utility Namespace Reference

unresizable vector whose size is known at compile time, which may be allocated on the stack, and which indexes from 0. More...

Namespaces
	CSI
	excn
	factory
	file
	graph
	io
	json_spirit
	keys
	libsvm
	options
	pointer
	py
	serialization
	signals
	sql_database
	tag
	thread
	tools
	type_traits
	xsd_util

Classes
class	BitSet
	Simple bit set. More...
class	BitVector
	Simple bit vector. More...
class	Bound
	Bound value class. More...
class	CSI_Sequence
	Class to hold all Terminal ASCII codes as static data for CSI_Sequence. Note: that on non-tty terminals the codes will not print to avoid polution of Rosetta logs. More...
struct	DenseBoolMap
	This struct condenses N boolean values into roughly N bits, saving roughly 4x memory. NUM_ELEMS parameter takes in the number of boolean values. BASE_INDEX parameter takes in the index of the first value. The recommended way to use this struct is with an enum. See core::scoring::hbonds::graph::AtomInfo for an example. More...
class	DereferenceIterator
	const_iterator class for SilentFileData container. More...
class	fixedsizearray0
class	fixedsizearray0const_iterator
class	fixedsizearray0iterator
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...
struct	UtilityExitException
class	vector0
	std::vector with assert-checked bounds More...
class	vector0< bool, A >
	std::vector with assert-checked bounds: bool specialization More...
class	vector1
	std::vector with 1-based indexing More...
class	vector1< bool, A >
	std::vector with 1-based indexing: bool specialization More...
class	vectorL
	std::vector with L-based indexing More...
class	vectorL< L, bool, A >
	std::vector with L-based indexing: bool specialization More...
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	DateFormat { PDB_FORMAT = 1 }
	Enumeration of acceptable date formats. More...
enum	simulate_mpi_message_type {   smpi_char = 1, smpi_integer, smpi_size, smpi_string,   smpi_double, smpi_integers, smpi_sizes, smpi_doubles }

