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...

class	deep_copy_vector1

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...

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

struct	RawType< T & >

struct	RawType< T * >

struct	UtilityExitException

class	fixedsizearray0

class	fixedsizearray1

class	FixedSizeLexicographicalIterator

class	heap

class	list_element

class	in_place_list

class	predicate_cmp_filename

class	Inline_File_Provider_Hook

class	Inline_File_Provider

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

class	Enumerate1

class	SimpleRange1

class	LexicographicalIterator

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

struct	history_queue_struct

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	SimulateMPIMessage

class	SimulateMPIData

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

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...

class	small_vectorL

struct	SortFirst

struct	SortSecond

struct	StrongT

class	VBWrapper

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...

struct	Version

class	VirtualBase
	Base class for Polymorphic classes All classes in Rosetta used polymorphically (that is, where a pointer/reference to a base type can point/reference a derived type) should inherit from this class. More...

Typedefs
typedef void(*	UtilityExitCallBack) ()

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

template<typename T , std::size_t BUFFER_SIZE>
using	small_vector0 = small_vectorL< T, 0, BUFFER_SIZE >

template<typename T , std::size_t BUFFER_SIZE>
using	small_vector1 = small_vectorL< T, 1, BUFFER_SIZE >

template<typename Key >
using	StrongReal = StrongT< platform::Real, Key >

template<typename Key >
using	StrongSize = StrongT< platform::Size, Key >

typedef utility::pointer::shared_ptr< VirtualBase >	VirtualBaseOP

typedef utility::pointer::shared_ptr< VirtualBase const >	VirtualBaseCOP

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	swap4_aligned (void *v, long ndata)

void	encode6bit (const unsigned char *memory, unsigned int length, std::string &jar)
	Given a block of memory (with memory pointing to the first byte) and a byte count (length), convert every three bytes of memory into four bytes of ASCII characters, and populate the string (jar) with those characters. More...

platform::Size	decode6bit (unsigned char *memory, std::string const &jar, platform::Size const maxbytes)
	Given 3N bytes of memory to fill, and a string containing 4N characters, decode the characters (interpreting 4 bytes of ASCII text as 3 binary bytes) and populate the block of memory. More...

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 short goodbytes)

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...

static std::string const	CRASH_FILE ("ROSETTA_CRASH.log")

static std::string	APPNAME ("UNKNOWN APPLICATION")

static std::string	OPTIONS ("NO OPTIONS SPECIFIED")

static std::string const	HEADER ("##############################################################################################################\n" "#\n" "# Rosetta crash log. Please submit the contents of this file to http://crash.rosettacommons.org/\n" "# or use the script Rosetta/main/source/scripts/python/public/report_crashes.py\n" "#\n\n")

void	signal_handler (int signal)

void	terminate_handler ()

void	install_crash_handler ()
	Set the crash handler for non-standard crashes (e.g. segfaults) Should only be called once at startup. More...

void	set_application_name (char const *appname)
	Set the application name that this was launched as. Should only be called once on startup. More...

void	set_options_string (std::string const &options)
	Set the string representation of the options to be used in the crash report Should only be called once on startup. More...

void	set_show_crash_report_on_console (bool setting)
	If passed true, any backtrace will show up on stderr in addition to the crash report file. More...

void	save_crash_report (char const *message="(none)", std::string const &file="(none)", int const line=0)
	Save a crash report to the crash reporter file. More...

void	save_crash_report (char const *message, std::string const &file, int line, std::string const &traceback)

void	save_crash_report_to_file (char const *message, std::string const &file, int line, std::string const &traceback)

void	save_crash_report_to_console (char const *, std::string const &, int, std::string const &traceback)

void	save_crash_report (std::string const &message, std::string const &file="(none)", int const line=0)
	Save a crash report to the crash reporter file. More...

void	save_crash_report (std::string const &message, std::string const &file, int const line, std::string const &traceback)

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=nullptr)
	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 nullptr, 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_handler (char const *file, int const line, std::string const &message)

void	exit_with_user_fixable_issue (char const *file, int line, std::string const &message)
	Exit in cases where there's a clear issue the user can fix. More...

void	exit (char const *file, int const line, std::string const &message, int const)
	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...

NORETURN_ATTR void	exit (char const *file, int const line, int const status=1)
	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...

SimpleRange1	enumerate1 (platform::Size const max_inclusive)
	iterate from [1, max_inclusive] More...

template<typename T >
SimpleRange1	indices1 (utility::vector1< T > const &v)
	iterate from [1, c.size()] 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)

std::string	payload (SimulateMPIMessageOP msg)

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 >	string_vector_from_char_vector (utility::vector1< char > const &char_vect)

bool	parse_boolean (std::stringstream &stream, std::string const &errmsg)
	Given a stringstream in which the next block of text is any string representing "true" or any string representing "false", parse this as a Boolean, and return an informative error message if we fail. More...

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)
	@breif 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 const &st)
	convert a string to a float, returns -1 on failure More...

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

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

platform::Real	string2Real (std::string const &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)
	@breif 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	ltrim (std::string &s, const std::string &drop)
	Remove any characters in "drop" from the front of the string. More...

void	rtrim (std::string &s, const std::string &drop)
	Remove any characters in "drop" from the back of the string. 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_atom_name (std::string const &s)
	Pad an atom name to the pdb format. 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< utility::vector1< int >, utility::vector1< char >, utility::vector1< 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< utility::vector1< int >, utility::vector1< char >, utility::vector1< 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, utility::vector1< int > &resnum, utility::vector1< char > &chains, utility::vector1< 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	replace_first_in (std::string const &source, std::string const &from, std::string const &to)
	Generate new string from 'source' by replacing the first occurrence 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...

void	copy_to_cstr_buffer (std::string const &str, char *buffer, platform::Size buffer_length)
	Copy the contents of a string to a given C-style string buffer (with the given maximum length) The output will be truncated if greater than length, and null terminator will be added. 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 >
void	parse_out (std::stringstream &stream, T &recipient, std::string const &errmsg)
	Parse out some data of type T from a stringstream, and throw an error with a message if the operation fails. More...

template<class T >
void	parse_out (std::stringstream &stream, T &recipient)
	Parse out some data of type T from a stringstream, and throw an error with a message if the operation fails. More...

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 >
utility::pointer::shared_ptr< VBWrapper< T > >	make_shared_vb_wrapper (T val)

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	max2 (vector1< T > const &input)
	Find the second 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 >
T	min2 (vector1< T > const &input)
	Find the SECOND 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 bool	show_crash_report_on_console_ = false

std::terminate_handler	old_terminate_handler_ = nullptr

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.

#include <iostream> // debug only

determines all possible rings in a graph.

Project headers.

