1\hypertarget{params_2basic_8h}{}\doxysection{Vienna\+RNA/params/basic.h File Reference}
2\label{params_2basic_8h}\index{ViennaRNA/params/basic.h@{ViennaRNA/params/basic.h}}
3
4
5Functions to deal with sets of energy parameters.
6
7
8Include dependency graph for basic.\+h\+:
9\nopagebreak
10\begin{figure}[H]
11\begin{center}
12\leavevmode
13\includegraphics[width=350pt]{params_2basic_8h__incl}
14\end{center}
15\end{figure}
16This graph shows which files directly or indirectly include this file\+:
17\nopagebreak
18\begin{figure}[H]
19\begin{center}
20\leavevmode
21\includegraphics[width=350pt]{params_2basic_8h__dep__incl}
22\end{center}
23\end{figure}
24\doxysubsection*{Data Structures}
25\begin{DoxyCompactItemize}
26\item
27struct \mbox{\hyperlink{group__energy__parameters_structvrna__param__s}{vrna\+\_\+param\+\_\+s}}
28\begin{DoxyCompactList}\small\item\em The datastructure that contains temperature scaled energy parameters.  \mbox{\hyperlink{group__energy__parameters_structvrna__param__s}{More...}}\end{DoxyCompactList}\item
29struct \mbox{\hyperlink{group__energy__parameters_structvrna__exp__param__s}{vrna\+\_\+exp\+\_\+param\+\_\+s}}
30\begin{DoxyCompactList}\small\item\em The data structure that contains temperature scaled Boltzmann weights of the energy parameters.  \mbox{\hyperlink{group__energy__parameters_structvrna__exp__param__s}{More...}}\end{DoxyCompactList}\end{DoxyCompactItemize}
31\doxysubsection*{Typedefs}
32\begin{DoxyCompactItemize}
33\item
34typedef struct \mbox{\hyperlink{group__energy__parameters_structvrna__param__s}{vrna\+\_\+param\+\_\+s}} \mbox{\hyperlink{group__energy__parameters_ga8a69ca7d787e4fd6079914f5343a1f35}{vrna\+\_\+param\+\_\+t}}
35\begin{DoxyCompactList}\small\item\em Typename for the free energy parameter data structure \mbox{\hyperlink{group__energy__parameters_gad0e3e7e74bdc50d1709d40c92993185e}{vrna\+\_\+params}}. \end{DoxyCompactList}\item
36typedef struct \mbox{\hyperlink{group__energy__parameters_structvrna__exp__param__s}{vrna\+\_\+exp\+\_\+param\+\_\+s}} \mbox{\hyperlink{group__energy__parameters_ga01d8b92fe734df8d79a6169482c7d8d8}{vrna\+\_\+exp\+\_\+param\+\_\+t}}
37\begin{DoxyCompactList}\small\item\em Typename for the Boltzmann factor data structure \mbox{\hyperlink{group__energy__parameters_gab1f3016f96aa96bff020cdd904605afa}{vrna\+\_\+exp\+\_\+params}}. \end{DoxyCompactList}\item
38typedef struct \mbox{\hyperlink{group__energy__parameters_structvrna__param__s}{vrna\+\_\+param\+\_\+s}} \mbox{\hyperlink{group__energy__parameters_ga857dde86357d306cc902f0d8b2797659}{paramT}}
39\begin{DoxyCompactList}\small\item\em Old typename of \mbox{\hyperlink{group__energy__parameters_structvrna__param__s}{vrna\+\_\+param\+\_\+s}}. \end{DoxyCompactList}\item
40typedef struct \mbox{\hyperlink{group__energy__parameters_structvrna__exp__param__s}{vrna\+\_\+exp\+\_\+param\+\_\+s}} \mbox{\hyperlink{group__energy__parameters_ga8bffe1828e2cbec101769f5cc0b1535b}{pf\+\_\+paramT}}
41\begin{DoxyCompactList}\small\item\em Old typename of \mbox{\hyperlink{group__energy__parameters_structvrna__exp__param__s}{vrna\+\_\+exp\+\_\+param\+\_\+s}}. \end{DoxyCompactList}\end{DoxyCompactItemize}
