tools.cpp

/*
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
TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/

#include "tools.hpp"

#include <stdarg.h>

namespace Clustering {
namespace Tools {

void
write_fes(std::string fname, std::vector<float> fes) {
  std::ofstream ofs(fname);
  if (ofs.fail()) {
    std::cerr << "error: cannot open file '" << fname << "'" << std::endl;
    exit(EXIT_FAILURE);
  } else {
    ofs << std::scientific;
    for (float f: fes) {
      ofs << f << "\n";
    }
  }
}

void
write_pops(std::string fname, std::vector<std::size_t> pops) {
  // technically the same ...
  write_clustered_trajectory(fname, pops);
}

std::vector<std::size_t>
read_clustered_trajectory(std::string filename) {
  std::vector<std::size_t> traj;
  std::ifstream ifs(filename);
  if (ifs.fail()) {
    std::cerr << "error: cannot open file '" << filename << "'" << std::endl;
    exit(EXIT_FAILURE);
  } else {
    while (ifs.good()) {
      std::size_t buf;
      ifs >> buf;
      if ( ! ifs.fail()) {
        traj.push_back(buf);
      }
    }
  }
  return traj;
}

void
write_clustered_trajectory(std::string filename, std::vector<std::size_t> traj) {
  std::ofstream ofs(filename);
  if (ofs.fail()) {
    std::cerr << "error: cannot open file '" << filename << "'" << std::endl;
    exit(EXIT_FAILURE);
  } else {
    for (std::size_t c: traj) {
      ofs << c << "\n";
    }
  }
}


std::string
stringprintf(const std::string& str, ...) {
  unsigned int size = 256;
  va_list args;
  char* buf = (char*) malloc(size * sizeof(char));
  va_start(args, str);
  while (size <= (unsigned int) vsnprintf(buf, size, str.c_str(), args)) {
    size *= 2;
    buf = (char*) realloc(buf, size * sizeof(char));
  }
  va_end(args);
  std::string result(buf);
  free(buf);
  return result;
}

std::vector<float>
read_free_energies(std::string filename) {
  return read_single_column<float>(filename);
}

std::pair<Neighborhood, Neighborhood>
read_neighborhood(const std::string fname) {
  Neighborhood nh;
  Neighborhood nh_high_dens;
  std::ifstream ifs(fname);
  if (ifs.fail()) {
    std::cerr << "error: cannot open file '" << fname << "' for reading." << std::endl;
    exit(EXIT_FAILURE);
  } else {
    std::size_t i=0;
    while (ifs.good()) {
      std::size_t buf1;
      float buf2;
      std::size_t buf3;
      float buf4;
      ifs >> buf1;
      ifs >> buf2;
      ifs >> buf3;
      ifs >> buf4;
      if ( ! ifs.fail()) {
        nh[i] = std::pair<std::size_t, float>(buf1, buf2);
        nh_high_dens[i] = std::pair<std::size_t, float>(buf3, buf4);
        ++i;
      }
    }
  }
  return {nh, nh_high_dens};
}

void
write_neighborhood(const std::string fname,
                   const Neighborhood& nh,
                   const Neighborhood& nh_high_dens) {
  std::ofstream ofs(fname);
  auto p = nh.begin();
  auto p_hd = nh_high_dens.begin();
  while (p != nh.end() && p_hd != nh_high_dens.end()) {
    // first: key (not used)
    // second: neighbor
    // second.first: id; second.second: squared dist
    ofs << p->second.first    << " " << p->second.second    << " "
        << p_hd->second.first << " " << p_hd->second.second << "\n";
    ++p;
    ++p_hd;
  }
}

std::map<std::size_t, std::size_t>
microstate_populations(std::vector<std::size_t> traj) {
  std::map<std::size_t, std::size_t> populations;
  for (std::size_t state: traj) {
    if (populations.count(state) == 0) {
      populations[state] = 1;
    } else {
      ++populations[state];
    }
  }
  return populations;
}

} // end namespace Tools
} // end namespace Clustering