From e803afb2574bf82b8a1b3c981568995a74a40476 Mon Sep 17 00:00:00 2001 From: Rodrigo Vargas Honorato Date: Wed, 28 Aug 2024 16:50:02 +0200 Subject: [PATCH] Expand documentation on how to set distances in the `tbl` configuration file (#20) * Expand documentation * tweak text --- docs/src/configuration_file.md | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/docs/src/configuration_file.md b/docs/src/configuration_file.md index 7a08685..0416adf 100644 --- a/docs/src/configuration_file.md +++ b/docs/src/configuration_file.md @@ -48,6 +48,11 @@ A minimal configuration file would look like this: - `surface_as_passive`: if true, the passive residues are defined based on the surface accessibility of the residues (_requires structure_) - `filter_buried`: if true, the buried residues are filtered out (_requires structure_) - `filter_buried_cutoff`: the cutoff to consider a residue as buried, default = 0.7 (_requires structure_) +- `target_distance`: the distance to consider two residues as interacting, default = 2.0 (_see Note_) +- `lower_margin`: the lower bound correction subtracted from the `target_distance` to define the lower distance boundary. +- `upper_margin`: the upper bound correction added to the target_distance to define the upper distance boundary. + +> **Note**: Check [this paper](https://doi.org/10.1038/s41596-018-0018-5) for a deeper explanation about the target distance and the margins. The default value of 2.0Å (which might seem short) is used because of the way the effective distance is calculated from all pairwise combinations of atom it will always be shorter than the shortest distance measured. A configuration file with optional fields would look like this: @@ -140,3 +145,15 @@ Optional fields are: - type: float - description: the cutoff to consider a residue as buried, default = 0.7 - requires: `structure` + +- `target_distance` + - type: float + - description: the distance to consider two residues as interacting, default = 2.0 + +- `lower_margin` + - type: float + - description: the lower bound correction subtracted from the `target_distance` to define the lower distance boundary + +- `upper_margin` + - type: float + - description: the upper bound correction added to the target_distance to define the upper distance boundary