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Expand documentation on how to set distances in the tbl configuration file #20

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Aug 28, 2024
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Expand documentation on how to set distances in the tbl configuration file #20

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rvhonorato Aug 28, 2024
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rvhonorato Aug 28, 2024
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5 changes: 5 additions & 0 deletions docs/src/configuration_file.md
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Expand Up @@ -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
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- `lower_margin`: the lower margin to consider two residues as interacting, default = 2.0
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- `upper_margin`: the upper margin to consider two residues as interacting, default = 0.0

Note: Check [this paper](https://doi.org/10.1038/s41596-018-0018-5) for a deeper explanation about the target distance and the margins

A configuration file with optional fields would look like this:

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