Functions
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<typename U >
void	swap (BitVector< U > &a, BitVector< U > &b)
	swap( BitVector, BitVector ) More...
bool	stdout_is_tty ()
CSI_Sequence	CSI_Nothing ()
CSI_Sequence	CSI_Reset ()
CSI_Sequence	CSI_Bold ()
CSI_Sequence	CSI_Underline ()
CSI_Sequence	CSI_Black ()
CSI_Sequence	CSI_Red ()
CSI_Sequence	CSI_Green ()
CSI_Sequence	CSI_Yellow ()
CSI_Sequence	CSI_Blue ()
CSI_Sequence	CSI_Magenta ()
CSI_Sequence	CSI_Cyan ()
CSI_Sequence	CSI_White ()
CSI_Sequence	CSI_Default ()
CSI_Sequence	CSI_bgBlack ()
CSI_Sequence	CSI_bgRed ()
CSI_Sequence	CSI_bgGreen ()
CSI_Sequence	CSI_bgYellow ()
CSI_Sequence	CSI_bgBlue ()
CSI_Sequence	CSI_bgMagenta ()
CSI_Sequence	CSI_bgCyan ()
CSI_Sequence	CSI_bgWhite ()
CSI_Sequence	CSI_bgDefault ()
std::string	get_current_date (DateFormat const format)
	Return current date in the requested format. 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 (char 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, char const *file, int const line, std::string const &message, int const status)
	Conditional Exit with file + line + message + optional status. More...
void	exit (char const *file, int const line, int const status=1) NORETURN
	Exit with file + line + optional status. More...
void	exit (int const status, char 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<class K , class V >
void	map_merge (std::map< K, V > &destination_map, std::map< K, V > const &source_map)
	Append the second map to the first For one-liner convenience (esp. for map return values.) 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...
platform::Size	modulo (int const &a, int const &b)
	modulo of an input integer a (can be negative) with respect to unsigned integer b 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)
platform::Size	receive_size_from_node (int source)
	Use MPI to receive a single unsigned (usually 64-bit) integer from a particular node. More...
void	send_size_to_node (int destination, platform::Size message)
	Use MPI to send a single unsigned (usually 64-bit) integer to a particular node. More...
utility::vector1< platform::Size >	receive_sizes_from_node (int source)
	Use MPI to receive a vector of integers from a particular node. More...
void	send_sizes_to_node (int destination, utility::vector1< platform::Size > 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)
bool	isnan (platform::Real const &val)
bool	isinf (platform::Real const &val)
bool	isfinite (platform::Real const &val)
platform::Real	round (platform::Real const &val)
platform::Real	copysign (platform::Real const &x, platform::Real const &y)
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	operator== (history_queue_struct const &a, history_queue_struct const &b)
std::string	msg_name (simulate_mpi_message_type msg_type)
void	print_message (SimulateMPIMessageCOP msg, std::ostream &os)
template<platform::SSize L, typename T >
utility::vector1< platform::Size >	argsort (utility::vectorL< L, T > const &v)
template<platform::SSize L, typename T >
utility::vector1< platform::Real >	fractional_rank (utility::vectorL< L, T > const &v)
	Return the fractional rank of a list of numbers. More...
template<platform::SSize L, class T , typename std::enable_if< utility::type_traits::has_insertion_operator_s< T >::value >::type * = nullptr>
std::ostream &	operator<< (std::ostream &os, utility::vectorL< L, T > const &v)
	Output function for utility::vectorL object. More...
template<class T , platform::Size S>
std::ostream &	operator<< (std::ostream &os, utility::fixedsizearray1< T, S > const &v)
	Output function for utility::fixedsizearray0 object. More...
static std::string const	UPPERCASE_LETTERS ("ABCDEFGHIJKLMNOPQRSTUVWXYZ")
static std::string const	LOWERCASE_LETTERS ("abcdefghijklmnopqrstuvwxyz")
static std::string const	LETTERS (UPPERCASE_LETTERS+LOWERCASE_LETTERS)
static std::string const	NUMERALS ("0123456789")
static std::string const	UPPERCASE_ALPHANUMERICS (UPPERCASE_LETTERS+NUMERALS)
static std::string const	LOWERCASE_ALPHANUMERICS (LOWERCASE_LETTERS+NUMERALS)
static std::string const	ALPHANUMERICS (LETTERS+NUMERALS)
utility::vector1< std::string >	split (std::string const &s)
	split given std::string using ' ' symbol. More...
utility::vector1< std::string >	split_whitespace (std::string const &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::vector< std::string >	split_by_newlines (std::string const &s)
std::string	upper (std::string const &s)
	Make a string Uppercase. More...
std::string	lower (std::string const &s)
	Make a string Lowercase More...
utility::vector1< std::string >	quoted_split (std::string const &s)
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	replace_spaces (std::string const &string_w_spaces, std::string const &replacement)
	replace 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...
std::string	Real2string (platform::Real, std::size_t const decimal_places)
	convert a Real to string at a number of decimal places, optionally pad left. More...
std::string	fmt_real (platform::Real, platform::Size const pad_left_newlen, std::size_t const decimal_places)
	convert a Real to a string, padding left with spaces until total number of char on left is equal to pad_lef_n More...
void	string2uint (const std::string &x, unsigned int *const 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...
bool	contains (std::string const &haystack, std::string const &needle)
	Does the string contain the other string? This is purely convenience as I hate the C++ syntax to do this. More...
void	slurp (std::istream &in, std::string &out)
	Take all of the contents from the std::istream "in" and put them in the std::string "out". More...
void	trim (std::string &s, const std::string &drop=" ")
	Remove any charachters in "drop" from the front and back of the string. Use strip() for the value-return version. More...
std::string	strip (std::string const &source, std::string const &drop)
	Return a copy of the string with leading and trailing characters removed Any charachters in drop will be removed For the in place version, see trim() More...
std::string	pad_left (std::string const &s, platform::Size const newlen, char pad_with=' ')
	Add char to the left of the string. More...
std::string	pad_right (std::string const &s, platform::Size const newlen, char pad_with=' ')
	Add char to the right of a string. More...
std::string	strip (std::string const &source, char c=' ')
	Return a copy of the string with leading and trailing characters removed. 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)
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...
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, utility::vector1< std::string > segid_vector, char const delimiter)
std::string	make_segtag_with_dashes (utility::vector1< int > res_vector, utility::vector1< std::string > segid_vector, char const delimiter)
std::string	make_tag (utility::vector1< int > res_vector)
std::tuple< std::vector< int > , std::vector< char > , std::vector< std::string > >	get_resnum_and_chain_and_segid (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...
std::tuple< std::vector< int > , std::vector< char > , std::vector< std::string > >	get_resnum_and_chain (std::string const &s)
	for those who have a legacy interface that can't touch segids. More...
std::pair< std::vector< int > , std::vector< std::string > >	get_resnum_and_segid (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, std::vector< std::string > &segids)
	helper function for get_resnum_and_chain More...
bool	get_resnum_and_segid_from_one_tag (std::string const &tag, std::vector< int > &resnum, std::vector< std::string > &chains)
	helper function for get_resnum_and_chain More...
platform::Size	get_num_digits (platform::Size value)
std::string	replace_in (std::string const &source, std::string const &from, std::string const &to)
	Generate new string from 'source' by replacing all occurrences of 'from' to 'to' string. More...
std::string	remove_from_string (std::string const &source, std::string const &erase_str)
	Call boost to erase all instances of erase_str from source. More...
template<class T >
std::string	to_string (const T &t)
template<>
std::string	to_string< char > (const char &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)
template<class T >
std::string	join (utility::vector1< T > const &vector, std::string const &connector)
	combine vector with anything More...
template<platform::SSize L>
std::string	join (vectorL< L, std::string > const &s, std::string const &connector)
	Join vector of strings in to single string. More...
std::string	trim (std::string const &s, std::string const &drop=" ")
	Ambiguious with the trim( std::string & s ) – Deprecated: use strip() instead for return-value trimming. More...
template<class T >
std::string	pad_left (const T &t, platform::Size const newlen, char pad_width= ' ')
	Add char to the left of the string. More...
template<class T >
std::string	pad_right (const T &t, platform::Size const newlen, char pad_width= ' ')
	Add char to the right of a string. 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)
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...
std::string	timestamp_millis ()
	Generate timestamp string with millis. More...
std::string	timestamp_millis_short ()
	Generate timestamp string with millis, short format. 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 >
void	nmers_worker (utility::vector1< T > const &vec, utility::vector1< T > &combination, utility::vector1< utility::vector1< T > > &power_sets, int const offset, int const kk, int const kk_orig)
	Function invoked by nmers_of (and itself) to generate the power sets of a vector of size kk_orig. More...
template<class T >
utility::vector1 < utility::vector1< T > >	nmers_of (utility::vector1< T > const &vec, int const kk)
	Returns all vector of kk-mer vectors made from combinations of the elements of vec. Returns a vector containing only the empty vector if 0-mers are requested (rather than a zero length vector). 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<typename T >
platform::Size	binary_search_ranges (utility::vector1< T > const &range_array, T query)
	Find the index into the input range array such that range_array[ index ] <= query < range_array[ index + 1 ] or if index+1 would be off the end of the array, then simply the last index in the array (for which range_array[ index ] <= query holds). Each entry in range_array represents the lower boundry (inclusive) for a range, so that range i is defined by ( range_array[ i ], range_array[i+1] - 1 ) except for the last range, which is from range_array[ range_array.size() ] to infinity. T must be a discrete type. range_array must be sorted. range_array[ 1 ] must be as small as the smallest possible query. More...
template<platform::SSize L, typename T >
bool	is_finite (utility::vectorL< L, T > const &vect)
	Are any of the values contained in the vector non-finite (NaN, inf) 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) = nullptr
	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 0.

