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Rosetta
3.7
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All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Properties Friends Macros Pages
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Rosetta
3.7
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comment 0 More...
Namespaces | |
| excn | |
| factory | |
| file | |
| graph | |
| io | |
| json_spirit | |
| keys | |
| libsvm | |
| options | |
| pointer | |
| py | |
| serialization | |
| signals | |
| sql_database | |
| tag | |
| thread | |
| tools | |
Classes | |
| struct | A |
| A molecular system including residues, kinematics, and energies. More... | |
| 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... | |
Enumerations | |
| enum | simulate_mpi_message_type { smpi_char = 1, smpi_integer, smpi_string, smpi_double, smpi_integers, smpi_doubles } |
Functions | |
| std::ostream & | operator<< (std::ostream &os, A const &a) |
| A const | foo () |
| Copies <src> into the pose where it remains possible that two Poses may point to each other in non-const ways or share non-bitwise constant data between them (E.g. the AtomTree observer system). More... | |
| 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<typename U > | |
| void | swap (BitVector< U > &a, BitVector< U > &b) |
| swap( 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<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) |
| bool | is_true_string (std::string const &value_str) |
| String accepted as a true value? More... | |
| bool | is_false_string (std::string const &value_str) |
| String accepted as a false value? More... | |
| std::string | make_tag_with_dashes (utility::vector1< int > res_vector, char const delimiter= ' ') |
| Compactifies vectors of ints: 1 2 3 9 10 11 to "1-3 9-11". More... | |
| std::string | make_tag_with_dashes (utility::vector1< int > res_vector, utility::vector1< char > chain_vector, 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) |
| 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... | |
comment 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.
unresizable vector whose size is known at compile time, which may be allocated on the stack, and which indexes from 0.
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() ) );
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
This detects rings in residues!
#include <core/pose/signals/DestructionEvent.hh> – Illegal and unneccessary
Predefined functions for Tracer IO We originally moved them out of name spaces so we can use them right away - without specifying it. Returned to utility namespace, as some compilers did not find the operator otherwise! – rhiju
| typedef utility::pointer::shared_ptr< heap const > utility::heapCOP |
| typedef utility::pointer::shared_ptr< heap > utility::heapOP |
| typedef utility::pointer::shared_ptr< Inline_File_Provider_Hook const > utility::Inline_File_Provider_HookCOP |
| typedef utility::pointer::shared_ptr< Inline_File_Provider_Hook > utility::Inline_File_Provider_HookOP |
| typedef utility::pointer::shared_ptr< SimulateMPIMessage const > utility::SimulateMPIMessageCOP |
| typedef utility::pointer::shared_ptr< SimulateMPIMessage > utility::SimulateMPIMessageOP |
| typedef pointer::shared_ptr< subset_mapping const> utility::subset_mappingCOP |
| typedef pointer::shared_ptr< subset_mapping > utility::subset_mappingOP |
| typedef void(* utility::UtilityExitCallBack)(void) |
| typedef vector0< char > utility::vector0_char |
| typedef vector0< long int > utility::vector0_long |
| typedef vector0< signed char > utility::vector0_schar |
| typedef vector0< short int > utility::vector0_short |
| typedef vector0< unsigned char > utility::vector0_uchar |
| typedef vector0< unsigned int > utility::vector0_uint |
| typedef vector0< unsigned long int > utility::vector0_ulong |
| typedef vector0< unsigned short int > utility::vector0_ushort |
| typedef vector1< char > utility::vector1_char |
| typedef vector1< long int > utility::vector1_long |
| typedef vector1< signed char > utility::vector1_schar |
| typedef vector1< short int > utility::vector1_short |
| typedef vector1< std::size_t > utility::vector1_size |
| typedef vector1< std::size_t > utility::vector1_size_t |
| typedef vector1< unsigned char > utility::vector1_uchar |
| typedef vector1< unsigned int > utility::vector1_uint |
| typedef vector1< unsigned long int > utility::vector1_ulong |
| typedef vector1< unsigned short int > utility::vector1_ushort |
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 | |
| void utility::add_exit_callback | ( | UtilityExitCallBack | cb | ) |
Add additional callback function that will be called before standard exit(…) is executed. [Note: do not confuse this function with 'set_main_exit_callback' which is replacing the end behavior of exit(…)].
