unresizable vector whose size is known at compile time, which may be allocated on the stack, and which indexes from 1. More...

Namespaces
	excn

	factory

	file

	graph

	io

	json_spirit

	keys

	libsvm

	lua

	options

	pointer

	py

	signals

	sql_database

	tag

	thread

	tools

Classes
class	BitSet
	Simple bit set. More...

class	BitVector
	Simple bit vector. More...

class	Bound
	Bound value class. More...

class	DereferenceIterator
	const_iterator class for SilentFileData container. More...

class	EXCN_utility_exit

class	Factory

class	FactoryRegister

class	fixedsizearray1

class	fixedsizearray1const_iterator

class	fixedsizearray1iterator

class	FixedSizeLexicographicalIterator

class	heap

struct	history_queue_struct

class	in_place_list

class	Inline_File_Provider

class	Inline_File_Provider_Hook

class	LexicographicalIterator

class	list_element

class	OrderedTuple
	The ordered tuple takes a container class T and defines comparison operators so that the tuple may be sorted. More...

class	predicate_cmp_filename

struct	RawType
	Meta-programming classes to provide the pointer type for down_cast. More...

struct	RawType< T & >

struct	RawType< T * >

class	recent_history_queue
	A class for keeping track of a subset of elements in a set that are pushed into a queue in a certain order, and which fall off the end of the queue in ther order in which they arrive. Elements in the set can be bumped to the front of the queue. More...

class	Show

class	SimulateMPI
	singleton class storing simulated MPI state More...

class	SimulateMPIData

class	SimulateMPIMessage

class	SingletonBase
	SingletonBase is meant to serve as a base class for singleton classes in Rosetta handling the initialization of the singleton in a thread-safe way. More...

struct	SortFirst

struct	SortSecond

class	subset_mapping
	This class handles the bookeeping to map between a set of integer ids in the "source" enumeration to a subset of those ids – the destination enumartion. Elements in the source enumeration that do not map to elements in the destination enumeration are represented by the value 0. Both enumerations should count from 1. Once the class has been initialized, this class offers O(1) mapping between elements in the enumerations. More...

class	vector0
	std::vector with assert-checked bounds More...

class	vector0< bool, A >
	std::vector with assert-checked bounds: bool specialization

class	vector1
	std::vector with 1-based indexing More...

class	vector1< bool, A >
	std::vector with 1-based indexing: bool specialization

class	vectorL
	std::vector with L-based indexing More...

class	vectorL< L, bool, A >
	std::vector with L-based indexing: bool specialization

struct	vectorL_IndexSelector
	vectorL index type selector: Nonnegative lower index non-specialization More...

struct	vectorL_IndexSelector< false >
	vectorL index type selector: Negative lower index specialization More...

struct	vectorL_ZeroSelector
	vectorL lower index zero selector: Nonzero lower index non-specialization More...

struct	vectorL_ZeroSelector< false >
	vectorL lower index zero selector: Zero lower index specialization More...

Typedefs
typedef void(*	UtilityExitCallBack )(void)

typedef utility::pointer::shared_ptr < heap >	heapOP

typedef utility::pointer::shared_ptr < heap const >	heapCOP

typedef utility::pointer::shared_ptr < Inline_File_Provider_Hook >	Inline_File_Provider_HookOP

typedef utility::pointer::shared_ptr < Inline_File_Provider_Hook const >	Inline_File_Provider_HookCOP

typedef pointer::shared_ptr < subset_mapping >	subset_mappingOP

typedef pointer::shared_ptr < subset_mapping const >	subset_mappingCOP

typedef utility::pointer::shared_ptr < SimulateMPIMessage >	SimulateMPIMessageOP

typedef utility::pointer::shared_ptr < SimulateMPIMessage const >	SimulateMPIMessageCOP

typedef vector0< bool >	vector0_bool

typedef vector0< short int >	vector0_short

typedef vector0< int >	vector0_int

typedef vector0< long int >	vector0_long

typedef vector0< unsigned short int >	vector0_ushort

typedef vector0< unsigned int >	vector0_uint

typedef vector0< unsigned long int >	vector0_ulong

typedef vector0< platform::Size >	vector0_size_t

typedef vector0< platform::Size >	vector0_size

typedef vector0< platform::SSize >	vector0_ssize_t

typedef vector0< platform::SSize >	vector0_ssize

typedef vector0< float >	vector0_float

typedef vector0< double >	vector0_double

typedef vector0< long double >	vector0_longdouble

typedef vector0< char >	vector0_char

typedef vector0< unsigned char >	vector0_uchar

typedef vector0< signed char >	vector0_schar

typedef vector1< bool >	vector1_bool

typedef vector1< short int >	vector1_short

typedef vector1< int >	vector1_int

typedef vector1< long int >	vector1_long

typedef vector1< unsigned short int >	vector1_ushort

typedef vector1< unsigned int >	vector1_uint

typedef vector1< unsigned long int >	vector1_ulong

typedef vector1< std::size_t >	vector1_size_t

typedef vector1< std::size_t >	vector1_size

typedef vector1< platform::SSize >	vector1_ssize_t

typedef vector1< platform::SSize >	vector1_ssize

typedef vector1< float >	vector1_float

typedef vector1< double >	vector1_double

typedef vector1< long double >	vector1_longdouble

typedef vector1< char >	vector1_char

typedef vector1< unsigned char >	vector1_uchar

typedef vector1< signed char >	vector1_schar

Enumerations
enum	simulate_mpi_message_type { smpi_char = 1, smpi_integer, smpi_string, smpi_double, smpi_integers, smpi_doubles }

Functions
void	sys_sleep (double const seconds)
	Sleep for a specified number of seconds. More...

void	rand_sleep ()

std::string	timestamp ()
	Generate timestamp string. More...

std::string	timestamp_short ()
	Generate timestamp string, short format. More...

void	encode6bit (const unsigned char *memory, unsigned int length, std::string &jar)

int	decode6bit (unsigned char *memory, const std::string &jar)

void	swap4_aligned (void *v, long ndata)

unsigned char	code_to_6bit (unsigned char _6bit)

unsigned char	code_from_6bit (unsigned char _8bit)

void	encode_24_to_32 (unsigned char i0, unsigned char i1, unsigned char i2, unsigned char &o0, unsigned char &o1, unsigned char &o2, unsigned char &o3)

void	decode_32_to_24 (unsigned char i0, unsigned char i1, unsigned char i2, unsigned char i3, unsigned char &o0, unsigned char &o1, unsigned char &o2)

template<typename B >
BitSet< B >	operator+ (BitSet< B > const &a, BitSet< B > const &b)
	BitSet + BitSet: Union. More...

template<typename B >
BitSet< B >	operator\| (BitSet< B > const &a, BitSet< B > const &b)
	BitSet \| BitSet: Union. More...

template<typename B >
BitSet< B >	operator- (BitSet< B > const &a, BitSet< B > const &b)
	BitSet - BitSet: Difference. More...

template<typename B >
void	swap (BitSet< B > &a, BitSet< B > &b)
	swap( BitSet, BitSet ) More...

template<typename B >
bool	operator== (BitSet< B > const &a, BitSet< B > const &b)
	BitSet == BitSet. More...

template<typename B >
bool	operator!= (BitSet< B > const &a, BitSet< B > const &b)
	BitSet != BitSet. More...

template<typename B >
BitVector< B >	operator+ (BitVector< B > const &a, BitVector< B > const &b)
	BitVector + BitVector: Union. More...

template<typename B >
BitVector< B >	operator\| (BitVector< B > const &a, BitVector< B > const &b)
	BitVector \| BitVector: Union. More...

template<typename B >
BitVector< B >	operator- (BitVector< B > const &a, BitVector< B > const &b)
	BitVector - BitVector: Difference. More...

template<typename B >
void	swap (BitVector< B > &a, BitVector< B > &b)
	swap( BitVector, BitVector ) More...

template<typename B >
bool	operator== (BitVector< B > const &a, BitVector< B > const &b)
	BitVector == BitVector. More...

template<typename B >
bool	operator!= (BitVector< B > const &a, BitVector< B > const &b)
	BitVector != BitVector. More...

template<class Target , class Source >
Target	down_cast (Source &s)
	Fast assert-checked polymorphic down-cast: reference argument. More...

template<class Target , class Source >
Target	down_cast (Source *p)
	Fast assert-checked polymorphic down-cast: pointer argument. More...

void	set_main_exit_callback (UtilityExitCallBack=0)
	Set call back funtion that will be called on utility::exit. Use this function to overload default behavior of sys.exit to more appropriate to your application Defaut value for callback function is 0, whicth mean no sys exit is called. More...

std::vector < UtilityExitCallBack > &	get_all_exit_callbacks ()
	Array to hold all additional exit-callbacks. More...

