utility Namespace Reference

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

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

Classes
class	BitSet
	Simple bit set. More...
class	BitVector
	Simple bit vector. More...
class	Bound
	Bound value class. More...
class	CSI_Sequence
	Class to hold all Terminal ASCII codes as static data for CSI_Sequence. Note: that on non-tty terminals all codes will initialized as empty to avoid polution of Rosetta logs. More...
class	DereferenceIterator
	const_iterator class for SilentFileData container. More...
class	EXCN_utility_exit
class	fixedsizearray0
class	fixedsizearray0const_iterator
class	fixedsizearray0iterator
class	fixedsizearray1
class	fixedsizearray1const_iterator
class	fixedsizearray1iterator
class	FixedSizeLexicographicalIterator
class	heap
struct	history_queue_struct
class	in_place_list
class	Inline_File_Provider
class	Inline_File_Provider_Hook
class	LexicographicalIterator
class	list_element
class	OrderedTuple
	The ordered tuple takes a container class T and defines comparison operators so that the tuple may be sorted. More...
class	predicate_cmp_filename
struct	RawType
	Meta-programming classes to provide the pointer type for down_cast. More...
struct	RawType< T & >
struct	RawType< T * >
class	recent_history_queue
	A class for keeping track of a subset of elements in a set that are pushed into a queue in a certain order, and which fall off the end of the queue in ther order in which they arrive. Elements in the set can be bumped to the front of the queue. More...
class	Show
class	SimulateMPI
	singleton class storing simulated MPI state More...
class	SimulateMPIData
class	SimulateMPIMessage
class	SingletonBase
	SingletonBase is meant to serve as a base class for singleton classes in Rosetta handling the initialization of the singleton in a thread-safe way. More...
struct	SortFirst
struct	SortSecond
class	subset_mapping
	This class handles the bookeeping to map between a set of integer ids in the "source" enumeration to a subset of those ids – the destination enumartion. Elements in the source enumeration that do not map to elements in the destination enumeration are represented by the value 0. Both enumerations should count from 1. Once the class has been initialized, this class offers O(1) mapping between elements in the enumerations. More...
class	vector0
	std::vector with assert-checked bounds More...
class	vector0< bool, A >
	std::vector with assert-checked bounds: bool specialization More...
class	vector1
	std::vector with 1-based indexing More...
class	vector1< bool, A >
	std::vector with 1-based indexing: bool specialization More...
class	vectorL
	std::vector with L-based indexing More...
class	vectorL< L, bool, A >
	std::vector with L-based indexing: bool specialization More...
struct	vectorL_IndexSelector
	vectorL index type selector: Nonnegative lower index non-specialization More...
struct	vectorL_IndexSelector< false >
	vectorL index type selector: Negative lower index specialization More...
struct	vectorL_ZeroSelector
	vectorL lower index zero selector: Nonzero lower index non-specialization More...
struct	vectorL_ZeroSelector< false >
	vectorL lower index zero selector: Zero lower index specialization More...

Typedefs
typedef void(*	UtilityExitCallBack )(void)
typedef utility::pointer::shared_ptr < heap >	heapOP
typedef utility::pointer::shared_ptr < heap const >	heapCOP
typedef utility::pointer::shared_ptr < Inline_File_Provider_Hook >	Inline_File_Provider_HookOP
typedef utility::pointer::shared_ptr < Inline_File_Provider_Hook const >	Inline_File_Provider_HookCOP
typedef pointer::shared_ptr < subset_mapping >	subset_mappingOP
typedef pointer::shared_ptr < subset_mapping const >	subset_mappingCOP
typedef utility::pointer::shared_ptr < SimulateMPIMessage >	SimulateMPIMessageOP
typedef utility::pointer::shared_ptr < SimulateMPIMessage const >	SimulateMPIMessageCOP
typedef vector0< bool >	vector0_bool
typedef vector0< short int >	vector0_short
typedef vector0< int >	vector0_int
typedef vector0< long int >	vector0_long
typedef vector0< unsigned short int >	vector0_ushort
typedef vector0< unsigned int >	vector0_uint
typedef vector0< unsigned long int >	vector0_ulong
typedef vector0< platform::Size >	vector0_size_t
typedef vector0< platform::Size >	vector0_size
typedef vector0< platform::SSize >	vector0_ssize_t
typedef vector0< platform::SSize >	vector0_ssize
typedef vector0< float >	vector0_float
typedef vector0< double >	vector0_double
typedef vector0< long double >	vector0_longdouble
typedef vector0< char >	vector0_char
typedef vector0< unsigned char >	vector0_uchar
typedef vector0< signed char >	vector0_schar
typedef vector1< bool >	vector1_bool
typedef vector1< short int >	vector1_short
typedef vector1< int >	vector1_int
typedef vector1< long int >	vector1_long
typedef vector1< unsigned short int >	vector1_ushort
typedef vector1< unsigned int >	vector1_uint
typedef vector1< unsigned long int >	vector1_ulong
typedef vector1< std::size_t >	vector1_size_t
typedef vector1< std::size_t >	vector1_size
typedef vector1< platform::SSize >	vector1_ssize_t
typedef vector1< platform::SSize >	vector1_ssize
typedef vector1< float >	vector1_float
typedef vector1< double >	vector1_double
typedef vector1< long double >	vector1_longdouble
typedef vector1< char >	vector1_char
typedef vector1< unsigned char >	vector1_uchar
typedef vector1< signed char >	vector1_schar