References get_all_exit_callbacks().
|
static |
| void utility::arg_greatest_several | ( | vector1< T > const & | input, |
| vector1< typename vector1< T >::Size > & | arg_list | ||
| ) |
Finds indices of the n largest items in input vector, where n is size of the arg_list vector. The indices are reported in decreasing sorted order by the value of the corresponding position in the input vector. If m is the size of the input vector, then this function is O( m n**2)
If arg_list has more entries than input, then it is resized at the end of this function to have as many entries as the input.
References test.T200_Scoring::ii, and insert_middle().
| void utility::arg_least_several | ( | vector1< T > const & | input, |
| vector1< typename vector1< T >::Size > & | arg_list | ||
| ) |
Finds indices of the n smallest items in input vector, where n is size of the arg_list vector. The indices are reported in increasing sorted order by the value of the corresponding position in the input vector. If m is the size of the input vector, then this function is O( m n**2)
If arg_list has more entries than input, then it is resized at the end of this function to have as many entries as the input.
References test.T200_Scoring::ii, and insert_middle().
| vector1< T >::Size utility::arg_max | ( | vector1< T > const & | input | ) |
find the index of the largest value in a vector
class T must provide an operator < () and operator = (). Error if input.size() == 0
References debug_assert, test.T200_Scoring::ii, and test.T007_TracerIO::T.
| vector1< T >::Size utility::arg_min | ( | vector1< T > const & | input | ) |
find the index of the smallest value in a vector
class T must provide an operator < () and operator = (). Error if input.size() == 0
References debug_assert, test.T200_Scoring::ii, and test.T007_TracerIO::T.
Referenced by numeric::geometry::vector_normal_to_ring_plane_of_best_fit().
| int utility::argmax | ( | const std::vector< T > & | iterable | ) |
Returns the argument whose value is maximal according to operator>.
Adheres to STL numbering (0-indexed).
| int utility::argmax | ( | const utility::vector1< T > & | iterable | ) |
Returns the argument whose value is maximal according to operator>.
Adheres to Rosetta numbering (1-indexed).
| int utility::argmin | ( | const std::vector< T > & | iterable | ) |
Returns the argument whose value is minimal according to operator<.
Adheres to STL numbering (0-indexed).
| int utility::argmin | ( | const utility::vector1< T > & | iterable | ) |
Returns the argument whose value is minimal according to operator<.
Adheres to Rosetta numbering (1-indexed).
|
inline |
Referenced by decode_32_to_24().
|
inline |
uuencode
Referenced by encode_24_to_32().
| int utility::cond_exit | ( | bool | condition, |
| std::string const & | file, | ||
| int const | line, | ||
| std::string const & | message, | ||
| int const | status | ||
| ) |
Conditional Exit with file + line + message + optional status.
Conditional Exit with file + line + message + optional status. WIll exit if the condition is not met!
References exit().
|
inline |
Referenced by numeric::xyzTransform< numeric::Real >::to_quaternion(), and numeric::statistics::w().
| int utility::decode6bit | ( | unsigned char * | memory, |
| const std::string & | jar | ||
| ) |
References decode_32_to_24().
|
inline |
References code_from_6bit().
Referenced by decode6bit().
|
inline |
Fast assert-checked polymorphic down-cast: reference argument.
References debug_assert, and basic::options::OptionKeys::in::file::s.
Referenced by utility::options::OptionCollection::operator()(), and utility::options::OptionCollection::operator[]().
|
inline |
Fast assert-checked polymorphic down-cast: pointer argument.
References debug_assert, and basic::options::OptionKeys::score::fiber_diffraction::p.
| void utility::encode6bit | ( | const unsigned char * | memory, |
| unsigned int | length, | ||
| std::string & | jar | ||
| ) |
References encode_24_to_32(), and make_symmdef_file_denovo::length.
|
inline |
References code_to_6bit().
Referenced by encode6bit().
| bool utility::endswith | ( | std::string const & | haystack, |
| std::string const & | needle | ||
| ) |
True iff haystack ends with needle.
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, | ||
| std::string const & | message, | ||
| int const | status | ||
| ) |
Exit with file + line + message + optional status.
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, maybe_throw_on_next_assertion_failure(), and print_backtrace().