#include <iosfwd> // 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

◆ heapCOP

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

◆ heapOP

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

◆ Inline_File_Provider_HookCOP

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

◆ Inline_File_Provider_HookOP

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

◆ SimulateMPIMessageCOP

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

◆ SimulateMPIMessageOP

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

◆ small_vector0

template<typename T , std::size_t BUFFER_SIZE>

using utility::small_vector0 = typedef small_vectorL< T, 0, BUFFER_SIZE >

◆ small_vector1

template<typename T , std::size_t BUFFER_SIZE>

using utility::small_vector1 = typedef small_vectorL< T, 1, BUFFER_SIZE >

◆ StrongReal

template<typename Key >

using utility::StrongReal = typedef StrongT< platform::Real, Key >

◆ StrongSize

template<typename Key >

using utility::StrongSize = typedef StrongT< platform::Size, Key >

◆ subset_mappingCOP

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

◆ subset_mappingOP

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

◆ UtilityExitCallBack

typedef void(* utility::UtilityExitCallBack) ()

◆ vector0_bool

typedef vector0< bool > utility::vector0_bool

◆ vector0_char

typedef vector0< char > utility::vector0_char

◆ vector0_double

typedef vector0< double > utility::vector0_double

◆ vector0_float

typedef vector0< float > utility::vector0_float

◆ vector0_int

typedef vector0< int > utility::vector0_int

◆ vector0_long

typedef vector0< long int > utility::vector0_long

◆ vector0_longdouble

typedef vector0< long double > utility::vector0_longdouble

◆ vector0_schar

typedef vector0< signed char > utility::vector0_schar

◆ vector0_short

typedef vector0< short int > utility::vector0_short

◆ vector0_size

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

◆ vector0_size_t

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

◆ vector0_ssize

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

◆ vector0_ssize_t

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

◆ vector0_uchar

typedef vector0< unsigned char > utility::vector0_uchar

◆ vector0_uint

typedef vector0< unsigned int > utility::vector0_uint

◆ vector0_ulong

typedef vector0< unsigned long int > utility::vector0_ulong

◆ vector0_ushort

typedef vector0< unsigned short int > utility::vector0_ushort

◆ vector1_bool

typedef vector1< bool > utility::vector1_bool

◆ vector1_char

typedef vector1< char > utility::vector1_char

◆ vector1_double

typedef vector1< double > utility::vector1_double

◆ vector1_float

typedef vector1< float > utility::vector1_float

◆ vector1_int

typedef vector1< int > utility::vector1_int

◆ vector1_long

typedef vector1< long int > utility::vector1_long

◆ vector1_longdouble

typedef vector1< long double > utility::vector1_longdouble

◆ vector1_schar

typedef vector1< signed char > utility::vector1_schar

◆ vector1_short

typedef vector1< short int > utility::vector1_short

◆ vector1_size

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

◆ vector1_size_t

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

◆ vector1_ssize

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

◆ vector1_ssize_t

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

◆ vector1_uchar

typedef vector1< unsigned char > utility::vector1_uchar

◆ vector1_uint

typedef vector1< unsigned int > utility::vector1_uint

◆ vector1_ulong

typedef vector1< unsigned long int > utility::vector1_ulong

◆ vector1_ushort

typedef vector1< unsigned short int > utility::vector1_ushort

◆ VirtualBaseCOP

typedef utility::pointer::shared_ptr< VirtualBase const > utility::VirtualBaseCOP

◆ VirtualBaseOP

typedef utility::pointer::shared_ptr< VirtualBase > utility::VirtualBaseOP

Enumeration Type Documentation

◆ DateFormat

enum utility::DateFormat

Enumeration of acceptable date formats.

Enumerator
PDB_FORMAT

◆ simulate_mpi_message_type

enum utility::simulate_mpi_message_type

@detail 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

◆ add_exit_callback()

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().

◆ ALPHANUMERICS()

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

static

◆ APPNAME()

static std::string utility::APPNAME ( "UNKNOWN APPLICATION" )

static

Referenced by save_crash_report_to_file(), and set_application_name().

◆ arg_greatest_several()

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 create_a3b_hbs::ii, gaussian-sampling::input, insert_middle(), beta_nonlocal::jj, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::n.

Referenced by analyze_poses_for_convergence(), and main().

◆ arg_least_several()

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 create_a3b_hbs::ii, gaussian-sampling::input, insert_middle(), beta_nonlocal::jj, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::n.

Referenced by main().

◆ arg_max()

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, create_a3b_hbs::ii, and gaussian-sampling::input.

Referenced by MetalSiteFinderMover::apply(), main(), and numeric::linear_algebra::minimum_bounding_ellipse().

◆ arg_min()

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, create_a3b_hbs::ii, and gaussian-sampling::input.

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

◆ argmax() [1/2]

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().

◆ argmax() [2/2]

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).

◆ argmin() [1/2]

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).

Referenced by main().

◆ argmin() [2/2]

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).

◆ argsort()

template<platform::SSize L, typename T >

utility::vector1< platform::Size > utility::argsort ( utility::vectorL< L, T > const & v )

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::idx, spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::L, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

Referenced by fractional_rank().

◆ binary_search_ranges()

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(), cache_trajectory::query, and upper().

◆ code_from_6bit()

unsigned char utility::code_from_6bit ( unsigned char _8bit )

inline

Referenced by decode_32_to_24().

◆ code_to_6bit()

unsigned char utility::code_to_6bit ( unsigned char _6bit )

inline

uuencode

Referenced by encode_24_to_32().

◆ cond_exit()

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(), evaluate_beta_mutants::file, line, and pyrosetta.utility.array::message.

◆ contains()

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 lactamize::find_lactams(), SphereGrinder(), and test_Vec().

◆ copy_to_cstr_buffer()

void utility::copy_to_cstr_buffer	(	std::string const &	str,
		char *	buffer,
		platform::Size	buffer_length
	)

Copy the contents of a string to a given C-style string buffer (with the given maximum length) The output will be truncated if greater than length, and null terminator will be added.

To be clear, this is only to be used for limited situations. Avoiding c-style strings is preferred.

References str().

Referenced by interface_residue_ddg(), and is_interface_residue().

◆ copysign()

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

inline

References x, and predPRE::y.

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

◆ CRASH_FILE()

static std::string const utility::CRASH_FILE ( "ROSETTA_CRASH.log" )

static

Referenced by save_crash_report_to_file().

◆ CSI_bgBlack()

CSI_Sequence utility::CSI_bgBlack ( )

inline

References utility::CSI::bgBlack.

◆ CSI_bgBlue()

CSI_Sequence utility::CSI_bgBlue ( )

inline

References utility::CSI::bgBlue.

Referenced by main(), and ui::network::B::run().

◆ CSI_bgCyan()

CSI_Sequence utility::CSI_bgCyan ( )

inline

References utility::CSI::bgCyan.

◆ CSI_bgDefault()

CSI_Sequence utility::CSI_bgDefault ( )

inline

References utility::CSI::bgDefault.

◆ CSI_bgGreen()

CSI_Sequence utility::CSI_bgGreen ( )

inline

References utility::CSI::bgGreen.

Referenced by ui::network::B::run().

◆ CSI_bgMagenta()

CSI_Sequence utility::CSI_bgMagenta ( )

inline

References utility::CSI::bgMagenta.

◆ CSI_bgRed()

CSI_Sequence utility::CSI_bgRed ( )

inline

References utility::CSI::bgRed.

Referenced by ui::network::B::run().

◆ CSI_bgWhite()

CSI_Sequence utility::CSI_bgWhite ( )

inline

References utility::CSI::bgWhite.

