<k_left; j++)
ASSERT_NE(neighbors_set.find(floats[i-j-1]),neighbors_set.end());
for (int j=0; j<k_right; j++)
ASSERT_NE(neighbors_set.find(floats[i+j+1]),neighbors_set.end());
}
}
Floats CysteineCrossLinkData::get_omegas(Floats fmods, double omega0) const {
Floats omegas;
for (unsigned n = 0; n < fmods.size(); ++n) {
double cumul = 0;
double cumul2 = 0;
for (unsigned j = 1; j < omega_grid_.size(); ++j) {
double omj = omega_grid_[j];
double omjm1 = omega_grid_[j - 1];
double dom = omj - omjm1;
double priorj = get_omega_prior(omj, omega0);
double priorjm1 = get_omega_prior(omjm1, omega0);
double pj = get_element(fexp_, fmods[n], omj) * priorj;
double pjm1 = get_element(fexp_, fmods[n], omjm1) * priorjm1;
double pj2 = get_element(fexp_, fmods[n], omj) * priorj * omj;
double pjm12 = get_element(fexp_, fmods[n], omjm1) * priorjm1 * omjm1;
cumul += (pj + pjm1) / 2.0 * dom;
cumul2 += (pj2 + pjm12) / 2.0 * dom;
}
omegas.push_back(cumul2 / cumul);
}
return omegas;
}
Floats FStudentT::evaluate_derivative_FX(const Floats FXs) const {
Floats dervs;
double c = (N_ + nu_) / IMP::square(sigma_) / (nu_ + t2_);
for (unsigned int i = 0; i < FXs.size(); i++) {
dervs.push_back(c * (FXs[i] - FM_));
}
return dervs;
}
Floats ReplicaExchange::create_temperatures(double tmin,double tmax,int nrep)
{
Floats temp;
double tfact=exp(log(tmax/tmin)/double(nrep-1));
for(int i=0;i<nrep;++i) {
temp.push_back(tmin*pow(tfact,i));
}
return temp;
}
FloatsList GaussianProcessInterpolationRestraint::get_hessian(bool) const {
IMP_Eigen::MatrixXd tmp(get_hessian());
FloatsList ret;
for (unsigned i = 0; i < tmp.rows(); ++i) {
Floats buf;
for (unsigned j = 0; j < tmp.cols(); ++j) buf.push_back(tmp(i, j));
ret.push_back(buf);
}
return ret;
}
Floats CrossLinkData::get_marginal_elements(double sigma, Floats dists) const {
Floats probs;
unsigned is = get_closest(sigma_grid_, sigma);
for (unsigned n = 0; n < dists.size(); n++) {
unsigned id = get_closest(dist_grid_, dists[n]);
probs.push_back(grid_[is][id]);
}
return probs;
}
FloatsList GaussianProcessInterpolation::get_data_variance() const {
FloatsList ret;
IMP_Eigen::MatrixXd S(get_S());
for (unsigned i = 0; i < M_; i++) {
Floats val;
for (unsigned j = 0; j < M_; j++) val.push_back(S(i, j));
ret.push_back(val);
}
return ret;
}
Floats CysteineCrossLinkData::get_nonmarginal_elements(double fexp,
Floats fmods,
double omega) const {
Floats probs;
for (unsigned n = 0; n < fmods.size(); n++) {
probs.push_back(get_element(fexp, fmods[n], omega));
}
return probs;
}
IMPISD_BEGIN_NAMESPACE
CysteineCrossLinkData::CysteineCrossLinkData(double fexp, Floats fmod_grid,
Floats omega_grid,
Floats omega0_grid, int prior_type)
: Object("Data Structure for CysteineCrossLinkRestraint %1%") {
prior_type_ = prior_type;
// fexp is the experimental frequency
// fmod is the model frequency
// omega0 is the typical value for omega, i.e., the experimental uncertainty
// this constructor calculates the marginal likelihood using a
// truncated gaussian function
// to account for outliers
// Store omega0 grid
omega0_grid_ = omega0_grid;
// Store the fmod grid
fmod_grid_ = fmod_grid;
// Store omega grid
omega_grid_ = omega_grid;
fexp_ = fexp;
for (unsigned k = 0; k < omega0_grid_.size(); ++k) {
double omega0 = omega0_grid_[k];
Floats grid;
for (unsigned i = 0; i < fmod_grid_.size(); ++i) {
double fmod = fmod_grid_[i];
double cumul = 0;
for (unsigned j = 1; j < omega_grid_.size(); ++j) {
double omj = omega_grid_[j];
double omjm1 = omega_grid_[j - 1];
double dom = omj - omjm1;
double priorj = get_omega_prior(omj, omega0);