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

STL Headers.

determines all possible rings in a graph.

Project headers.

#include <iostream> // debug only

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

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

Utility headers

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

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

---

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

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::DateFormat

Enumeration of acceptable date formats.

Enumerator
PDB_FORMAT

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_size
smpi_string
smpi_double
smpi_integers
smpi_sizes
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().

static std::string const utility::ALPHANUMERICS ( LETTERS+  NUMERALS )

static

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 test.T200_Scoring::ii, and insert_middle().

Referenced by analyze_poses_for_convergence().

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 test.T200_Scoring::ii, and 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 test.T200_Scoring::ii.

Referenced by MetalSiteFinderMover::apply().

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 test.T200_Scoring::ii.

Referenced by MetalSiteFinderMover::apply(), and numeric::geometry::vector_normal_to_ring_plane_of_best_fit().

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).

Referenced by MPDomainAssembly::apply().

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).

template<platform::SSize L, typename T >

utility::vector1< platform::Size > utility::argsort

(

utility::vectorL< L, T > const &

v

)

References ObjexxFCL::format::L(), and test.T850_SubClassing::v.

Referenced by fractional_rank().

template<typename T >

platform::Size utility::binary_search_ranges	(	utility::vector1< T > const &	range_array,
		T	query
	)

Find the index into the input range array such that range_array[ index ] <= query < range_array[ index + 1 ] or if index+1 would be off the end of the array, then simply the last index in the array (for which range_array[ index ] <= query holds). Each entry in range_array represents the lower boundry (inclusive) for a range, so that range i is defined by ( range_array[ i ], range_array[i+1] - 1 ) except for the last range, which is from range_array[ range_array.size() ] to infinity. T must be a discrete type. range_array must be sorted. range_array[ 1 ] must be as small as the smallest possible query.

References lower(), and upper().

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,
		char 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().

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

Does the string contain the other string? This is purely convenience as I hate the C++ syntax to do this.

References make_symmdef_file_denovo::pos.

Referenced by SphereGrinder().

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().

CSI_Sequence utility::CSI_bgBlack ( )

inline

References utility::CSI::bgBlack.

CSI_Sequence utility::CSI_bgBlue ( )

inline

References utility::CSI::bgBlue.

CSI_Sequence utility::CSI_bgCyan ( )

inline

References utility::CSI::bgCyan.

CSI_Sequence utility::CSI_bgDefault ( )

inline

References utility::CSI::bgDefault.

CSI_Sequence utility::CSI_bgGreen ( )

inline

References utility::CSI::bgGreen.

CSI_Sequence utility::CSI_bgMagenta ( )

inline

References utility::CSI::bgMagenta.

CSI_Sequence utility::CSI_bgRed ( )

inline

References utility::CSI::bgRed.

CSI_Sequence utility::CSI_bgWhite ( )

inline

References utility::CSI::bgWhite.

CSI_Sequence utility::CSI_bgYellow ( )

inline

References utility::CSI::bgYellow.

CSI_Sequence utility::CSI_Black ( )

inline

References utility::CSI::Black.