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

Functions
void	sys_sleep (double const seconds)
	Sleep for a specified number of seconds. More...
void	rand_sleep ()
std::string	timestamp ()
	Generate timestamp string. More...
std::string	timestamp_short ()
	Generate timestamp string, short format. More...
void	encode6bit (const unsigned char *memory, unsigned int length, std::string &jar)
int	decode6bit (unsigned char *memory, const std::string &jar)
void	swap4_aligned (void *v, long ndata)
unsigned char	code_to_6bit (unsigned char _6bit)
unsigned char	code_from_6bit (unsigned char _8bit)
void	encode_24_to_32 (unsigned char i0, unsigned char i1, unsigned char i2, unsigned char &o0, unsigned char &o1, unsigned char &o2, unsigned char &o3)
void	decode_32_to_24 (unsigned char i0, unsigned char i1, unsigned char i2, unsigned char i3, unsigned char &o0, unsigned char &o1, unsigned char &o2)
template<typename B >
BitSet< B >	operator+ (BitSet< B > const &a, BitSet< B > const &b)
	BitSet + BitSet: Union. More...
template<typename B >
BitSet< B >	operator| (BitSet< B > const &a, BitSet< B > const &b)
	BitSet | BitSet: Union. More...
template<typename B >
BitSet< B >	operator- (BitSet< B > const &a, BitSet< B > const &b)
	BitSet - BitSet: Difference. More...
template<typename B >
void	swap (BitSet< B > &a, BitSet< B > &b)
	swap( BitSet, BitSet ) More...
template<typename B >
bool	operator== (BitSet< B > const &a, BitSet< B > const &b)
	BitSet == BitSet. More...
template<typename B >
bool	operator!= (BitSet< B > const &a, BitSet< B > const &b)
	BitSet != BitSet. More...
template<typename B >
BitVector< B >	operator+ (BitVector< B > const &a, BitVector< B > const &b)
	BitVector + BitVector: Union. More...
template<typename B >
BitVector< B >	operator| (BitVector< B > const &a, BitVector< B > const &b)
	BitVector | BitVector: Union. More...
template<typename B >
BitVector< B >	operator- (BitVector< B > const &a, BitVector< B > const &b)
	BitVector - BitVector: Difference. More...
template<typename B >
void	swap (BitVector< B > &a, BitVector< B > &b)
	swap( BitVector, BitVector ) More...
template<typename B >
bool	operator== (BitVector< B > const &a, BitVector< B > const &b)
	BitVector == BitVector. More...
template<typename B >
bool	operator!= (BitVector< B > const &a, BitVector< B > const &b)
	BitVector != BitVector. More...
template<class Target , class Source >
Target	down_cast (Source &s)
	Fast assert-checked polymorphic down-cast: reference argument. More...
template<class Target , class Source >
Target	down_cast (Source *p)
	Fast assert-checked polymorphic down-cast: pointer argument. More...
void	set_main_exit_callback (UtilityExitCallBack=0)
	Set call back funtion that will be called on utility::exit. Use this function to overload default behavior of sys.exit to more appropriate to your application Defaut value for callback function is 0, whicth mean no sys exit is called. More...
std::vector < UtilityExitCallBack > &	get_all_exit_callbacks ()
	Array to hold all additional exit-callbacks. More...
void	add_exit_callback (UtilityExitCallBack)
	Add additional callback function that will be called before standard exit(…) is executed. [Note: do not confuse this function with 'set_main_exit_callback' which is replacing the end behavior of exit(…)]. More...
void	remove_exit_callback (UtilityExitCallBack)
	Remove additional callback function that was previously added by using add_exit_callback. More...
void	exit (std::string const &file, int const line, std::string const &message, int const status)
	Exit with file + line + message + optional status. More...
int	cond_exit (bool condition, std::string const &file, int const line, std::string const &message, int const status)
	Conditional Exit with file + line + message + optional status. More...
void	exit (std::string const &file, int const line, int const status=1) NORETURN
	Exit with file + line + optional status. More...
void	exit (int const status, std::string const &file, int const line)
	Exit with file + line + status. More...
template<typename BidirectionalIterator , typename T >
BidirectionalIterator	find_closest (BidirectionalIterator first, BidirectionalIterator last, const T &value)
	Returns an iterator on the sorted range [first, last) nearest to value. If value is equidistant between adjacent elements, the lesser is returned. More...
template<class T >
bool	has_key (std::map< T, T > a_map, T key)
template<class T >
bool	has_key (std::map< T, T > const &a_map, T const &key)
	Does the map have the key? More...
template<typename T >
int	argmin (const std::vector< T > &iterable)
	Returns the argument whose value is minimal according to operator<. More...
template<typename T >
int	argmin (const utility::vector1< T > &iterable)
	Returns the argument whose value is minimal according to operator<. More...
template<typename T >
int	argmax (const std::vector< T > &iterable)
	Returns the argument whose value is maximal according to operator>. More...
template<typename T >
int	argmax (const utility::vector1< T > &iterable)
	Returns the argument whose value is maximal according to operator>. More...
int	mpi_rank ()
int	mpi_nprocs ()
int	receive_integer_from_anyone ()
	Use MPI to wait until some node sends an integer – usually its own mpi_rank so that it can send further messages. More...
std::string	receive_string_from_node (int source)
	Use MPI to receive a string from a particular node. More...
void	send_string_to_node (int destination, std::string const &message)
char	receive_char_from_node (int source)
	Use MPI to receive a single char from a particular node. More...
void	send_char_to_node (int destination, char message)
int	receive_integer_from_node (int source)
	Use MPI to receive a single integer from a particular node. More...
void	send_integer_to_node (int destination, int message)
utility::vector1< int >	receive_integers_from_node (int source)
	Use MPI to receive a vector of integers from a particular node. More...
void	send_integers_to_node (int destination, utility::vector1< int > const &message)
double	receive_double_from_node (int source)
	Use MPI to receive a single double from a particular node. More...
void	send_double_to_node (int destination, double message)
utility::vector1< double >	receive_doubles_from_node (int source)
	Use MPI to receive a vector of doubles from a particular node. More...
void	send_doubles_to_node (int destination, utility::vector1< double > const &message)
platform::Size	get_undefined_size ()
	Get a numeric value for Size that represents an "undefined" value. More...
bool	is_undefined (platform::Size const &val)
	Check if a Size is undefined (i.e has the same value as utility::get_undefined_size() ) More...
platform::Real	get_undefined_real ()
	Get a numeric value for Real that represents an "undefined" value. More...
bool	is_undefined (platform::Real const &val)
	Check if a Real is undefined (i.e has the same value as utility::get_undefined_real() ) More...
bool	is_nan (platform::Real const &val)
bool	is_inf (platform::Real const &val)
platform::Real	round (platform::Real const &val)
platform::Real	copysign (platform::Real const &x, platform::Real const &y)
bool	operator== (history_queue_struct const &a, history_queue_struct const &b)
std::string	msg_name (simulate_mpi_message_type msg_type)
template<typename T1 , typename T2 >
std::ostream &	operator<< (std::ostream &os, std::pair< T1, T2 > const &v)
	Output function for std::pair object. More...
template<typename T1 , typename T2 >
std::ostream &	operator<< (std::ostream &os, std::map< T1, T2 > const &m)
	Output function for std::map object. More...
template<typename T >
std::ostream &	operator<< (std::ostream &os, std::list< T > const &l)
	Output function for std::list object. More...
template<platform::SSize L, class T >
std::ostream &	operator<< (std::ostream &os, utility::vectorL< L, T > const &v)
	Output function for utility::vector1 object. More...
static std::string const	UPPERCASE_LETTERS ("ABCDEFGHIJKLMNOPQRSTUVWXYZ")
static std::string const	LOWERCASE_LETTERS ("abcdefghijklmnopqrstuvwxyz")
static std::string const	LETTERS (UPPERCASE_LETTERS+LOWERCASE_LETTERS)
static std::string const	NUMERALS ("0123456789")
static std::string const	UPPERCASE_ALPHANUMERICS (UPPERCASE_LETTERS+NUMERALS)
static std::string const	LOWERCASE_ALPHANUMERICS (LOWERCASE_LETTERS+NUMERALS)
static std::string const	ALPHANUMERICS (LETTERS+NUMERALS)
utility::vector1< std::string >	split (const std::string &s)
	split given std::string using ' ' symbol. More...
utility::vector1< std::string >	split_whitespace (const std::string &s)
	split given std::string using whitespace as a separator. Unlike string_split_multi_delim(), any group of mixed whitespace counts only as a single seperator. More...
std::vector< std::string >	split_by_newlines (std::string const &s)
std::string	join (utility::vector1< std::string > const &s, std::string const &connector)
	combine strings with anything More...
std::string	join (std::vector< std::string > const &s, std::string const &connector)
	combine strings with anything More...
std::string	replace_spaces (std::string const &string_w_spaces, std::string const &replacement)
	replace space separations in a string with a connector such as '_' More...
std::list< std::string >	split_to_list (const std::string &s)
	split given std::string using ' ' symbol. More...
std::set< std::string >	split_to_set (std::string const &s)
	split given std::string to a set using ' ' symbol. More...
utility::vector1< std::string >	string_split (std::string const &in, char splitchar)
utility::vector1< std::string >	string_split_simple (std::string const &in, char splitchar= ' ')
	split to vector1< std::string > using arbitrary split character, but no empty strings (closer to python string::split) More...
utility::vector1< std::string >	string_split_multi_delim (std::string const &in, std::string splitchars)
float	string2float (std::string st)
	convert a string to a float, returns -1 on failure More...
int	string2int (std::string st)
	convert a string to an int, returns -1 on failure More...
platform::Size	string2Size (std::string st)
	convert a string to a Size, returns numeric::get_undefined_size() on failure More...
platform::Real	string2Real (std::string st)
	convert a string to a Real, returns numeric::get_undefined_real() on failure More...
std::string	Real2string (platform::Real, std::size_t const decimal_places)
	convert a Real to string at a number of decimal places, optionally pad left. More...
std::string	fmt_real (platform::Real, platform::Size const pad_left_newlen, std::size_t const decimal_places)
	convert a Real to a string, padding left with spaces until total number of char on left is equal to pad_lef_n More...
void	string2uint (const std::string &x, unsigned int *y)
bool	trimmed_compare (std::string const &s1, std::string const &s2)
	compares two strings ignoring leading and trailing spaces More...
bool	startswith (std::string const &haystack, std::string const &needle)
	True iff haystack starts with needle. More...
bool	endswith (std::string const &haystack, std::string const &needle)
	True iff haystack ends with needle. More...
void	slurp (std::istream &in, std::string &out)
void	trim (std::string &s, const std::string &drop=" ")
	Remove any charachters in "drop" from the front and back of the string. Use strip() for the value-return version. More...
std::string	strip (std::string const &source, std::string const &drop)
	Return a copy of the string with leading and trailing characters removed Any charachters in drop will be removed For the in place version, see trim() More...
std::string	pad_left (std::string s, platform::Size const newlen, char pad_with=' ')
	Add char to the left of the string. More...
std::string	pad_right (std::string 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)
std::string	make_tag_with_dashes (utility::vector1< int > res_vector, char const delimiter= ' ')
	Compactifies vectors of ints: 1 2 3 9 10 11 to "1-3 9-11". More...