double priorjm1 = get_omega_prior(omjm1, omega0);
double pj = get_element(fexp_, fmod, omj) * priorj;
double pjm1 = get_element(fexp_, fmod, omjm1) * priorjm1;
cumul += (pj + pjm1) / 2.0 * dom;
}
grid.push_back(cumul);
}
grid_.push_back(grid);
}
}
FloatsList GaussianProcessInterpolation::get_posterior_covariance_hessian(
Floats x, bool) const {
IMP_Eigen::MatrixXd mat(get_posterior_covariance_hessian(x));
FloatsList ret;
for (unsigned j = 0; j < mat.rows(); j++) {
Floats tmp;
for (unsigned i = 0; i < mat.cols(); i++) tmp.push_back(mat(i, j));
ret.push_back(tmp);
}
return ret;
}
Floats CysteineCrossLinkData::get_marginal_elements(Floats fmods,
double omega0) const {
Floats probs;
unsigned is = get_closest(omega0_grid_, omega0);
for (unsigned n = 0; n < fmods.size(); n++) {
unsigned id = get_closest(fmod_grid_, fmods[n]);
probs.push_back(grid_[is][id]);
}
return probs;
}
void ProbabilisticAnchorGraph::set_particle_probabilities_on_anchors(
Particle *p, FittingSolutionRecords sols) {
IMP_USAGE_CHECK(sols.size() > 0, "no solutions provided\n");
IMP_NEW(algebra::NearestNeighborD<3>, nn, (positions_));
Ints anchor_counters;
anchor_counters.insert(anchor_counters.end(), positions_.size(), 0);
for (unsigned int i = 0; i < sols.size(); i++) {
algebra::Vector3D loc = sols[i].get_fit_transformation().get_transformed(
core::XYZ(p).get_coordinates());
anchor_counters[nn->get_nearest_neighbor(loc)]++;
}
Floats probs;
for (unsigned int i = 0; i < anchor_counters.size(); i++) {
probs.push_back(1. * anchor_counters[i] / sols.size());
}
particle_to_anchor_probabilities_[p] = probs;
}
Floats CrossLinkData::get_omegas(double sigma, Floats dists) const {
Floats omegas;
for (unsigned n = 0; n < dists.size(); ++n) {
double cumul = 0;
double cumul2 = 0;
if (!bias_) {
for (unsigned j = 1; j < omega_grid_.size(); ++j) {
double omj = omega_grid_[j];
double omjm1 = omega_grid_[j - 1];
double dom = omj - omjm1;
double pj = get_unbiased_element(dists[n], omj * sigma) / omj;
double pjm1 = get_unbiased_element(dists[n], omjm1 * sigma) / omjm1;
double pj2 = get_unbiased_element(dists[n], omj * sigma);
double pjm12 = get_unbiased_element(dists[n], omjm1 * sigma);
cumul += (pj + pjm1) / 2.0 * dom;
cumul2 += (pj2 + pjm12) / 2.0 * dom;
}
}
if (bias_) {
for (unsigned j = 1; j < omega_grid_.size(); ++j) {
double omj = omega_grid_[j];
double omjm1 = omega_grid_[j - 1];
double dom = omj - omjm1;
double pj = get_biased_element(dists[n], omj * sigma) / omj;
double pjm1 = get_biased_element(dists[n], omjm1 * sigma) / omjm1;
double pj2 = get_biased_element(dists[n], omj * sigma);
double pjm12 = get_biased_element(dists[n], omjm1 * sigma);
cumul += (pj + pjm1) / 2.0 * dom;
cumul2 += (pj2 + pjm12) / 2.0 * dom;
}
}
omegas.push_back(cumul2 / cumul);
}
return omegas;
}
Floats ChainStatisticsOptimizerState::get_diffusion_coefficients() const {
if (positions_.empty()) return Floats();
base::Vector<algebra::Vector3Ds >
displacements(positions_[0].size(),
algebra::Vector3Ds( positions_.size()-1));
for (unsigned int i=1; i< positions_.size(); ++i) {
algebra::Transformation3D rel
= algebra::get_transformation_aligning_first_to_second(positions_[i-1],
positions_[i]);
for (unsigned int j=0; j < positions_[i].size(); ++j) {
displacements[j][i-1]= rel.get_transformed(positions_[i-1][j])
- positions_[i][j];
}
}
Floats ret;
for (unsigned int i=0; i < displacements.size(); ++i) {
ret.push_back(atom::get_diffusion_coefficient(displacements[i],
get_period()*get_dt()));
}
return ret;
}
/* Apply the restraint to two atoms, two Scales, one experimental value.