CSI_Sequence utility::CSI_Blue ( )

inline

References utility::CSI::Blue.

CSI_Sequence utility::CSI_Bold ( )

inline

References utility::CSI::Bold.

Referenced by exit(), and handle_assert_failure().

CSI_Sequence utility::CSI_Cyan ( )

inline

References utility::CSI::Cyan.

CSI_Sequence utility::CSI_Default ( )

inline

References utility::CSI::Default.

CSI_Sequence utility::CSI_Green ( )

inline

References utility::CSI::Green.

CSI_Sequence utility::CSI_Magenta ( )

inline

References utility::CSI::Magenta.

CSI_Sequence utility::CSI_Nothing ( )

inline

Functions to return CSI_Seqeunce objects. These are not static constants, due to the static initilization order fiasco.

References utility::CSI::Nothing.

Referenced by basic::TracerImpl::TracerImpl().

CSI_Sequence utility::CSI_Red ( )

inline

References utility::CSI::Red.

Referenced by exit(), and handle_assert_failure().

CSI_Sequence utility::CSI_Reset ( )

inline

References utility::CSI::Reset.

Referenced by exit(), and handle_assert_failure().

CSI_Sequence utility::CSI_Underline ( )

inline

References utility::CSI::Underline.

CSI_Sequence utility::CSI_White ( )

inline

References utility::CSI::White.

CSI_Sequence utility::CSI_Yellow ( )

inline

References utility::CSI::Yellow.

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, and basic::options::OptionKeys::in::file::s.

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, and basic::options::OptionKeys::score::fiber_diffraction::p.

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

References encode_24_to_32(), and make_symmdef_file_denovo::length.

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	(	char const *	file,
		int const	line,
		std::string const &	message,
		int const	status
	)

Exit with file + line + message + optional status.

References begin, utility::io::oc::cerr, utility::io::izstream::close(), CSI_Bold(), CSI_Red(), CSI_Reset(), erraser_single_res_analysis::data, utility::io::ocstream::flush(), get_all_exit_callbacks(), ObjexxFCL::getline(), utility::file::gzip(), main_exit_callback, maybe_throw_on_next_assertion_failure(), test.T008_Serialization::oss, and print_backtrace().

Referenced by cond_exit(), exit(), main(), print_ddgs(), and rhiju_pdbstats().

void utility::exit ( char const *  file, int const  line, int const  status = 1  )

inline

Exit with file + line + optional status.

References exit().

void utility::exit ( int const  status, char 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().

Referenced by composite_sequences_from_cmd_line(), main(), poses_from_cmd_line(), and sequences_from_cmd_line().

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(), CREATE_EXCEPTION, ObjexxFCL::getline(), test.T200_Scoring::ii, line, and utility::options::OptionKeys::options::table::text.

Referenced by convert(), utility::io::GeneralFileContents::GeneralFileContents(), utility::io::FileContentsMap::get_file_contents(), utility::io::FileContentsMap::get_file_contents_ref(), basic::resource_manager::ResourceManager::initialize_from_commandline(), and reverse_convert().

std::string utility::filename

(

const std::string &

path

)

References utility::file::FileName::base(), utility::file::FileName::extension(), and demo.D060_Folding::f.

Referenced by utility::io::mpi_stream::basic_mpi_streambuf< Elem, Tr, ElemA, ByteT, ByteAT >::basic_mpi_streambuf(), utility::io::GeneralFileManager::create_instance(), 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.

References assign_charges::first.

std::string utility::fmt_real	(	platform::Real	num,
		platform::Size	pad_left_n,
		std::size_t const	decimal_places
	)

convert a Real to a string, padding left with spaces until total number of char on left is equal to pad_lef_n

References pad_left(), Real2string(), and basic::options::OptionKeys::in::file::s.

template<platform::SSize L, typename T >

utility::vector1< platform::Real > utility::fractional_rank

(

utility::vectorL< L, T > const &

v

)

Return the fractional rank of a list of numbers.

References argsort(), basic::options::OptionKeys::frags::j, and value.

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

template<class T >

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

inline

References name, basic::options::OptionKeys::mh::match::ss, test.T007_TracerIO::T, basic::options::OptionKeys::in::file::t, DRRAFTER::type, 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().

std::string utility::get_current_date

(

DateFormat const

format

)

Return current date in the requested format.

References version::date, PDB_FORMAT, and basic::options::OptionKeys::in::file::t.

platform::Size utility::get_num_digits

(

platform::Size

value

)

std::tuple< std::vector< int >, std::vector< char >, std::vector< std::string > > utility::get_resnum_and_chain

(

std::string const &

s

)

for those who have a legacy interface that can't touch segids.

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

References get_resnum_and_chain_and_segid().

std::tuple< std::vector< int >, std::vector< char >, std::vector< std::string > > utility::get_resnum_and_chain_and_segid	(	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 basic::options::OptionKeys::run::chain, get_resnum_and_chain_from_one_tag(), replace_in(), clean_pdb_keep_ligand::resnum, string_split(), and basic::options::OptionKeys::in::file::tags.