void	add_exit_callback (UtilityExitCallBack)
	Add additional callback function that will be called before standard exit(…) is executed. [Note: do not confuse this function with 'set_main_exit_callback' which is replacing the end behavior of exit(…)]. More...

void	remove_exit_callback (UtilityExitCallBack)
	Remove additional callback function that was previously added by using add_exit_callback. More...

void	exit (std::string const &file, int const line, std::string const &message, int const status)
	Exit with file + line + message + optional status. More...

int	cond_exit (bool condition, std::string const &file, int const line, std::string const &message, int const status)
	Conditional Exit with file + line + message + optional status. More...

void	exit (std::string const &file, int const line, int const status=1) NORETURN
	Exit with file + line + optional status. More...

void	exit (int const status, std::string const &file, int const line)
	Exit with file + line + status. More...

template<typename BidirectionalIterator , typename T >
BidirectionalIterator	find_closest (BidirectionalIterator first, BidirectionalIterator last, const T &value)
	Returns an iterator on the sorted range [first, last) nearest to value. If value is equidistant between adjacent elements, the lesser is returned. More...

template<typename T >
int	argmin (const std::vector< T > &iterable)
	Returns the argument whose value is minimal according to operator<. More...

template<typename T >
int	argmin (const utility::vector1< T > &iterable)
	Returns the argument whose value is minimal according to operator<. More...

template<typename T >
int	argmax (const std::vector< T > &iterable)
	Returns the argument whose value is maximal according to operator>. More...

template<typename T >
int	argmax (const utility::vector1< T > &iterable)
	Returns the argument whose value is maximal according to operator>. More...

int	mpi_rank ()

int	mpi_nprocs ()

int	receive_integer_from_anyone ()
	Use MPI to wait until some node sends an integer – usually its own mpi_rank so that it can send further messages. More...

std::string	receive_string_from_node (int source)
	Use MPI to receive a string from a particular node. More...

void	send_string_to_node (int destination, std::string const &message)

char	receive_char_from_node (int source)
	Use MPI to receive a single char from a particular node. More...

void	send_char_to_node (int destination, char message)

int	receive_integer_from_node (int source)
	Use MPI to receive a single integer from a particular node. More...

void	send_integer_to_node (int destination, int message)

utility::vector1< int >	receive_integers_from_node (int source)
	Use MPI to receive a vector of integers from a particular node. More...

void	send_integers_to_node (int destination, utility::vector1< int > const &message)

double	receive_double_from_node (int source)
	Use MPI to receive a single double from a particular node. More...

void	send_double_to_node (int destination, double message)

utility::vector1< double >	receive_doubles_from_node (int source)
	Use MPI to receive a vector of doubles from a particular node. More...

void	send_doubles_to_node (int destination, utility::vector1< double > const &message)

platform::Size	get_undefined_size ()
	Get a numeric value for Size that represents an "undefined" value. More...

bool	is_undefined (platform::Size const &val)
	Check if a Size is undefined (i.e has the same value as utility::get_undefined_size() ) More...

platform::Real	get_undefined_real ()
	Get a numeric value for Real that represents an "undefined" value. More...

bool	is_undefined (platform::Real const &val)
	Check if a Real is undefined (i.e has the same value as utility::get_undefined_real() ) More...

bool	is_nan (platform::Real const &val)

bool	is_inf (platform::Real const &val)

platform::Real	round (platform::Real const &val)

platform::Real	copysign (platform::Real const &x, platform::Real const &y)

bool	operator== (history_queue_struct const &a, history_queue_struct const &b)

std::string	msg_name (simulate_mpi_message_type msg_type)

template<typename T1 , typename T2 >
std::ostream &	operator<< (std::ostream &os, std::pair< T1, T2 > const &v)
	Output function for std::pair object. More...

template<class T >
std::ostream &	operator<< (std::ostream &os, std::vector< T > const &v)
	Output function for std::vector object. More...

template<class T >
std::ostream &	operator<< (std::ostream &os, utility::vector1< T > const &v)
	Output function for utility::vector1 object. More...

template<typename T1 , typename T2 >
std::ostream &	operator<< (std::ostream &os, std::map< T1, T2 > const &m)
	Output function for std::map object. More...

template<typename T >
std::ostream &	operator<< (std::ostream &os, std::list< T > const &l)
	Output function for std::list object. More...

void	ReadFromFileOrDie (const std::string &filename, std::string *contents)
	Reads the contents of <filename> into <contents>, preserving newline characters. Aborts if an error is encoutered. More...

utility::vector1< std::string >	split (const std::string &s)
	split given std::string using ' ' symbol. More...

utility::vector1< std::string >	split_whitespace (const std::string &s)
	split given std::string using whitespace as a separator. Unlike string_split_multi_delim(), any group of mixed whitespace counts only as a single seperator. More...

std::string	join (utility::vector1< std::string > const &s, std::string const &connector)
	combine strings with anything More...

std::string	join (std::vector< std::string > const &s, std::string const &connector)
	combine strings with anything More...

std::string	join (std::string const &string_w_spaces, std::string const &connector)
	join space separations in a string with a connector such as '_' More...

std::list< std::string >	split_to_list (const std::string &s)
	split given std::string using ' ' symbol. More...

std::set< std::string >	split_to_set (std::string const &s)
	split given std::string to a set using ' ' symbol. More...

utility::vector1< std::string >	string_split (std::string const &in, char splitchar)

utility::vector1< std::string >	string_split_simple (std::string const &in, char splitchar= ' ')
	split to vector1< std::string > using arbitrary split character, but no empty strings (closer to python string::split) More...

utility::vector1< std::string >	string_split_multi_delim (std::string const &in, std::string splitchars)

float	string2float (std::string st)
	convert a string to a float, returns -1 on failure More...

int	string2int (std::string st)
	convert a string to an int, returns -1 on failure More...

platform::Size	string2Size (std::string st)
	convert a string to a Size, returns numeric::get_undefined_size() on failure More...

platform::Real	string2Real (std::string st)
	convert a string to a Real, returns numeric::get_undefined_real() on failure More...

void	string2uint (const std::string &x, unsigned int *y)

bool	trimmed_compare (std::string const &s1, std::string const &s2)
	compares two strings ignoring leading and trailing spaces More...

bool	startswith (std::string const &haystack, std::string const &needle)
	True iff haystack starts with needle. More...

bool	endswith (std::string const &haystack, std::string const &needle)
	True iff haystack ends with needle. More...

void	slurp (std::istream &in, std::string &out)

void	trim (std::string &s, const std::string &drop)

std::string	trim (std::string const &s, std::string const &drop=" ")
	create a new string that drops all the unwanted substrings of the original string. More...

void	add_spaces_left_align (std::string &st, std::size_t const newlen)
	adds spaces to a left aligned string until a given length is reached More...

void	add_spaces_right_align (std::string &st, std::size_t const newlen)
	adds spaces to a right aligned string until a given length is reached More...

bool	is_string_numeric (std::string const &input)

std::string	file_contents (std::string const &file_name)
	Read the entire contents of a file into a string. All end-of-line characters are replaced by "\n". Throws a utility::excn::EXCN_msg_exception if the file cannot be opened. More...

std::string	file_basename (const std::string &full_path)

std::string	filename (const std::string &path)

std::string	pathname (const std::string &path)

std::string	replace_environment_variables (std::string input)
	find all environment variables with the form ${VARIABLE} and replace with the contents of that environment variable. if the environment variable does not exist, return string::npos More...

std::string	string_to_sha1 (std::string const &input_string)

std::string	make_tag_with_dashes (utility::vector1< int > res_vector, char const delimiter= ' ')
	Compactifies vectors of ints: 1 2 3 9 10 11 to "1-3 9-11". More...

std::string	make_tag_with_dashes (utility::vector1< int > res_vector, utility::vector1< char > chain_vector, char const delimiter)

std::string	make_tag (utility::vector1< int > res_vector)

std::pair< std::vector< int > , std::vector< char > >	get_resnum_and_chain (std::string const &s, bool &string_is_ok)
	converts string like "1-3 20-22" or "A:1-5 B:20-22" to vectors containing resnums and chains. More...

bool	get_resnum_and_chain_from_one_tag (std::string const &tag, std::vector< int > &resnum, std::vector< char > &chains)
	helper function for get_resnum_and_chain More...

platform::Size	get_num_digits (platform::Size value)

std::string	replace_in (std::string const name_in, std::string const find_string, std::string const replace_string)
	find/replace strings within input string. More...

template<class T >
std::string	join (utility::vector1< T > const &vector, std::string const &connector)
	combine vector with anything More...

bool	same_ignoring_spaces (std::string const &s1, std::string const &s2)
	Compares two strings, ignoring spaces. Useful for comparing atom name strings which have pdb-alignment built into them. Slightly dangerous if you consider the fact that atom names in the PDB are different for different indentation rules: ' CA ' is c-alpha. 'CA ' is calcium. More...