*/
double
AmbiguousNOERestraint::unprotected_evaluate(DerivativeAccumulator *accum) const
{
IMP_OBJECT_LOG;
IMP_USAGE_CHECK(get_model(),
"You must at least register the restraint with the model"
<< " before calling evaluate.");
/* compute Icalc = 1/(gamma*d^6) where d = (sum d_i^-6)^(-1/6) */
double vol = 0;
Floats vols;
IMP_CONTAINER_FOREACH(PairContainer, pc_,
{
core::XYZ d0(get_model(), _1[0]);
core::XYZ d1(get_model(), _1[1]);
algebra::Vector3D c0 = d0.get_coordinates();
algebra::Vector3D c1 = d1.get_coordinates();
//will raise an error if c0 == c1
double tmp = 1.0/(c0-c1).get_squared_magnitude();
vols.push_back(IMP::cube(tmp)); // store di^-6
vol += vols.back();
});
CrossLinkData::CrossLinkData(Floats dist_grid, Floats omega_grid,
Floats sigma_grid, Floats pot_x_grid,
Floats pot_value_grid, double don, double doff,
int prior_type)
: Object("Data Structure for CrossLinkMSRestraint %1%") {
prior_type_ = prior_type;
bias_ = true;
// this constructor calculates the marginal likelihood using a biasing
// potential
// obtained from Free energy calculations.
// Store dist grid
dist_grid_ = dist_grid;
// Store omega grid
omega_grid_ = omega_grid;
// Store sigma grid
sigma_grid_ = sigma_grid;
// Store the potential x coordinates
pot_x_grid_ = pot_x_grid;
// Store the normalized potential
double cumul = 0;
for (unsigned j = 1; j < pot_value_grid.size(); ++j) {
double xj = pot_x_grid_[j];
double xjm1 = pot_x_grid_[j - 1];
double dx = xj - xjm1;
double pj = pot_value_grid[j];
double pjm1 = pot_value_grid[j - 1];
cumul += (pj + pjm1) / 2.0 * dx;
}
for (unsigned i = 0; i < pot_value_grid.size(); ++i) {
pot_value_grid_.push_back(pot_value_grid[i] / cumul);
}
for (unsigned k = 0; k < sigma_grid_.size(); ++k) {
double sigma = sigma_grid_[k];
Floats grid;
for (unsigned i = 0; i < dist_grid_.size(); ++i) {
double dist = dist_grid_[i];
double cumul = 0;
for (unsigned j = 1; j < omega_grid_.size(); ++j) {
double omj = omega_grid_[j];
double omjm1 = omega_grid_[j - 1];
double dom = omj - omjm1;
double pj;
double pjm1;
if (prior_type_ == 0) {
pj = get_biased_element(dist, omj * sigma) / omj;
pjm1 = get_biased_element(dist, omjm1 * sigma) / omjm1;
} else {
pj = get_biased_element(dist, omj) * get_omega_prior(omj, sigma);
pjm1 =
get_biased_element(dist, omjm1) * get_omega_prior(omjm1, sigma);
}
cumul += (pj + pjm1) / 2.0 * dom;
}
// switching cumul to zero between don and doff
if (dist > doff) {
cumul = 0.;
}
if (dist > don && dist <= doff) {
cumul *= pow(doff * doff - dist * dist, 2) *
(doff * doff + 2. * dist * dist - 3. * don * don) /
pow(doff * doff - don * don, 3);
}
grid.push_back(cumul);
}
grid_.push_back(grid);
}
}
IMPISD_BEGIN_NAMESPACE
CrossLinkData::CrossLinkData(Floats dist_grid, Floats omega_grid,
Floats sigma_grid, double lexp, double don,
double doff, int prior_type)
: Object("Data Structure for CrossLinkMSRestraint %1%") {
prior_type_ = prior_type;
lexp_ = lexp;
bias_ = false;
// this constructor calculates the marginal likelihood using a theta function