Referenced by get_resnum_and_chain(), 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,
		std::vector< std::string > &	segids
	)

helper function for get_resnum_and_chain

References basic::options::OptionKeys::run::chain, clean_pdb_keep_ligand::count, and ObjexxFCL::ints_of().

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

std::pair< std::vector< int >, std::vector< std::string > > utility::get_resnum_and_segid	(	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.

References get_resnum_and_segid_from_one_tag(), replace_in(), clean_pdb_keep_ligand::resnum, tag, and basic::options::OptionKeys::in::file::tags.

bool utility::get_resnum_and_segid_from_one_tag	(	std::string const &	tag,
		std::vector< int > &	resnum,
		std::vector< std::string > &	segids
	)

helper function for get_resnum_and_chain

References ObjexxFCL::ints_of(), and runtime_assert.

Referenced by get_resnum_and_segid().

platform::Real utility::get_undefined_real ( )

inline

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

References max().

Referenced by is_undefined(), and 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 test.T200_Scoring::ii, and swap().

Referenced by arg_greatest_several(), and arg_least_several().

bool utility::is_false_string

(

std::string const &

value_str

)

String accepted as a false value?

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

template<platform::SSize L, typename T >

bool utility::is_finite

(

utility::vectorL< L, T > const &

vect

)

Are any of the values contained in the vector non-finite (NaN, inf)

References isfinite(), and test.T850_SubClassing::v.

bool utility::is_string_numeric

(

std::string const &

input

)

bool utility::is_true_string

(

std::string const &

value_str

)

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 get_undefined_real(), isinf(), and isnan().

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

inline

Referenced by is_finite(), numeric::xyzVector< core::Real >::is_finite(), and numeric::xyzMatrix< T >::is_finite().

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

inline

Referenced by is_undefined(), and numeric::statistics::w().

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

inline

Referenced by numeric::xyzTransform< numeric::Real >::bad(), numeric::xyzTransform< numeric::Real >::badfast(), numeric::statistics::Dawson(), numeric::statistics::errf(), is_undefined(), main(), numeric::xyzTransform< numeric::Real >::rt6(), and numeric::statistics::w().

template<class T >

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

combine vector with anything

References begin.

template<platform::SSize L>

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

Join vector of strings in to single string.

References begin.

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

combine strings with anything

References begin.

Referenced by basic::database::make_compound_statement(), and replace_spaces().

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

combine strings with anything

References begin.

static std::string const utility::LETTERS ( UPPERCASE_LETTERS+  LOWERCASE_LETTERS )

static

std::string utility::lower

(

std::string const &

s

)

Make a string Lowercase

References basic::options::OptionKeys::in::file::s, and basic::options::OptionKeys::mp::transform::transform.

Referenced by numeric::random::binary_search_cdf(), binary_search_ranges(), numeric::geometry::hashing::SixDCoordinateBinner::bounding_volume_from_index(), numeric::interpolation::Histogram< typename, typename >::derivative_linear(), erraser_wrapper::erraser_minimize(), erraser_util::extract_pdb(), numeric::kdtree::get_percentile_bounds(), numeric::kdtree::hr_intersects_hs(), numeric::interpolation::Histogram< typename, typename >::interpolate_linear(), numeric::kdtree::nearest_neighbor(), erraser_util::rna_rosetta_ready_set(), erraser_wrapper::seq_rebuild_new(), erraser_wrapper::SWA_rebuild_erraser(), numeric::kdtree::transform_percentile(), and numeric::kdtree::transform_percentile_single_pt().

static std::string const utility::LOWERCASE_ALPHANUMERICS ( LOWERCASE_LETTERS+  NUMERALS )

static

static std::string const utility::LOWERCASE_LETTERS ( "abcdefghijklmnopqrstuvwxyz"  )

static

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

References runtime_assert, amino_acids::size, ObjexxFCL::string_of(), and tag.

std::string utility::make_tag

(

utility::vector1< int >

res_vector

)

References ObjexxFCL::string_of(), and 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".

References chains.

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

References runtime_assert, ObjexxFCL::string_of(), strip(), and tag.

template<class K , class V >

void utility::map_merge	(	std::map< K, V > &	destination_map,
		std::map< K, V > const &	source_map
	)

Append the second map to the first For one-liner convenience (esp. for map return values.)

In C++17 this is std::map::merge(), but until then ...

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 test.T200_Scoring::ii.

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

inline

max( short int, short int )

Referenced by MetalSiteFinderMover::apply(), and 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 )

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 )

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 test.T200_Scoring::ii.

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().

platform::Size utility::modulo ( int const &  a, int const &  b  )

inline

modulo of an input integer a (can be negative) with respect to unsigned integer b

Most folks use C's "a % b" operator but it gives funny behavior for negative a. This version came out of stack overflow.

References ObjexxFCL::abs().

