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;
}
/// A thread-safe version of CalcSummary. BlockFile::CalcSummary
/// uses a static summary array across the class, which we can't use.
/// Get a buffer containing a summary block describing this sample
/// data. This must be called by derived classes when they
/// are constructed, to allow them to construct their summary data,
/// after which they should write that data to their disk file.
///
/// This method also has the side effect of setting the mMin, mMax,
/// and mRMS members of this class.
///
/// Unlike BlockFile's implementation You SHOULD DELETE the returned buffer.
/// this is protected so it shouldn't be hard to deal with - just override
/// all BlockFile methods that use this method.
///
/// @param buffer A buffer containing the sample data to be analyzed
/// @param len The length of the sample data
/// @param format The format of the sample data.
void *ODDecodeBlockFile::CalcSummary(samplePtr buffer, size_t len,
sampleFormat format, ArrayOf<char> &cleanup)
{
cleanup.reinit(mSummaryInfo.totalSummaryBytes);
char* localFullSummary = cleanup.get();
memcpy(localFullSummary, bheaderTag, bheaderTagLen);
float *summary64K = (float *)(localFullSummary + mSummaryInfo.offset64K);
float *summary256 = (float *)(localFullSummary + mSummaryInfo.offset256);
Floats floats;
float *fbuffer;
//mchinen: think we can hack this - don't allocate and copy if we don't need to.,
if(format==floatSample)
{
fbuffer = (float*)buffer;
}
else
{
floats.reinit(len);
fbuffer = floats.get();
CopySamples(buffer, format,
(samplePtr)fbuffer, floatSample, len);
}
BlockFile::CalcSummaryFromBuffer(fbuffer, len, summary256, summary64K);
return localFullSummary;
}
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 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;
}
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;
}
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;
}
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;
}
void write_cmm(const std::string &cmm_filename,
const std::string &marker_set_name, const AnchorsData &ad) {
Floats radii;
// algebra::get_enclosing_sphere(dpa.get_cluster_vectors(i));
radii.insert(radii.begin(), ad.get_number_of_points(), 5.);
std::ofstream out;
out.open(cmm_filename.c_str(), std::ios::out);
write_cmm_helper(out, marker_set_name, ad.points_, ad.edges_, radii);
out.close();
}
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;
}
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;
}
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);
}
}
algebra::Vector3Ds ProbabilisticAnchorGraph::get_particle_anchors(
Particle *p, float min_prob) const {
Floats probs = get_particle_probabilities(p);
algebra::Vector3Ds anchors;
for (unsigned int i = 0; i < probs.size(); i++) {
if (probs[i] >= min_prob) {
anchors.push_back(positions_[i]);
}
}
return anchors;
}
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;
}
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;
}
algebra::VectorKD get_embedding(const Subset &s,
const Assignment &a,
ParticleStatesTable *pst){
Floats embed;
for (unsigned int i=0; i< s.size(); ++i) {
algebra::VectorKD cur
= pst->get_particle_states(s[i])->get_embedding(a[i]);
embed.insert(embed.end(), cur.coordinates_begin(),
cur.coordinates_end());
}
return embed;
}
IMPCORE_BEGIN_NAMESPACE
OpenCubicSpline::OpenCubicSpline(const Floats &values,
Float minrange, Float spacing,
bool extend) :
spacing_(spacing), inverse_spacing_(1.0/spacing_),
spline_(values, spacing_, inverse_spacing_),
minrange_(minrange), maxrange_(minrange_ + spacing_ * (values.size() - 1)),
extend_(extend)
{
IMP_USAGE_CHECK(spacing >0, "The spacing between values must be positive.");
IMP_USAGE_CHECK(values.size() >=1, "You must provide at least one value.");
}
IMPALGEBRA_BEGIN_NAMESPACE
LinearFit2D::LinearFit2D(const algebra::Vector2Ds& data,
const Floats &errors) {
// check that there are at least 3 points
IMP_USAGE_CHECK(data.size() > 1,
"At least 2 points are required for LinearFit2D "
<< data.size() << " given");
