mpp.hpp

/*
Copyright (c) 2015, Florian Sittel (www.lettis.net)
All rights reserved.

Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:

1. Redistributions of source code must retain the above copyright notice,
   this list of conditions and the following disclaimer.

2. Redistributions in binary form must reproduce the above copyright notice,
   this list of conditions and the following disclaimer in the documentation
   and/or other materials provided with the distribution.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY
EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT
SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR
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EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
#pragma once

#include <vector>
#include <map>
#include <set>
#include <stdexcept>

#include <boost/program_options.hpp>
#include <boost/numeric/ublas/matrix_sparse.hpp>
#include <boost/numeric/ublas/io.hpp>

#include "tools.hpp"

namespace Clustering {
  namespace MPP {
    using SparseMatrixF = boost::numeric::ublas::mapped_matrix<float>;
    using Neighborhood = Clustering::Tools::Neighborhood;
    SparseMatrixF
    transition_counts(std::vector<std::size_t> trajectory, std::vector<std::size_t> concat_limits, std::size_t n_lag_steps);
    SparseMatrixF
    row_normalized_transition_probabilities(SparseMatrixF count_matrix, std::set<std::size_t> microstate_names);
    std::map<std::size_t, std::size_t>
    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>>
    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>
    microstate_populations(std::vector<std::size_t> clusters, std::set<std::size_t> cluster_names);
    std::map<std::size_t, float>
    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>
    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>
    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>>
    fixed_metastability_clustering(std::vector<std::size_t> initial_trajectory,
                                   std::vector<std::size_t> concat_limits,
                                   float q_min,
                                   std::size_t lagtime,
                                   std::vector<float> free_energy);
    void
    main(boost::program_options::variables_map args);
  } // end namespace Clustering::MPP
} // end namespace Clustering