std::string	make_tag_with_dashes (utility::vector1< int > res_vector, utility::vector1< char > chain_vector, char const delimiter)
std::string	make_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::pair< std::vector< int > , std::vector< char > >	get_resnum_and_chain (std::string const &s, bool &string_is_ok)
	converts string like "1-3 20-22" or "A:1-5 B:20-22" to vectors containing resnums and chains. More...
std::pair< std::vector< int > , std::vector< char > >	get_resnum_and_chain (std::string const &s)
	converts string like "1-3 20-22" or "A:1-5 B:20-22" to vectors containing resnums and chains. More...
std::pair< std::vector< int > , std::vector< std::string > >	get_resnum_and_segid (std::string const &s, bool &string_is_ok)
	converts string like "1-3 20-22" or "A:1-5 B:20-22" to vectors containing resnums and chains. More...
bool	get_resnum_and_chain_from_one_tag (std::string const &tag, std::vector< int > &resnum, std::vector< char > &chains)
	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...
template<class T >
std::string	to_string (const T &t)
template<class T >
T const	from_string (std::string const &s, T)
template<class T >
utility::vector1< T > const	string_split (std::string const &in, char splitchar, T)
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)
bool	is_true_string (std::string const &value_str)
	String accepted as a true value? More...
bool	is_false_string (std::string const &value_str)
	String accepted as a false value? More...
short int	min (short int const a, short int const b)
	min( short int, short int ) More...
int	min (int const a, int const b)
	min( int, int ) More...
long int	min (long int const a, long int const b)
	min( long int, long int ) More...
unsigned short int	min (unsigned short int const a, unsigned short int const b)
	min( unsigned short int, unsigned short int ) More...
unsigned int	min (unsigned int const a, unsigned int const b)
	min( unsigned int, unsigned int ) More...
unsigned long int	min (unsigned long int const a, unsigned long int const b)
	min( unsigned long int, unsigned long int ) More...
float	min (float const a, float const b)
	min( float, float ) More...
double	min (double const a, double const b)
	min( double, double ) More...
long double	min (long double const a, long double const b)
	min( long double, long double ) More...
template<typename T >
T const &	min (T const &a, T const &b, T const &c)
	min( a, b, c ) More...
template<typename T >
T const &	min (T const &a, T const &b, T const &c, T const &d)
	min( a, b, c, d ) More...
template<typename T >
T const &	min (T const &a, T const &b, T const &c, T const &d, T const &e)
	min( a, b, c, d, e ) More...
template<typename T >
T const &	min (T const &a, T const &b, T const &c, T const &d, T const &e, T const &f)
	min( a, b, c, d, e, f ) More...
short int	max (short int const a, short int const b)
	max( short int, short int ) More...
int	max (int const a, int const b)
	max( int, int ) More...
long int	max (long int const a, long int const b)
	max( long int, long int ) More...
unsigned short int	max (unsigned short int const a, unsigned short int const b)
	max( unsigned short int, unsigned short int ) More...
unsigned int	max (unsigned int const a, unsigned int const b)
	max( unsigned int, unsigned int ) More...
unsigned long int	max (unsigned long int const a, unsigned long int const b)
	max( unsigned long int, unsigned long int ) More...
float	max (float const a, float const b)
	max( float, float ) More...
double	max (double const a, double const b)
	max( double, double ) More...
long double	max (long double const a, long double const b)
	max( long double, long double ) More...
template<typename T >
T const &	max (T const &a, T const &b, T const &c)
	max( a, b, c ) More...
template<typename T >
T const &	max (T const &a, T const &b, T const &c, T const &d)
	max( a, b, c, d ) More...
template<typename T >
T const &	max (T const &a, T const &b, T const &c, T const &d, T const &e)
	max( a, b, c, d, e ) More...
template<typename T >
T const &	max (T const &a, T const &b, T const &c, T const &d, T const &e, T const &f)
	max( a, b, c, d, e, f ) More...
template<class T >
T	max (vector1< T > const &input)
	Find the largest value in a vector. More...
template<class T >
T	min (vector1< T > const &input)
	Find the smallest value in a vector. More...
template<class T >
vector1< T >::Size	arg_max (vector1< T > const &input)
	find the index of the largest value in a vector More...
template<class T >
vector1< T >::Size	arg_min (vector1< T > const &input)
	find the index of the smallest value in a vector More...
template<class T >
void	insert_middle (vector1< T > &vect, typename vector1< T >::Size const position, T const new_value, bool expand)
template<class T >
void	arg_greatest_several (vector1< T > const &input, vector1< typename vector1< T >::Size > &arg_list)
	Finds indices of the n largest items in input vector, where n is size of the arg_list vector. The indices are reported in decreasing sorted order by the value of the corresponding position in the input vector. If m is the size of the input vector, then this function is O( m n**2) More...
template<class T >
void	arg_least_several (vector1< T > const &input, vector1< typename vector1< T >::Size > &arg_list)
	Finds indices of the n smallest items in input vector, where n is size of the arg_list vector. The indices are reported in increasing sorted order by the value of the corresponding position in the input vector. If m is the size of the input vector, then this function is O( m n**2) More...
template<platform::SSize L, typename T , typename A >
bool	operator== (vectorL< L, T, A > const &a, vectorL< L, T, A > const &b)
	vectorL == vectorL More...
template<platform::SSize L, typename T , typename A >
bool	operator!= (vectorL< L, T, A > const &a, vectorL< L, T, A > const &b)
	vectorL != vectorL More...
template<platform::SSize L, typename T , typename A >
bool	operator< (vectorL< L, T, A > const &a, vectorL< L, T, A > const &b)
	vectorL < vectorL More...
template<platform::SSize L, typename T , typename A >
bool	operator<= (vectorL< L, T, A > const &a, vectorL< L, T, A > const &b)
	vectorL <= vectorL More...
template<platform::SSize L, typename T , typename A >
bool	operator>= (vectorL< L, T, A > const &a, vectorL< L, T, A > const &b)
	vectorL >= vectorL More...
template<platform::SSize L, typename T , typename A >
bool	operator> (vectorL< L, T, A > const &a, vectorL< L, T, A > const &b)
	vectorL > vectorL More...
template<platform::SSize L, typename T , typename A >
bool	operator== (vectorL< L, T, A > const &a, std::vector< T, A > const &b)
	vectorL == std::vector More...
template<platform::SSize L, typename T , typename A >
bool	operator!= (vectorL< L, T, A > const &a, std::vector< T, A > const &b)
	vectorL != std::vector More...
template<platform::SSize L, typename T , typename A >
bool	operator< (vectorL< L, T, A > const &a, std::vector< T, A > const &b)
	vectorL < std::vector More...
template<platform::SSize L, typename T , typename A >
bool	operator<= (vectorL< L, T, A > const &a, std::vector< T, A > const &b)
	vectorL <= std::vector More...
template<platform::SSize L, typename T , typename A >
bool	operator>= (vectorL< L, T, A > const &a, std::vector< T, A > const &b)
	vectorL >= std::vector More...
template<platform::SSize L, typename T , typename A >
bool	operator> (vectorL< L, T, A > const &a, std::vector< T, A > const &b)
	vectorL > std::vector More...
template<platform::SSize L, typename T , typename A >
bool	operator== (std::vector< T, A > const &a, vectorL< L, T, A > const &b)
	std::vector == vectorL More...
template<platform::SSize L, typename T , typename A >
bool	operator!= (std::vector< T, A > const &a, vectorL< L, T, A > const &b)
	std::vector != vectorL More...
template<platform::SSize L, typename T , typename A >
bool	operator< (std::vector< T, A > const &a, vectorL< L, T, A > const &b)
	std::vector < vectorL More...
template<platform::SSize L, typename T , typename A >
bool	operator<= (std::vector< T, A > const &a, vectorL< L, T, A > const &b)
	std::vector <= vectorL More...
template<platform::SSize L, typename T , typename A >
bool	operator>= (std::vector< T, A > const &a, vectorL< L, T, A > const &b)
	std::vector >= vectorL More...
template<platform::SSize L, typename T , typename A >
bool	operator> (std::vector< T, A > const &a, vectorL< L, T, A > const &b)
	std::vector > vectorL More...
template<platform::SSize L, typename T , typename A >
void	swap (vectorL< L, T, A > &a, vectorL< L, T, A > &b)
	swap( vectorL, vectorL ) More...
template<platform::SSize L, typename T , typename A >
void	swap (vectorL< L, T, A > &a, std::vector< T, A > &b)
	swap( vectorL, std::vector ) More...
template<platform::SSize L, typename T , typename A >
void	swap (std::vector< T, A > &a, vectorL< L, T, A > &b)
	swap( std::vector, vectorL ) More...
template<platform::SSize L, typename A >
bool	operator== (vectorL< L, bool, A > const &a, vectorL< L, bool, A > const &b)
	vectorL == vectorL More...
template<platform::SSize L, typename A >
bool	operator!= (vectorL< L, bool, A > const &a, vectorL< L, bool, A > const &b)
	vectorL != vectorL More...
template<platform::SSize L, typename A >
bool	operator< (vectorL< L, bool, A > const &a, vectorL< L, bool, A > const &b)
	vectorL < vectorL More...
template<platform::SSize L, typename A >
bool	operator<= (vectorL< L, bool, A > const &a, vectorL< L, bool, A > const &b)
	vectorL <= vectorL More...
template<platform::SSize L, typename A >
bool	operator>= (vectorL< L, bool, A > const &a, vectorL< L, bool, A > const &b)
	vectorL >= vectorL More...
template<platform::SSize L, typename A >
bool	operator> (vectorL< L, bool, A > const &a, vectorL< L, bool, A > const &b)
	vectorL > vectorL More...
template<platform::SSize L, typename A >
bool	operator== (vectorL< L, bool, A > const &a, std::vector< bool, A > const &b)
	vectorL == std::vector More...
template<platform::SSize L, typename A >
bool	operator!= (vectorL< L, bool, A > const &a, std::vector< bool, A > const &b)
	vectorL != std::vector More...
template<platform::SSize L, typename A >
bool	operator< (vectorL< L, bool, A > const &a, std::vector< bool, A > const &b)
	vectorL < std::vector More...
template<platform::SSize L, typename A >
bool	operator<= (vectorL< L, bool, A > const &a, std::vector< bool, A > const &b)
	vectorL <= std::vector More...
template<platform::SSize L, typename A >
bool	operator>= (vectorL< L, bool, A > const &a, std::vector< bool, A > const &b)
	vectorL >= std::vector More...
template<platform::SSize L, typename A >
bool	operator> (vectorL< L, bool, A > const &a, std::vector< bool, A > const &b)
	vectorL > std::vector More...
template<platform::SSize L, typename A >
bool	operator== (std::vector< bool, A > const &a, vectorL< L, bool, A > const &b)
	std::vector == vectorL More...
template<platform::SSize L, typename A >
bool	operator!= (std::vector< bool, A > const &a, vectorL< L, bool, A > const &b)
	std::vector != vectorL More...
template<platform::SSize L, typename A >
bool	operator< (std::vector< bool, A > const &a, vectorL< L, bool, A > const &b)
	std::vector < vectorL More...
template<platform::SSize L, typename A >
bool	operator<= (std::vector< bool, A > const &a, vectorL< L, bool, A > const &b)
	std::vector <= vectorL More...
template<platform::SSize L, typename A >
bool	operator>= (std::vector< bool, A > const &a, vectorL< L, bool, A > const &b)
	std::vector >= vectorL More...
template<platform::SSize L, typename A >
bool	operator> (std::vector< bool, A > const &a, vectorL< L, bool, A > const &b)
	std::vector > vectorL More...
template<platform::SSize L, typename A >
void	swap (vectorL< L, bool, A > &a, vectorL< L, bool, A > &b)
	swap( vectorL, vectorL ) More...
template<platform::SSize L, typename A >
void	swap (vectorL< L, bool, A > &a, std::vector< bool, A > &b)
	swap( vectorL, std::vector ) More...
template<platform::SSize L, typename A >
void	swap (std::vector< bool, A > &a, vectorL< L, bool, A > &b)
	swap( std::vector, vectorL ) More...

