About DNA/RNA parameters

[simonecodispoti]

Hi all,
short question about the model parameters given as seq_dep_file : what are all the possible parameters that can be changed?
For example, In the default file of average parameters for the DNA model these are all the given options:

""""""""""""""""""""""""""""""
STCK_FACT_EPS = 0.180004

STCK_G_C = 1.6491556
STCK_C_G = 1.6491556
STCK_G_G = 1.6491556
STCK_C_C = 1.6491556
STCK_G_A = 1.6491556
STCK_T_C = 1.6491556
STCK_A_G = 1.6491556
STCK_C_T = 1.6491556
STCK_T_G = 1.6491556
STCK_C_A = 1.6491556
STCK_G_T = 1.6491556
STCK_A_C = 1.6491556
STCK_A_T = 1.6491556
STCK_T_A = 1.6491556
STCK_A_A = 1.6491556
STCK_T_T = 1.6491556

HYDR_A_T = 1.0678
HYDR_T_A = 1.0678
HYDR_C_G = 1.0678
HYDR_G_C = 1.0678
"""""""""""""""""""""""""""

Are there other parameters that can be edited? In the RNA file I see also the Cross Stacking interactions modified for example. It would be helpful to have in the documentation all the possible MACROS setting these interactions, together with their possible "physical" range.

Thanks for the attention!
I think anyone would benefit from this. Maybe is something already stated somewhere, but I couldn't find :0

[lorenzo-rovigatti]

Hi, and thanks for the suggestion. For RNA, you can have a look at the src/Interactions/rna_model.h for the list of options that can be set from the sequence-dependence file. For DNA, the list of user-definable settings is limited to those that are set in the seq_dep_file.

[simonecodispoti]

Thanks a lot for the reply!
So, if I understood correctly, I can edit only the MACROS I wrote above using the seq_dep_file for DNA? I had a look at src/Interactions/rna_model.h, but I couldn't find the same keywords (like e.g. HYDR_A_T ), even though it's clear that all the interactions are listed there. Because I suppose these files are not to be changed directly (it's part of the source code) what would be the most extensive seq_dep_file as input?

Thanks again :)

[lorenzo-rovigatti]

Apologies, I misremember. What is read from the seq_dep_files can be found in the init() functions of the RNAInteraction and DNAInteractions classes. With oxRNA, you can specify an additional file (with the external_model key) where you can change all the options listed in rna_model.h.

[simonecodispoti]

Now it's clear!

Thanks again,
Simone