// to approximate the propensity of the linker
// Store dist grid
dist_grid_ = dist_grid;
// Store omega grid
omega_grid_ = omega_grid;
// Store sigma grid
sigma_grid_ = sigma_grid;
for (unsigned k = 0; k < sigma_grid_.size(); ++k) {
double sigma = sigma_grid_[k];
Floats grid;
for (unsigned i = 0; i < dist_grid_.size(); ++i) {
double dist = dist_grid_[i];
double cumul = 0;
for (unsigned j = 1; j < omega_grid_.size(); ++j) {
double omj = omega_grid_[j];
double omjm1 = omega_grid_[j - 1];
double dom = omj - omjm1;
double pj;
double pjm1;
if (prior_type_ == 0) {
pj = get_biased_element(dist, omj * sigma) / omj;
pjm1 = get_biased_element(dist, omjm1 * sigma) / omjm1;
} else {
pj = get_biased_element(dist, omj) * get_omega_prior(omj, sigma);
pjm1 =
get_biased_element(dist, omjm1) * get_omega_prior(omjm1, sigma);
}
cumul += (pj + pjm1) / 2.0 * dom;
}
// switching cumul to zero between don and doff
if (dist > doff) {
cumul = 0.;
}
if (dist > don && dist <= doff) {
cumul *= pow(doff * doff - dist * dist, 2) *
(doff * doff + 2. * dist * dist - 3. * don * don) /
pow(doff * doff - don * don, 3);
}
grid.push_back(cumul);
}
grid_.push_back(grid);
}
}
IMPCNMULTIFIT_BEGIN_NAMESPACE
Floats get_rmsd_for_models(const std::string param_filename,
const std::string trans_filename,
const std::string ref_filename, int start_model,
int end_model) {
std::string protein_filename, surface_filename;
int cn_symm_deg;
std::cout << "============= parameters ============" << std::endl;
std::cout << "params filename : " << param_filename << std::endl;
std::cout << "trans filename : " << trans_filename << std::endl;
std::cout << "ref filename : " << ref_filename << std::endl;
std::cout << "start index to rmsd : " << start_model << std::endl;
std::cout << "end index to rmsd : " << end_model << std::endl;
std::cout << "=====================================" << std::endl;
internal::Parameters params(param_filename.c_str());
protein_filename = params.get_unit_pdb_fn();
cn_symm_deg = params.get_cn_symm();
IMP_NEW(Model, mdl, ());
atom::Hierarchy asmb_ref;
atom::Hierarchies mhs;
// read the monomer
core::XYZs model_xyzs;
for (int i = 0; i < cn_symm_deg; i++) {
atom::Hierarchy h =
atom::read_pdb(protein_filename, mdl, new atom::CAlphaPDBSelector());
atom::Chain c = atom::get_chain(
atom::Residue(atom::get_residue(atom::Atom(core::get_leaves(h)[0]))));
c.set_id(std::string(1, char(65 + i)));
atom::add_radii(h);
atom::create_rigid_body(h);
mhs.push_back(h);
Particles leaves = core::get_leaves(h);
for (Particles::iterator it = leaves.begin(); it != leaves.end();
it++) {
model_xyzs.push_back(core::XYZ(*it));
}
}
// read the transformations
multifit::FittingSolutionRecords recs =
multifit::read_fitting_solutions(trans_filename.c_str());
// read the reference structure
asmb_ref = atom::read_pdb(ref_filename, mdl, new atom::CAlphaPDBSelector());
atom::Hierarchies ref_chains =
atom::Hierarchies(atom::get_by_type(asmb_ref, atom::CHAIN_TYPE));