Variables
static CSI_Sequence const	CSI_Reset ("\x1b[0m")
static CSI_Sequence const	CSI_Bold ("\x1b[1m")
static CSI_Sequence const	CSI_Underline ("\x1b[4m")
static CSI_Sequence const	CSI_Black ("\x1b[30m")
static CSI_Sequence const	CSI_Red ("\x1b[31m")
static CSI_Sequence const	CSI_Green ("\x1b[32m")
static CSI_Sequence const	CSI_Yellow ("\x1b[33m")
static CSI_Sequence const	CSI_Blue ("\x1b[34m")
static CSI_Sequence const	CSI_Magenta ("\x1b[35m")
static CSI_Sequence const	CSI_Cyan ("\x1b[36m")
static CSI_Sequence const	CSI_White ("\x1b[37m")
static CSI_Sequence const	CSI_bgBlack ("\x1b[40m")
static CSI_Sequence const	CSI_bgRed ("\x1b[41m")
static CSI_Sequence const	CSI_bgGreen ("\x1b[42m")
static CSI_Sequence const	CSI_bgYellow ("\x1b[43m")
static CSI_Sequence const	CSI_bgBlue ("\x1b[44m")
static CSI_Sequence const	CSI_bgMagenta ("\x1b[45m")
static CSI_Sequence const	CSI_bgCyan ("\x1b[46m")
static CSI_Sequence const	CSI_bgWhite ("\x1b[47m")
static void(*	main_exit_callback )(void)=0
	Place holder for 'end-action' of utility::exit(…) More...

Detailed Description

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

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

STL Headers.

determines all possible rings in a graph.

#include <iostream> // debug only

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

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

Author

Oliver Lange

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

Typedef Documentation

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

Definition at line 24 of file heap.fwd.hh.

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

Definition at line 22 of file heap.fwd.hh.

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

Definition at line 33 of file inline_file_provider.hh.

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

Definition at line 30 of file inline_file_provider.hh.

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

Definition at line 24 of file SimulateMPI.fwd.hh.

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

Definition at line 21 of file SimulateMPI.fwd.hh.

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

Definition at line 23 of file integer_mapping.fwd.hh.

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

Definition at line 21 of file integer_mapping.fwd.hh.