Referenced by cond_exit(), exit(), main(), print_ddgs(), and rhiju_pdbstats().
Exit with file + line + optional status.
References exit().
Exit with file + line + status.
References exit().
| std::string utility::file_basename | ( | const std::string & | full_path | ) |
References filename().
Referenced by composite_sequences_from_cmd_line(), main(), poses_from_cmd_line(), and sequences_from_cmd_line().
| std::string utility::file_contents | ( | std::string const & | file_name | ) |
Read the entire contents of a file into a string. All end-of-line characters are replaced by "\n". Throws a utility::excn::EXCN_msg_exception if the file cannot be opened.
References utility::io::izstream::close(), 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 | ) |
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().
| BidirectionalIterator utility::find_closest | ( | BidirectionalIterator | first, |
| BidirectionalIterator | last, | ||
| const T & | value | ||
| ) |
Returns an iterator on the sorted range [first, last) nearest to value. If value is equidistant between adjacent elements, the lesser is returned.
References assign_charges::first.
| std::string utility::fmt_real | ( | platform::Real | num, |
| platform::Size | pad_left_n, | ||
| std::size_t const | decimal_places | ||
| ) |
convert a Real to a string, padding left with spaces until total number of char on left is equal to pad_lef_n
References pad_left(), Real2string(), and basic::options::OptionKeys::in::file::s.
| A const utility::foo | ( | ) |
Copies <src> into the pose where it remains possible that two Poses may point to each other in non-const ways or share non-bitwise constant data between them (E.g. the AtomTree observer system).
example(s): test_pose.assign(pose) See also: Pose
References ObjexxFCL::format::A().
Referenced by tools.CppParser.CppFunction::getSimpleArgsType(), and tools.CppParser.CppFunction::writeCallbackCode().
|
inline |
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.
Referenced by add_exit_callback(), exit(), and remove_exit_callback().
| platform::Size utility::get_num_digits | ( | platform::Size | value | ) |
| std::pair< std::vector< int >, std::vector< char > > utility::get_resnum_and_chain | ( | std::string const & | s, |
| bool & | string_is_ok | ||
| ) |
converts string like "1-3 20-22" or "A:1-5 B:20-22" to vectors containing resnums and chains.
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.
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
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.
References get_resnum_and_segid_from_one_tag(), replace_in(), clean_pdb_keep_ligand::resnum, tag, and basic::options::OptionKeys::in::file::tags.
| bool utility::get_resnum_and_segid_from_one_tag | ( | std::string const & | tag, |
| std::vector< int > & | resnum, | ||
| std::vector< std::string > & | segids | ||
| ) |
helper function for get_resnum_and_chain
References ObjexxFCL::ints_of(), and runtime_assert.
Referenced by get_resnum_and_segid().
|
inline |
Get a numeric value for Real that represents an "undefined" value.
Referenced by string2Real().
|
inline |
Get a numeric value for Size that represents an "undefined" value.
References max().
Referenced by is_undefined(), and string2Size().
| bool utility::has_key | ( | std::map< T, T > | a_map, |
| T | key | ||
| ) |
| bool utility::has_key | ( | std::map< T, T > const & | a_map, |
| T const & | key | ||
| ) |
Does the map have the key?
| void utility::insert_middle | ( | vector1< T > & | vect, |
| typename vector1< T >::Size const | position, | ||
| T const | new_value, | ||
| bool | expand | ||
| ) |
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 | ) |
String accepted as a false value?
Referenced by utility::tag::Tag::getOption(), and utility::options::BooleanOption::is_false_value().
|
inline |
References numeric::isinf().
Referenced by numeric::statistics::w().
|
inline |
References numeric::isnan().
Referenced by numeric::xyzTransform< numeric::Real >::bad(), numeric::xyzTransform< numeric::Real >::badfast(), numeric::alignment::QCP_Kernel< double >::calc_rmsd_Theobald_method(), numeric::statistics::Dawson(), numeric::statistics::errf(), numeric::xyzTransform< numeric::Real >::rt6(), and numeric::statistics::w().
| bool utility::is_string_numeric | ( | std::string const & | input | ) |
| bool utility::is_true_string | ( | std::string const & | value_str | ) |
String accepted as a true value?