IMP_USAGE_CHECK(errors.empty() || errors.size()==data.size(),
"Either there must be no error bars given or one per"
<< " point.");
find_regression(data, errors);
evaluate_error(data, errors);
}
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;
}
IMPSCOREFUNCTOR_BEGIN_INTERNAL_NAMESPACE
RawOpenCubicSpline::RawOpenCubicSpline(const Floats &values, double spacing,
double inverse_spacing)
: values_(values) {
IMP_USAGE_CHECK(spacing > 0, "The spacing between values must be positive.");
IMP_USAGE_CHECK(values.size() >= 1, "You must provide at least one value.");
int npoints = values_.size();
// Precalculate second derivatives for a natural cubic spline (open) by
// inversion of the tridiagonal matrix (Thomas algorithm)
second_derivs_.resize(npoints);
Floats tmp(npoints);
// Forward elimination phase
second_derivs_[0] = 0.;
tmp[0] = 0.;
double inverse_doublespacing = 1.0 / (spacing + spacing);
for (int i = 1; i < npoints - 1; ++i) {
Float m = 0.5 * second_derivs_[i - 1] + 2.;
second_derivs_[i] = -0.5 / m;
tmp[i] = (6. * ((values_[i + 1] - values_[i]) * inverse_spacing -
(values_[i] - values_[i - 1]) * inverse_spacing) *
inverse_doublespacing -
0.5 * tmp[i - 1]) /
m;
}
// Backward substitution phase
second_derivs_[npoints - 1] = 0.;
for (int i = npoints - 2; i >= 0; --i) {
second_derivs_[i] = second_derivs_[i] * second_derivs_[i + 1] + tmp[i];
}
/*IMP_LOG_TERSE( "Initialized spline with " << values.size() << " values "
<< "with spacing " << spacing << std::endl);*/
}
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;
}
IMPCORE_BEGIN_NAMESPACE
RigidBodyUmbrella::RigidBodyUmbrella(kernel::Model *m, kernel::ParticleIndex pi,
kernel::ParticleIndex ref, Floats x0,
double alpha, double k, std::string name)
: Restraint(m, name), pi_(pi), ref_(ref), x0_(x0), alpha_(alpha),
k_(k) {
IMP_USAGE_CHECK(x0.size() == 7, "Wrong size for x0, should be 7");
}
void FStudentT::do_update_sufficient_statistics(Floats FXs) {
N_ = FXs.size();
sumFX_ = FXs[0];
sumFX2_ = IMP::square(FXs[0]);
LogJX_ = 0.;
for (unsigned int i = 1; i < N_; ++i) {
sumFX_ += FXs[i];
sumFX2_ += IMP::square(FXs[i]);
}
}
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);
}
IMPISD_BEGIN_NAMESPACE
GaussianProcessInterpolation::GaussianProcessInterpolation(
FloatsList x, Floats sample_mean, Floats sample_std, unsigned n_obs,
UnivariateFunction *mean_function, BivariateFunction *covariance_function,
Particle *sigma, double sparse_cutoff)
: Object("GaussianProcessInterpolation%1%"),
x_(x),
n_obs_(n_obs),
mean_function_(mean_function),
covariance_function_(covariance_function),
sigma_(sigma),
cutoff_(sparse_cutoff) {
// O(M)
// store dimensions
M_ = x.size();
N_ = x[0].size();
sigma_val_ = Scale(sigma_).get_nuisance();
// basic checks
IMP_USAGE_CHECK(sample_mean.size() == M_,
"sample_mean should have the same size as x");
IMP_USAGE_CHECK(sample_std.size() == M_,
"sample_std should have the same size as x");
IMP_USAGE_CHECK(mean_function->get_ndims_x() == N_,
"mean_function should have " << N_ << " input dimensions");
IMP_USAGE_CHECK(mean_function->get_ndims_y() == 1,
"mean_function should have 1 output dimension");
IMP_USAGE_CHECK(covariance_function->get_ndims_x1() == N_,
"covariance_function should have "
<< N_ << " input dimensions for first vector");
IMP_USAGE_CHECK(covariance_function->get_ndims_x2() == N_,
"covariance_function should have "
<< N_ << " input dimensions for second vector");
IMP_USAGE_CHECK(covariance_function->get_ndims_y() == 1,
"covariance_function should have 1 output dimension");
// set all flags to false = need update.
force_mean_update();
force_covariance_update();
// compute needed matrices
compute_I(sample_mean);
compute_S(sample_std);
}
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;
}
void LinearFit2D::evaluate_error(const algebra::Vector2Ds& data,
const Floats &errors) {
error_ = 0.0;
for(unsigned int i=0; i<data.size(); i++) {
double diff = (a_*data[i][0] + b_ - data[i][1]);
if (!errors.empty()) {
diff/=errors[i];
}
error_ += diff*diff;
}
//std::cerr << error_ << std::endl;
}
/* 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();
});