Referenced by numeric::interpolation::get_val().

int utility::mpi_nprocs

(

)

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

Referenced by basic::TracerImpl::calculate_visibility(), and main().

int utility::mpi_rank

(

)

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

Referenced by basic::TracerImpl::calculate_visibility(), main(), 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, smpi_size, smpi_sizes, and smpi_string.

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

template<class T >

utility::vector1< utility::vector1< T > > utility::nmers_of	(	utility::vector1< T > const &	vec,
		int const	kk
	)

Returns all vector of kk-mer vectors made from combinations of the elements of vec. Returns a vector containing only the empty vector if 0-mers are requested (rather than a zero length vector).

References nmers_worker().

template<class T >

void utility::nmers_worker	(	utility::vector1< T > const &	vec,
		utility::vector1< T > &	combination,
		utility::vector1< utility::vector1< T > > &	power_sets,
		int const	offset,
		int const	kk,
		int const	kk_orig
	)

Function invoked by nmers_of (and itself) to generate the power sets of a vector of size kk_orig.

References test.T200_Scoring::ii.

Referenced by nmers_of().

static std::string const utility::NUMERALS ( "0123456789"  )

static

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.

References basic::options::OptionKeys::in::file::s.

template<typename B >

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

BitVector + BitVector: Union.

References basic::options::OptionKeys::score::fiber_diffraction::b, and basic::options::OptionKeys::in::file::s.

template<typename B >

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

BitSet - BitSet: Difference.

References test.T009_Exceptions::e, and basic::options::OptionKeys::in::file::s.

template<typename B >

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

BitVector - BitVector: Difference.

References basic::options::OptionKeys::score::fiber_diffraction::b, and basic::options::OptionKeys::in::file::s.

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 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,
		vectorL< L, T, A > const &	b
	)

vectorL < 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, class T , typename std::enable_if< utility::type_traits::has_insertion_operator_s< T >::value >::type * = nullptr>

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

Output function for utility::vectorL object.

References test.T850_SubClassing::v.

template<class T , platform::Size S>

std::ostream& utility::operator<<	(	std::ostream &	os,
		utility::fixedsizearray1< T, S > const &	v
	)

Output function for utility::fixedsizearray0 object.

References test.T850_SubClassing::v.

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 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,
		vectorL< L, T, A > const &	b
	)

vectorL >= 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.

References basic::options::OptionKeys::in::file::s.

template<typename B >

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

BitVector | BitVector: Union.

References basic::options::OptionKeys::score::fiber_diffraction::b, and basic::options::OptionKeys::in::file::s.

template<class T >

std::string utility::pad_left	(	const T &	t,
		platform::Size const	newlen,
		char	pad_width = ' '
	)

Add char to the left of the string.

References pad_left(), basic::options::OptionKeys::in::file::s, and to_string().

std::string utility::pad_left	(	std::string const &	s,
		platform::Size const	newlen,
		char	pad_with
	)

Add char to the left of the string.

References basic::options::OptionKeys::ufv::right, and basic::options::OptionKeys::in::file::s.

Referenced by fmt_real(), and pad_left().

template<class T >

std::string utility::pad_right	(	const T &	t,
		platform::Size const	newlen,
		char	pad_width = ' '
	)

Add char to the right of a string.

References pad_right(), basic::options::OptionKeys::in::file::s, and to_string().

std::string utility::pad_right	(	std::string const &	s,
		platform::Size const	newlen,
		char	pad_with
	)

Add char to the right of a string.

References basic::options::OptionKeys::ufv::left, and basic::options::OptionKeys::in::file::s.

Referenced by pad_right().

std::string utility::pathname

(

const std::string &

path

)

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

void utility::print_message	(	SimulateMPIMessageCOP	msg,
		std::ostream &	os
	)

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

Referenced by utility::SimulateMPI::print_unprocessed_incoming_messages(), and utility::SimulateMPI::print_unprocessed_outgoing_messages().

utility::vector1< std::string > utility::quoted_split

(

std::string const &

s

)

Split a string by whitespace, but obey single and double quote marks, like the bash commandline

References test.T200_Scoring::ii, and basic::options::OptionKeys::cutoutdomain::start.

Referenced by utility::options::VectorOption::set_value().

void utility::rand_sleep

(

)

References sys_sleep().

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

std::string utility::Real2string	(	platform::Real	num,
		std::size_t const	decimal_places
	)

convert a Real to string at a number of decimal places, optionally pad left.

References basic::options::OptionKeys::optE::fixed.

Referenced by fmt_real().

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().

Referenced by main().

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().

Referenced by main().

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().

platform::Size utility::receive_size_from_node

(

int

source

)

Use MPI to receive a single unsigned (usually 64-bit) integer from a particular node.

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

utility::vector1< platform::Size > utility::receive_sizes_from_node

(

int

source

)

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

References utility::SimulateMPI::receive_sizes_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::mpi::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 begin, and get_all_exit_callbacks().

std::string utility::remove_from_string	(	std::string const &	source,
		std::string const &	remove
	)

Call boost to erase all instances of erase_str from source.