Referenced by utility::tag::Tag::getOption(), and utility::options::BooleanOption::is_true_value().
|
inline |
Check if a Size is undefined (i.e has the same value as utility::get_undefined_size() )
References get_undefined_size().
|
inline |
Check if a Real is undefined (i.e has the same value as utility::get_undefined_real() )
References numeric::isinf(), and numeric::isnan().
| std::string utility::join | ( | utility::vector1< std::string > const & | s, |
| std::string const & | connector | ||
| ) |
combine strings with anything
References begin.
Referenced by basic::database::make_compound_statement(), and replace_spaces().
| std::string utility::join | ( | std::vector< std::string > const & | s, |
| std::string const & | connector | ||
| ) |
combine strings with anything
References begin.
| std::string utility::join | ( | utility::vector1< T > const & | vector, |
| std::string const & | connector | ||
| ) |
combine vector with anything
References begin.
| std::string utility::join | ( | vectorL< L, std::string > const & | s, |
| std::string const & | connector | ||
| ) |
Join vector of strings in to single string.
References begin.
|
static |
|
static |
|
static |
| std::string utility::make_segtag_with_dashes | ( | utility::vector1< int > | res_vector, |
| utility::vector1< std::string > | segid_vector, | ||
| char const | delimiter | ||
| ) |
References runtime_assert, amino_acids::size, ObjexxFCL::string_of(), and tag.
| std::string utility::make_tag | ( | utility::vector1< int > | res_vector | ) |
References ObjexxFCL::string_of(), and tag.
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".
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 | ||
| ) |
References runtime_assert, ObjexxFCL::string_of(), and tag.
| T utility::max | ( | vector1< T > const & | input | ) |
Find the largest value in a vector.
class T must provide an operator < () and operator = (). Error if input.size() == 0
References debug_assert, test.T200_Scoring::ii, and test.T007_TracerIO::T.
Referenced by max().
|
inline |
max( a, b, c )
|
inline |
max( a, b, c, d )
References max().
|
inline |
|
inline |
Referenced by min().
| T utility::min | ( | vector1< T > const & | input | ) |
Find the smallest value in a vector.
class T must provide an operator < () and operator = (). Error if input.size() == 0
References debug_assert, test.T200_Scoring::ii, and test.T007_TracerIO::T.
|
inline |
min( a, b, c )
|
inline |
min( a, b, c, d )
References min().
|
inline |
|
inline |
| int utility::mpi_nprocs | ( | ) |
References utility::SimulateMPI::mpi_nprocs(), and utility::SimulateMPI::simulate_mpi().
Referenced by basic::Tracer::calculate_visibility(), and main().
| int utility::mpi_rank | ( | ) |
| std::string utility::msg_name | ( | simulate_mpi_message_type | msg_type | ) |
References smpi_char, smpi_double, smpi_doubles, smpi_integer, smpi_integers, and smpi_string.
Referenced by utility::SimulateMPIData::pop_next_message_for_node_of_type(), and utility::SimulateMPIData::pop_next_message_of_type().
|
static |
| bool utility::operator!= | ( | vectorL< L, bool, A > const & | a, |
| std::vector< bool, A > const & | b | ||
| ) |
vectorL != std::vector
| bool utility::operator!= | ( | std::vector< bool, A > const & | a, |
| vectorL< L, bool, A > const & | b | ||
| ) |
std::vector != vectorL
| bool utility::operator!= | ( | vectorL< L, T, A > const & | a, |
| std::vector< T, A > const & | b | ||
| ) |
vectorL != std::vector
| bool utility::operator!= | ( | std::vector< T, A > const & | a, |
| vectorL< L, T, A > const & | b | ||
| ) |
std::vector != vectorL
| BitSet< B > utility::operator+ | ( | BitSet< B > const & | a, |
| BitSet< B > const & | b | ||
| ) |
References basic::options::OptionKeys::in::file::s.
| BitVector< B > utility::operator+ | ( | BitVector< B > const & | a, |
| BitVector< B > const & | b | ||
| ) |
| BitSet< B > utility::operator- | ( | BitSet< B > const & | a, |
| BitSet< B > const & | b | ||
| ) |
References basic::options::OptionKeys::in::file::s.
| BitVector< B > utility::operator- | ( | BitVector< B > const & | a, |
| BitVector< B > const & | b | ||
| ) |
BitVector - BitVector: Difference.