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

Definition at line 142 of file exit.hh.

typedef vector0< bool > utility::vector0_bool

Definition at line 44 of file vector0.fwd.hh.

typedef vector0< char > utility::vector0_char

Definition at line 62 of file vector0.fwd.hh.

typedef vector0< double > utility::vector0_double

Definition at line 60 of file vector0.fwd.hh.

typedef vector0< float > utility::vector0_float

Definition at line 59 of file vector0.fwd.hh.

typedef vector0< int > utility::vector0_int

Definition at line 50 of file vector0.fwd.hh.

typedef vector0< long int > utility::vector0_long

Definition at line 51 of file vector0.fwd.hh.

typedef vector0< long double > utility::vector0_longdouble

Definition at line 61 of file vector0.fwd.hh.

typedef vector0< signed char > utility::vector0_schar

Definition at line 64 of file vector0.fwd.hh.

typedef vector0< short int > utility::vector0_short

Definition at line 49 of file vector0.fwd.hh.

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

Definition at line 56 of file vector0.fwd.hh.

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

Definition at line 55 of file vector0.fwd.hh.

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

Definition at line 58 of file vector0.fwd.hh.

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

Definition at line 57 of file vector0.fwd.hh.

typedef vector0< unsigned char > utility::vector0_uchar

Definition at line 63 of file vector0.fwd.hh.

typedef vector0< unsigned int > utility::vector0_uint

Definition at line 53 of file vector0.fwd.hh.

typedef vector0< unsigned long int > utility::vector0_ulong

Definition at line 54 of file vector0.fwd.hh.

typedef vector0< unsigned short int > utility::vector0_ushort

Definition at line 52 of file vector0.fwd.hh.

typedef vector1< bool > utility::vector1_bool

Definition at line 44 of file vector1.fwd.hh.

typedef vector1< char > utility::vector1_char

Definition at line 62 of file vector1.fwd.hh.

typedef vector1< double > utility::vector1_double

Definition at line 60 of file vector1.fwd.hh.

typedef vector1< float > utility::vector1_float

Definition at line 59 of file vector1.fwd.hh.

typedef vector1< int > utility::vector1_int

Definition at line 50 of file vector1.fwd.hh.

typedef vector1< long int > utility::vector1_long

Definition at line 51 of file vector1.fwd.hh.

typedef vector1< long double > utility::vector1_longdouble

Definition at line 61 of file vector1.fwd.hh.

typedef vector1< signed char > utility::vector1_schar

Definition at line 64 of file vector1.fwd.hh.

typedef vector1< short int > utility::vector1_short

Definition at line 49 of file vector1.fwd.hh.

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

Definition at line 56 of file vector1.fwd.hh.

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

Definition at line 55 of file vector1.fwd.hh.

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

Definition at line 58 of file vector1.fwd.hh.

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

Definition at line 57 of file vector1.fwd.hh.

typedef vector1< unsigned char > utility::vector1_uchar

Definition at line 63 of file vector1.fwd.hh.

typedef vector1< unsigned int > utility::vector1_uint

Definition at line 53 of file vector1.fwd.hh.

typedef vector1< unsigned long int > utility::vector1_ulong

Definition at line 54 of file vector1.fwd.hh.

typedef vector1< unsigned short int > utility::vector1_ushort

Definition at line 52 of file vector1.fwd.hh.

Enumeration Type Documentation

enum utility::simulate_mpi_message_type

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

Enumerator
smpi_char
smpi_integer
smpi_string
smpi_double
smpi_integers
smpi_doubles

Definition at line 45 of file SimulateMPI.hh.

Function Documentation

void utility::add_exit_callback

(

UtilityExitCallBack

cb

)

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

Definition at line 66 of file exit.cc.

References get_all_exit_callbacks().

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

static

template<class T >

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

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

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

Definition at line 138 of file vector1.functions.hh.

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

template<class T >

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

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

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

Definition at line 170 of file vector1.functions.hh.

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

template<class T >

vector1< T >::Size utility::arg_max

(

vector1< T > const &

input

)

find the index of the largest value in a vector

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

Definition at line 65 of file vector1.functions.hh.

References debug_assert, test.T200_Scoring::ii, and test.T007_TracerIO::T.

template<class T >

vector1< T >::Size utility::arg_min

(

vector1< T > const &

input

)

find the index of the smallest value in a vector

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

Definition at line 86 of file vector1.functions.hh.

References debug_assert, test.T200_Scoring::ii, and test.T007_TracerIO::T.

Referenced by numeric::geometry::vector_normal_to_ring_plane_of_best_fit().

template<typename T >

int utility::argmax

(

const std::vector< T > &

iterable

)

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

Adheres to STL numbering (0-indexed).

Definition at line 67 of file minmax.hh.

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).

Definition at line 85 of file minmax.hh.

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).

Definition at line 29 of file minmax.hh.

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).

Definition at line 47 of file minmax.hh.

unsigned char utility::code_from_6bit ( unsigned char  _8bit )

inline

Definition at line 52 of file Binary_Util.hh.

Referenced by decode_32_to_24().

unsigned char utility::code_to_6bit ( unsigned char  _6bit )

inline

uuencode

Definition at line 46 of file Binary_Util.hh.

Referenced by encode_24_to_32().

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

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

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

Definition at line 184 of file exit.cc.

References exit().

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

inline

Definition at line 76 of file numbers.hh.

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

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

Definition at line 54 of file Binary_Util.cc.

References decode_32_to_24().

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

inline

Definition at line 77 of file Binary_Util.hh.

References code_from_6bit().

Referenced by decode6bit().

template<class Target , class Source >

Target utility::down_cast ( Source &  s )

inline

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

Note

Usage: down_cast< Type & > where Type can be const-qualified

For down-casting when you know the cast is valid

Can't use for hierarchies with virtual base classes

Assert intentionally won't compile if a virtual base class is present

Definition at line 44 of file down_cast.hh.

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

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

template<class Target , class Source >

Target utility::down_cast ( Source *  p )

inline

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

Note

Usage: down_cast< Type * > where Type can be const-qualified

For down-casting when you know the cast is valid

Can't use for hierarchies with virtual base classes

Assert intentionally won't compile if a virtual base class is present

Definition at line 60 of file down_cast.hh.

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

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

Definition at line 25 of file Binary_Util.cc.

References encode_24_to_32(), and make_symmdef_file_denovo::length.

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

inline

Definition at line 61 of file Binary_Util.hh.

References code_to_6bit().

Referenced by encode6bit().

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

True iff haystack ends with needle.

Definition at line 299 of file string_util.cc.

Referenced by tools.CppParser.CppType::getFile(), tools.CppParser.CppFunction::getReturnValuePolicyString(), tools.CppParser.CppFunction::isWrapable(), and exclude::set_default_call_policies().

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

inline

Exit with file + line + optional status.

Definition at line 118 of file exit.hh.

References exit().

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

Exit with file + line + message + optional status.

Definition at line 108 of file exit.cc.

References begin, utility::io::oc::cerr, utility::io::izstream::close(), app.delta_score_per_mutation::data, utility::io::ocstream::flush(), get_all_exit_callbacks(), ObjexxFCL::getline(), utility::file::gzip(), main_exit_callback, and print_backtrace().

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

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

inline

Exit with file + line + status.

Note

Deprecated: For backwards compatibility with earlier version

Definition at line 133 of file exit.hh.

References exit().

std::string utility::file_basename

(

const std::string &

full_path

)

Definition at line 428 of file string_util.cc.

References filename().

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

std::string utility::file_contents

(

std::string const &

file_name

)

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

Definition at line 405 of file string_util.cc.

References utility::io::izstream::close(), ObjexxFCL::getline(), test.T200_Scoring::ii, line, and utility::options::OptionKeys::options::table::text.

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

std::string utility::filename

(

const std::string &

path

)

Definition at line 432 of file string_util.cc.

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

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

template<typename BidirectionalIterator , typename T >

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

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

Definition at line 26 of file iter_util.hh.

References assign_charges::first.

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

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

Definition at line 259 of file string_util.cc.

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

template<class T >

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

inline

Definition at line 61 of file string_util.hh.