void	replace_in (std::string &s, const char from, const char *to)

template<class T >
std::string	to_string (const T &t)

template<class T >
T const	from_string (std::string const &s, T)

template<class T >
utility::vector1< T > const	string_split (std::string const &in, char splitchar, T)

bool	is_true_string (std::string const &value_str)
	String accepted as a true value? More...

bool	is_false_string (std::string const &value_str)
	String accepted as a false value? More...

short int	min (short int const a, short int const b)
	min( short int, short int ) More...

int	min (int const a, int const b)
	min( int, int ) More...

long int	min (long int const a, long int const b)
	min( long int, long int ) More...

unsigned short int	min (unsigned short int const a, unsigned short int const b)
	min( unsigned short int, unsigned short int ) More...

unsigned int	min (unsigned int const a, unsigned int const b)
	min( unsigned int, unsigned int ) More...

unsigned long int	min (unsigned long int const a, unsigned long int const b)
	min( unsigned long int, unsigned long int ) More...

float	min (float const a, float const b)
	min( float, float ) More...

double	min (double const a, double const b)
	min( double, double ) More...

long double	min (long double const a, long double const b)
	min( long double, long double ) More...

template<typename T >
T const &	min (T const &a, T const &b, T const &c)
	min( a, b, c ) More...

template<typename T >
T const &	min (T const &a, T const &b, T const &c, T const &d)
	min( a, b, c, d ) More...

template<typename T >
T const &	min (T const &a, T const &b, T const &c, T const &d, T const &e)
	min( a, b, c, d, e ) More...

template<typename T >
T const &	min (T const &a, T const &b, T const &c, T const &d, T const &e, T const &f)
	min( a, b, c, d, e, f ) More...

short int	max (short int const a, short int const b)
	max( short int, short int ) More...

int	max (int const a, int const b)
	max( int, int ) More...

long int	max (long int const a, long int const b)
	max( long int, long int ) More...

unsigned short int	max (unsigned short int const a, unsigned short int const b)
	max( unsigned short int, unsigned short int ) More...

unsigned int	max (unsigned int const a, unsigned int const b)
	max( unsigned int, unsigned int ) More...

unsigned long int	max (unsigned long int const a, unsigned long int const b)
	max( unsigned long int, unsigned long int ) More...

float	max (float const a, float const b)
	max( float, float ) More...

double	max (double const a, double const b)
	max( double, double ) More...

long double	max (long double const a, long double const b)
	max( long double, long double ) More...

template<typename T >
T const &	max (T const &a, T const &b, T const &c)
	max( a, b, c ) More...

template<typename T >
T const &	max (T const &a, T const &b, T const &c, T const &d)
	max( a, b, c, d ) More...

template<typename T >
T const &	max (T const &a, T const &b, T const &c, T const &d, T const &e)
	max( a, b, c, d, e ) More...

template<typename T >
T const &	max (T const &a, T const &b, T const &c, T const &d, T const &e, T const &f)
	max( a, b, c, d, e, f ) More...

template<class T >
T	max (vector1< T > const &input)
	Find the largest value in a vector. More...

template<class T >
T	min (vector1< T > const &input)
	Find the smallest value in a vector. More...

template<class T >
vector1< T >::Size	arg_max (vector1< T > const &input)
	find the index of the largest value in a vector More...

template<class T >
vector1< T >::Size	arg_min (vector1< T > const &input)
	find the index of the smallest value in a vector More...

template<class T >
void	insert_middle (vector1< T > &vect, typename vector1< T >::Size const position, T const new_value, bool expand)

template<class T >
void	arg_greatest_several (vector1< T > const &input, vector1< typename vector1< T >::Size > &arg_list)
	Finds indices of the n largest items in input vector, where n is size of the arg_list vector. The indices are reported in decreasing sorted order by the value of the corresponding position in the input vector. If m is the size of the input vector, then this function is O( m n**2) More...

template<class T >
void	arg_least_several (vector1< T > const &input, vector1< typename vector1< T >::Size > &arg_list)
	Finds indices of the n smallest items in input vector, where n is size of the arg_list vector. The indices are reported in increasing sorted order by the value of the corresponding position in the input vector. If m is the size of the input vector, then this function is O( m n**2) More...

template<platform::SSize L, typename T , typename A >
bool	operator== (vectorL< L, T, A > const &a, vectorL< L, T, A > const &b)
	vectorL == vectorL More...

template<platform::SSize L, typename T , typename A >
bool	operator!= (vectorL< L, T, A > const &a, vectorL< L, T, A > const &b)
	vectorL != vectorL More...

template<platform::SSize L, typename T , typename A >
bool	operator< (vectorL< L, T, A > const &a, vectorL< L, T, A > const &b)
	vectorL < vectorL More...

template<platform::SSize L, typename T , typename A >
bool	operator<= (vectorL< L, T, A > const &a, vectorL< L, T, A > const &b)
	vectorL <= vectorL More...

template<platform::SSize L, typename T , typename A >
bool	operator>= (vectorL< L, T, A > const &a, vectorL< L, T, A > const &b)
	vectorL >= vectorL More...

template<platform::SSize L, typename T , typename A >
bool	operator> (vectorL< L, T, A > const &a, vectorL< L, T, A > const &b)
	vectorL > vectorL More...

template<platform::SSize L, typename T , typename A >
bool	operator== (vectorL< L, T, A > const &a, std::vector< T, A > const &b)
	vectorL == std::vector More...

template<platform::SSize L, typename T , typename A >
bool	operator!= (vectorL< L, T, A > const &a, std::vector< T, A > const &b)
	vectorL != std::vector More...

template<platform::SSize L, typename T , typename A >
bool	operator< (vectorL< L, T, A > const &a, std::vector< T, A > const &b)
	vectorL < std::vector More...

template<platform::SSize L, typename T , typename A >
bool	operator<= (vectorL< L, T, A > const &a, std::vector< T, A > const &b)
	vectorL <= std::vector More...

template<platform::SSize L, typename T , typename A >
bool	operator>= (vectorL< L, T, A > const &a, std::vector< T, A > const &b)
	vectorL >= std::vector More...

template<platform::SSize L, typename T , typename A >
bool	operator> (vectorL< L, T, A > const &a, std::vector< T, A > const &b)
	vectorL > std::vector More...

template<platform::SSize L, typename T , typename A >
bool	operator== (std::vector< T, A > const &a, vectorL< L, T, A > const &b)
	std::vector == vectorL More...

template<platform::SSize L, typename T , typename A >
bool	operator!= (std::vector< T, A > const &a, vectorL< L, T, A > const &b)
	std::vector != vectorL More...

template<platform::SSize L, typename T , typename A >
bool	operator< (std::vector< T, A > const &a, vectorL< L, T, A > const &b)
	std::vector < vectorL More...

template<platform::SSize L, typename T , typename A >
bool	operator<= (std::vector< T, A > const &a, vectorL< L, T, A > const &b)
	std::vector <= vectorL More...

template<platform::SSize L, typename T , typename A >
bool	operator>= (std::vector< T, A > const &a, vectorL< L, T, A > const &b)
	std::vector >= vectorL More...

template<platform::SSize L, typename T , typename A >
bool	operator> (std::vector< T, A > const &a, vectorL< L, T, A > const &b)
	std::vector > vectorL More...

template<platform::SSize L, typename T , typename A >
void	swap (vectorL< L, T, A > &a, vectorL< L, T, A > &b)
	swap( vectorL, vectorL ) More...

template<platform::SSize L, typename T , typename A >
void	swap (vectorL< L, T, A > &a, std::vector< T, A > &b)
	swap( vectorL, std::vector ) More...

template<platform::SSize L, typename T , typename A >
void	swap (std::vector< T, A > &a, vectorL< L, T, A > &b)
	swap( std::vector, vectorL ) More...

template<platform::SSize L, typename A >
bool	operator== (vectorL< L, bool, A > const &a, vectorL< L, bool, A > const &b)
	vectorL == vectorL More...

template<platform::SSize L, typename A >
bool	operator!= (vectorL< L, bool, A > const &a, vectorL< L, bool, A > const &b)
	vectorL != vectorL More...

template<platform::SSize L, typename A >
bool	operator< (vectorL< L, bool, A > const &a, vectorL< L, bool, A > const &b)
	vectorL < vectorL More...

template<platform::SSize L, typename A >
bool	operator<= (vectorL< L, bool, A > const &a, vectorL< L, bool, A > const &b)
	vectorL <= vectorL More...

template<platform::SSize L, typename A >
bool	operator>= (vectorL< L, bool, A > const &a, vectorL< L, bool, A > const &b)
	vectorL >= vectorL More...