References basic::options::OptionKeys::score::fiber_diffraction::b, and basic::options::OptionKeys::in::file::s.
| bool utility::operator< | ( | vectorL< L, bool, A > const & | a, |
| std::vector< bool, A > const & | b | ||
| ) |
vectorL < std::vector
| bool utility::operator< | ( | std::vector< bool, A > const & | a, |
| vectorL< L, bool, A > const & | b | ||
| ) |
std::vector < vectorL
| bool utility::operator< | ( | vectorL< L, T, A > const & | a, |
| std::vector< T, A > const & | b | ||
| ) |
vectorL < std::vector
| bool utility::operator< | ( | std::vector< T, A > const & | a, |
| vectorL< L, T, A > const & | b | ||
| ) |
std::vector < vectorL
| std::ostream& utility::operator<< | ( | std::ostream & | os, |
| A const & | a | ||
| ) |
References utility::A::value.
| std::ostream & utility::operator<< | ( | std::ostream & | os, |
| utility::vectorL< L, T > const & | v | ||
| ) |
Output function for utility::vector1 object.
References test.T850_SubClassing::v.
| bool utility::operator<= | ( | vectorL< L, bool, A > const & | a, |
| std::vector< bool, A > const & | b | ||
| ) |
vectorL <= std::vector
| bool utility::operator<= | ( | std::vector< bool, A > const & | a, |
| vectorL< L, bool, A > const & | b | ||
| ) |
std::vector <= vectorL
| bool utility::operator<= | ( | vectorL< L, T, A > const & | a, |
| std::vector< T, A > const & | b | ||
| ) |
vectorL <= std::vector
| bool utility::operator<= | ( | std::vector< T, A > const & | a, |
| vectorL< L, T, A > const & | b | ||
| ) |
std::vector <= vectorL
|
inline |
| bool utility::operator== | ( | vectorL< L, bool, A > const & | a, |
| std::vector< bool, A > const & | b | ||
| ) |
vectorL == std::vector
| bool utility::operator== | ( | std::vector< bool, A > const & | a, |
| vectorL< L, bool, A > const & | b | ||
| ) |
std::vector == vectorL
| bool utility::operator== | ( | vectorL< L, T, A > const & | a, |
| std::vector< T, A > const & | b | ||
| ) |
vectorL == std::vector
| bool utility::operator== | ( | std::vector< T, A > const & | a, |
| vectorL< L, T, A > const & | b | ||
| ) |
std::vector == vectorL
| bool utility::operator> | ( | vectorL< L, bool, A > const & | a, |
| std::vector< bool, A > const & | b | ||
| ) |
vectorL > std::vector
| bool utility::operator> | ( | std::vector< bool, A > const & | a, |
| vectorL< L, bool, A > const & | b | ||
| ) |
std::vector > vectorL
| bool utility::operator> | ( | vectorL< L, T, A > const & | a, |
| std::vector< T, A > const & | b | ||
| ) |
vectorL > std::vector
| bool utility::operator> | ( | std::vector< T, A > const & | a, |
| vectorL< L, T, A > const & | b | ||
| ) |
std::vector > vectorL
| bool utility::operator>= | ( | vectorL< L, bool, A > const & | a, |
| std::vector< bool, A > const & | b | ||
| ) |
vectorL >= std::vector
| bool utility::operator>= | ( | std::vector< bool, A > const & | a, |
| vectorL< L, bool, A > const & | b | ||
| ) |
std::vector >= vectorL
| bool utility::operator>= | ( | vectorL< L, T, A > const & | a, |
| std::vector< T, A > const & | b | ||
| ) |
vectorL >= std::vector
| bool utility::operator>= | ( | std::vector< T, A > const & | a, |
| vectorL< L, T, A > const & | b | ||
| ) |
std::vector >= vectorL
| BitSet< B > utility::operator| | ( | BitSet< B > const & | a, |
| BitSet< B > const & | b | ||
| ) |
References basic::options::OptionKeys::in::file::s.
| BitVector< B > utility::operator| | ( | BitVector< B > const & | a, |
| BitVector< B > const & | b | ||
| ) |
| std::string utility::pad_left | ( | const T & | t, |
| platform::Size const | newlen, | ||
| char | pad_width = ' ' |
||
| ) |
Add char to the left of the string.
