Salt Corrections
All relevant functions to compute salt correction at a given salt concentration and temperature.
The corrections for loop and stack are taken from Einert and Netz [2011].
All corrections returned are in units of \(\text{dcal} \cdot \text{mol}^{-1}\).
Functions
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double vrna_salt_loop(int L, double salt, double T, double backbonelen)
- #include <ViennaRNA/params/salt.h>
Get salt correction for a loop at a given salt concentration and temperature.
- Parameters:
L – backbone number in loop
salt – salt concentration (M)
T – absolute temperature (K)
backbonelen – Backbone Length, phosphate-to-phosphate distance (typically 6 for RNA, 6.76 for DNA)
- Returns:
Salt correction for loop in dcal/mol
-
int vrna_salt_loop_int(int L, double salt, double T, double backbonelen)
- #include <ViennaRNA/params/salt.h>
Get salt correction for a loop at a given salt concentration and temperature.
This functions is same as vrna_salt_loop but returns rounded salt correction in integer
See also
- Parameters:
L – backbone number in loop
salt – salt concentration (M)
T – absolute temperature (K)
backbonelen – Backbone Length, phosphate-to-phosphate distance (typically 6 for RNA, 6.76 for DNA)
- Returns:
Rounded salt correction for loop in dcal/mol
-
int vrna_salt_stack(double salt, double T, double hrise)
- #include <ViennaRNA/params/salt.h>
Get salt correction for a stack at a given salt concentration and temperature.
- Parameters:
salt – salt concentration (M)
T – absolute temperature (K)
hrise – Helical Rise (typically 2.8 for RNA, 3.4 for DNA)
- Returns:
Rounded salt correction for stack in dcal/mol
-
void vrna_salt_ml(double saltLoop[], int lower, int upper, int *m, int *b)
- #include <ViennaRNA/params/salt.h>
Fit linear function to loop salt correction.
For a given range of loop size (backbone number), we perform a linear fitting on loop salt correction
\[ \text{Loop correction} \approx m \cdot L + b. \]See also
- Parameters:
saltLoop – List of loop salt correction of size from 1
lower – Define the size lower bound for fitting
upper – Define the size upper bound for fitting
m – pointer to store the parameter m in fitting result
b – pointer to store the parameter b in fitting result
-
int vrna_salt_duplex_init(vrna_md_t *md)
- #include <ViennaRNA/params/salt.h>
Get salt correction for duplex initialization at a given salt concentration.
- Parameters:
md – Model details data structure that specfifies salt concentration in buffer (M)
- Returns:
Rounded correction for duplex initialization in dcal/mol
-
double vrna_salt_loop(int L, double salt, double T, double backbonelen)