template<platform::SSize L, typename A >
bool	operator> (vectorL< L, bool, A > const &a, vectorL< L, bool, A > const &b)
	vectorL > vectorL More...

template<platform::SSize L, typename A >
bool	operator== (vectorL< L, bool, A > const &a, std::vector< bool, A > const &b)
	vectorL == std::vector More...

template<platform::SSize L, typename A >
bool	operator!= (vectorL< L, bool, A > const &a, std::vector< bool, A > const &b)
	vectorL != std::vector More...

template<platform::SSize L, typename A >
bool	operator< (vectorL< L, bool, A > const &a, std::vector< bool, A > const &b)
	vectorL < std::vector More...

template<platform::SSize L, typename A >
bool	operator<= (vectorL< L, bool, A > const &a, std::vector< bool, A > const &b)
	vectorL <= std::vector More...

template<platform::SSize L, typename A >
bool	operator>= (vectorL< L, bool, A > const &a, std::vector< bool, A > const &b)
	vectorL >= std::vector More...

template<platform::SSize L, typename A >
bool	operator> (vectorL< L, bool, A > const &a, std::vector< bool, A > const &b)
	vectorL > std::vector More...

template<platform::SSize L, typename A >
bool	operator== (std::vector< bool, A > const &a, vectorL< L, bool, A > const &b)
	std::vector == vectorL More...

template<platform::SSize L, typename A >
bool	operator!= (std::vector< bool, A > const &a, vectorL< L, bool, A > const &b)
	std::vector != vectorL More...

template<platform::SSize L, typename A >
bool	operator< (std::vector< bool, A > const &a, vectorL< L, bool, A > const &b)
	std::vector < vectorL More...

template<platform::SSize L, typename A >
bool	operator<= (std::vector< bool, A > const &a, vectorL< L, bool, A > const &b)
	std::vector <= vectorL More...

template<platform::SSize L, typename A >
bool	operator>= (std::vector< bool, A > const &a, vectorL< L, bool, A > const &b)
	std::vector >= vectorL More...

template<platform::SSize L, typename A >
bool	operator> (std::vector< bool, A > const &a, vectorL< L, bool, A > const &b)
	std::vector > vectorL More...

template<platform::SSize L, typename A >
void	swap (vectorL< L, bool, A > &a, vectorL< L, bool, A > &b)
	swap( vectorL, vectorL ) More...

template<platform::SSize L, typename A >
void	swap (vectorL< L, bool, A > &a, std::vector< bool, A > &b)
	swap( vectorL, std::vector ) More...

template<platform::SSize L, typename A >
void	swap (std::vector< bool, A > &a, vectorL< L, bool, A > &b)
	swap( std::vector, vectorL ) More...

Variables
static void(*	main_exit_callback )(void)=0
	Place holder for 'end-action' of utility::exit(…) More...

Detailed Description

unresizable vector whose size is known at compile time, which may be allocated on the stack, and which indexes from 1.

#include <core/conformation/signals/GeneralEvent.hh> – Illegal and unneccessary

STL Headers.

determines all possible rings in a graph.

#include <iostream> // debug only

if you have a container of OPs: i.e., typedef std::list< SilentStructOP > SilentStructs; you can now call this function with the SilentStructs container instead of the SilentFileData objects by my_func( DereferenceIterator< SilentStructs >( decoys().begin() ), DereferenceIterator< SilentStructs >( decoys().end() ) );

Author: Oliver Lange

RingDetection

Hanser, Th., Jauffret, Ph., Kaufmann, G., "A New Algorithm for Exhaustive Ring Perception in a Molecular Graph", Laboratoire de Modeles Informatiques Appliques a la Synthese, URA 405 du CNRS, Universite Louis Pasteur, 67000 Strasbourg, France, Received May 15, 1996

Date: 02/13/2014

This detects rings in residues!

Author: Steven Combs (steve.nosp@m.n.co.nosp@m.mbs1@.nosp@m.gmai.nosp@m.l.com), Ralf Mueller, Jeff Menden; Ken Jung

#include <core/pose/signals/DestructionEvent.hh> – Illegal and unneccessary

Typedef Documentation

typedef utility::pointer::shared_ptr< heap const > utility::heapCOP

typedef utility::pointer::shared_ptr< heap > utility::heapOP

typedef utility::pointer::shared_ptr< Inline_File_Provider_Hook const > utility::Inline_File_Provider_HookCOP

typedef utility::pointer::shared_ptr< Inline_File_Provider_Hook > utility::Inline_File_Provider_HookOP

typedef utility::pointer::shared_ptr< SimulateMPIMessage const > utility::SimulateMPIMessageCOP

typedef utility::pointer::shared_ptr< SimulateMPIMessage > utility::SimulateMPIMessageOP

typedef pointer::shared_ptr< subset_mapping const> utility::subset_mappingCOP

typedef pointer::shared_ptr< subset_mapping > utility::subset_mappingOP

typedef void(* utility::UtilityExitCallBack)(void)

typedef vector0< bool > utility::vector0_bool

typedef vector0< char > utility::vector0_char

typedef vector0< double > utility::vector0_double

typedef vector0< float > utility::vector0_float

typedef vector0< int > utility::vector0_int

typedef vector0< long int > utility::vector0_long

typedef vector0< long double > utility::vector0_longdouble

typedef vector0< signed char > utility::vector0_schar

typedef vector0< short int > utility::vector0_short

typedef vector0< platform::Size > utility::vector0_size

typedef vector0< platform::Size > utility::vector0_size_t

typedef vector0< platform::SSize > utility::vector0_ssize

typedef vector0< platform::SSize > utility::vector0_ssize_t

typedef vector0< unsigned char > utility::vector0_uchar

typedef vector0< unsigned int > utility::vector0_uint

typedef vector0< unsigned long int > utility::vector0_ulong

typedef vector0< unsigned short int > utility::vector0_ushort

typedef vector1< bool > utility::vector1_bool

typedef vector1< char > utility::vector1_char

typedef vector1< double > utility::vector1_double

typedef vector1< float > utility::vector1_float

typedef vector1< int > utility::vector1_int

typedef vector1< long int > utility::vector1_long

typedef vector1< long double > utility::vector1_longdouble

typedef vector1< signed char > utility::vector1_schar

typedef vector1< short int > utility::vector1_short

typedef vector1< std::size_t > utility::vector1_size

typedef vector1< std::size_t > utility::vector1_size_t

typedef vector1< platform::SSize > utility::vector1_ssize

typedef vector1< platform::SSize > utility::vector1_ssize_t

typedef vector1< unsigned char > utility::vector1_uchar

typedef vector1< unsigned int > utility::vector1_uint

typedef vector1< unsigned long int > utility::vector1_ulong

typedef vector1< unsigned short int > utility::vector1_ushort

Enumeration Type Documentation

enum utility::simulate_mpi_message_type

This is for unit testing mpi code in a single processor. The idea is to buffer the messages in the SimulateMPIData stored in the SimulateMPI. To use this class, call initialize_simulation( nprocs ), then set the mpi rank can be set manually, and the functions in mpi_util are usable. By setting the mpi_rank to a different processor, other messages can be sent and received. See test/utility/simulate_mpi.cxxtest for examples.

Enumerator
smpi_char
smpi_integer
smpi_string
smpi_double
smpi_integers
smpi_doubles

Function Documentation

void utility::add_exit_callback ( UtilityExitCallBack cb )

Add additional callback function that will be called before standard exit(…) is executed. [Note: do not confuse this function with 'set_main_exit_callback' which is replacing the end behavior of exit(…)].

References get_all_exit_callbacks().

void utility::add_spaces_left_align	(	std::string &	st,
		std::size_t const	newlen
	)

adds spaces to a left aligned string until a given length is reached

void utility::add_spaces_right_align	(	std::string &	st,
		std::size_t const	newlen
	)

adds spaces to a right aligned string until a given length is reached

template<class T >

void utility::arg_greatest_several	(	vector1< T > const &	input,
		vector1< typename vector1< T >::Size > &	arg_list
	)

Finds indices of the n largest items in input vector, where n is size of the arg_list vector. The indices are reported in decreasing sorted order by the value of the corresponding position in the input vector. If m is the size of the input vector, then this function is O( m n**2)

If arg_list has more entries than input, then it is resized at the end of this function to have as many entries as the input.

References insert_middle().

template<class T >

void utility::arg_least_several	(	vector1< T > const &	input,
		vector1< typename vector1< T >::Size > &	arg_list
	)

Finds indices of the n smallest items in input vector, where n is size of the arg_list vector. The indices are reported in increasing sorted order by the value of the corresponding position in the input vector. If m is the size of the input vector, then this function is O( m n**2)

If arg_list has more entries than input, then it is resized at the end of this function to have as many entries as the input.