References pad_left(), basic::options::OptionKeys::in::file::s, and to_string().
| std::string utility::pad_left | ( | std::string | s, |
| platform::Size const | newlen, | ||
| char | pad_with | ||
| ) |
Add char to the left of the string.
References basic::options::OptionKeys::ufv::right, and basic::options::OptionKeys::in::file::s.
Referenced by fmt_real(), and pad_left().
| std::string utility::pad_right | ( | const T & | t, |
| platform::Size const | newlen, | ||
| char | pad_width = ' ' |
||
| ) |
Add char to the right of a string.
References pad_right(), basic::options::OptionKeys::in::file::s, and to_string().
| std::string utility::pad_right | ( | std::string | s, |
| platform::Size const | newlen, | ||
| char | pad_with | ||
| ) |
Add char to the right of a string.
References basic::options::OptionKeys::ufv::left, and basic::options::OptionKeys::in::file::s.
Referenced by pad_right().
| std::string utility::pathname | ( | const std::string & | path | ) |
References utility::file::FileName::path().
| void utility::rand_sleep | ( | ) |
References sys_sleep().
Referenced by utility::file::file_delete(), utility::file::trytry_ifstream_open(), and utility::file::trytry_ofstream_open().
| std::string utility::Real2string | ( | platform::Real | num, |
| std::size_t const | decimal_places | ||
| ) |
convert a Real to string at a number of decimal places, optionally pad left.
References basic::options::OptionKeys::optE::fixed.
Referenced by fmt_real().
| char utility::receive_char_from_node | ( | int | source | ) |
Use MPI to receive a single char from a particular node.
References utility::SimulateMPI::receive_char_from_node(), and utility::SimulateMPI::simulate_mpi().
Use MPI to receive a single double from a particular node.
References utility::SimulateMPI::receive_double_from_node(), and utility::SimulateMPI::simulate_mpi().
| utility::vector1< double > utility::receive_doubles_from_node | ( | int | source | ) |
Use MPI to receive a vector of doubles from a particular node.
References utility::SimulateMPI::receive_doubles_from_node(), and utility::SimulateMPI::simulate_mpi().
| int utility::receive_integer_from_anyone | ( | ) |
Use MPI to wait until some node sends an integer – usually its own mpi_rank so that it can send further messages.
References utility::SimulateMPI::receive_integer_from_anyone(), and utility::SimulateMPI::simulate_mpi().
Referenced by main().
Use MPI to receive a single integer from a particular node.
References utility::SimulateMPI::receive_integer_from_node(), and utility::SimulateMPI::simulate_mpi().
Referenced by main().
| utility::vector1< int > utility::receive_integers_from_node | ( | int | source | ) |
Use MPI to receive a vector of integers from a particular node.
References utility::SimulateMPI::receive_integers_from_node(), and utility::SimulateMPI::simulate_mpi().
| std::string utility::receive_string_from_node | ( | int | source | ) |
Use MPI to receive a string from a particular node.
References utility::SimulateMPI::receive_string_from_node(), and utility::SimulateMPI::simulate_mpi().
Referenced by basic::mpi::request_data_from_head_node().
| void utility::remove_exit_callback | ( | UtilityExitCallBack | cb | ) |
Remove additional callback function that was previously added by using add_exit_callback.
References begin, and get_all_exit_callbacks().
| std::string utility::replace_environment_variables | ( | std::string | input | ) |
find all environment variables with the form ${VARIABLE} and replace with the contents of that environment variable. if the environment variable does not exist, return string::npos
References basic::options::OptionKeys::cutoutdomain::end, 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().
|
inline |
| std::string utility::replace_in | ( | std::string const & | name_in, |
| std::string const & | find_string, | ||
| std::string const & | replace_string | ||
| ) |
Generate new string from 'source' by replacing all occurrences of 'from' to 'to' string.
References name, and make_symmdef_file_denovo::pos.
