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docs: explain how to use modified base energy param presets
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marcom committed Apr 16, 2024
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Expand Up @@ -282,6 +282,33 @@ inverse_pf_fold("AAAAAAA", "((...))") # => ("GCCAAGC", 2.0244526863098145 kcal
ViennaRNA.init_rand_seed(42)
```

### Modified bases energy parameter presets

Energy parameters for modified bases can be used via ViennaRNA's soft
constraints mechanism.

```julia
using ViennaRNA
fc = FoldCompound("AAACCCUUU")
partfn(fc) # -0.0025467473022687203 kcal mol^-1
ViennaRNA.sc_mod_pseudouridine!(fc, [7,8,9]) # modify positions 7, 8, 9
partfn(fc) # -0.004713416050703315 kcal mol^-1
```

These functions are currently available:
```
sc_mod_7DA!
sc_mod_dihydrouridine!
sc_mod_inosine!
sc_mod_m6A!
sc_mod_pseudouridine!
sc_mod_purine!
```
Please refer to the
[ViennaRNA section on modified bases](https://www.tbi.univie.ac.at/RNA/ViennaRNA/doc/html/modified_bases.html)
for more details.


## Reducing memory usage

When creating many `FoldCompound`s, running `finalize` manually will
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