mpp.hpp File Reference
Most Probable Path Clustering. More...
#include <vector>#include <map>#include <set>#include <stdexcept>#include <string>#include <boost/program_options.hpp>#include <boost/numeric/ublas/matrix_sparse.hpp>#include <boost/numeric/ublas/io.hpp>#include "tools.hpp"
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Namespaces | |
| Clustering | |
| general namespace for clustering package | |
| Clustering::MPP | |
| functions related to "Most Probable Path"-clustering | |
Typedefs | |
| using | Clustering::MPP::SparseMatrixF = boost::numeric::ublas::mapped_matrix< float > |
| BOOST implementation of a sparse matrix for floats. | |
| using | Clustering::MPP::Neighborhood = Clustering::Tools::Neighborhood |
| Neighborhood per frame. | |
Functions | |
| SparseMatrixF | Clustering::MPP::read_transition_probabilities (std::string fname) |
| read (row-normalized) transition matrix from file | |
| SparseMatrixF | Clustering::MPP::transition_counts (std::vector< std::size_t > trajectory, std::vector< std::size_t > concat_limits, std::size_t n_lag_steps, std::size_t i_max) |
| SparseMatrixF | Clustering::MPP::weighted_transition_counts (std::vector< std::size_t > trajectory, std::vector< std::size_t > concat_limits, std::size_t n_lag_steps) |
| SparseMatrixF | Clustering::MPP::row_normalized_transition_probabilities (SparseMatrixF count_matrix, std::set< std::size_t > microstate_names) |
| compute transition matrix from counts by normalization of rows | |
| SparseMatrixF | Clustering::MPP::updated_transition_probabilities (SparseMatrixF transition_matrix, std::map< std::size_t, std::size_t > sinks, std::map< std::size_t, std::size_t > pops) |
| update transition matrix after lumping states into sinks | |
| std::map< std::size_t, std::size_t > | Clustering::MPP::single_step_future_state (SparseMatrixF transition_matrix, std::set< std::size_t > cluster_names, float q_min, std::map< std::size_t, float > min_free_energy) |
| std::map< std::size_t, std::vector< std::size_t > > | Clustering::MPP::most_probable_path (std::map< std::size_t, std::size_t > future_state, std::set< std::size_t > cluster_names) |
| std::map< std::size_t, std::size_t > | Clustering::MPP::microstate_populations (std::vector< std::size_t > clusters, std::set< std::size_t > cluster_names) |
| compute cluster populations | |
| std::map< std::size_t, float > | Clustering::MPP::microstate_min_free_energy (const std::vector< std::size_t > &clustering, const std::vector< float > &free_energy) |
| std::map< std::size_t, std::size_t > | Clustering::MPP::path_sinks (std::vector< std::size_t > clusters, std::map< std::size_t, std::vector< std::size_t >> mpp, SparseMatrixF transition_matrix, std::set< std::size_t > cluster_names, float q_min, std::vector< float > free_energy) |
| std::vector< std::size_t > | Clustering::MPP::lumped_trajectory (std::vector< std::size_t > trajectory, std::map< std::size_t, std::size_t > sinks) |
| std::tuple< std::vector< std::size_t >, std::map< std::size_t, std::size_t >, SparseMatrixF > | Clustering::MPP::fixed_metastability_clustering (std::vector< std::size_t > initial_trajectory, SparseMatrixF trans_prob, float q_min, std::vector< float > free_energy) |
| run clustering for given Q_min value | |
| void | Clustering::MPP::main (boost::program_options::variables_map args) |
| MPP clustering control function and user interface. More... | |