◆ CSI_bgYellow()

CSI_Sequence utility::CSI_bgYellow ( )

inline

References utility::CSI::bgYellow.

◆ CSI_Black()

CSI_Sequence utility::CSI_Black ( )

inline

References utility::CSI::Black.

Referenced by ui::network::B::run().

◆ CSI_Blue()

CSI_Sequence utility::CSI_Blue ( )

inline

References utility::CSI::Blue.

◆ CSI_Bold()

CSI_Sequence utility::CSI_Bold ( )

inline

References utility::CSI::Bold.

Referenced by exit_handler(), handle_assert_failure(), and main().

◆ CSI_Cyan()

CSI_Sequence utility::CSI_Cyan ( )

inline

References utility::CSI::Cyan.

◆ CSI_Default()

CSI_Sequence utility::CSI_Default ( )

inline

References utility::CSI::Default.

◆ CSI_Green()

CSI_Sequence utility::CSI_Green ( )

inline

References utility::CSI::Green.

Referenced by main().

◆ CSI_Magenta()

CSI_Sequence utility::CSI_Magenta ( )

inline

References utility::CSI::Magenta.

Referenced by utility::excn::Exception::display(), utility::excn::UserCorrectableIssue::display(), and save_crash_report_to_console().

◆ CSI_Nothing()

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_Red()

CSI_Sequence utility::CSI_Red ( )

inline

References utility::CSI::Red.

Referenced by basic::random::determine_random_number_seed(), exit_handler(), handle_assert_failure(), and main().

◆ CSI_Reset()

CSI_Sequence utility::CSI_Reset ( )

inline

References utility::CSI::Reset.

Referenced by basic::random::determine_random_number_seed(), utility::excn::Exception::display(), utility::excn::UserCorrectableIssue::display(), exit_handler(), handle_assert_failure(), main(), ui::network::B::run(), and save_crash_report_to_console().

◆ CSI_Underline()

CSI_Sequence utility::CSI_Underline ( )

inline

References utility::CSI::Underline.

Referenced by basic::random::determine_random_number_seed().

◆ CSI_White()

CSI_Sequence utility::CSI_White ( )

inline

References utility::CSI::White.

◆ CSI_Yellow()

CSI_Sequence utility::CSI_Yellow ( )

inline

References utility::CSI::Yellow.

Referenced by main().

◆ decode6bit()

platform::Size utility::decode6bit	(	unsigned char *	memory,
		std::string const &	jar,
		platform::Size const	maxbytes
	)

Given 3*N bytes of memory to fill, and a string containing 4*N characters, decode the characters (interpreting 4 bytes of ASCII text as 3 binary bytes) and populate the block of memory.

Parameters

[in]	memory	A pointer to the first byte of memory to fill. It is assumed that we're filling a contiguous block of memory.
[in]	jar	The string containing the characters that will be decoded and converted to bytes.
[in]	maxbytes	The maximum number of bytes to put into the memory pointed to by the "memory" pointer. (i.e. The size of the array that we're filling).

Note: Assumes memory already allocated!!! There is no direct check for vector overflows, since this function has no knowlege of what it is that it's filling (or how big the object is). The function relies on maxbytes to prevent overflows.

Returns: The number of bytes filled.

Author: Originally author unknown. Revised in 2021 by Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

References decode_32_to_24(), create_a3b_hbs::i, and min().

◆ 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 short	goodbytes
	)

inline

References code_from_6bit().

Referenced by decode6bit().

◆ down_cast() [1/2]

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 docking::s.

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

◆ down_cast() [2/2]

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 kmeans_adaptive_kernel_density_bb_dependent_rotlib::p.

◆ encode6bit()

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

Given a block of memory (with memory pointing to the first byte) and a byte count (length), convert every three bytes of memory into four bytes of ASCII characters, and populate the string (jar) with those characters.

Note that decode6bit requires the length of the memory block into which the contents of jar will be extracted, so the length of the memory location here should be stored somehow if one hopes to accurately reproduce the bytes stored.

References encode_24_to_32(), create_a3b_hbs::i, oop_conformations::length, and PREcst::linewidth.

◆ encode_24_to_32()

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

inline

References code_to_6bit().

Referenced by encode6bit().

◆ endswith()

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

True iff haystack ends with needle.

◆ enumerate1()

SimpleRange1 utility::enumerate1 ( platform::Size const max_inclusive )

inline

iterate from [1, max_inclusive]

USAGE: for( platform::Size const index : enumerate1( vec.size() ) )

Referenced by indices1().

◆ exit() [1/3]

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

inline

Exit with file + line + optional status.

References exit(), evaluate_beta_mutants::file, and line.

◆ exit() [2/3]

NORETURN_ATTR void utility::exit	(	char const *	file,
		int const	line,
		std::string const &	message,
		int const
	)

Exit with file + line + message + optional status.

References exit_handler(), evaluate_beta_mutants::file, line, and pyrosetta.utility.array::message.

Referenced by align_conformations(), cond_exit(), dna_dr_loop_test(), exit(), find_centerest_residue(), loop_rebuilding_test(), main(), mg_pdbstats_test(), my_main(), polar_pdbstats_test(), print_ddgs(), rhiju_pdbstats(), set_inverso_conformation_main_chain(), and set_inverso_conformation_side_chain().

◆ exit() [3/3]

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(), evaluate_beta_mutants::file, and line.

◆ exit_handler()

void utility::exit_handler	(	char const *	file,
		int const	line,
		std::string const &	message
	)

References begin, utility::io::oc::cerr, CSI_Bold(), CSI_Red(), CSI_Reset(), data, evaluate_beta_mutants::file, utility::io::ocstream::flush(), get_all_exit_callbacks(), getline(), utility::file::gzip(), line, maybe_throw_on_next_assertion_failure(), pyrosetta.utility.array::message, and test.T008_Serialization::oss.

Referenced by exit(), and exit_with_user_fixable_issue().

◆ exit_with_user_fixable_issue()

NORETURN_ATTR void utility::exit_with_user_fixable_issue	(	char const *	file,
		int	line,
		std::string const &	message
	)

Exit in cases where there's a clear issue the user can fix.

References exit_handler(), evaluate_beta_mutants::file, line, and pyrosetta.utility.array::message.

◆ file_basename()

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

◆ file_contents()

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, getline(), create_a3b_hbs::ii, line, and utility::options::OptionKeys::options::table::text.

Referenced by convert(), utility::io::GeneralFileContents::GeneralFileContents(), utility::io::GeneralFileContentsVector::GeneralFileContentsVector(), utility::io::FileContentsMap::get_file_contents(), utility::io::FileContentsMap::get_file_contents_ref(), basic::resource_manager::ResourceManager::initialize_from_commandline(), basic::citation_manager::CitationManager::load_rosetta_citations_from_database(), reverse_convert(), and utility::tag::XMLErrorHandler::set_file_contents().

◆ filename()

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

References create_a3b_hbs::f, and closure_error::path.

◆ find_closest()

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 create_a3b_hbs::first, and value.

◆ fmt_real()

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

@breif 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 docking::s.