Referenced by get_resnum_and_chain(), 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 | ||
| ) |
|
inline |
References round().
|
inline |
Compares two strings, ignoring spaces. Useful for comparing atom name strings which have pdb-alignment built into them. Slightly dangerous if you consider the fact that atom names in the PDB are different for different indentation rules: ' CA ' is c-alpha. 'CA ' is calcium.
| void utility::send_char_to_node | ( | int | destination, |
| char | message | ||
| ) |
| void utility::send_doubles_to_node | ( | int | destination, |
| utility::vector1< double > const & | message | ||
| ) |
References utility::SimulateMPI::send_integer_to_node(), and utility::SimulateMPI::simulate_mpi().
Referenced by main().
| void utility::send_integers_to_node | ( | int | destination, |
| utility::vector1< int > const & | message | ||
| ) |
| void utility::send_string_to_node | ( | int | destination, |
| std::string const & | message | ||
| ) |
References utility::SimulateMPI::send_string_to_node(), and utility::SimulateMPI::simulate_mpi().
Referenced by basic::mpi::request_data_from_head_node(), and basic::mpi::send_data_to_head_node().
| void utility::set_main_exit_callback | ( | UtilityExitCallBack | my_callback | ) |
Set call back funtion that will be called on utility::exit. Use this function to overload default behavior of sys.exit to more appropriate to your application Defaut value for callback function is 0, whicth mean no sys exit is called.
References main_exit_callback.
Referenced by set_pyexit_callback(), and utility::py::PyExitCallback::set_PyExitCallBack().
| void utility::slurp | ( | std::istream & | in, |
| std::string & | out | ||
| ) |
References ObjexxFCL::getline(), and line.
| utility::vector1< std::string > utility::split | ( | const std::string & | s | ) |
split given std::string using ' ' symbol.
References numeric::add(), and basic::options::OptionKeys::cutoutdomain::start.
Referenced by basic::mpi::DbMoverMessageListener::deserialize_data(), replace_spaces(), and basic::Tracer::set_ios_hook().
| std::vector< std::string > utility::split_by_newlines | ( | std::string const & | s | ) |
Split string by new line symbols, return vector of string.
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.
References numeric::add(), and basic::options::OptionKeys::cutoutdomain::start.
Referenced by utility::options::OptionCollection::load_option_from_file().
| std::set< std::string > utility::split_to_set | ( | const std::string & | s | ) |
split given std::string to a set using ' ' symbol.
split given std::string using ' ' symbol.
References numeric::add(), and basic::options::OptionKeys::cutoutdomain::start.
| utility::vector1< std::string > utility::split_whitespace | ( | const std::string & | s | ) |
split given std::string using whitespace as a separator. Unlike string_split_multi_delim(), any group of mixed whitespace counts only as a single seperator.
References basic::options::OptionKeys::mh::match::ss.
| bool utility::startswith | ( | std::string const & | haystack, |
| std::string const & | needle | ||
| ) |
True iff haystack starts with needle.
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
References basic::options::OptionKeys::mh::match::ss.
| int utility::string2int | ( | std::string | st | ) |
convert a string to an int, returns -1 on failure
convert a string to an int
References basic::options::OptionKeys::mh::match::ss.
Referenced by basic::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
References get_undefined_real(), and basic::options::OptionKeys::mh::match::ss.
| platform::Size utility::string2Size | ( | std::string | st | ) |
convert a string to a Size, returns numeric::get_undefined_size() on failure
References get_undefined_size(), and basic::options::OptionKeys::mh::match::ss.
| void utility::string2uint | ( | const std::string & | x, |
| unsigned int * | y | ||
| ) |
References basic::options::OptionKeys::mh::match::ss, and y().
|
inline |
| utility::vector1< std::string > utility::string_split | ( | std::string const & | in, |
| char | splitchar = ' ' |
||
| ) |
split to vector1< std::string > using arbitrary split character
References basic::options::OptionKeys::frags::j.