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

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

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

(

)

Array to hold all additional exit-callbacks.

Definition at line 60 of file exit.cc.

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

platform::Size utility::get_num_digits

(

platform::Size

value

)

Definition at line 764 of file string_util.cc.

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

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

Author

rhiju

Definition at line 630 of file string_util.cc.

References basic::options::OptionKeys::run::chain, get_resnum_and_chain_from_one_tag(), replace_in(), clean_pdb_keep_ligand::resnum, string_split(), and basic::options::OptionKeys::in::file::tags.

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

std::pair< std::vector< int >, std::vector< char > > utility::get_resnum_and_chain

(

std::string const &

s

)

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

Definition at line 646 of file string_util.cc.

References get_resnum_and_chain().

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

helper function for get_resnum_and_chain

Definition at line 695 of file string_util.cc.

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

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

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

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

Definition at line 652 of file string_util.cc.

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

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

helper function for get_resnum_and_chain

Definition at line 734 of file string_util.cc.

References ObjexxFCL::ints_of(), and runtime_assert.

Referenced by get_resnum_and_segid().

platform::Real utility::get_undefined_real ( )

inline

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

Definition at line 50 of file numbers.hh.

Referenced by string2Real().

platform::Size utility::get_undefined_size ( )

inline

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

Definition at line 38 of file numbers.hh.

References max().

Referenced by is_undefined(), and string2Size().

template<class T >

bool utility::has_key	(	std::map< T, T >	a_map,
		T	key
	)

Definition at line 20 of file map_util.cc.

Referenced by app.pyrosetta_toolkit.modules.DesignBreakdown.SequenceResults::add_residue(), and options::main().

template<class T >

bool utility::has_key	(	std::map< T, T > const &	a_map,
		T const &	key
	)

Does the map have the key?

template<class T >

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

Definition at line 103 of file vector1.functions.hh.

References test.T200_Scoring::ii, swap(), and test.T007_TracerIO::T.

Referenced by arg_greatest_several(), and arg_least_several().

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

inline

String accepted as a false value?

Definition at line 345 of file string_util.hh.

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

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

inline

Definition at line 66 of file numbers.hh.

References numeric::isinf().

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

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

inline

Definition at line 61 of file numbers.hh.

References numeric::isnan().

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

bool utility::is_string_numeric

(

std::string const &

input

)

Definition at line 390 of file string_util.cc.

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

inline

String accepted as a true value?

Definition at line 324 of file string_util.hh.

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

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

inline

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

Definition at line 44 of file numbers.hh.

References get_undefined_size().

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

inline

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

Definition at line 56 of file numbers.hh.

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

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

combine strings with anything

Definition at line 93 of file string_util.cc.

References begin.

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

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

combine strings with anything

Definition at line 103 of file string_util.cc.

References begin.

template<class T >

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

combine vector with anything

Definition at line 119 of file string_util.hh.

References begin.

template<platform::SSize L>

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

Join vector of strings in to single string.

Definition at line 135 of file string_util.hh.

References begin.

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

static

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

static

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

static

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

Definition at line 566 of file string_util.cc.

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

std::string utility::make_tag

(

utility::vector1< int >

res_vector

)

Definition at line 611 of file string_util.cc.

References ObjexxFCL::string_of(), and tag.

Referenced by prepare_threaded_model().

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".

Definition at line 508 of file string_util.cc.

References chains.

Referenced by prepare_threaded_model().

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

Definition at line 520 of file string_util.cc.

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

template<class T >

T utility::max

(

vector1< T > const &

input

)

Find the largest value in a vector.

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

Definition at line 31 of file vector1.functions.hh.

References debug_assert, test.T200_Scoring::ii, and test.T007_TracerIO::T.

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

inline

max( short int, short int )

Definition at line 163 of file utility.functions.hh.

Referenced by max().

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

inline

max( int, int )

Definition at line 172 of file utility.functions.hh.

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

inline

max( long int, long int )

Definition at line 181 of file utility.functions.hh.

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

inline

max( unsigned short int, unsigned short int )

Definition at line 190 of file utility.functions.hh.

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

inline

max( unsigned int, unsigned int )

Definition at line 199 of file utility.functions.hh.

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

inline

max( unsigned long int, unsigned long int )

Definition at line 208 of file utility.functions.hh.

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

inline

max( float, float )

Definition at line 217 of file utility.functions.hh.

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

inline

max( double, double )

Definition at line 226 of file utility.functions.hh.

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

inline

max( long double, long double )

Definition at line 235 of file utility.functions.hh.

template<typename T >

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

inline

max( a, b, c )

Definition at line 249 of file utility.functions.hh.

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 )

Definition at line 259 of file utility.functions.hh.

References max().

template<typename T >

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

inline

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

Definition at line 269 of file utility.functions.hh.

References max(), and max().

template<typename T >

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

inline

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

Definition at line 279 of file utility.functions.hh.

References max(), and max().

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

inline

min( short int, short int )

Definition at line 35 of file utility.functions.hh.

Referenced by min().

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

inline

min( int, int )

Definition at line 44 of file utility.functions.hh.

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

Definition at line 48 of file vector1.functions.hh.

References debug_assert, test.T200_Scoring::ii, and test.T007_TracerIO::T.

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

inline

min( long int, long int )

Definition at line 53 of file utility.functions.hh.

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

inline

min( unsigned short int, unsigned short int )

Definition at line 62 of file utility.functions.hh.

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

inline

min( unsigned int, unsigned int )

Definition at line 71 of file utility.functions.hh.

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

inline

min( unsigned long int, unsigned long int )

Definition at line 80 of file utility.functions.hh.

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

inline

min( float, float )

Definition at line 89 of file utility.functions.hh.

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

inline

min( double, double )

Definition at line 98 of file utility.functions.hh.

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

inline

min( long double, long double )

Definition at line 107 of file utility.functions.hh.

template<typename T >

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

inline

min( a, b, c )

Definition at line 121 of file utility.functions.hh.

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 )

Definition at line 131 of file utility.functions.hh.

References min().

template<typename T >

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

inline

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

Definition at line 141 of file utility.functions.hh.

References min(), and min().

template<typename T >

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

inline

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

Definition at line 151 of file utility.functions.hh.

References min(), and min().

int utility::mpi_nprocs

(

)

Definition at line 265 of file mpi_util.cc.

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

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

int utility::mpi_rank

(

)

Definition at line 254 of file mpi_util.cc.

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

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

std::string utility::msg_name

(

simulate_mpi_message_type

msg_type

)

Definition at line 21 of file SimulateMPI.cc.

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

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

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

static

template<typename B >

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

BitSet != BitSet.

Definition at line 358 of file BitSet.hh.

template<typename B >

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

BitVector != BitVector.

Definition at line 408 of file BitVector.hh.

template<platform::SSize L, typename A >

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

vectorL != vectorL

template<platform::SSize L, typename A >

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

vectorL != std::vector

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

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

vectorL != vectorL

template<platform::SSize L, typename A >

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

std::vector != vectorL

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

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

vectorL != std::vector

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

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

std::vector != vectorL

template<typename B >

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

BitSet + BitSet: Union.

Definition at line 216 of file BitSet.hh.

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

template<typename B >

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

BitVector + BitVector: Union.

Definition at line 238 of file BitVector.hh.

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

template<typename B >

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

BitSet - BitSet: Difference.

Definition at line 240 of file BitSet.hh.

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

template<typename B >

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

BitVector - BitVector: Difference.

Definition at line 262 of file BitVector.hh.

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

template<platform::SSize L, typename A >

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

vectorL < vectorL

template<platform::SSize L, typename A >

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

vectorL < std::vector

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

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

vectorL < vectorL

template<platform::SSize L, typename A >

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

std::vector < vectorL

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

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

vectorL < std::vector

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

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

std::vector < vectorL

template<typename T1 , typename T2 >

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

Output function for std::pair object.