References insert_middle().

template<class T >

vector1< T >::Size utility::arg_max ( vector1< T > const & input )

find the index of the largest value in a vector

class T must provide an operator < () and operator = (). Error if input.size() == 0

References debug_assert, and basic::T().

template<class T >

vector1< T >::Size utility::arg_min ( vector1< T > const & input )

find the index of the smallest value in a vector

class T must provide an operator < () and operator = (). Error if input.size() == 0

References debug_assert, and basic::T().

template<typename T >

int utility::argmax ( const std::vector< T > & iterable )

Returns the argument whose value is maximal according to operator>.

Adheres to STL numbering (0-indexed).

template<typename T >

int utility::argmax ( const utility::vector1< T > & iterable )

Returns the argument whose value is maximal according to operator>.

Adheres to Rosetta numbering (1-indexed).

template<typename T >

int utility::argmin ( const std::vector< T > & iterable )

Returns the argument whose value is minimal according to operator<.

Adheres to STL numbering (0-indexed).

template<typename T >

int utility::argmin ( const utility::vector1< T > & iterable )

Returns the argument whose value is minimal according to operator<.

Adheres to Rosetta numbering (1-indexed).

unsigned char utility::code_from_6bit ( unsigned char _8bit )

inline

Referenced by decode_32_to_24().

unsigned char utility::code_to_6bit ( unsigned char _6bit )

inline

uuencode

Referenced by encode_24_to_32().

int utility::cond_exit	(	bool	condition,
		std::string const &	file,
		int const	line,
		std::string const &	message,
		int const	status
	)

Conditional Exit with file + line + message + optional status.

Conditional Exit with file + line + message + optional status. WIll exit if the condition is not met!

References exit().

platform::Real utility::copysign	(	platform::Real const &	x,
		platform::Real const &	y
	)

inline

Referenced by numeric::xyzTransform< numeric::Real >::to_quaternion(), and numeric::statistics::w().

int utility::decode6bit	(	unsigned char *	memory,
		const std::string &	jar
	)

References decode_32_to_24().

void utility::decode_32_to_24	(	unsigned char	i0,
		unsigned char	i1,
		unsigned char	i2,
		unsigned char	i3,
		unsigned char &	o0,
		unsigned char &	o1,
		unsigned char &	o2
	)

inline

References code_from_6bit().

Referenced by decode6bit().

template<class Target , class Source >

Target utility::down_cast ( Source & s )

inline

Fast assert-checked polymorphic down-cast: reference argument.

Note: Usage: down_cast< Type & > where Type can be const-qualified; For down-casting when you know the cast is valid; Can't use for hierarchies with virtual base classes; Assert intentionally won't compile if a virtual base class is present

References debug_assert.

Referenced by utility::options::OptionCollection::operator()(), and utility::options::OptionCollection::operator[]().

template<class Target , class Source >

Target utility::down_cast ( Source * p )

inline

Fast assert-checked polymorphic down-cast: pointer argument.

Note: Usage: down_cast< Type * > where Type can be const-qualified; For down-casting when you know the cast is valid; Can't use for hierarchies with virtual base classes; Assert intentionally won't compile if a virtual base class is present

References debug_assert.

void utility::encode6bit	(	const unsigned char *	memory,
		unsigned int	length,
		std::string &	jar
	)

References encode_24_to_32().

void utility::encode_24_to_32	(	unsigned char	i0,
		unsigned char	i1,
		unsigned char	i2,
		unsigned char &	o0,
		unsigned char &	o1,
		unsigned char &	o2,
		unsigned char &	o3
	)

inline

References code_to_6bit().

Referenced by encode6bit().

bool utility::endswith	(	std::string const &	haystack,
		std::string const &	needle
	)

True iff haystack ends with needle.

void utility::exit	(	std::string const &	file,
		int const	line,
		std::string const &	message,
		int const	status
	)

Exit with file + line + message + optional status.

References basic::options::OptionKeys::begin, utility::io::oc::cerr, utility::io::izstream::close(), utility::io::ocstream::flush(), get_all_exit_callbacks(), utility::io::getline(), utility::file::gzip(), main_exit_callback, and print_backtrace().

Referenced by cond_exit(), and exit().

void utility::exit	(	std::string const &	file,
		int const	line,
		int const	status = `1`
	)

inline

Exit with file + line + optional status.

References exit().

void utility::exit	(	int const	status,
		std::string const &	file,
		int const	line
	)

inline

Exit with file + line + status.

Note: Deprecated: For backwards compatibility with earlier version

References exit().

std::string utility::file_basename ( const std::string & full_path )

References filename().

std::string utility::file_contents ( std::string const & file_name )

Read the entire contents of a file into a string. All end-of-line characters are replaced by "\n". Throws a utility::excn::EXCN_msg_exception if the file cannot be opened.

References utility::io::izstream::close(), utility::io::getline(), line, and utility::options::OptionKeys::options::table::text.

Referenced by utility::io::FileContentsMap::get_file_contents(), and utility::io::FileContentsMap::get_file_contents_ref().

std::string utility::filename ( const std::string & path )

References utility::file::FileName::base(), and utility::file::FileName::extension().

Referenced by utility::io::mpi_stream::basic_mpi_streambuf< Elem, Tr, ElemA, ByteT, ByteAT >::basic_mpi_streambuf(), utility::file::file_basename(), file_basename(), utility::io::FileContentsMap::get_file_contents(), utility::io::FileContentsMap::get_file_contents_ref(), and utility::Inline_File_Provider::is_black_listed_file().

template<typename BidirectionalIterator , typename T >

BidirectionalIterator utility::find_closest	(	BidirectionalIterator	first,
		BidirectionalIterator	last,
		const T &	value
	)

Returns an iterator on the sorted range [first, last) nearest to value. If value is equidistant between adjacent elements, the lesser is returned.

template<class T >

T const utility::from_string	(	std::string const &	s,
		T
	)

inline

References name, basic::T(), and utility_exit_with_message.

Referenced by numeric::comma_seperated_string_to_xyz(), numeric::expression_parser::ArithmeticScanner::scan_literal(), and numeric::interpolation::spline_from_file().

std::vector< UtilityExitCallBack >& utility::get_all_exit_callbacks ( )

Array to hold all additional exit-callbacks.

Referenced by add_exit_callback(), exit(), and remove_exit_callback().

platform::Size utility::get_num_digits ( platform::Size value )

std::pair< std::vector< int >, std::vector< char > > utility::get_resnum_and_chain	(	std::string const &	s,
		bool &	string_is_ok
	)

converts string like "1-3 20-22" or "A:1-5 B:20-22" to vectors containing resnums and chains.

Author: rhiju

References get_resnum_and_chain_from_one_tag(), replace_in(), and string_split().

Referenced by utility::options::ResidueChainVectorOption::resnum_and_chain(), and utility::options::ResidueChainVectorOption::values_of().

bool utility::get_resnum_and_chain_from_one_tag	(	std::string const &	tag,
		std::vector< int > &	resnum,
		std::vector< char > &	chains
	)

helper function for get_resnum_and_chain

Referenced by get_resnum_and_chain(), and utility::options::ResidueChainVectorOption::value_of().

platform::Real utility::get_undefined_real ( )

inline

Get a numeric value for Real that represents an "undefined" value.

Referenced by string2Real().

platform::Size utility::get_undefined_size ( )

inline

Get a numeric value for Size that represents an "undefined" value.

References max().

Referenced by is_undefined(), and string2Size().

template<class T >

void utility::insert_middle	(	vector1< T > &	vect,
		typename vector1< T >::Size const	position,
		T const	new_value,
		bool	expand
	)

References swap(), and basic::T().

Referenced by arg_greatest_several(), and arg_least_several().

bool utility::is_false_string ( std::string const & value_str )

inline

String accepted as a false value?

Referenced by utility::tag::Tag::getOption(), and utility::options::BooleanOption::is_false_value().

bool utility::is_inf ( platform::Real const & val )

inline

References numeric::isinf().

Referenced by numeric::statistics::w().

bool utility::is_nan ( platform::Real const & val )

inline

References numeric::isnan().

Referenced by numeric::xyzTransform< numeric::Real >::bad(), numeric::xyzTransform< numeric::Real >::badfast(), numeric::alignment::QCP_Kernel< double >::calc_rmsd_Theobald_method(), numeric::statistics::Dawson(), numeric::statistics::errf(), numeric::xyzTransform< numeric::Real >::rt6(), and numeric::statistics::w().

bool utility::is_string_numeric ( std::string const & input )

bool utility::is_true_string ( std::string const & value_str )

inline

String accepted as a true value?