std::cout << "number of records:" << recs.size() << std::endl;
Floats rmsd;
std::ofstream out;
out.open("rmsd.output");
if (end_model < 0 || end_model >= static_cast<int>(recs.size())) {
end_model = recs.size() - 1;
}
for (int i = start_model; i >= 0 && i <= end_model; ++i) {
algebra::Transformation3D t1 = recs[i].get_dock_transformation();
algebra::Transformation3D t2 = recs[i].get_fit_transformation();
algebra::Transformation3D t2_inv = t1.get_inverse();
transform_cn_assembly(mhs, t1);
for (unsigned int j = 0; j < model_xyzs.size(); j++) {
model_xyzs[j]
.set_coordinates(t2.get_transformed(model_xyzs[j].get_coordinates()));
}
std::cout << mhs.size() << "," << ref_chains.size() << std::endl;
Float cn_rmsd = get_cn_rmsd(mhs, ref_chains);
out << " trans:" << i << " rmsd: " << cn_rmsd
<< " cc: " << 1. - recs[i].get_fitting_score() << std::endl;
rmsd.push_back(cn_rmsd);
for (unsigned int j = 0; j < model_xyzs.size(); j++) {
model_xyzs[j].set_coordinates(
t2_inv.get_transformed(model_xyzs[j].get_coordinates()));
}
/* std::stringstream ss;
ss<<"asmb_"<<i<<".pdb";
atom::write_pdb(mhs,ss.str());*/
transform_cn_assembly(mhs, t1.get_inverse());
}
out.close();
return rmsd;
}
Floats GaussianProcessInterpolation::get_data_mean() const {
Floats ret;
IMP_Eigen::VectorXd I(get_I());
for (unsigned i = 0; i < M_; i++) ret.push_back(I(i));
return ret;
}
IMP_Eigen::MatrixXd
GaussianProcessInterpolation::get_posterior_covariance_hessian(Floats x) const {
const_cast<GaussianProcessInterpolation *>(this)->update_flags_covariance();
// get how many and which particles are optimized
unsigned mnum = get_number_of_m_particles();
std::vector<bool> mopt;
unsigned mnum_opt = 0;
for (unsigned i = 0; i < mnum; i++) {
mopt.push_back(get_m_particle_is_optimized(i));
if (mopt.back()) mnum_opt++;
}
unsigned Onum = get_number_of_Omega_particles();
std::vector<bool> Oopt;
unsigned Onum_opt = 0;
for (unsigned i = 0; i < Onum; i++) {
Oopt.push_back(get_Omega_particle_is_optimized(i));
if (Oopt.back()) Onum_opt++;
}
// total number of optimized particles
unsigned num_opt = mnum_opt + Onum_opt;
// whether sigma is optimized
unsigned sigma_opt = Oopt[0] ? 1 : 0;
// cov_opt: number of optimized covariance particles without counting sigma
unsigned cov_opt = Onum_opt - sigma_opt;
// init matrix and fill with zeros at mean particle's indices
// dprior_cov(q,q)/(dsigma d.) is also zero
IMP_Eigen::MatrixXd ret(IMP_Eigen::MatrixXd::Zero(num_opt, num_opt));
// build vector of dcov(q,q)/dp1dp2 with p1 and p2 covariance particles
FloatsList xv;
xv.push_back(x);
FloatsList tmplist;
for (unsigned pa = 0; pa < Onum; ++pa) {
if (!Oopt[pa]) continue; // skip not optimized particles
if (pa == 0) continue; // skip sigma even when it is optimized
Floats tmp;
for (unsigned pb = pa; pb < Onum; ++pb) {
if (!Oopt[pb]) continue; // skip not optimized particles
// sigma has already been skipped
tmp.push_back(covariance_function_->get_second_derivative_matrix(
pa - 1, pb - 1, xv)(0, 0));
}
tmplist.push_back(tmp);
}