◆ fractional_rank()

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(), create_a3b_hbs::i, create_a3b_hbs::j, create_a3b_hbs::k, kmeans_adaptive_kernel_density_bb_dependent_rotlib::v, and value.

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

◆ from_string()

template<class T >

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

inline

References docking::s, challenge::ss, predPRE::t, pyrosetta.distributed.cluster.exceptions::T, and utility_exit_with_message.

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

◆ get_all_exit_callbacks()

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

Array to hold all additional exit-callbacks.

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

◆ get_current_date()

std::string utility::get_current_date ( DateFormat const format )

Return current date in the requested format.

References ObjexxFCL::date(), enumerate_junctions::default, pyrosetta.tests.distributed.test_dask::format, localtime(), PDB_FORMAT, and predPRE::t.

◆ get_num_digits()

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

References value.

◆ get_resnum_and_chain()

std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< 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(), and docking::s.

Referenced by my_main().

◆ get_resnum_and_chain_and_segid()

std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< 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 predPRE::chain, get_resnum_and_chain_from_one_tag(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, replace_in(), predPRE::resnum, docking::s, string_split(), and extract_by_sidechain_sasa_score::tags.

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

◆ get_resnum_and_chain_from_one_tag()

bool utility::get_resnum_and_chain_from_one_tag	(	std::string const &	tag,
		utility::vector1< int > &	resnum,
		utility::vector1< char > &	chains,
		utility::vector1< std::string > &	segids
	)

helper function for get_resnum_and_chain

References predPRE::chain, chains, count, ObjexxFCL::ints_of(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, predPRE::resnum, and tag.

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

◆ get_resnum_and_segid()

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(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, replace_in(), predPRE::resnum, docking::s, tag, and extract_by_sidechain_sasa_score::tags.

◆ get_resnum_and_segid_from_one_tag()

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(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, predPRE::resnum, runtime_assert, and tag.

Referenced by get_resnum_and_segid().

◆ get_undefined_real()

platform::Real utility::get_undefined_real ( )

inline

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

References max().

Referenced by initialize_atoms(), is_undefined(), and string2Real().

◆ get_undefined_size()

platform::Size utility::get_undefined_size ( )

inline

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

References max().

Referenced by initialize_elements(), is_undefined(), and string2Size().

◆ HEADER()

static std::string const utility::HEADER ( "##############################################################################################################\n" "#\n" "# Rosetta crash log. Please submit the contents of this file to http://crash.rosettacommons.org/\n" "# or use the script Rosetta/main/source/scripts/python/public/report_crashes.py\n" "#\n\n" )

static

Referenced by save_crash_report_to_file().

◆ indices1()

template<typename T >

SimpleRange1 utility::indices1 ( utility::vector1< T > const & v )

inline

iterate from [1, c.size()]

USAGE: for( platform::Size const index : indices1( vec1 ) )

References enumerate1(), and kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

◆ insert_middle()

template<class T >

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

References create_a3b_hbs::ii, and swap().

Referenced by arg_greatest_several(), and arg_least_several().

◆ install_crash_handler()

void utility::install_crash_handler ( )

Set the crash handler for non-standard crashes (e.g. segfaults) Should only be called once at startup.

References old_terminate_handler_, signal_handler(), and terminate_handler().

◆ is_false_string()

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

String accepted as a false value?

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

◆ is_finite()

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 kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

◆ is_string_numeric()

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

References gaussian-sampling::input, and correlation_time::loc.

◆ is_true_string()

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

String accepted as a true value?

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

◆ is_undefined() [1/2]

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().

◆ is_undefined() [2/2]

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().

◆ isfinite()

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

inline

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

◆ isinf()

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

inline

Referenced by compare_times::compare_times(), is_undefined(), main(), numeric::statistics::w(), detail::write(), and detail::write_nonfinite().

◆ isnan()

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

inline

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

◆ join() [1/4]

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

combine strings with anything

References begin, and docking::s.

◆ join() [2/4]

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

combine strings with anything

References begin, and docking::s.

Referenced by InjectorMover::hash(), main(), basic::database::make_compound_statement(), replace_spaces(), and scan_hbond_jumps().

◆ join() [3/4]

template<class T >

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

combine vector with anything

References begin.

◆ join() [4/4]

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, and docking::s.

◆ LETTERS()

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

static

Referenced by superimpose_A_to_all().

◆ lower()

std::string utility::lower ( std::string const & s )

@breif Make a string Lowercase

References docking::s, and basic::options::OptionKeys::mp::transform::transform.

Referenced by binary_search_ranges(), and utility::tag::integer_range_restriction().

◆ LOWERCASE_ALPHANUMERICS()

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

static

◆ LOWERCASE_LETTERS()

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

static

◆ ltrim()

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

Remove any characters in "drop" from the front of the string.

References docking::s.

Referenced by trim().

◆ make_segtag_with_dashes()

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

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, runtime_assert, subloop_histogram::size, ObjexxFCL::string_of(), and tag.

◆ make_shared_vb_wrapper()

template<class T >

utility::pointer::shared_ptr<VBWrapper<T> > utility::make_shared_vb_wrapper ( T val )

◆ make_tag()

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

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, ObjexxFCL::string_of(), and tag.

◆ make_tag_with_dashes() [1/2]

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, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::n.

◆ make_tag_with_dashes() [2/2]

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 kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, runtime_assert, ObjexxFCL::string_of(), strip(), and tag.

◆ map_merge()

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 ...

◆ max() [1/14]

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

inline

max( double, double )

References a, and compute_difference::b.

◆ max() [2/14]

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

inline

max( float, float )

References a, and compute_difference::b.

◆ max() [3/14]

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

inline

max( int, int )

References a, and compute_difference::b.

◆ max() [4/14]

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

inline

max( long double, long double )

References a, and compute_difference::b.

◆ max() [5/14]

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

inline

max( long int, long int )

References a, and compute_difference::b.

◆ max() [6/14]

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

inline

max( short int, short int )

References a, and compute_difference::b.

Referenced by MetalSiteFinderMover::apply(), dump_energy_kinemage(), max(), print_passed(), and test_Vec().

◆ max() [7/14]

template<typename T >

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

inline

max( a, b, c )

References a, compute_difference::b, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::c.

◆ max() [8/14]

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 a, compute_difference::b, kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, and max().

◆ max() [9/14]

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 a, compute_difference::b, kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, test.T009_Exceptions::e, max(), and max().

◆ max() [10/14]

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 a, compute_difference::b, kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, test.T009_Exceptions::e, create_a3b_hbs::f, max(), and max().

◆ max() [11/14]

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

inline

max( unsigned int, unsigned int )

References a, and compute_difference::b.

◆ max() [12/14]

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

inline

max( unsigned long int, unsigned long int )

References a, and compute_difference::b.

◆ max() [13/14]

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

inline

max( unsigned short int, unsigned short int )

References a, and compute_difference::b.

◆ max() [14/14]

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, create_a3b_hbs::ii, and gaussian-sampling::input.

◆ max2()

template<class T >

T utility::max2 ( vector1< T > const & input )

Find the second largest value in a vector.

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

References debug_assert, create_a3b_hbs::ii, and gaussian-sampling::input.