Referenced by utility::tag::Tag::getOption(), and utility::options::BooleanOption::is_true_value().

bool utility::is_undefined ( platform::Size const & val )

inline

Check if a Size is undefined (i.e has the same value as utility::get_undefined_size() )

References get_undefined_size().

bool utility::is_undefined ( platform::Real const & val )

inline

Check if a Real is undefined (i.e has the same value as utility::get_undefined_real() )

References numeric::isinf(), and numeric::isnan().

template<class T >

std::string utility::join	(	utility::vector1< T > const &	vector,
		std::string const &	connector
	)

combine vector with anything

References basic::options::OptionKeys::begin.

std::string utility::join	(	utility::vector1< std::string > const &	s,
		std::string const &	connector
	)

combine strings with anything

References basic::options::OptionKeys::begin.

Referenced by join(), options::main(), basic::database::make_compound_statement(), and options_class::writeToFile().

std::string utility::join	(	std::vector< std::string > const &	s,
		std::string const &	connector
	)

combine strings with anything

References basic::options::OptionKeys::begin.

std::string utility::join	(	std::string const &	string_w_spaces,
		std::string const &	connector
	)

join space separations in a string with a connector such as '_'

References join(), split(), and trim().

std::string utility::make_tag ( utility::vector1< int > res_vector )

References tag.

std::string utility::make_tag_with_dashes	(	utility::vector1< int >	res_vector,
		char const	delimiter
	)

Compactifies vectors of ints: 1 2 3 9 10 11 to "1-3 9-11".

std::string utility::make_tag_with_dashes	(	utility::vector1< int >	res_vector,
		utility::vector1< char >	chain_vector,
		char const	delimiter
	)

References runtime_assert, and tag.

template<class T >

T utility::max ( vector1< T > const & input )

Find the largest value in a vector.

class T must provide an operator < () and operator = (). Error if input.size() == 0

References debug_assert, and basic::T().

short int utility::max	(	short int const	a,
		short int const	b
	)

inline

max( short int, short int )

Referenced by max().

int utility::max	(	int const	a,
		int const	b
	)

inline

max( int, int )

long int utility::max	(	long int const	a,
		long int const	b
	)

inline

max( long int, long int )

unsigned short int utility::max	(	unsigned short int const	a,
		unsigned short int const	b
	)

inline

max( unsigned short int, unsigned short int )

unsigned int utility::max	(	unsigned int const	a,
		unsigned int const	b
	)

inline

max( unsigned int, unsigned int )

unsigned long int utility::max	(	unsigned long int const	a,
		unsigned long int const	b
	)

inline

max( unsigned long int, unsigned long int )

float utility::max	(	float const	a,
		float const	b
	)

inline

max( float, float )

double utility::max	(	double const	a,
		double const	b
	)

inline

max( double, double )

long double utility::max	(	long double const	a,
		long double const	b
	)

inline

max( long double, long double )

template<typename T >

T const& utility::max	(	T const &	a,
		T const &	b,
		T const &	c
	)

inline

max( a, b, c )

template<typename T >

T const& utility::max	(	T const &	a,
		T const &	b,
		T const &	c,
		T const &	d
	)

inline

max( a, b, c, d )

References max().

template<typename T >

T const& utility::max	(	T const &	a,
		T const &	b,
		T const &	c,
		T const &	d,
		T const &	e
	)

inline

max( a, b, c, d, e )

References max(), and max().

template<typename T >

T const& utility::max	(	T const &	a,
		T const &	b,
		T const &	c,
		T const &	d,
		T const &	e,
		T const &	f
	)

inline

max( a, b, c, d, e, f )

References max(), and max().

short int utility::min	(	short int const	a,
		short int const	b
	)

inline

min( short int, short int )

Referenced by min().

int utility::min	(	int const	a,
		int const	b
	)

inline

min( int, int )

template<class T >

T utility::min ( vector1< T > const & input )

Find the smallest value in a vector.

class T must provide an operator < () and operator = (). Error if input.size() == 0

References debug_assert, and basic::T().

long int utility::min	(	long int const	a,
		long int const	b
	)

inline

min( long int, long int )

unsigned short int utility::min	(	unsigned short int const	a,
		unsigned short int const	b
	)

inline

min( unsigned short int, unsigned short int )

unsigned int utility::min	(	unsigned int const	a,
		unsigned int const	b
	)

inline

min( unsigned int, unsigned int )

unsigned long int utility::min	(	unsigned long int const	a,
		unsigned long int const	b
	)

inline

min( unsigned long int, unsigned long int )

float utility::min	(	float const	a,
		float const	b
	)

inline

min( float, float )

double utility::min	(	double const	a,
		double const	b
	)

inline

min( double, double )

long double utility::min	(	long double const	a,
		long double const	b
	)

inline

min( long double, long double )

template<typename T >

T const& utility::min	(	T const &	a,
		T const &	b,
		T const &	c
	)

inline

min( a, b, c )

template<typename T >

T const& utility::min	(	T const &	a,
		T const &	b,
		T const &	c,
		T const &	d
	)

inline

min( a, b, c, d )

References min().

template<typename T >

T const& utility::min	(	T const &	a,
		T const &	b,
		T const &	c,
		T const &	d,
		T const &	e
	)

inline

min( a, b, c, d, e )

References min(), and min().

template<typename T >

T const& utility::min	(	T const &	a,
		T const &	b,
		T const &	c,
		T const &	d,
		T const &	e,
		T const &	f
	)

inline

min( a, b, c, d, e, f )

References min(), and min().

int utility::mpi_nprocs ( )

References utility::SimulateMPI::mpi_nprocs(), and utility::SimulateMPI::simulate_mpi().

Referenced by basic::Tracer::calculate_visibility().

int utility::mpi_rank ( )

References utility::SimulateMPI::mpi_rank(), and utility::SimulateMPI::simulate_mpi().

Referenced by basic::Tracer::calculate_visibility(), utility::options::mpi_safe_std_err(), and basic::database::resolve_db_partition().

std::string utility::msg_name ( simulate_mpi_message_type msg_type )

References smpi_char, smpi_double, smpi_doubles, smpi_integer, smpi_integers, and smpi_string.

Referenced by utility::SimulateMPIData::pop_next_message_for_node_of_type(), and utility::SimulateMPIData::pop_next_message_of_type().

template<typename B >

bool utility::operator!=	(	BitSet< B > const &	a,
		BitSet< B > const &	b
	)

BitSet != BitSet.

template<typename B >

bool utility::operator!=	(	BitVector< B > const &	a,
		BitVector< B > const &	b
	)

BitVector != BitVector.

template<platform::SSize L, typename A >

bool utility::operator!=	(	vectorL< L, bool, A > const &	a,
		vectorL< L, bool, A > const &	b
	)

vectorL != vectorL

template<platform::SSize L, typename A >

bool utility::operator!=	(	vectorL< L, bool, A > const &	a,
		std::vector< bool, A > const &	b
	)

vectorL != std::vector

template<platform::SSize L, typename T , typename A >

bool utility::operator!=	(	vectorL< L, T, A > const &	a,
		vectorL< L, T, A > const &	b
	)

vectorL != vectorL

template<platform::SSize L, typename A >

bool utility::operator!=	(	std::vector< bool, A > const &	a,
		vectorL< L, bool, A > const &	b
	)

std::vector != vectorL

template<platform::SSize L, typename T , typename A >

bool utility::operator!=	(	vectorL< L, T, A > const &	a,
		std::vector< T, A > const &	b
	)

vectorL != std::vector

template<platform::SSize L, typename T , typename A >

bool utility::operator!=	(	std::vector< T, A > const &	a,
		vectorL< L, T, A > const &	b
	)

std::vector != vectorL

template<typename B >

BitSet< B > utility::operator+	(	BitSet< B > const &	a,
		BitSet< B > const &	b
	)

BitSet + BitSet: Union.

template<typename B >

BitVector< B > utility::operator+	(	BitVector< B > const &	a,
		BitVector< B > const &	b
	)

BitVector + BitVector: Union.

template<typename B >

BitSet< B > utility::operator-	(	BitSet< B > const &	a,
		BitSet< B > const &	b
	)

BitSet - BitSet: Difference.

template<typename B >

BitVector< B > utility::operator-	(	BitVector< B > const &	a,
		BitVector< B > const &	b
	)

BitVector - BitVector: Difference.

template<platform::SSize L, typename A >

bool utility::operator<	(	vectorL< L, bool, A > const &	a,
		vectorL< L, bool, A > const &	b
	)

vectorL < vectorL

template<platform::SSize L, typename A >

bool utility::operator<	(	vectorL< L, bool, A > const &	a,
		std::vector< bool, A > const &	b
	)

vectorL < std::vector

template<platform::SSize L, typename T , typename A >

bool utility::operator<	(	vectorL< L, T, A > const &	a,
		vectorL< L, T, A > const &	b
	)

vectorL < vectorL

template<platform::SSize L, typename A >

bool utility::operator<	(	std::vector< bool, A > const &	a,
		vectorL< L, bool, A > const &	b
	)

std::vector < vectorL

template<platform::SSize L, typename T , typename A >

bool utility::operator<	(	vectorL< L, T, A > const &	a,
		std::vector< T, A > const &	b
	)

vectorL < std::vector

template<platform::SSize L, typename T , typename A >

bool utility::operator<	(	std::vector< T, A > const &	a,
		vectorL< L, T, A > const &	b
	)

std::vector < vectorL

template<typename T1 , typename T2 >

std::ostream & utility::operator<<	(	std::ostream &	os,
		std::pair< T1, T2 > const &	v
	)

Output function for std::pair object.

