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Adds documentation about eager reparation in foldx
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docs/protein-optimization/using_poli/objective_repository/foldx_sasa.md

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@@ -20,6 +20,21 @@ If you are interested in computing both a protein's stability and it's SASA scor
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- `~/foldx/rotabase.txt`: a text file necessary for `foldx` to run.
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- A `wildtype_pdb_file`: a (repaired) pdb file of the wildtype.
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:::{admonition} We can repair the file for you
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:class: dropdown
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By default, we will assume you are passing a repaired `pdb` file to us (indeed, we check if the filename contains `_Repair`). If you want us to repair the file for you and keep it in a cache, you can add the `eager_repair=True` keyword argument to the `create` method.
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Otherwise, pre-repair your files using e.g.
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```bash
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~/foldx/foldx --command=RepairPDB --pdb your_file.pdb --water -CRYSTAL --pH 7.0
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```
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In our repairing process, we also remove heteroatoms using [`pdbtools`](https://www.bonvinlab.org/pdb-tools/).
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:::
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## How to run
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You can either run this objective function in your current environment (assuming that you have the correct dependencies installed), or you can run it in an isolated environment.

docs/protein-optimization/using_poli/objective_repository/foldx_stability.md

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@@ -19,6 +19,21 @@ If you are interested in computing both a protein's stability and it's SASA scor
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- `~/foldx/rotabase.txt`: a text file necessary for `foldx` to run.
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- A `wildtype_pdb_file`: a (repaired) pdb file of the wildtype.
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:::{admonition} We can repair the file for you
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:class: dropdown
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By default, we will assume you are passing a repaired `pdb` file to us (indeed, we check if the filename contains `_Repair`). If you want us to repair the file for you and keep it in a cache, you can add the `eager_repair=True` keyword argument to the `create` method.
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Otherwise, pre-repair your files using e.g.
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```bash
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~/foldx/foldx --command=RepairPDB --pdb your_file.pdb --water -CRYSTAL --pH 7.0
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```
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In our repairing process, we also remove heteroatoms using [`pdbtools`](https://www.bonvinlab.org/pdb-tools/).
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:::
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## How to run
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You can either run this objective function in your current environment (assuming that you have the correct dependencies installed), or you can run it in an isolated environment.

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