◆ min() [1/14]

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

inline

min( double, double )

References a, and compute_difference::b.

◆ min() [2/14]

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

inline

min( float, float )

References a, and compute_difference::b.

◆ min() [3/14]

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

inline

min( int, int )

References a, and compute_difference::b.

◆ min() [4/14]

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

inline

min( long double, long double )

References a, and compute_difference::b.

◆ min() [5/14]

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

inline

min( long int, long int )

References a, and compute_difference::b.

◆ min() [6/14]

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

inline

min( short int, short int )

References a, and compute_difference::b.

Referenced by HemeReplace::apply(), dump_energy_kinemage(), get_boltzmann_probabilities(), min(), print_passed(), and test_Vec().

◆ min() [7/14]

template<typename T >

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

inline

min( a, b, c )

References a, compute_difference::b, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::c.

◆ min() [8/14]

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 a, compute_difference::b, kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, and min().

◆ min() [9/14]

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 a, compute_difference::b, kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, test.T009_Exceptions::e, min(), and min().

◆ min() [10/14]

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 a, compute_difference::b, kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, test.T009_Exceptions::e, create_a3b_hbs::f, min(), and min().

◆ min() [11/14]

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

inline

min( unsigned int, unsigned int )

References a, and compute_difference::b.

◆ min() [12/14]

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

inline

min( unsigned long int, unsigned long int )

References a, and compute_difference::b.

◆ min() [13/14]

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

inline

min( unsigned short int, unsigned short int )

References a, and compute_difference::b.

◆ min() [14/14]

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, create_a3b_hbs::ii, and gaussian-sampling::input.

◆ min2()

template<class T >

T utility::min2 ( vector1< T > const & input )

Find the SECOND smallest value in a vector.

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

References debug_assert, create_a3b_hbs::ii, and gaussian-sampling::input.

◆ modulo()

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 a, ObjexxFCL::abs(), and compute_difference::b.

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

◆ mpi_nprocs()

int utility::mpi_nprocs ( )

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

Referenced by basic::TracerImpl::calculate_visibility(), protocols::jd2::RECONMPIJobDistributor::go(), protocols::jd2::RECONMPIJobDistributor::go_hardcoded(), and main().

◆ mpi_rank()

int utility::mpi_rank ( )

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

Referenced by basic::TracerImpl::calculate_visibility(), protocols::jd2::RECONMPIJobDistributor::design_this_nodes_pose(), basic::random::determine_random_number_seed(), protocols::jd2::RECONMPIJobDistributor::find_consensus_sequence(), protocols::jd2::RECONMPIJobDistributor::get_new_job_id(), protocols::jd2::RECONMPIJobDistributor::go(), protocols::jd2::RECONMPIJobDistributor::go_hardcoded(), main(), utility::options::mpi_safe_std_err(), protocols::jd2::RECONMPIJobDistributor::pick_consensus_AA(), basic::database::resolve_db_partition(), MPI_Refinement_Launcher::run(), and MPI_LoopHash_Launcher::run().

◆ msg_name()

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().

◆ nmers_of()

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 kk, nmers_worker(), and vec().

◆ 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 create_a3b_hbs::ii, enumerate_junctions::int, kk, offset, and vec().

Referenced by nmers_of().

◆ NUMERALS()

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

static

◆ operator!=() [1/8]

template<typename B >

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

BitSet != BitSet.

◆ operator!=() [2/8]

template<typename B >

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

BitVector != BitVector.

◆ operator!=() [3/8]

template<platform::SSize L, typename A >

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

std::vector != vectorL

◆ operator!=() [4/8]

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

◆ operator!=() [5/8]

template<platform::SSize L, typename A >

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

vectorL != std::vector

◆ operator!=() [6/8]

template<platform::SSize L, typename A >

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

vectorL != vectorL

◆ operator!=() [7/8]

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

◆ operator!=() [8/8]

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

◆ operator+() [1/2]

template<typename B >

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

BitSet + BitSet: Union.

◆ operator+() [2/2]

template<typename B >

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

BitVector + BitVector: Union.

◆ operator-() [1/2]

template<typename B >

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

BitSet - BitSet: Difference.

◆ operator-() [2/2]

template<typename B >

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

BitVector - BitVector: Difference.

◆ operator<() [1/6]

template<platform::SSize L, typename A >

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

std::vector < vectorL

◆ operator<() [2/6]

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

◆ operator<() [3/6]

template<platform::SSize L, typename A >

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

vectorL < std::vector

◆ operator<() [4/6]

template<platform::SSize L, typename A >

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

vectorL < vectorL

◆ operator<() [5/6]

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

◆ operator<() [6/6]

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

◆ operator<<() [1/2]

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 create_a3b_hbs::i, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

◆ operator<<() [2/2]

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 create_a3b_hbs::i, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

◆ operator<=() [1/6]

template<platform::SSize L, typename A >

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

std::vector <= vectorL

◆ operator<=() [2/6]

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

◆ operator<=() [3/6]

template<platform::SSize L, typename A >

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

vectorL <= std::vector

◆ operator<=() [4/6]

template<platform::SSize L, typename A >

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

vectorL <= vectorL

◆ operator<=() [5/6]

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

◆ operator<=() [6/6]

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

◆ operator==() [1/9]

template<typename B >

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

BitSet == BitSet.

◆ operator==() [2/9]

template<typename B >

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

BitVector == BitVector.

◆ operator==() [3/9]

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

inline

References a, and compute_difference::b.

◆ operator==() [4/9]

template<platform::SSize L, typename A >

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

std::vector == vectorL

◆ operator==() [5/9]

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

◆ operator==() [6/9]

template<platform::SSize L, typename A >

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

vectorL == std::vector

◆ operator==() [7/9]

template<platform::SSize L, typename A >

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

vectorL == vectorL

◆ operator==() [8/9]

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

◆ operator==() [9/9]

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

◆ operator>() [1/6]

template<platform::SSize L, typename A >

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

std::vector > vectorL

◆ operator>() [2/6]

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

◆ operator>() [3/6]

template<platform::SSize L, typename A >

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

vectorL > std::vector

◆ operator>() [4/6]

template<platform::SSize L, typename A >

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

vectorL > vectorL

◆ operator>() [5/6]

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

◆ operator>() [6/6]

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

◆ operator>=() [1/6]

template<platform::SSize L, typename A >

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

std::vector >= vectorL

◆ operator>=() [2/6]

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

◆ operator>=() [3/6]

template<platform::SSize L, typename A >

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

vectorL >= std::vector

◆ operator>=() [4/6]

template<platform::SSize L, typename A >

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

vectorL >= vectorL

◆ operator>=() [5/6]

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

◆ operator>=() [6/6]

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

◆ operator|() [1/2]

template<typename B >

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

BitSet | BitSet: Union.

◆ operator|() [2/2]

template<typename B >

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

BitVector | BitVector: Union.

◆ OPTIONS()

static std::string utility::OPTIONS ( "NO OPTIONS SPECIFIED" )

static

Referenced by save_crash_report_to_file(), and set_options_string().

