Expand documentation on how to set distances in the tbl configurati…

…on file (#20)

* Expand documentation

* tweak text

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