42\doxysubsection*{Functions}
43\begin{DoxyCompactItemize}
44\item
45\mbox{\hyperlink{group__energy__parameters_ga8a69ca7d787e4fd6079914f5343a1f35}{vrna\+\_\+param\+\_\+t}} $\ast$ \mbox{\hyperlink{group__energy__parameters_gad0e3e7e74bdc50d1709d40c92993185e}{vrna\+\_\+params}} (\mbox{\hyperlink{group__model__details_ga1f8a10e12a0a1915f2a4eff0b28ea17c}{vrna\+\_\+md\+\_\+t}} $\ast$md)
46\begin{DoxyCompactList}\small\item\em Get a data structure containing prescaled free energy parameters. \end{DoxyCompactList}\item
47\mbox{\hyperlink{group__energy__parameters_ga8a69ca7d787e4fd6079914f5343a1f35}{vrna\+\_\+param\+\_\+t}} $\ast$ \mbox{\hyperlink{group__energy__parameters_ga4bffa39f26e7746148444dd8a8426eca}{vrna\+\_\+params\+\_\+copy}} (\mbox{\hyperlink{group__energy__parameters_ga8a69ca7d787e4fd6079914f5343a1f35}{vrna\+\_\+param\+\_\+t}} $\ast$par)
48\begin{DoxyCompactList}\small\item\em Get a copy of the provided free energy parameters. \end{DoxyCompactList}\item
49\mbox{\hyperlink{group__energy__parameters_ga01d8b92fe734df8d79a6169482c7d8d8}{vrna\+\_\+exp\+\_\+param\+\_\+t}} $\ast$ \mbox{\hyperlink{group__energy__parameters_gab1f3016f96aa96bff020cdd904605afa}{vrna\+\_\+exp\+\_\+params}} (\mbox{\hyperlink{group__model__details_ga1f8a10e12a0a1915f2a4eff0b28ea17c}{vrna\+\_\+md\+\_\+t}} $\ast$md)
50\begin{DoxyCompactList}\small\item\em Get a data structure containing prescaled free energy parameters already transformed to Boltzmann factors. \end{DoxyCompactList}\item
51\mbox{\hyperlink{group__energy__parameters_ga01d8b92fe734df8d79a6169482c7d8d8}{vrna\+\_\+exp\+\_\+param\+\_\+t}} $\ast$ \mbox{\hyperlink{group__energy__parameters_gaf78c09e685e6eef4100b1a41d4042550}{vrna\+\_\+exp\+\_\+params\+\_\+comparative}} (unsigned int n\+\_\+seq, \mbox{\hyperlink{group__model__details_ga1f8a10e12a0a1915f2a4eff0b28ea17c}{vrna\+\_\+md\+\_\+t}} $\ast$md)
52\begin{DoxyCompactList}\small\item\em Get a data structure containing prescaled free energy parameters already transformed to Boltzmann factors (alifold version) \end{DoxyCompactList}\item
53\mbox{\hyperlink{group__energy__parameters_ga01d8b92fe734df8d79a6169482c7d8d8}{vrna\+\_\+exp\+\_\+param\+\_\+t}} $\ast$ \mbox{\hyperlink{group__energy__parameters_ga70bc46be7cfa5434a71efe241c4f0609}{vrna\+\_\+exp\+\_\+params\+\_\+copy}} (\mbox{\hyperlink{group__energy__parameters_ga01d8b92fe734df8d79a6169482c7d8d8}{vrna\+\_\+exp\+\_\+param\+\_\+t}} $\ast$par)
54\begin{DoxyCompactList}\small\item\em Get a copy of the provided free energy parameters (provided as Boltzmann factors) \end{DoxyCompactList}\item
55void \mbox{\hyperlink{group__energy__parameters_ga5d1909208f7ea3baa98b75afaa1f62ca}{vrna\+\_\+params\+\_\+subst}} (\mbox{\hyperlink{group__fold__compound_ga1b0cef17fd40466cef5968eaeeff6166}{vrna\+\_\+fold\+\_\+compound\+\_\+t}} $\ast$vc, \mbox{\hyperlink{group__energy__parameters_ga8a69ca7d787e4fd6079914f5343a1f35}{vrna\+\_\+param\+\_\+t}} $\ast$par)