◆ pad_atom_name()

std::string utility::pad_atom_name ( std::string const & s )

Pad an atom name to the pdb format.

References CREATE_EXCEPTION, and docking::s.

◆ pad_left() [1/2]

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(), docking::s, predPRE::t, and to_string().

◆ pad_left() [2/2]

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 docking::s.

Referenced by fmt_real(), and pad_left().

◆ pad_right() [1/2]

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(), docking::s, predPRE::t, and to_string().

◆ pad_right() [2/2]

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 docking::s.

Referenced by main(), and pad_right().

◆ parse_boolean()

bool utility::parse_boolean	(	std::stringstream &	stream,
		std::string const &	errmsg
	)

Given a stringstream in which the next block of text is any string representing "true" or any string representing "false", parse this as a Boolean, and return an informative error message if we fail.

Author: Vikram K. Mulligan

References errmsg(), is_false_string(), is_true_string(), and runtime_assert_string_msg.

◆ parse_out() [1/2]

template<class T >

void utility::parse_out	(	std::stringstream &	stream,
		T &	recipient
	)

inline

Parse out some data of type T from a stringstream, and throw an error with a message if the operation fails.

Version with a default error message.

Author: Vikram K. Mulligan.

References parse_out().

◆ parse_out() [2/2]

template<class T >

void utility::parse_out	(	std::stringstream &	stream,
		T &	recipient,
		std::string const &	errmsg
	)

inline

Parse out some data of type T from a stringstream, and throw an error with a message if the operation fails.

Version with a custom error message.

Author: Vikram K. Mulligan.

References errmsg(), and runtime_assert_string_msg.

Referenced by parse_out().

◆ pathname()

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

References closure_error::path, and utility::file::FileName::path().

Referenced by main().

◆ payload()

std::string utility::payload ( SimulateMPIMessageOP msg )

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

Referenced by utility::SimulateMPI::incoming_message_queue_is_empty(), utility::SimulateMPI::outgoing_message_queue_is_empty(), RosettaJob::request_job_from_server(), and ui::task::TaskSyncer_TaskStrategy::subscribe().

◆ print_message()

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().

◆ quoted_split()

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 create_a3b_hbs::ii, create_a3b_hbs::r, docking::s, and basic::options::OptionKeys::cutoutdomain::start.

Referenced by basic::citation_manager::Citation::parse_authors(), and utility::options::VectorOption::set_value().

◆ rand_sleep()

void utility::rand_sleep ( )

References sys_sleep().

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

◆ Real2string()

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().

◆ receive_char_from_node()

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().

◆ receive_double_from_node()

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().

Referenced by main(), protocols::jd2::RECONMPIJobDistributor::pick_consensus_AA(), and run_parallel_docking().

◆ receive_doubles_from_node()

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().

Referenced by main(), and run_parallel_docking().

◆ receive_integer_from_anyone()

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().

◆ receive_integer_from_node()

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 protocols::jd2::RECONMPIJobDistributor::design_this_nodes_pose(), main(), and run_parallel_docking().

◆ receive_integers_from_node()

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().

Referenced by main().

◆ receive_size_from_node()

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().

◆ receive_sizes_from_node()

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().

◆ receive_string_from_node()

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 protocols::jd2::RECONMPIJobDistributor::design_this_nodes_pose(), protocols::jd2::RECONMPIJobDistributor::find_consensus_sequence(), protocols::jd2::RECONMPIJobDistributor::go_hardcoded(), main(), protocols::jd2::RECONMPIJobDistributor::pick_consensus_AA(), and basic::mpi::request_data_from_head_node().

◆ remove_exit_callback()

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().

◆ remove_from_string()

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.

References erraser_util::remove().

◆ replace_environment_variables()

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 end, gaussian-sampling::input, basic::options::OptionKeys::cutoutdomain::start, and utility_exit_with_message.

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

◆ replace_first_in()

std::string utility::replace_first_in	(	std::string const &	source,
		std::string const &	from,
		std::string const &	to
	)

Generate new string from 'source' by replacing the first occurrence of 'from' to 'to' string.

Author: Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

References make_symmdef_file_denovo::pos, and replace_string().

◆ replace_in() [1/2]

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

inline

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, and docking::s.

◆ replace_in() [2/2]

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 make_symmdef_file_denovo::pos, and replace_string().

Referenced by RNA_ScoreMover::apply(), get_resnum_and_chain_and_segid(), get_resnum_and_segid(), get_rmsd(), basic::tensorflow_manager::get_tensorflow_compilation_instructions(), mg_modeler_test(), mg_pdbstats_test(), morph_pdbs_test(), numeric::read_tensor_from_file(), and numeric::write_tensor_to_file().

◆ replace_spaces()

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().

◆ round()

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

inline

References round().

◆ rtrim()

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

Remove any characters in "drop" from the back of the string.

References docking::s.

Referenced by trim().

◆ same_ignoring_spaces()

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.

References basic::options::OptionKeys::stepwise::s1, and basic::options::OptionKeys::stepwise::s2.

◆ save_crash_report() [1/4]

void utility::save_crash_report	(	char const *	message,
		std::string const &	file,
		int	line,
		std::string const &	traceback
	)

References evaluate_beta_mutants::file, line, pyrosetta.utility.array::message, save_crash_report_to_console(), save_crash_report_to_file(), and show_crash_report_on_console_.

◆ save_crash_report() [2/4]

void utility::save_crash_report	(	char const *	message,
		std::string const &	file,
		int	line
	)

Save a crash report to the crash reporter file.

References backtrace_string(), evaluate_beta_mutants::file, line, and pyrosetta.utility.array::message.

Referenced by utility::excn::Exception::crash_log(), handle_assert_failure(), save_crash_report(), signal_handler(), and terminate_handler().

◆ save_crash_report() [3/4]

void utility::save_crash_report	(	std::string const &	message,
		std::string const &	file,
		int const	line,
		std::string const &	traceback
	)

inline

References evaluate_beta_mutants::file, line, pyrosetta.utility.array::message, and save_crash_report().

◆ save_crash_report() [4/4]

void utility::save_crash_report	(	std::string const &	message,
		std::string const &	file = `"(none)"`,
		int const	line = `0`
	)

inline

Save a crash report to the crash reporter file.

References evaluate_beta_mutants::file, line, pyrosetta.utility.array::message, and save_crash_report().

◆ save_crash_report_to_console()

void utility::save_crash_report_to_console	(	char const *	,
		std::string const &	,
		int	,
		std::string const &	traceback
	)

References utility::io::oc::cerr, CSI_Magenta(), and CSI_Reset().

Referenced by save_crash_report().

◆ save_crash_report_to_file()

void utility::save_crash_report_to_file	(	char const *	message,
		std::string const &	file,
		int	line,
		std::string const &	traceback
	)

References job_manager::app, APPNAME(), utility::io::oc::cerr, CRASH_FILE(), utility::Version::date(), evaluate_beta_mutants::file, get_extras(), HEADER(), line, pyrosetta.utility.array::message, MODE(), OPTIONS(), OS_VER(), erraser_single_res_analysis::out, and utility::Version::version().

Referenced by save_crash_report().