Referenced by calc_scores(), basic::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(), utility::tag::XMLErrorHandler::set_file_contents(), and numeric::interpolation::spline_from_file().
| utility::vector1< std::string > utility::string_split_multi_delim | ( | std::string const & | in, |
| std::string | splitchars = " \t" |
||
| ) |
split to vector< std::string > using any of arbitrary split characters
References basic::options::OptionKeys::frags::j.
| utility::vector1< std::string > utility::string_split_simple | ( | std::string const & | in, |
| char | splitchar | ||
| ) |
split to vector1< std::string > using arbitrary split character, but no empty strings (closer to python string::split)
split to vector1< std::string > using arbitrary split character, but no empty strings (closer to python string::split)
References basic::options::OptionKeys::frags::j.
| std::string utility::string_to_sha1 | ( | std::string const & | input_string | ) |
References fmt::hex().
| std::string utility::strip | ( | std::string const & | s, |
| std::string const & | drop | ||
| ) |
| std::string utility::strip | ( | std::string const & | source, |
| char | c | ||
| ) |
Return a copy of the string with leading and trailing characters removed.
References begin, basic::options::OptionKeys::cutoutdomain::end, and basic::options::OptionKeys::score::fiber_diffraction::p.
swap( BitSet, BitSet )
Referenced by swap().
swap( BitVector, BitVector )
| void utility::swap | ( | BitVector< U > & | a, |
| BitVector< U > & | b | ||
| ) |
swap( BitVector, BitVector )
| void utility::swap | ( | vectorL< L, bool, A > & | a, |
| vectorL< L, bool, A > & | b | ||
| ) |
swap( vectorL, vectorL )
References basic::options::OptionKeys::score::fiber_diffraction::a, and swap().
| void utility::swap | ( | vectorL< L, bool, A > & | a, |
| std::vector< bool, A > & | b | ||
| ) |
swap( vectorL, std::vector )
References basic::options::OptionKeys::score::fiber_diffraction::a, and swap().
| void utility::swap | ( | std::vector< bool, A > & | a, |
| vectorL< L, bool, A > & | b | ||
| ) |
swap( std::vector, vectorL )
|
inline |
swap( vectorL, vectorL )
References basic::options::OptionKeys::score::fiber_diffraction::a, and swap().
|
inline |
swap( vectorL, std::vector )
References basic::options::OptionKeys::score::fiber_diffraction::a, and swap().
|
inline |
swap( std::vector, vectorL )
|
inline |
References app.delta_score_per_mutation::data.
| void utility::sys_sleep | ( | double const | seconds | ) |
Sleep for a specified number of seconds.
References utility::io::oc::cout, BuildBindings::Sleep(), and x().
Referenced by rand_sleep().
| std::string utility::timestamp | ( | ) |
Generate timestamp string.
Referenced by basic::Tracer::prepend_channel_name(), and timestamp_short().
| std::string utility::timestamp_short | ( | ) |
Generate timestamp string, short format.
References timestamp().
|
inline |
References basic::options::OptionKeys::mh::match::ss, and basic::options::OptionKeys::in::file::t.
Referenced by IdentifyCDRClusters::apply(), binder::bind_member_functions_for_call_back(), correct_dunbrack(), binder::function_arguments_for_lambda(), binder::function_arguments_for_py_overload(), binder::Context::generate(), numeric::expression_parser::ExpressionCreator::handle_function_expression(), numeric::expression_parser::SimpleExpressionCreator::handle_variable_expression(), utility::tag::integer_range_restriction(), binder::line_number(), utility::tag::XMLErrorHandler::lines_near_error(), main(), make_fragments(), pad_left(), pad_right(), utility::SimulateMPIData::pop_next_message_for_node_of_type(), utility::SimulateMPIData::pop_next_message_of_type(), utility::tag::XMLSchemaComplexTypeGeneratorImpl::prepare_subelement_single_instance_optional(), 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().
|
inline |
| void utility::trim | ( | std::string & | s, |
| const std::string & | drop | ||
| ) |
Remove any charachters in "drop" from the front and back of the string. Use strip() for the value-return version.
Referenced by utility::io::get_lines_from_file_data(), spanfile_for_each_chain(), spanfile_from_pdb(), strip(), and basic::database::write_schema_to_database().
| bool utility::trimmed_compare | ( | std::string const & | s1, |
| std::string const & | s2 | ||
| ) |
compares two strings ignoring leading and trailing spaces
compares two strings ignoring leading and trailing spaces
References ObjexxFCL::space().
|
static |
|
static |
| 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") |
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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") |
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static |
Place holder for 'end-action' of utility::exit(…)
Referenced by exit(), and set_main_exit_callback().
1.8.7