56\begin{DoxyCompactList}\small\item\em Update/\+Reset energy parameters data structure within a \mbox{\hyperlink{group__fold__compound_ga1b0cef17fd40466cef5968eaeeff6166}{vrna\+\_\+fold\+\_\+compound\+\_\+t}}. \end{DoxyCompactList}\item
57void \mbox{\hyperlink{group__energy__parameters_ga8e7ac4fab3b0cc03afbc134eaafb3525}{vrna\+\_\+exp\+\_\+params\+\_\+subst}} (\mbox{\hyperlink{group__fold__compound_ga1b0cef17fd40466cef5968eaeeff6166}{vrna\+\_\+fold\+\_\+compound\+\_\+t}} $\ast$vc, \mbox{\hyperlink{group__energy__parameters_ga01d8b92fe734df8d79a6169482c7d8d8}{vrna\+\_\+exp\+\_\+param\+\_\+t}} $\ast$params)
58\begin{DoxyCompactList}\small\item\em Update the energy parameters for subsequent partition function computations. \end{DoxyCompactList}\item
59void \mbox{\hyperlink{group__energy__parameters_gad607bc3a5b5da16400e2ca4ea5560233}{vrna\+\_\+exp\+\_\+params\+\_\+rescale}} (\mbox{\hyperlink{group__fold__compound_ga1b0cef17fd40466cef5968eaeeff6166}{vrna\+\_\+fold\+\_\+compound\+\_\+t}} $\ast$vc, double $\ast$mfe)
60\begin{DoxyCompactList}\small\item\em Rescale Boltzmann factors for partition function computations. \end{DoxyCompactList}\item
61void \mbox{\hyperlink{group__energy__parameters_gac40dc82e48a72a97cfc58b9da08a7792}{vrna\+\_\+params\+\_\+reset}} (\mbox{\hyperlink{group__fold__compound_ga1b0cef17fd40466cef5968eaeeff6166}{vrna\+\_\+fold\+\_\+compound\+\_\+t}} $\ast$vc, \mbox{\hyperlink{group__model__details_ga1f8a10e12a0a1915f2a4eff0b28ea17c}{vrna\+\_\+md\+\_\+t}} $\ast$md\+\_\+p)
62\begin{DoxyCompactList}\small\item\em Reset free energy parameters within a \mbox{\hyperlink{group__fold__compound_ga1b0cef17fd40466cef5968eaeeff6166}{vrna\+\_\+fold\+\_\+compound\+\_\+t}} according to provided, or default model details. \end{DoxyCompactList}\item
63void \mbox{\hyperlink{group__energy__parameters_gaa5409218068be84d7b50c78fbdaa85a9}{vrna\+\_\+exp\+\_\+params\+\_\+reset}} (\mbox{\hyperlink{group__fold__compound_ga1b0cef17fd40466cef5968eaeeff6166}{vrna\+\_\+fold\+\_\+compound\+\_\+t}} $\ast$vc, \mbox{\hyperlink{group__model__details_ga1f8a10e12a0a1915f2a4eff0b28ea17c}{vrna\+\_\+md\+\_\+t}} $\ast$md\+\_\+p)
64\begin{DoxyCompactList}\small\item\em Reset Boltzmann factors for partition function computations within a \mbox{\hyperlink{group__fold__compound_ga1b0cef17fd40466cef5968eaeeff6166}{vrna\+\_\+fold\+\_\+compound\+\_\+t}} according to provided, or default model details. \end{DoxyCompactList}\item
65\mbox{\hyperlink{group__energy__parameters_ga01d8b92fe734df8d79a6169482c7d8d8}{vrna\+\_\+exp\+\_\+param\+\_\+t}} $\ast$ \mbox{\hyperlink{group__energy__parameters_gabf3b9271c41dd3fac02d56e0b02b3344}{get\+\_\+scaled\+\_\+pf\+\_\+parameters}} (void)
66\item
67\mbox{\hyperlink{group__energy__parameters_ga01d8b92fe734df8d79a6169482c7d8d8}{vrna\+\_\+exp\+\_\+param\+\_\+t}} $\ast$ \mbox{\hyperlink{group__energy__parameters_gaef2b931c7e9d4ffb0a5c33df50ec2068}{get\+\_\+boltzmann\+\_\+factors}} (double \mbox{\hyperlink{group__model__details_gab4b11c8d9c758430960896bc3fe82ead}{temperature}}, double beta\+Scale, \mbox{\hyperlink{group__model__details_ga1f8a10e12a0a1915f2a4eff0b28ea17c}{vrna\+\_\+md\+\_\+t}} md, double \mbox{\hyperlink{group__model__details_gad3b22044065acc6dee0af68931b52cfd}{pf\+\_\+scale}})