Predefined functions for Tracer IO We originally moved them out of name spaces so we can use them right away - without specifying it. Returned to utility namespace, as some compilers did not find the operator otherwise! – rhiju

template<class T >

std::ostream& utility::operator<<	(	std::ostream &	os,
		std::vector< T > const &	v
	)

Output function for std::vector object.

template<class T >

std::ostream& utility::operator<<	(	std::ostream &	os,
		utility::vector1< T > const &	v
	)

Output function for utility::vector1 object.

template<typename T1 , typename T2 >

std::ostream& utility::operator<<	(	std::ostream &	os,
		std::map< T1, T2 > const &	m
	)

Output function for std::map object.

template<typename T >

std::ostream& utility::operator<<	(	std::ostream &	os,
		std::list< T > const &	l
	)

Output function for std::list object.

template<platform::SSize L, typename A >

bool utility::operator<=	(	vectorL< L, bool, A > const &	a,
		vectorL< L, bool, A > const &	b
	)

vectorL <= vectorL

template<platform::SSize L, typename A >

bool utility::operator<=	(	vectorL< L, bool, A > const &	a,
		std::vector< bool, A > const &	b
	)

vectorL <= std::vector

template<platform::SSize L, typename T , typename A >

bool utility::operator<=	(	vectorL< L, T, A > const &	a,
		vectorL< L, T, A > const &	b
	)

vectorL <= vectorL

template<platform::SSize L, typename A >

bool utility::operator<=	(	std::vector< bool, A > const &	a,
		vectorL< L, bool, A > const &	b
	)

std::vector <= vectorL

template<platform::SSize L, typename T , typename A >

bool utility::operator<=	(	vectorL< L, T, A > const &	a,
		std::vector< T, A > const &	b
	)

vectorL <= std::vector

template<platform::SSize L, typename T , typename A >

bool utility::operator<=	(	std::vector< T, A > const &	a,
		vectorL< L, T, A > const &	b
	)

std::vector <= vectorL

bool utility::operator==	(	history_queue_struct const &	a,
		history_queue_struct const &	b
	)

inline

References utility::history_queue_struct::element_in_rh, utility::history_queue_struct::more_ancient_ptr, and utility::history_queue_struct::more_recent_ptr.

template<typename B >

bool utility::operator==	(	BitSet< B > const &	a,
		BitSet< B > const &	b
	)

BitSet == BitSet.

template<typename B >

bool utility::operator==	(	BitVector< B > const &	a,
		BitVector< B > const &	b
	)

BitVector == BitVector.

template<platform::SSize L, typename A >

bool utility::operator==	(	vectorL< L, bool, A > const &	a,
		vectorL< L, bool, A > const &	b
	)

vectorL == vectorL

template<platform::SSize L, typename A >

bool utility::operator==	(	vectorL< L, bool, A > const &	a,
		std::vector< bool, A > const &	b
	)

vectorL == std::vector

template<platform::SSize L, typename T , typename A >

bool utility::operator==	(	vectorL< L, T, A > const &	a,
		vectorL< L, T, A > const &	b
	)

vectorL == vectorL

template<platform::SSize L, typename A >

bool utility::operator==	(	std::vector< bool, A > const &	a,
		vectorL< L, bool, A > const &	b
	)

std::vector == vectorL

template<platform::SSize L, typename T , typename A >

bool utility::operator==	(	vectorL< L, T, A > const &	a,
		std::vector< T, A > const &	b
	)

vectorL == std::vector

template<platform::SSize L, typename T , typename A >

bool utility::operator==	(	std::vector< T, A > const &	a,
		vectorL< L, T, A > const &	b
	)

std::vector == vectorL

template<platform::SSize L, typename A >

bool utility::operator>	(	vectorL< L, bool, A > const &	a,
		vectorL< L, bool, A > const &	b
	)

vectorL > vectorL

template<platform::SSize L, typename A >

bool utility::operator>	(	vectorL< L, bool, A > const &	a,
		std::vector< bool, A > const &	b
	)

vectorL > std::vector

template<platform::SSize L, typename T , typename A >

bool utility::operator>	(	vectorL< L, T, A > const &	a,
		vectorL< L, T, A > const &	b
	)

vectorL > vectorL

template<platform::SSize L, typename A >

bool utility::operator>	(	std::vector< bool, A > const &	a,
		vectorL< L, bool, A > const &	b
	)

std::vector > vectorL

template<platform::SSize L, typename T , typename A >

bool utility::operator>	(	vectorL< L, T, A > const &	a,
		std::vector< T, A > const &	b
	)

vectorL > std::vector

template<platform::SSize L, typename T , typename A >

bool utility::operator>	(	std::vector< T, A > const &	a,
		vectorL< L, T, A > const &	b
	)

std::vector > vectorL

template<platform::SSize L, typename A >

bool utility::operator>=	(	vectorL< L, bool, A > const &	a,
		vectorL< L, bool, A > const &	b
	)

vectorL >= vectorL

template<platform::SSize L, typename A >

bool utility::operator>=	(	vectorL< L, bool, A > const &	a,
		std::vector< bool, A > const &	b
	)

vectorL >= std::vector

template<platform::SSize L, typename T , typename A >

bool utility::operator>=	(	vectorL< L, T, A > const &	a,
		vectorL< L, T, A > const &	b
	)

vectorL >= vectorL

template<platform::SSize L, typename A >

bool utility::operator>=	(	std::vector< bool, A > const &	a,
		vectorL< L, bool, A > const &	b
	)

std::vector >= vectorL

template<platform::SSize L, typename T , typename A >

bool utility::operator>=	(	vectorL< L, T, A > const &	a,
		std::vector< T, A > const &	b
	)

vectorL >= std::vector

template<platform::SSize L, typename T , typename A >

bool utility::operator>=	(	std::vector< T, A > const &	a,
		vectorL< L, T, A > const &	b
	)

std::vector >= vectorL

template<typename B >

BitSet< B > utility::operator\|	(	BitSet< B > const &	a,
		BitSet< B > const &	b
	)

BitSet | BitSet: Union.

template<typename B >

BitVector< B > utility::operator\|	(	BitVector< B > const &	a,
		BitVector< B > const &	b
	)

BitVector | BitVector: Union.

std::string utility::pathname ( const std::string & path )

References utility::file::FileName::path().

void utility::rand_sleep ( )

References sys_sleep().

Referenced by utility::file::file_delete(), utility::file::trytry_ifstream_open(), and utility::file::trytry_ofstream_open().

void utility::ReadFromFileOrDie	(	const std::string &	filename,
		std::string *	contents
	)

Reads the contents of <filename> into <contents>, preserving newline characters. Aborts if an error is encoutered.

References utility::io::getline(), line, and utility_exit_with_message.

char utility::receive_char_from_node ( int source )

Use MPI to receive a single char from a particular node.

References utility::SimulateMPI::receive_char_from_node(), and utility::SimulateMPI::simulate_mpi().

double utility::receive_double_from_node ( int source )

Use MPI to receive a single double from a particular node.

References utility::SimulateMPI::receive_double_from_node(), and utility::SimulateMPI::simulate_mpi().

utility::vector1< double > utility::receive_doubles_from_node ( int source )

Use MPI to receive a vector of doubles from a particular node.

References utility::SimulateMPI::receive_doubles_from_node(), and utility::SimulateMPI::simulate_mpi().

int utility::receive_integer_from_anyone ( )

Use MPI to wait until some node sends an integer – usually its own mpi_rank so that it can send further messages.

References utility::SimulateMPI::receive_integer_from_anyone(), and utility::SimulateMPI::simulate_mpi().

int utility::receive_integer_from_node ( int source )

Use MPI to receive a single integer from a particular node.

References utility::SimulateMPI::receive_integer_from_node(), and utility::SimulateMPI::simulate_mpi().

utility::vector1< int > utility::receive_integers_from_node ( int source )

Use MPI to receive a vector of integers from a particular node.

References utility::SimulateMPI::receive_integers_from_node(), and utility::SimulateMPI::simulate_mpi().

std::string utility::receive_string_from_node ( int source )

Use MPI to receive a string from a particular node.