◆ send_char_to_node()

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

References pyrosetta.utility.array::message, utility::SimulateMPI::send_char_to_node(), and utility::SimulateMPI::simulate_mpi().

◆ send_double_to_node()

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

References pyrosetta.utility.array::message, utility::SimulateMPI::send_double_to_node(), and utility::SimulateMPI::simulate_mpi().

Referenced by main(), protocols::jd2::RECONMPIJobDistributor::pick_consensus_AA(), and run_parallel_docking().

◆ send_doubles_to_node()

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

References pyrosetta.utility.array::message, utility::SimulateMPI::send_doubles_to_node(), and utility::SimulateMPI::simulate_mpi().

Referenced by main(), and run_parallel_docking().

◆ send_integer_to_node()

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

References pyrosetta.utility.array::message, utility::SimulateMPI::send_integer_to_node(), and utility::SimulateMPI::simulate_mpi().

Referenced by protocols::jd2::RECONMPIJobDistributor::design_this_nodes_pose(), main(), and run_parallel_docking().

◆ send_integers_to_node()

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

References pyrosetta.utility.array::message, utility::SimulateMPI::send_integers_to_node(), and utility::SimulateMPI::simulate_mpi().

Referenced by main().

◆ send_size_to_node()

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 pyrosetta.utility.array::message, utility::SimulateMPI::send_size_to_node(), and utility::SimulateMPI::simulate_mpi().

◆ send_sizes_to_node()

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

References pyrosetta.utility.array::message, utility::SimulateMPI::send_sizes_to_node(), and utility::SimulateMPI::simulate_mpi().

◆ send_string_to_node()

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

References pyrosetta.utility.array::message, utility::SimulateMPI::send_string_to_node(), and utility::SimulateMPI::simulate_mpi().

Referenced by protocols::jd2::RECONMPIJobDistributor::design_this_nodes_pose(), protocols::jd2::RECONMPIJobDistributor::find_consensus_sequence(), protocols::jd2::RECONMPIJobDistributor::go_hardcoded(), main(), protocols::jd2::RECONMPIJobDistributor::pick_consensus_AA(), basic::mpi::request_data_from_head_node(), and basic::mpi::send_data_to_head_node().

◆ set_application_name()

void utility::set_application_name ( char const * appname )

Set the application name that this was launched as. Should only be called once on startup.

References APPNAME().

◆ set_main_exit_callback()

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 nullptr, whicth mean no sys exit is called.

References main_exit_callback.

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

◆ set_options_string()

void utility::set_options_string ( std::string const & options )

Set the string representation of the options to be used in the crash report Should only be called once on startup.

References OPTIONS(), and options.

◆ set_show_crash_report_on_console()

void utility::set_show_crash_report_on_console ( bool setting )

If passed true, any backtrace will show up on stderr in addition to the crash report file.

References show_crash_report_on_console_.

◆ signal_handler()

void utility::signal_handler ( int signal )

References enumerate_junctions::default, pyrosetta.utility.array::message, and save_crash_report().

Referenced by install_crash_handler(), and self-test::main().

◆ slurp()

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(), main(), and sequence_tolerance_mf_main().

◆ split()

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

split given std::string using ' ' symbol.

References numeric::add(), create_a3b_hbs::i, create_a3b_hbs::r, docking::s, and basic::options::OptionKeys::cutoutdomain::start.

Referenced by MPFindInterfaceTestMover::apply(), CrystFFTDock::apply(), protocols::surface_docking::AntibodyInfoRMLoader::create_resource(), basic::mpi::DbMoverMessageListener::deserialize_data(), MPInterfaceStatistics::get_number_hbonds(), get_pair_keys_from_list(), replace_spaces(), and basic::TracerImpl::set_ios_hook().

◆ split_by_newlines()

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, create_a3b_hbs::i, create_a3b_hbs::r, docking::s, and basic::options::OptionKeys::cutoutdomain::start.

Referenced by basic::citation_manager::Citation::initialize_from_string(), main(), and basic::citation_manager::CitationManager::populate_doi_rosetta_citation_map().

◆ split_to_list()

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

split given std::string using ' ' symbol.

References numeric::add(), create_a3b_hbs::i, create_a3b_hbs::r, docking::s, and basic::options::OptionKeys::cutoutdomain::start.

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

◆ split_to_set()

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(), create_a3b_hbs::i, create_a3b_hbs::r, docking::s, and basic::options::OptionKeys::cutoutdomain::start.

◆ split_whitespace()

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, create_a3b_hbs::r, docking::s, and challenge::ss.

Referenced by read_complex_type().

◆ startswith()

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

True iff haystack starts with needle.

Referenced by DRRAFTER_util::graph_from_ss().

◆ stdout_is_tty()

bool utility::stdout_is_tty ( )

References build::stdout.

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

◆ string2float()

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

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

convert a string to a float

References create_a3b_hbs::i, and challenge::ss.

◆ string2int()

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

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

convert a string to an int

References create_a3b_hbs::i, and challenge::ss.

Referenced by basic::TracerImpl::calculate_tracer_level(), basic::mpi::DbMoverMessageListener::deserialize_data(), get_pair_keys_from_list(), get_pos_from_fragfn(), main(), process_ss_str(), and PoseAndData::set_file_name().

◆ string2Real()

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

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

References get_undefined_real(), create_a3b_hbs::i, and challenge::ss.

◆ string2Size()

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

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

References get_undefined_size(), create_a3b_hbs::i, and challenge::ss.

Referenced by TestQuickRelaxMover::apply(), MPInterfaceStatistics::get_number_pi_stacking(), and apps::pilot::frankdt::import_motifs().

◆ string2uint()

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

References debug_assert, challenge::ss, x, and predPRE::y.

◆ string_split() [1/2]

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

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

References create_a3b_hbs::i, and create_a3b_hbs::j.

Referenced by MyScoreMover::apply(), ColorByLipidType::apply(), FindOptimalHydrophobicThk::apply(), MPFindInterfaceTestMover::apply(), byres_analysis(), calc_scores(), MPInterfaceStatistics::calculate_interfaces(), basic::TracerImpl::calculate_tracer_level(), check_inputs_for_errors(), numeric::comma_seperated_string_to_xyz(), DeleteSegments::DeleteSegments(), dna_motif_matcher(), dostuff(), MPInterfaceStatistics::get_number_hbonds(), get_pos_from_fragfn(), get_res_data_ss(), get_resnum_and_chain_and_segid(), utility::xsd_util::get_tag_name(), basic::resource_manager::locator::FileListResourceLocator::locate_resource_stream(), main(), motif_dna_packer_design(), opt_bicelle_params(), opt_double_vesicle_params(), opt_vesicle_params(), basic::resource_manager::locator::FileSystemResourceLocator::parse_my_tag(), process_file_list(), rna_design_test(), ScoreFragmentSetMover::run(), ConsensusFragmentMover::run(), SolutionRescoreMover::run(), scan_hbond_jumps(), set_basic_dock_options(), utility::tag::XMLErrorHandler::set_file_contents(), PoseAndData::set_file_name(), setup_coord_csts(), and numeric::interpolation::spline_from_file().

