documentation/monster/three_modes_compared.md
## Three modes
> This page is a bit out of date as the full mode now includes various corrections, for automatic merging,
> but the conclusion is the same. `none` mode of merging —i.e. mapping the followup molecule to each hit is the best
> even when there are incorrect inspiration hits.
As [discussed](../../README.md), it has three main parts:
* the pipeline (Victor class)
* the minimiser (Egor class) and
* the followup placing algorithm (Fragmenstein class)
The latter has three modes as discussed in [the fragmenstein page](monster.md): "full-merging", "partial-merging" and "no-merging" for mapping.
Each has advantages and disadvantage. For the [covid](../covid.md) data, an analysis was done to figure out which.
50 followups were randomly chosen and placed with the three modes (165 total poses were done, +10% for safety).
The medians of the various scores are:
| mode | ∆∆G [kcal/mol] | concatenated RMSD [Å] | Number of constrained atoms | Runtime [s] |
|:--------|---------:|----------:|----------------------:|----------:|
| full | -3.55336 | 0.940974 | 12 | 16.6215 |
| none | -4.02654 | 1.0435 | 14 | 17.5834 |
| partial | -3.23976 | 0.970151 | 13 | 16.7117 |
No merging mapping is better for both number of atoms used and the ∆∆G_bind.
It scored worse for time and slightly for RMSD.
It is clear that the no merging mapping when it fails it fails badly.
So let's look solely at all ∆∆G < 0 ones:
The outliers in ∆∆G are caused by erroneous hits being claimed to be inspirations.
Here is one of these, WAR-XCH-b6889685-63 in the same colours as the graphs:
Namely the outlier is chosen as an inspiration and the bond length is not violated as the atoms from the mapped parts are
not neighbours, so the 3 Å limit does not apply. Curiously, full-merger mapped to one cluster, while partial merger to the loner.
The time problem is substantial for the none.
.
These are the offenders:
| | name | mode | ∆∆G | comRMSD | N_constrained_atoms | runtime | N_hits |
|----:|:--------------------|:--------|----------:|----------:|----------------------:|----------:|---------:|
| 36 | JAG-SYN-9c2cd0bd-13 | none | nan | nan | 18 | 2164.83 | 6 |
| 156 | WAR-XCH-b6889685-20 | none | -5.81899 | 1.43685 | 10 | 528.47 | 5 |
| 93 | CHR-SOS-1f323c23-1 | none | -7.99253 | 0.65989 | 16 | 85.4308 | 5 |
| 98 | RAM-SYN-2a37ce6c-4 | partial | -8.13456 | 2.2751 | 11 | 79.835 | 4 |
| 153 | DRA-CSI-47e38074-1 | none | -4.02654 | 1.0435 | 13 | 67.3437 | 6 |
The `JAG-SYN-9c2cd0bd-13` has nothing wrong with it. It dies after the igor step due to sanitisation (fixed).
The "none" mode excluded the following `['x0689', 'x0691', 'x0692', 'x0705', 'x0708']`,
As a human at first glance I would have excluded `['x0689', 'x0692', 'x0705', 'x0708']`, so keeping `['x0691', 'x0731']`,
but looking better at it, `'x0691'` would be in the list. So perfect!
However, 33 minutes is not an acceptable runtime.