68\begin{DoxyCompactList}\small\item\em Get precomputed Boltzmann factors of the loop type dependent energy contributions with independent thermodynamic temperature. \end{DoxyCompactList}\item
69\mbox{\hyperlink{group__energy__parameters_ga01d8b92fe734df8d79a6169482c7d8d8}{vrna\+\_\+exp\+\_\+param\+\_\+t}} $\ast$ \mbox{\hyperlink{group__energy__parameters_ga665a446ba8ff211e551297a8fa36ec27}{get\+\_\+boltzmann\+\_\+factor\+\_\+copy}} (\mbox{\hyperlink{group__energy__parameters_ga01d8b92fe734df8d79a6169482c7d8d8}{vrna\+\_\+exp\+\_\+param\+\_\+t}} $\ast$parameters)
70\begin{DoxyCompactList}\small\item\em Get a copy of already precomputed Boltzmann factors. \end{DoxyCompactList}\item
71\mbox{\hyperlink{group__energy__parameters_ga01d8b92fe734df8d79a6169482c7d8d8}{vrna\+\_\+exp\+\_\+param\+\_\+t}} $\ast$ \mbox{\hyperlink{group__energy__parameters_ga0ccf4e1be085a573533fd6b9da2d8cf9}{get\+\_\+scaled\+\_\+alipf\+\_\+parameters}} (unsigned int n\+\_\+seq)
72\begin{DoxyCompactList}\small\item\em Get precomputed Boltzmann factors of the loop type dependent energy contributions (alifold variant) \end{DoxyCompactList}\item
73\mbox{\hyperlink{group__energy__parameters_ga01d8b92fe734df8d79a6169482c7d8d8}{vrna\+\_\+exp\+\_\+param\+\_\+t}} $\ast$ \mbox{\hyperlink{group__energy__parameters_ga2aa1d87c97f35d2e4121634a17556829}{get\+\_\+boltzmann\+\_\+factors\+\_\+ali}} (unsigned int n\+\_\+seq, double \mbox{\hyperlink{group__model__details_gab4b11c8d9c758430960896bc3fe82ead}{temperature}}, double beta\+Scale, \mbox{\hyperlink{group__model__details_ga1f8a10e12a0a1915f2a4eff0b28ea17c}{vrna\+\_\+md\+\_\+t}} md, double \mbox{\hyperlink{group__model__details_gad3b22044065acc6dee0af68931b52cfd}{pf\+\_\+scale}})
74\begin{DoxyCompactList}\small\item\em Get precomputed Boltzmann factors of the loop type dependent energy contributions (alifold variant) with independent thermodynamic temperature. \end{DoxyCompactList}\item
75\mbox{\hyperlink{group__energy__parameters_ga8a69ca7d787e4fd6079914f5343a1f35}{vrna\+\_\+param\+\_\+t}} $\ast$ \mbox{\hyperlink{group__energy__parameters_ga541f2cf7436e9bc939b0a49b24baf987}{scale\+\_\+parameters}} (void)
76\begin{DoxyCompactList}\small\item\em Get precomputed energy contributions for all the known loop types. \end{DoxyCompactList}\item
77\mbox{\hyperlink{group__energy__parameters_ga8a69ca7d787e4fd6079914f5343a1f35}{vrna\+\_\+param\+\_\+t}} $\ast$ \mbox{\hyperlink{group__energy__parameters_ga7fa6a000d7c16feab939f2c4ee626197}{get\+\_\+scaled\+\_\+parameters}} (double \mbox{\hyperlink{group__model__details_gab4b11c8d9c758430960896bc3fe82ead}{temperature}}, \mbox{\hyperlink{group__model__details_ga1f8a10e12a0a1915f2a4eff0b28ea17c}{vrna\+\_\+md\+\_\+t}} md)
78\begin{DoxyCompactList}\small\item\em Get precomputed energy contributions for all the known loop types. \end{DoxyCompactList}\end{DoxyCompactItemize}
79
80
81\doxysubsection{Detailed Description}
82Functions to deal with sets of energy parameters.
83
84