◆ string_split() [2/2]

template<class T >

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

inline

References create_a3b_hbs::i, create_a3b_hbs::j, challenge::ss, predPRE::t, pyrosetta.distributed.cluster.exceptions::T, and utility_exit_with_message.

◆ string_split_multi_delim()

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 create_a3b_hbs::i, and create_a3b_hbs::j.

Referenced by main().

◆ string_split_simple()

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)

References create_a3b_hbs::i, and create_a3b_hbs::j.

Referenced by utility::io::GeneralFileContentsVector::GeneralFileContentsVector(), MetalSiteFinderMover::initialize_from_options(), and main().

◆ string_to_sha1()

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

References create_a3b_hbs::i.

◆ string_vector_from_char_vector()

utility::vector1< std::string > utility::string_vector_from_char_vector ( utility::vector1< char > const & char_vect )

References to_string< char >().

◆ strip() [1/2]

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

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

References begin, kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, end, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::p.

◆ strip() [2/2]

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 docking::s, and trim().

Referenced by utility::xsd_util::generate_human_readable_documentation(), basic::citation_manager::Citation::initialize_from_string(), main(), make_tag_with_dashes(), basic::citation_manager::Citation::parse_authors(), basic::citation_manager::Citation::parse_string_entry(), basic::citation_manager::Citation::parse_year(), basic::citation_manager::CitationManager::populate_doi_rosetta_citation_map(), and trim().

◆ swap() [1/9]

template<typename B >

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

swap( BitSet, BitSet )

Referenced by swap().

◆ swap() [2/9]

template<typename B >

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

swap( BitVector, BitVector )

◆ swap() [3/9]

template<typename U >

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

swap( BitVector, BitVector )

◆ swap() [4/9]

template<platform::SSize L, typename A >

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

swap( std::vector, vectorL )

References a, and compute_difference::b.

◆ swap() [5/9]

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 )

References a, and compute_difference::b.

◆ swap() [6/9]

template<platform::SSize L, typename A >

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

swap( vectorL, std::vector )

References a, compute_difference::b, and swap().

◆ swap() [7/9]

template<platform::SSize L, typename A >

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

swap( vectorL, vectorL )

References a, compute_difference::b, and swap().

◆ swap() [8/9]

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 a, compute_difference::b, and swap().

◆ swap() [9/9]

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 a, compute_difference::b, and swap().

◆ swap4_aligned()

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

References data, create_a3b_hbs::i, N, spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::ndata, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

◆ sys_sleep()

void utility::sys_sleep ( double const seconds )

Sleep for a specified number of seconds.

References utility::io::oc::cout, enumerate_junctions::int, and x.

Referenced by rand_sleep().

◆ terminate_handler()

void utility::terminate_handler ( )

References test.T009_Exceptions::e, old_terminate_handler_, and save_crash_report().

Referenced by install_crash_handler().

◆ timestamp()

std::string utility::timestamp ( )

Generate timestamp string.

References localtime().

Referenced by basic::TracerImpl::prepend_channel_name(), timestamp_millis(), timestamp_millis_short(), and timestamp_short().

◆ timestamp_millis()

std::string utility::timestamp_millis ( )

Generate timestamp string with millis.

References localtime(), docking::s, predPRE::t, and timestamp().

◆ timestamp_millis_short()

std::string utility::timestamp_millis_short ( )

Generate timestamp string with millis, short format.

References localtime(), docking::s, predPRE::t, and timestamp().

◆ timestamp_short()

std::string utility::timestamp_short ( )

Generate timestamp string, short format.

References localtime(), and timestamp().

◆ to_string()

template<class T >

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

inline

Note: : If your type is int/Size/Real, you're probably better off with std::to_string()

References challenge::ss, and predPRE::t.

◆ to_string< char >()

template<>

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

inline

References predPRE::t.

Referenced by main(), and string_vector_from_char_vector().

◆ trim() [1/2]

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.

References ltrim(), rtrim(), and docking::s.

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

◆ trim() [2/2]

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 docking::s, and strip().

◆ trimmed_compare()

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

compares two strings ignoring leading and trailing spaces

References basic::options::OptionKeys::stepwise::s1, basic::options::OptionKeys::stepwise::s2, and sign::space.

◆ upper()

std::string utility::upper ( std::string const & s )

Make a string Uppercase.

References docking::s, and basic::options::OptionKeys::mp::transform::transform.

Referenced by binary_search_ranges(), utility::tag::Tag::getOption(), and utility::tag::integer_range_restriction().

◆ UPPERCASE_ALPHANUMERICS()

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

static

◆ UPPERCASE_LETTERS()

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

static

Referenced by PoseWrap::dump_pdb(), and dumpsym().

Variable Documentation

◆ main_exit_callback

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

static

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

Referenced by set_main_exit_callback().

◆ old_terminate_handler_

std::terminate_handler utility::old_terminate_handler_ = nullptr

Referenced by install_crash_handler(), and terminate_handler().

◆ show_crash_report_on_console_

bool utility::show_crash_report_on_console_ = false

static

Referenced by save_crash_report(), and set_show_crash_report_on_console().

Namespaces

Classes

Typedefs

Enumerations

Functions

Variables

Detailed Description

Typedef Documentation

◆ heapCOP

◆ heapOP

◆ Inline_File_Provider_HookCOP

◆ Inline_File_Provider_HookOP

◆ SimulateMPIMessageCOP

◆ SimulateMPIMessageOP

◆ small_vector0

◆ small_vector1

◆ StrongReal

◆ StrongSize

◆ subset_mappingCOP

◆ subset_mappingOP

◆ UtilityExitCallBack

◆ vector0_bool

◆ vector0_char

◆ vector0_double

◆ vector0_float

◆ vector0_int

◆ vector0_long

◆ vector0_longdouble

◆ vector0_schar

◆ vector0_short

◆ vector0_size

◆ vector0_size_t

◆ vector0_ssize

◆ vector0_ssize_t

◆ vector0_uchar

◆ vector0_uint

◆ vector0_ulong

◆ vector0_ushort

◆ vector1_bool

◆ vector1_char

◆ vector1_double

◆ vector1_float

◆ vector1_int

◆ vector1_long

◆ vector1_longdouble

◆ vector1_schar

◆ vector1_short

◆ vector1_size

◆ vector1_size_t

◆ vector1_ssize

◆ vector1_ssize_t

◆ vector1_uchar

◆ vector1_uint

◆ vector1_ulong

◆ vector1_ushort

◆ VirtualBaseCOP

◆ VirtualBaseOP

Enumeration Type Documentation

◆ DateFormat

◆ simulate_mpi_message_type

Function Documentation

◆ add_exit_callback()

◆ ALPHANUMERICS()

◆ APPNAME()

◆ arg_greatest_several()

◆ arg_least_several()

◆ arg_max()

◆ arg_min()

◆ argmax() [1/2]

◆ argmax() [2/2]

◆ argmin() [1/2]

◆ argmin() [2/2]

◆ argsort()

◆ binary_search_ranges()

◆ code_from_6bit()

◆ code_to_6bit()

◆ cond_exit()

◆ contains()

◆ copy_to_cstr_buffer()

◆ copysign()