#include "IntaRNA/intarna_config.h"#include <algorithm>#include <cassert>#include "easylogging++.h"#include <stdexcept>#include <boost/lexical_cast.hpp>#include <cmath>#include <limits>#include <iostream>#include <string>
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Namespaces | |
| namespace | IntaRNA |
Macros | |
| #define | INTARNA_IN_DEBUG_MODE 1 |
| central flag whether or not debug mode is enabled | |
| #define | INTARNA_NOT_IMPLEMENTED(message) |
| #define | INTARNA_CHECK_NOT_NULL(pointer, message) |
| #define | toString(x) boost::lexical_cast<std::string>(x) |
| #define | Z_log std::log |
| #define | Z_exp std::exp |
| #define | IntaRNA_precisionEpsilon std::sqrt(std::numeric_limits<float>::min()) |
| #define | E_2_Ekcal(e) ( static_cast<E_kcal_type>(e) / 100.0 ) |
| convert internal energy type to energy value in kcal/mol units | |
| #define | Ekcal_2_E(e) ( static_cast<E_type>(e * 100) ) |
| convert energy in kcal/mol units to internal energy type | |
| #define | E_2_Z(e) ( static_cast<Z_type>(e) / 100.0 ) |
| convert E_type to Z_type | |
| #define | Z_2_E(e) ( static_cast<E_type>(e * 100) ) |
| convert Z_type to E_type | |
| #define | E_equal(e1, e2) ( e1 == e2 ) |
| check if two energies are equal | |
| #define | E_isNotINF(e) ( E_INF > e ) |
| check if a given energy is NOT set to E_INF | |
| #define | E_isINF(e) ( E_INF <= e ) |
| check if a given energy is set to E_INF | |
| #define | Z_equal(e1, e2) ( std::abs((e1)-(e2)) < IntaRNA_precisionEpsilon) |
| check if two energies are equal according to some epsilon | |
| #define | Z_isNotINF(e) ( std::numeric_limits<Z_type>::max() >= e ) |
| check if a given energy is NOT set to Z_INF | |
| #define | Z_isINF(e) ( std::numeric_limits<Z_type>::max() < e ) |
| check if a given energy is set to Z_INF | |
Typedefs | |
| typedef float | IntaRNA::E_kcal_type |
| type for energy values in kcal/mol units for in-/output only | |
| typedef int | IntaRNA::E_type |
| type for energy values (energy + accessibility [ED]) (internally) | |
| typedef double | IntaRNA::Z_type |
| type for probabilities, RT and Boltzmann values | |
Functions | |
| template<class T > | |
| void | INTARNA_CLEANUP (T *&pointer) |
| std::ostream * | IntaRNA::newOutputStream (const std::string &outName) |
| void | IntaRNA::deleteOutputStream (std::ostream *&outStream) |
| std::istream * | IntaRNA::newInputStream (const std::string &inName) |
| void | IntaRNA::deleteInputStream (std::istream *&inStream) |
Variables | |
| const E_type | IntaRNA::E_INF = (std::numeric_limits<E_type>::max() / 8) + 1 |
| const E_type | IntaRNA::E_MAX = E_INF / 2 |
| const Z_type | IntaRNA::Z_INF = std::numeric_limits<Z_type>::infinity() |
Macro Definition Documentation
◆ E_2_Ekcal
| #define E_2_Ekcal | ( | e | ) | ( static_cast<E_kcal_type>(e) / 100.0 ) |
convert internal energy type to energy value in kcal/mol units
◆ E_2_Z
| #define E_2_Z | ( | e | ) | ( static_cast<Z_type>(e) / 100.0 ) |
convert E_type to Z_type
◆ E_equal
| #define E_equal | ( | e1, | |
| e2 | |||
| ) | ( e1 == e2 ) |
check if two energies are equal
◆ E_isINF
| #define E_isINF | ( | e | ) | ( E_INF <= e ) |
check if a given energy is set to E_INF
◆ E_isNotINF
| #define E_isNotINF | ( | e | ) | ( E_INF > e ) |
check if a given energy is NOT set to E_INF
◆ Ekcal_2_E
| #define Ekcal_2_E | ( | e | ) | ( static_cast<E_type>(e * 100) ) |
convert energy in kcal/mol units to internal energy type
◆ INTARNA_CHECK_NOT_NULL
| #define INTARNA_CHECK_NOT_NULL | ( | pointer, | |
| message | |||
| ) |
Value:
if (pointer == NULL) { \
throw std::runtime_error( \
std::string("\nSTOP DUE TO NULL POINTER : ") \
+ message \
); }
◆ INTARNA_IN_DEBUG_MODE
| #define INTARNA_IN_DEBUG_MODE 1 |
central flag whether or not debug mode is enabled
◆ INTARNA_NOT_IMPLEMENTED
| #define INTARNA_NOT_IMPLEMENTED | ( | message | ) |
Value:
throw std::runtime_error( \
std::string("\nSTOP DUE TO MISSING IMPLEMENTATION : ") \
+ message \
);
◆ IntaRNA_precisionEpsilon
| #define IntaRNA_precisionEpsilon std::sqrt(std::numeric_limits<float>::min()) |
the delta difference range to consider two floating point values equivalent using sqrt(representable positive value closest to zero)
◆ toString
| #define toString | ( | x | ) | boost::lexical_cast<std::string>(x) |
◆ Z_2_E
| #define Z_2_E | ( | e | ) | ( static_cast<E_type>(e * 100) ) |
convert Z_type to E_type
◆ Z_equal
| #define Z_equal | ( | e1, | |
| e2 | |||
| ) | ( std::abs((e1)-(e2)) < IntaRNA_precisionEpsilon) |
check if two energies are equal according to some epsilon
◆ Z_exp
| #define Z_exp std::exp |
◆ Z_isINF
| #define Z_isINF | ( | e | ) | ( std::numeric_limits<Z_type>::max() < e ) |
check if a given energy is set to Z_INF
◆ Z_isNotINF
| #define Z_isNotINF | ( | e | ) | ( std::numeric_limits<Z_type>::max() >= e ) |
check if a given energy is NOT set to Z_INF
◆ Z_log
| #define Z_log std::log |
Function Documentation
◆ INTARNA_CLEANUP()
template<class T >
| void INTARNA_CLEANUP | ( | T *& | pointer | ) |