---

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

Definition at line 38 of file stream_util.hh.

References test.T850_SubClassing::v.

template<typename T1 , typename T2 >

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

Output function for std::map object.

Definition at line 50 of file stream_util.hh.

References basic::options::OptionKeys::score::fiber_diffraction::p.

template<typename T >

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

Output function for std::list object.

Definition at line 67 of file stream_util.hh.

References basic::options::OptionKeys::in::file::l, and basic::options::OptionKeys::score::fiber_diffraction::p.

template<platform::SSize L, class T >

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

Output function for utility::vector1 object.

Definition at line 83 of file stream_util.hh.

References test.T850_SubClassing::v.

template<platform::SSize L, typename A >

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

vectorL <= vectorL

template<platform::SSize L, typename A >

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

vectorL <= std::vector

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

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

vectorL <= vectorL

template<platform::SSize L, typename A >

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

std::vector <= vectorL

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

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

vectorL <= std::vector

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

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

std::vector <= vectorL

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

inline

Definition at line 42 of file recent_history_queue.hh.

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

template<typename B >

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

BitSet == BitSet.

Definition at line 348 of file BitSet.hh.

template<typename B >

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

BitVector == BitVector.

Definition at line 398 of file BitVector.hh.

template<platform::SSize L, typename A >

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

vectorL == vectorL

template<platform::SSize L, typename A >

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

vectorL == std::vector

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

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

vectorL == vectorL

template<platform::SSize L, typename A >

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

std::vector == vectorL

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

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

vectorL == std::vector

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

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

std::vector == vectorL

template<platform::SSize L, typename A >

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

vectorL > vectorL

template<platform::SSize L, typename A >

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

vectorL > std::vector

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

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

vectorL > vectorL

template<platform::SSize L, typename A >

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

std::vector > vectorL

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

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

vectorL > std::vector

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

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

std::vector > vectorL

template<platform::SSize L, typename A >

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

vectorL >= vectorL

template<platform::SSize L, typename A >

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

vectorL >= std::vector

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

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

vectorL >= vectorL

template<platform::SSize L, typename A >

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

std::vector >= vectorL

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

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

vectorL >= std::vector

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

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

std::vector >= vectorL

template<typename B >

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

BitSet | BitSet: Union.

Definition at line 228 of file BitSet.hh.

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

template<typename B >

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

BitVector | BitVector: Union.

Definition at line 250 of file BitVector.hh.

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

template<class T >

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

Add char to the left of the string.

Definition at line 248 of file string_util.hh.

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

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

Add char to the left of the string.

Definition at line 331 of file string_util.cc.

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

Referenced by fmt_real(), and pad_left().

template<class T >

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

Add char to the right of a string.

Definition at line 256 of file string_util.hh.

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

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

Add char to the right of a string.

Definition at line 340 of file string_util.cc.

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

Referenced by pad_right().

std::string utility::pathname

(

const std::string &

path

)

Definition at line 437 of file string_util.cc.

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

void utility::rand_sleep

(

)

Definition at line 79 of file basic_sys_util.cc.

References sys_sleep().

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

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

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

Definition at line 251 of file string_util.cc.

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

Referenced by fmt_real().

char utility::receive_char_from_node

(

int

source

)

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

Definition at line 312 of file mpi_util.cc.

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

double utility::receive_double_from_node

(

int

source

)

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

Definition at line 385 of file mpi_util.cc.

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

utility::vector1< double > utility::receive_doubles_from_node

(

int

source

)

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

Definition at line 409 of file mpi_util.cc.

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

int utility::receive_integer_from_anyone

(

)

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

Definition at line 276 of file mpi_util.cc.

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

Referenced by main().

int utility::receive_integer_from_node

(

int

source

)

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

Definition at line 336 of file mpi_util.cc.

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

Referenced by main().

utility::vector1< int > utility::receive_integers_from_node

(

int

source

)

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

Definition at line 360 of file mpi_util.cc.

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

std::string utility::receive_string_from_node

(

int

source

)

Use MPI to receive a string from a particular node.

Definition at line 288 of file mpi_util.cc.

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

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

void utility::remove_exit_callback

(

UtilityExitCallBack

cb

)

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

Definition at line 71 of file exit.cc.

References begin, and get_all_exit_callbacks().

std::string utility::replace_environment_variables

(

std::string

input

)

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

Definition at line 441 of file string_util.cc.

References basic::options::OptionKeys::cutoutdomain::end, app.surface_docking.surface_docking::input, basic::options::OptionKeys::cutoutdomain::start, and utility_exit_with_message.

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

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

inline

Definition at line 307 of file string_util.hh.

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.

Definition at line 769 of file string_util.cc.

References name, and make_symmdef_file_denovo::pos.

Referenced by get_resnum_and_chain(), get_resnum_and_segid(), mg_modeler_test(), and rna_score_test().

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 '_'

Definition at line 113 of file string_util.cc.

References join(), and split().

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

inline

Definition at line 71 of file numbers.hh.

References round().

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

inline

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

Definition at line 295 of file string_util.hh.

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

Definition at line 324 of file mpi_util.cc.

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

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

Definition at line 397 of file mpi_util.cc.

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

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

Definition at line 421 of file mpi_util.cc.

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

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

Definition at line 348 of file mpi_util.cc.

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

Referenced by main().

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

Definition at line 372 of file mpi_util.cc.

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

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

Definition at line 300 of file mpi_util.cc.

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

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

void utility::set_main_exit_callback

(

UtilityExitCallBack

my_callback

)

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

Definition at line 54 of file exit.cc.

References main_exit_callback.

Referenced by set_pyexit_callback(), and utility::py::PyExitCallback::set_PyExitCallBack().

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

Definition at line 305 of file string_util.cc.

References ObjexxFCL::getline(), and line.

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

(

const std::string &

s

)

split given std::string using ' ' symbol.

Definition at line 38 of file string_util.cc.

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

Referenced by app.pyrosetta_toolkit.modules.prettytable.prettytable.PrettyTable::_stringify_row(), BuildBindings::buildModule_All(), BuildBindings::buildModule_One(), app.pyrosetta_toolkit.modules.DesignBreakdown.DesignBreakdown::calculate_results(), BuildBindings::calculate_source_modification_date(), app.pyrosetta_toolkit.window_modules.design.ResfileDesignWindow.ResfileDesignWindow::check_for_residue_existance(), app.pyrosetta_toolkit.modules.tools.output::convert_PDBLIST_to_sqlite3db(), app.pyrosetta_toolkit.modules.ScoreAnalysis.ScoreAnalysis::copy_results(), basic::mpi::DbMoverMessageListener::deserialize_data(), arls_impl::find_programs(), BuildBindings::get_all_rosetta_objs(), BuildBindings::get_compiler_defines(), app.pyrosetta_toolkit.modules.tools.interfaces.Antibodies::getContactCDRs(), PhiPsi::hbond_record(), exclude::isFileInScons(), tools.CppParser.CppClass::isPublicMembersWrappable(), best_ifaceE::main(), get_scores::main(), prune_atdiff_top5pct::main(), BuildBindings::main(), app.pyrosetta_toolkit.window_modules.design.ResfileDesignWindow.ResfileDesignWindow::nextRes(), app.pyrosetta_toolkit.window_modules.ligand_ncaa_ptm_manager.ligand_ncaa_ptm_manager.ligand_ncaa_ptm_manager::open_param_or_patch(), app.pyrosetta_toolkit.modules.tools.output::output_molfile_to_params(), tools.CppParser.GccXML::parse(), app.pyrosetta_toolkit.window_modules.scorefunction.ScoreFxnControl.ScoreFxnControl::populateScoreList(), app.pyrosetta_toolkit.window_modules.design.ResfileDesignWindow.ResfileDesignWindow::prevRes(), app.pyrosetta_toolkit.modules.ScoreAnalysis.ScoreAnalysis::read_FASC(), app.pyrosetta_toolkit.modules.ScoreAnalysis.ScoreAnalysis::read_SC(), register_options(), app.pyrosetta_toolkit.window_modules.design.ResfileDesignWindow.ResfileDesignWindow::remove_from_current_designs_callback(), app.pyrosetta_toolkit.modules.tools.general_tools::renameandsave(), replace_spaces(), app.pyrosetta_toolkit.modules.calibur.calibur::ret_centers(), app.pyrosetta_toolkit.modules.tools.loops::return_residue_array(), run(), demo.D090_Ala_scan::scanning_analysis(), app.pyrosetta_toolkit.window_main.frames.SimpleAnalysisFrame.SimpleAnalysisFrame::score_loops(), basic::Tracer::set_ios_hook(), app.pyrosetta_toolkit.window_modules.design.ResfileDesignWindow.ResfileDesignWindow::updateInfo(), BuildBindings::windows_buildOneNamespace(), and tools.CppParser::wrapModule().

