tools.hpp File Reference

Tools mainly for IO and some other functions. More...

#include "config.hpp"
#include <string>
#include <vector>
#include <map>
#include <tuple>
#include <memory>
#include <iostream>
#include <mm_malloc.h>
#include "tools.hxx"

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Namespaces
	Clustering
	general namespace for clustering package
	Clustering::Tools
	additional tools used throughout the clustering package

Macros
#define	ASSUME_ALIGNED(c)   (c) = (float*) __builtin_assume_aligned( (c), DC_MEM_ALIGNMENT)
	needed for aligned memory allocation for Xeon Phi, SSE or AVX

Typedefs
using	Clustering::Tools::Neighbor = std::pair< std::size_t, float >
	matches neighbor's frame id to distance
using	Clustering::Tools::Neighborhood = std::map< std::size_t, Clustering::Tools::Neighbor >
	map frame id to neighbors

Functions
void	Clustering::Tools::write_pops (std::string fname, std::vector< std::size_t > pops, std::string header_comment, std::map< std::string, float > stringMap)
	write populations as column into given file
void	Clustering::Tools::write_fes (std::string fname, std::vector< float > fes, std::string header_comment, std::map< std::string, float > stringMap)
	write free energies as column into given file
std::vector< std::size_t >	Clustering::Tools::read_clustered_trajectory (std::string filename)
	read states from trajectory (given as plain text file)
void	Clustering::Tools::write_clustered_trajectory (std::string filename, std::vector< std::size_t > traj, std::string header_comment, std::map< std::string, float > stringMap)
	write state trajectory into plain text file
template<typename NUM >
std::vector< NUM >	Clustering::Tools::read_single_column (std::string filename)
	read single column of numbers from given file. number type (int, float, ...) given as template parameter
template<typename NUM >
void	Clustering::Tools::write_single_column (std::string filename, std::vector< NUM > dat, std::string header_comment, bool with_scientific_format=false)
	write single column of numbers to given file. number type (int, float, ...) given as template parameter
template<typename KEY , typename VAL >
void	Clustering::Tools::write_map (std::string filename, std::map< KEY, VAL > mapping, std::string header_comment, bool val_then_key=false)
	write key-value map to plain text file with key as first and value as second column
std::vector< float >	Clustering::Tools::read_free_energies (std::string filename)
	read free energies from plain text file
std::vector< std::size_t >	Clustering::Tools::read_concat_limits (std::string filename)
std::pair< Neighborhood, Neighborhood >	Clustering::Tools::read_neighborhood (const std::string filename)
void	Clustering::Tools::write_neighborhood (const std::string filename, const Neighborhood &nh, const Neighborhood &nh_high_dens, std::string header_comment, std::map< std::string, float > stringMap)
std::map< std::size_t, std::size_t >	Clustering::Tools::microstate_populations (std::vector< std::size_t > traj)
	compute microstate populations from clustered trajectory
template<typename NUM >
std::tuple< NUM *, std::size_t, std::size_t >	Clustering::Tools::read_coords (std::string filename, std::vector< std::size_t > usecols=std::vector< std::size_t >())
template<typename NUM >
void	Clustering::Tools::free_coords (NUM *coords)
	free memory pointing to coordinates
template<typename NUM >
std::vector< NUM >	Clustering::Tools::dim1_sorted_coords (const NUM *coords, std::size_t n_rows, std::size_t n_cols)
template<typename NUM >
std::vector< NUM >	Clustering::Tools::boxlimits (const std::vector< NUM > &xs, std::size_t boxsize, std::size_t n_rows, std::size_t n_cols)
template<typename NUM >
std::pair< std::size_t, std::size_t >	Clustering::Tools::min_max_box (const std::vector< NUM > &limits, NUM val, NUM radius)
	return indices of min and max boxes around value for given radius.
unsigned int	Clustering::Tools::min_multiplicator (unsigned int orig, unsigned int mult)
	return minimum multiplicator to fulfill result * mult >= orig
std::string	Clustering::Tools::stringprintf (const std::string &str,...)
	printf-version for std::string More...
template<typename NUM >
NUM	Clustering::Tools::string_to_num (const std::string &s)
	convert std::string to number of given template format
template<typename T >
std::vector< T >	Clustering::Tools::unique_elements (std::vector< T > xs)
	return distinct elements of vector
void	Clustering::Tools::check_concat_limits (std::vector< std::size_t > concat_limits, std::size_t n_frames)
	check if concat limits were passed correctly
void	Clustering::Tools::read_comments (std::string filename, std::map< std::string, float > &stringMap)
	read comments of stringMap from file. Comments should start with #@
float	Clustering::Tools::read_next_float (std::ifstream &ifs)
	read the next float of ifstream
void	Clustering::Tools::append_commentsMap (std::string &header_comment, std::map< std::string, float > &stringMap)
	append commentsMap to header comment

Detailed Description

Tools mainly for IO and some other functions.

See also

Clustering::Tools

Definition in file tools.hpp.