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
unsigned int	min_multiplicator (unsigned int orig, unsigned int mult)
	return minimum multiplicator to fulfill result * mult >= orig
void	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
void	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
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, std::string header_comment, std::map< std::string, float > stringMap)
	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 filename)
std::vector< std::size_t >	read_concat_limits (std::string filename)
void	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 >	microstate_populations (std::vector< std::size_t > traj)
	compute microstate populations from clustered trajectory
void	check_concat_limits (std::vector< std::size_t > concat_limits, std::size_t n_frames)
	check if concat limits were passed correctly
float	read_next_float (std::ifstream &ifs)
	read the next float of ifstream
void	read_comments (std::string filename, std::map< std::string, float > &stringMap)
	read comments of stringMap from file. Comments should start with #@
void	append_commentsMap (std::string &header_comment, std::map< std::string, float > &stringMap)
	append commentsMap to header comment
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, 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	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
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 >
std::vector< NUM >	dim1_sorted_coords (const NUM *coords, std::size_t n_rows, std::size_t n_cols)
template<typename NUM >
std::vector< NUM >	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 >	min_max_box (const std::vector< NUM > &limits, NUM val, NUM radius)
	return indices of min and max boxes around value for given radius.
template<typename NUM >
NUM	string_to_num (const std::string &s)
	convert std::string to number of given template format
template<typename T >
std::vector< T >	unique_elements (std::vector< T > xs)
	return distinct elements of vector

Detailed Description

additional tools used throughout the clustering package

This module contains helper functions. Most of them are for reading or writing files.

Function Documentation

boxlimits()

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
	)

separate into equally sized boxes and return min values of first dimension for given box. used for pruning in CUDA-accelerated code.

Definition at line 159 of file tools.hxx.

dim1_sorted_coords()

template<typename NUM >

std::vector< NUM > Clustering::Tools::dim1_sorted_coords	(	const NUM *	coords,
		std::size_t	n_rows,
		std::size_t	n_cols
	)

return std::vector with coords sorted along first dimension. uses row-based addressing (row*n_cols+col).

Definition at line 122 of file tools.hxx.

read_concat_limits()

std::vector< std::size_t > Clustering::Tools::read_concat_limits

(

std::string

filename

)

read conact limits takes length of the single trajectories.

Definition at line 133 of file tools.cpp.

read_coords()

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 41 of file tools.hxx.

read_neighborhood()

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 101 of file tools.cpp.

stringprintf()

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 80 of file tools.cpp.

write_neighborhood()

void Clustering::Tools::write_neighborhood	(	const std::string	fname,
		const Neighborhood &	nh,
		const Neighborhood &	nh_high_dens,
		std::string	header_comment,
		std::map< std::string, float >	stringMap
	)

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

Definition at line 144 of file tools.cpp.