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::cutoutdomain::end, basic::options::OptionKeys::cutoutdomain::start, 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
	)

Generate new string from 'source' by replacing all occurrences of 'from' to 'to' string.

References name, and make_symmdef_file_denovo::pos.

Referenced by get_resnum_and_chain_and_segid(), get_resnum_and_segid(), mg_modeler_test(), numeric::read_tensor_from_file(), rna_score_test(), and numeric::write_tensor_to_file().

std::string utility::replace_spaces	(	std::string const &	string_w_spaces,
		std::string const &	replacement
	)

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

References join(), and split().

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

inline

References round().

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().

Referenced by main().

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_size_to_node	(	int	destination,
		platform::Size	message
	)

Use MPI to send a single unsigned (usually 64-bit) integer to a particular node.

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

void utility::send_sizes_to_node	(	int	destination,
		utility::vector1< platform::Size > const &	message
	)

References utility::SimulateMPI::send_sizes_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::mpi::request_data_from_head_node(), and basic::mpi::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
	)

Take all of the contents from the std::istream "in" and put them in the std::string "out".

Useful for reading the full contents of a file into a string.

References basic::options::OptionKeys::cloud::block.

Referenced by basic::resource_manager::ResourceManager::initialize_from_commandline().

utility::vector1< std::string > utility::split

(

const std::string &

s

)

split given std::string using ' ' symbol.

References numeric::add(), and basic::options::OptionKeys::cutoutdomain::start.

Referenced by basic::mpi::DbMoverMessageListener::deserialize_data(), replace_spaces(), and basic::TracerImpl::set_ios_hook().

std::vector< std::string > utility::split_by_newlines

(

std::string const &

s

)

Note

This function also removes empty lines.

Split string by new line symbols, return vector of string.

References basic::options::OptionKeys::score::empty, and basic::options::OptionKeys::cutoutdomain::start.

std::list< std::string > utility::split_to_list

(

const std::string &

s

)

split given std::string using ' ' symbol.

split given std::string using ' ' symbol.

References numeric::add(), and basic::options::OptionKeys::cutoutdomain::start.

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(), and basic::options::OptionKeys::cutoutdomain::start.

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.

References test.T009_Exceptions::e, and basic::options::OptionKeys::mh::match::ss.

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

True iff haystack starts with needle.

bool utility::stdout_is_tty

(

)

Referenced by utility::CSI_Sequence::suppress_CSI_seq().

float utility::string2float

(

std::string

st

)

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

convert a string to a float

References basic::options::OptionKeys::mh::match::ss.

int utility::string2int

(

std::string

st

)

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

convert a string to an int

References basic::options::OptionKeys::mh::match::ss.

Referenced by basic::TracerImpl::calculate_tracer_level(), and basic::mpi::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(), and basic::options::OptionKeys::mh::match::ss.

platform::Size utility::string2Size

(

std::string

st

)

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

References get_undefined_size(), and basic::options::OptionKeys::mh::match::ss.

Referenced by apps::pilot::frankdt::import_motifs().

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

References debug_assert, basic::options::OptionKeys::mh::match::ss, and numeric::crick_equations::y().

template<class T >

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

inline

References basic::options::OptionKeys::frags::j, name, basic::options::OptionKeys::mh::match::ss, test.T007_TracerIO::T, basic::options::OptionKeys::in::file::t, DRRAFTER::type, and utility_exit_with_message.

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

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

References basic::options::OptionKeys::frags::j.

Referenced by calc_scores(), basic::TracerImpl::calculate_tracer_level(), numeric::comma_seperated_string_to_xyz(), get_resnum_and_chain_and_segid(), utility::xsd_util::get_tag_name(), basic::resource_manager::locator::FileListResourceLocator::locate_resource_stream(), main(), basic::resource_manager::locator::FileSystemResourceLocator::parse_my_tag(), ScoreFragmentSetMover::run(), ConsensusFragmentMover::run(), SolutionRescoreMover::run(), utility::tag::XMLErrorHandler::set_file_contents(), and numeric::interpolation::spline_from_file().

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

References basic::options::OptionKeys::frags::j.

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)

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

References basic::options::OptionKeys::frags::j.

Referenced by MetalSiteFinderMover::apply(), and main().

std::string utility::string_to_sha1

(

std::string const &

input_string

)

References fmt::hex().

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

Return a copy of the string with leading and trailing characters removed Any charachters in drop will be removed For the in place version, see trim()

References trim().

Referenced by utility::xsd_util::generate_human_readable_documentation(), make_tag_with_dashes(), and trim().

std::string utility::strip	(	std::string const &	source,
		char	c
	)

Return a copy of the string with leading and trailing characters removed.

References begin, basic::options::OptionKeys::cutoutdomain::end, and basic::options::OptionKeys::score::fiber_diffraction::p.

template<typename B >

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

swap( BitSet, BitSet )

Referenced by swap().

template<typename B >

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

swap( BitVector, BitVector )

template<typename U >

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

swap( BitVector, BitVector )

template<platform::SSize L, typename A >

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

swap( vectorL, vectorL )

References basic::options::OptionKeys::score::fiber_diffraction::a, and swap().

template<platform::SSize L, typename A >

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

swap( vectorL, std::vector )

References basic::options::OptionKeys::score::fiber_diffraction::a, and swap().

template<platform::SSize L, typename A >

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

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 )

References basic::options::OptionKeys::score::fiber_diffraction::a, and swap().