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.

Definition at line 71 of file string_util.cc.

References amino_acids::size, and basic::options::OptionKeys::cutoutdomain::start.

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

(

const std::string &

s

)

split given std::string using ' ' symbol.

split given std::string using ' ' symbol.

Definition at line 120 of file string_util.cc.

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

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

std::set< std::string > utility::split_to_set

(

const std::string &

s

)

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

split given std::string using ' ' symbol.

Definition at line 140 of file string_util.cc.

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

utility::vector1< std::string > utility::split_whitespace

(

const std::string &

s

)

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

Definition at line 58 of file string_util.cc.

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

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

True iff haystack starts with needle.

Definition at line 293 of file string_util.cc.

Referenced by BuildBindings::buildModule_One(), tools.CppParser.CppClass::getHeldType(), tools.CppParser.CppFunction::isWrapable(), and tools.CppParser.GccXML::parse().

float utility::string2float

(

std::string

st

)

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

convert a string to a float

Definition at line 208 of file string_util.cc.

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

int utility::string2int

(

std::string

st

)

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

convert a string to an int

Definition at line 219 of file string_util.cc.

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

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

platform::Real utility::string2Real

(

std::string

st

)

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

Definition at line 241 of file string_util.cc.

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

platform::Size utility::string2Size

(

std::string

st

)

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

Definition at line 230 of file string_util.cc.

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

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

Definition at line 271 of file string_util.cc.

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

template<class T >

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

inline

Definition at line 76 of file string_util.hh.

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

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

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

Definition at line 160 of file string_util.cc.

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

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

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

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

Definition at line 193 of file string_util.cc.

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

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

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

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

Definition at line 175 of file string_util.cc.

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

std::string utility::string_to_sha1

(

std::string const &

input_string

)

Definition at line 472 of file string_util.cc.

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()

Definition at line 323 of file string_util.cc.

References trim().

Referenced by trim().

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

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

Definition at line 350 of file string_util.cc.

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

template<typename B >

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

swap( BitSet, BitSet )

Definition at line 263 of file BitSet.hh.

template<typename B >

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

swap( BitVector, BitVector )

Definition at line 313 of file BitVector.hh.

template<platform::SSize L, typename A >

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

inline

swap( vectorL, vectorL )

Definition at line 760 of file vectorL_bool.hh.

References utility::vectorL< L, bool, A >::swap().

template<platform::SSize L, typename A >

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

inline

swap( vectorL, std::vector )

Definition at line 770 of file vectorL_bool.hh.

References utility::vectorL< L, bool, A >::swap().

template<platform::SSize L, typename A >

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

inline

swap( std::vector, vectorL )

Definition at line 780 of file vectorL_bool.hh.

References utility::vectorL< L, bool, A >::swap().

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 )

Definition at line 815 of file vectorL.hh.

References utility::vectorL< SSize, T, A >::swap().

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

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

inline

swap( vectorL, std::vector )

Definition at line 825 of file vectorL.hh.

References utility::vectorL< SSize, T, A >::swap().

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

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

inline

swap( std::vector, vectorL )

Definition at line 835 of file vectorL.hh.

References utility::vectorL< SSize, T, A >::swap().

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

inline

Definition at line 31 of file Binary_Util.hh.

References app.delta_score_per_mutation::data.

void utility::sys_sleep

(

double const

seconds

)

Sleep for a specified number of seconds.

Definition at line 51 of file basic_sys_util.cc.

References utility::io::oc::cout, BuildBindings::Sleep(), and x().

Referenced by rand_sleep().

std::string utility::timestamp

(

)

Generate timestamp string.

Definition at line 90 of file basic_sys_util.cc.

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

std::string utility::timestamp_short

(

)

Generate timestamp string, short format.

Definition at line 117 of file basic_sys_util.cc.

References timestamp().

template<class T >

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

inline

Definition at line 52 of file string_util.hh.

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

Referenced by numeric::expression_parser::ExpressionCreator::handle_function_expression(), numeric::expression_parser::SimpleExpressionCreator::handle_variable_expression(), main(), pad_left(), pad_right(), utility::SimulateMPIData::pop_next_message_for_node_of_type(), utility::SimulateMPIData::pop_next_message_of_type(), basic::database::schema_generator::DbText::print(), read_native_sequence_for_entity_elements(), basic::mpi::DbMoverMessageListener::request(), DockFragmentsMover::run(), numeric::expression_parser::ArithmeticScanner::scan(), numeric::expression_parser::ArithmeticScanner::scan_identifier(), numeric::expression_parser::ArithmeticScanner::scan_literal(), utility::subset_mapping::set_next_correspondence(), show(), numeric::expression_parser::LiteralToken::to_string(), numeric::expression_parser::FunctionToken::to_string(), numeric::xyzVector< core::Real >::to_string(), and numeric::expression_parser::ExpressionCreator::visit().

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.

Definition at line 228 of file string_util.hh.

References strip().

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

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

Definition at line 315 of file string_util.cc.

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

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

compares two strings ignoring leading and trailing spaces

compares two strings ignoring leading and trailing spaces

Definition at line 278 of file string_util.cc.

References ObjexxFCL::space().

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

static

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

static

Variable Documentation

CSI_Sequence const utility::CSI_bgBlack("\x1b[40m")

CSI_Sequence const utility::CSI_bgBlue("\x1b[44m")

CSI_Sequence const utility::CSI_bgCyan("\x1b[46m")

CSI_Sequence const utility::CSI_bgGreen("\x1b[42m")

CSI_Sequence const utility::CSI_bgMagenta("\x1b[45m")

CSI_Sequence const utility::CSI_bgRed("\x1b[41m")

CSI_Sequence const utility::CSI_bgWhite("\x1b[47m")

CSI_Sequence const utility::CSI_bgYellow("\x1b[43m")

CSI_Sequence const utility::CSI_Black("\x1b[30m")

CSI_Sequence const utility::CSI_Blue("\x1b[34m")

CSI_Sequence const utility::CSI_Bold("\x1b[1m")

CSI_Sequence const utility::CSI_Cyan("\x1b[36m")

CSI_Sequence const utility::CSI_Green("\x1b[32m")

CSI_Sequence const utility::CSI_Magenta("\x1b[35m")

CSI_Sequence const utility::CSI_Red("\x1b[31m")

CSI_Sequence const utility::CSI_Reset("\x1b[0m")

static

Constant static string objects to hold various ASCII CSI codes Codes below is all Hogwarts-approved magic numbers, so do not modify them. For reference see: http://en.wikipedia.org/wiki/ANSI_escape_code#CSI_codes

CSI_Sequence const utility::CSI_Underline("\x1b[4m")

CSI_Sequence const utility::CSI_White("\x1b[37m")

CSI_Sequence const utility::CSI_Yellow("\x1b[33m")

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

static

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

Definition at line 52 of file exit.cc.

Referenced by exit(), and set_main_exit_callback().