References utility::SimulateMPI::receive_string_from_node(), and utility::SimulateMPI::simulate_mpi().

Referenced by basic::message_listening::request_data_from_head_node().

void utility::remove_exit_callback ( UtilityExitCallBack cb )

Remove additional callback function that was previously added by using add_exit_callback.

References basic::options::OptionKeys::begin, and get_all_exit_callbacks().

std::string utility::replace_environment_variables ( std::string input )

find all environment variables with the form ${VARIABLE} and replace with the contents of that environment variable. if the environment variable does not exist, return string::npos

References basic::options::OptionKeys::end, and utility_exit_with_message.

Referenced by utility::options::OptionCollection::load_options_from_stream().

void utility::replace_in	(	std::string &	s,
		const char	from,
		const char *	to
	)

inline

std::string utility::replace_in	(	std::string const	name_in,
		std::string const	find_string,
		std::string const	replace_string
	)

find/replace strings within input string.

References name.

Referenced by get_resnum_and_chain().

platform::Real utility::round ( platform::Real const & val )

inline

bool utility::same_ignoring_spaces	(	std::string const &	s1,
		std::string const &	s2
	)

inline

Compares two strings, ignoring spaces. Useful for comparing atom name strings which have pdb-alignment built into them. Slightly dangerous if you consider the fact that atom names in the PDB are different for different indentation rules: ' CA ' is c-alpha. 'CA ' is calcium.

void utility::send_char_to_node	(	int	destination,
		char	message
	)

References utility::SimulateMPI::send_char_to_node(), and utility::SimulateMPI::simulate_mpi().

void utility::send_double_to_node	(	int	destination,
		double	message
	)

References utility::SimulateMPI::send_double_to_node(), and utility::SimulateMPI::simulate_mpi().

void utility::send_doubles_to_node	(	int	destination,
		utility::vector1< double > const &	message
	)

References utility::SimulateMPI::send_doubles_to_node(), and utility::SimulateMPI::simulate_mpi().

void utility::send_integer_to_node	(	int	destination,
		int	message
	)

References utility::SimulateMPI::send_integer_to_node(), and utility::SimulateMPI::simulate_mpi().

void utility::send_integers_to_node	(	int	destination,
		utility::vector1< int > const &	message
	)

References utility::SimulateMPI::send_integers_to_node(), and utility::SimulateMPI::simulate_mpi().

void utility::send_string_to_node	(	int	destination,
		std::string const &	message
	)

References utility::SimulateMPI::send_string_to_node(), and utility::SimulateMPI::simulate_mpi().

Referenced by basic::message_listening::request_data_from_head_node(), and basic::message_listening::send_data_to_head_node().

void utility::set_main_exit_callback ( UtilityExitCallBack my_callback )

Set call back funtion that will be called on utility::exit. Use this function to overload default behavior of sys.exit to more appropriate to your application Defaut value for callback function is 0, whicth mean no sys exit is called.

References main_exit_callback.

Referenced by utility::py::PyExitCallback::set_PyExitCallBack().

void utility::slurp	(	std::istream &	in,
		std::string &	out
	)

References utility::io::getline(), and line.

utility::vector1< std::string > utility::split ( const std::string & s )

split given std::string using ' ' symbol.

References numeric::add().

Referenced by basic::message_listening::DbMoverMessageListener::deserialize_data(), join(), and basic::Tracer::set_ios_hook().

std::list< std::string > utility::split_to_list ( const std::string & s )

split given std::string using ' ' symbol.

References numeric::add().

Referenced by utility::options::OptionCollection::load_option_from_file().

std::set< std::string > utility::split_to_set ( const std::string & s )

split given std::string to a set using ' ' symbol.

split given std::string using ' ' symbol.

References numeric::add().

utility::vector1< std::string > utility::split_whitespace ( const std::string & s )

split given std::string using whitespace as a separator. Unlike string_split_multi_delim(), any group of mixed whitespace counts only as a single seperator.

bool utility::startswith	(	std::string const &	haystack,
		std::string const &	needle
	)

True iff haystack starts with needle.

float utility::string2float ( std::string st )

convert a string to a float, returns -1 on failure

convert a string to a float

int utility::string2int ( std::string st )

convert a string to an int, returns -1 on failure

convert a string to an int

Referenced by basic::Tracer::calculate_tracer_level(), and basic::message_listening::DbMoverMessageListener::deserialize_data().

platform::Real utility::string2Real ( std::string st )

convert a string to a Real, returns numeric::get_undefined_real() on failure

References get_undefined_real().

platform::Size utility::string2Size ( std::string st )

convert a string to a Size, returns numeric::get_undefined_size() on failure

References get_undefined_size().

void utility::string2uint	(	const std::string &	x,
		unsigned int *	y
	)

References numeric::crick_equations::y().

utility::vector1< std::string > utility::string_split	(	std::string const &	in,
		char	splitchar = `' '`
	)

split to vector1< std::string > using arbitrary split character

Referenced by basic::Tracer::calculate_tracer_level(), numeric::comma_seperated_string_to_xyz(), get_resnum_and_chain(), basic::resource_manager::locator::FileListResourceLocator::locate_resource_stream(), and numeric::interpolation::spline_from_file().

template<class T >

utility::vector1<T> const utility::string_split	(	std::string const &	in,
		char	splitchar,
		T
	)

inline

References name, basic::T(), and utility_exit_with_message.

utility::vector1< std::string > utility::string_split_multi_delim	(	std::string const &	in,
		std::string	splitchars = `" \t"`
	)

split to vector< std::string > using any of arbitrary split characters

utility::vector1< std::string > utility::string_split_simple	(	std::string const &	in,
		char	splitchar
	)

split to vector1< std::string > using arbitrary split character, but no empty strings (closer to python string::split)

std::string utility::string_to_sha1 ( std::string const & input_string )

template<typename B >

void utility::swap	(	BitSet< B > &	a,
		BitSet< B > &	b
	)

swap( BitSet, BitSet )

template<typename B >

void utility::swap	(	BitVector< B > &	a,
		BitVector< B > &	b
	)

swap( BitVector, BitVector )

template<platform::SSize L, typename A >

void utility::swap	(	vectorL< L, bool, A > &	a,
		vectorL< L, bool, A > &	b
	)

inline

swap( vectorL, vectorL )

template<platform::SSize L, typename A >

void utility::swap	(	vectorL< L, bool, A > &	a,
		std::vector< bool, A > &	b
	)

inline

swap( vectorL, std::vector )

template<platform::SSize L, typename A >

void utility::swap	(	std::vector< bool, A > &	a,
		vectorL< L, bool, A > &	b
	)

inline

swap( std::vector, vectorL )

template<platform::SSize L, typename T , typename A >

void utility::swap	(	vectorL< L, T, A > &	a,
		vectorL< L, T, A > &	b
	)

inline

swap( vectorL, vectorL )

template<platform::SSize L, typename T , typename A >

void utility::swap	(	vectorL< L, T, A > &	a,
		std::vector< T, A > &	b
	)

inline

swap( vectorL, std::vector )

template<platform::SSize L, typename T , typename A >

void utility::swap	(	std::vector< T, A > &	a,
		vectorL< L, T, A > &	b
	)

inline

swap( std::vector, vectorL )

void utility::swap4_aligned	(	void *	v,
		long	ndata
	)

inline

void utility::sys_sleep ( double const seconds )

Sleep for a specified number of seconds.

References utility::io::oc::cout, and numeric::crick_equations::x().

Referenced by rand_sleep().

std::string utility::timestamp ( )

Generate timestamp string.

Referenced by basic::Tracer::prepend_channel_name(), and timestamp_short().

std::string utility::timestamp_short ( )

Generate timestamp string, short format.

References timestamp().

template<class T >

std::string utility::to_string ( const T & t )

inline

void utility::trim	(	std::string &	s,
		const std::string &	drop
	)

Referenced by join(), utility::options::OptionCollection::load(), utility::options::OptionCollection::load_options_from_stream(), basic::show_time(), numeric::interpolation::spline_from_file(), trim(), and basic::database::write_schema_to_database().

std::string utility::trim	(	std::string const &	s,
		std::string const &	drop
	)

create a new string that drops all the unwanted substrings of the original string.

References trim().

bool utility::trimmed_compare	(	std::string const &	s1,
		std::string const &	s2
	)

compares two strings ignoring leading and trailing spaces

Variable Documentation

void(* utility::main_exit_callback)(void)=0

static

Place holder for 'end-action' of utility::exit(…)

Referenced by exit(), and set_main_exit_callback().

Namespaces

Classes

Typedefs

Enumerations

Functions

Variables

Detailed Description

Typedef Documentation

Enumeration Type Documentation

Function Documentation

Variable Documentation