Clustering::Tools Namespace Reference

additional tools used throughout the clustering package More...

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

Functions
void	write_fes (std::string fname, std::vector< float > fes)
	write free energies as column into given file
void	write_pops (std::string fname, std::vector< std::size_t > pops)
	write populations as column into given file
std::vector< std::size_t >	read_clustered_trajectory (std::string filename)
	read states from trajectory (given as plain text file)
void	write_clustered_trajectory (std::string filename, std::vector< std::size_t > traj)
	write state trajectory into plain text file
std::string	stringprintf (const std::string &str,...)
	printf-version for std::string More...
std::vector< float >	read_free_energies (std::string filename)
	read free energies from plain text file
std::pair< Neighborhood, Neighborhood >	read_neighborhood (const std::string fname)
void	write_neighborhood (const std::string fname, const Neighborhood &nh, const Neighborhood &nh_high_dens)
std::map< std::size_t, std::size_t >	microstate_populations (std::vector< std::size_t > traj)
	compute microstate populations from clustered trajectory
template<typename NUM >
std::vector< NUM >	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	write_single_column (std::string filename, std::vector< NUM > dat, 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	write_map (std::string filename, std::map< KEY, VAL > mapping)
	write key-value map to plain text file with key as first and value as second column
template<typename NUM >
std::tuple< NUM *, std::size_t, std::size_t >	read_coords (std::string filename, std::vector< std::size_t > usecols=std::vector< std::size_t >())
template<typename NUM >
void	free_coords (NUM *coords)
	free memory pointing to coordinates
template<typename NUM >
NUM	string_to_num (const std::string &s)
	convert std::string to number of given template format

Detailed Description

additional tools used throughout the clustering package

Function Documentation

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>()
	)

read coordinates from space-separated ASCII file. will write data with precision of NUM-type into memory. format: [row * n_cols + col] return value: tuple of {data (unique_ptr<NUM> with custom deleter), n_rows (size_t), n_cols (size_t)}.

Definition at line 39 of file tools.hxx.

std::pair< Neighborhood, Neighborhood > Clustering::Tools::read_neighborhood

(

const std::string

fname

)

read neighborhood info from plain text file (two different neighborhoods: nearest neighbor (NN) and NN with higher density)

Definition at line 116 of file tools.cpp.

std::string Clustering::Tools::stringprintf	(	const std::string &	str,
			...
	)

printf-version for std::string

behaves like sprintf(char*, ...), but with c++ strings and returns the result

Parameters

str	pattern to be printed to

Returns

resulting string The function internally calls sprintf, but converts the result to a c++ string and returns that one. Problems of memory allocation are taken care of automatically.

Definition at line 95 of file tools.cpp.

void Clustering::Tools::write_neighborhood	(	const std::string	fname,
		const Neighborhood &	nh,
		const Neighborhood &	nh_high_dens
	)

write neighborhood info to plain text file (two different neighborhoods: nearest neighbor (NN) and NN with higher density)

Definition at line 145 of file tools.cpp.