for (unsigned pa_opt = 0; pa_opt < cov_opt; pa_opt++)
for (unsigned pb_opt = pa_opt; pb_opt < cov_opt; pb_opt++)
ret.bottomRightCorner(cov_opt, cov_opt)(pa_opt, pb_opt) =
tmplist[pa_opt][pb_opt - pa_opt];
// compute and store w(q) derivatives (skip mean particles)
IMP_Eigen::MatrixXd dwqdp(M_, Onum_opt);
for (unsigned i = 0, j = 0; i < Onum; i++)
if (Oopt[i]) dwqdp.col(j++) = get_wx_vector_derivative(x, i + mnum);
// add d2cov/(dw(q)_k * dw(q)_l) * dw(q)^k/dp_i * dw(q)^l/dp_j
ret.bottomRightCorner(cov_opt, cov_opt).noalias() +=
dwqdp.rightCols(cov_opt).transpose() * get_d2cov_dwq_dwq() *
dwqdp.rightCols(cov_opt);
// compute and store Omega derivatives (skip mean particles)
std::vector<IMP_Eigen::MatrixXd> dOmdp;
for (unsigned i = 0; i < Onum; i++) {
if (Oopt[i]) dOmdp.push_back(get_Omega_derivative(i));
}
// add d2cov/(dOm_kl * dOm_mn) * dOm^kl/dp_i * dOm^mn/dp_j
std::vector<std::vector<IMP_Eigen::MatrixXd> > d2covdo;
for (unsigned m = 0; m < M_; m++) {
std::vector<IMP_Eigen::MatrixXd> tmp;
for (unsigned n = 0; n < M_; n++) tmp.push_back(get_d2cov_dOm_dOm(x, m, n));
d2covdo.push_back(tmp);
}
for (unsigned i = 0; i < Onum_opt; i++) {
IMP_Eigen::MatrixXd tmp(M_, M_);
for (unsigned m = 0; m < M_; ++m)
for (unsigned n = 0; n < M_; ++n)
tmp(m, n) = (d2covdo[m][n].transpose() * dOmdp[i]).trace();
for (unsigned j = i; j < Onum_opt; j++)
ret.bottomRightCorner(Onum_opt, Onum_opt)(i, j) +=
(dOmdp[j].transpose() * tmp).trace();
}
for (unsigned i = 0; i < d2covdo.size(); i++) d2covdo[i].clear();
d2covdo.clear();
// compute cross-term
std::vector<IMP_Eigen::MatrixXd> d2covdwdo;
for (unsigned k = 0; k < M_; k++)
d2covdwdo.push_back(get_d2cov_dwq_dOm(x, k));
// compute derivative contribution into temporary
IMP_Eigen::MatrixXd tmpH(Onum_opt, Onum_opt);
for (unsigned i = 0; i < Onum_opt; i++) {
IMP_Eigen::VectorXd tmp(M_);
for (unsigned k = 0; k < M_; k++)
tmp(k) = (d2covdwdo[k].transpose() * dOmdp[i]).trace();
for (unsigned j = 0; j < Onum_opt; j++)
tmpH(i, j) = dwqdp.col(j).transpose() * tmp;
}
ret.bottomRightCorner(Onum_opt, Onum_opt) += tmpH + tmpH.transpose();
// deallocate unused stuff
// tmpH.resize(0,0);
d2covdwdo.clear();
dOmdp.clear();
// dwqdp.resize(0,0);
// dcov/dw_k * d2w^k/(dp_i dp_j)
IMP_Eigen::VectorXd dcwq(get_dcov_dwq(x));
for (unsigned i = 0; i < cov_opt; i++)
for (unsigned j = i; j < cov_opt; j++)
ret.bottomRightCorner(cov_opt, cov_opt)(i, j) +=
dcwq.transpose() *
get_wx_vector_second_derivative(x, mnum + 1 + i, mnum + 1 + j);
// dcwq.resize(0,0);
// dcov/dOm_kl * d2Om^kl/(dp_i dp_j), zero when p_i or p_j is sigma or mean
IMP_Eigen::MatrixXd dcOm(get_dcov_dOm(x));
for (unsigned i = 0; i < cov_opt; i++)
for (unsigned j = i; j < cov_opt; j++)
ret.bottomRightCorner(cov_opt, cov_opt)(i, j) +=
(dcOm.transpose() * get_Omega_second_derivative(i + 1, j + 1))
.trace();
// dcOm.resize(0,0);
// return as symmetric matrix
for (unsigned i = mnum_opt; i < num_opt; ++i)
for (unsigned j = mnum_opt + 1; j < num_opt; ++j) ret(j, i) = ret(i, j);
return ret;
}