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 )

References basic::options::OptionKeys::score::fiber_diffraction::a, and swap().

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

References erraser_single_res_analysis::data.

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::TracerImpl::prepend_channel_name(), timestamp_millis(), timestamp_millis_short(), and timestamp_short().

std::string utility::timestamp_millis

(

)

Generate timestamp string with millis.

References basic::options::OptionKeys::ms::ms, basic::options::OptionKeys::in::file::s, basic::options::OptionKeys::in::file::t, and timestamp().

std::string utility::timestamp_millis_short

(

)

Generate timestamp string with millis, short format.

References basic::options::OptionKeys::ms::ms, basic::options::OptionKeys::in::file::s, basic::options::OptionKeys::in::file::t, and timestamp().

std::string utility::timestamp_short

(

)

Generate timestamp string, short format.

References timestamp().

template<class T >

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

inline

References basic::options::OptionKeys::mh::match::ss, and basic::options::OptionKeys::in::file::t.

Referenced by IdentifyCDRClusters::apply(), utility::graph::block_allocation_error_message(), calc_rama_scores(), apps::pilot::frankdt::compare_segment_to_motif(), numeric::expression_parser::ExpressionCreator::handle_function_expression(), numeric::expression_parser::SimpleExpressionCreator::handle_variable_expression(), apps::pilot::frankdt::import_motifs(), utility::tag::integer_range_restriction(), utility::tag::XMLErrorHandler::lines_near_error(), main(), make_fragments(), utility::graph::neg_space_element_allocation_error_message(), zinc_stats::ZincStatisticGenerator::output_file(), pad_left(), pad_right(), utility::SimulateMPIData::pop_next_message_for_node_of_type(), utility::SimulateMPIData::pop_next_message_of_type(), Prepare(), utility::tag::XMLSchemaComplexTypeGeneratorImpl::prepare_subelement_single_instance_optional(), basic::database::schema_generator::DbText::print(), read_native_sequence_for_entity_elements(), basic::mpi::DbMoverMessageListener::request(), utility::SimulateMPIData::retrieve_next_message(), apps::pilot::frankdt::reverse_motif(), DockFragmentsMover::run(), numeric::expression_parser::ArithmeticScanner::scan(), numeric::expression_parser::ArithmeticScanner::scan_identifier(), numeric::expression_parser::ArithmeticScanner::scan_literal(), utility::subset_mapping::set_next_correspondence(), show(), apps::pilot::frankdt::store_segment_motif_match(), numeric::expression_parser::LiteralToken::to_string(), numeric::expression_parser::FunctionToken::to_string(), numeric::xyzVector< core::Real >::to_string(), numeric::Quaternion< T >::to_string(), and numeric::expression_parser::ExpressionCreator::visit().

template<>

std::string utility::to_string< char > ( const char &  t )

inline

References basic::options::OptionKeys::in::file::t.

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

inline

Ambiguious with the trim( std::string & s ) – Deprecated: use strip() instead for return-value trimming.

References strip().

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

Remove any charachters in "drop" from the front and back of the string. Use strip() for the value-return version.

Referenced by utility::io::get_lines_from_file_data(), spanfile_for_each_chain(), spanfile_from_pdb(), strip(), and basic::database::write_schema_to_database().

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

compares two strings ignoring leading and trailing spaces

compares two strings ignoring leading and trailing spaces

References ObjexxFCL::space().

std::string utility::upper

(

std::string const &

s

)

Make a string Uppercase.

References basic::options::OptionKeys::in::file::s, and basic::options::OptionKeys::mp::transform::transform.

Referenced by numeric::random::binary_search_cdf(), binary_search_ranges(), numeric::geometry::hashing::SixDCoordinateBinner::bounding_volume_from_index(), numeric::interpolation::Histogram< typename, typename >::derivative_linear(), numeric::kdtree::get_percentile_bounds(), numeric::kdtree::hr_intersects_hs(), numeric::interpolation::Histogram< typename, typename >::interpolate_linear(), pdb_to_molfile::main(), sidechain_cst_3::main(), arls_impl::main(), numeric::kdtree::nearest_neighbor(), numeric::kdtree::transform_percentile(), numeric::kdtree::transform_percentile_single_pt(), and fmt::BasicWriter< Char >::write_double().

static std::string const utility::UPPERCASE_ALPHANUMERICS ( UPPERCASE_LETTERS+  NUMERALS )

static

static std::string const utility::UPPERCASE_LETTERS ( "ABCDEFGHIJKLMNOPQRSTUVWXYZ"  )

static

Variable Documentation

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

static

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

Referenced by exit(), and set_main_exit_callback().