Update README.md

README.md

@@ -1,72 +1,83 @@
-## Installation
-
-Clone the repository `???`.  
-Then, extract the [FoldX](https://foldxsuite.crg.eu/products#foldx) distribution for your operating system into `external/foldx` in the cloned project folder, _make sure_ the binary is named `foldx`.  
-Finally, install the dependencies and check the installation works:  
-```bash
-pip install -r requirements.in
-python -m tests.inference
-```
-
-If the installation *fails*, or the application *crashes*, try to install *pinned dependencies* instead: `pip install -r requirements.txt`. Also check the table below.
-
-#### Tested configurations:
-
-| OS    | Python | PyTorch | Engine    | Project version                |
-|-------|--------|---------|-----------|--------------------------------|
-| Win 10 | 3.8.18 | 2.1.2   | CPU       | January 16, 2024               |
-| Linux | 3.9.19 | 2.1.2   | CPU       | January 16, 2024               | 
-| Linux | 3.8.13 | 1.10.0  | CUDA 11.3 | January 16, 2024                               | 
-
-### Usage
-
-```
-wrapper.py [-h] [-v] pdb-code [chain] wild-type location mutation
-
-Solubility change preditor:
-  Predicts the change in the solubility of a given protein variant
-
-positional arguments:
-  pdb-code       PDB code
-  chain          target chain          character; default=A
-  wild-type      wild-type residue(s)  amino-acid[n]
-  location       mutated position(s)   integer[n]
-  mutation       1 or n substituents   amino-acid|amino-acid[n]
-
-optional arguments:
-  -h, --help     show this help message and exit
-  -v, --verbose
-
-Amino acids can be specified by both 1- or 3-letter code.
-```
-
-Example usage (double-point mutant in [erythropoietin](https://www.rcsb.org/sequence/1EER))`and its outpus:
-```bash
-./wrapper.py 1EER F,R 48,150 D --verbose
-```
-
-```
-Predicted solubility change: 5.000398e-01 (solubilizing)
-```
-
-## Development
-
-### Reproducible environment
-
-`requirements.in` – project (direct) dependencies required for *inference*. Keep the PyTorch version specified here in sync with the link for the *pyg* wheels specified ibidem.
-
-`requirements.txt` – _resolved_ and _pinned_ dependencies based on the file above, a result of `pip install -r requirements.in && pip freeze` in a fresh Python environment.  
-note: `pip-compile` of pip-tools does not seem to work with complex PyTorch ecosystem 
-
-### Style guide
-#### Indentation
-Use tabs `\t` for an indentation, spaces (after tabs) for an alignment ([reasoning](https://stackoverflow.com/a/5048130/1908192), [reasoning2](https://www.reddit.com/r/javascript/comments/c8drjo/nobody_talks_about_the_real_reason_to_use_tabs/
-))
-
-#### Naming conventions (PEP8-based)
-module_name, CONSTANT_NAME, ClassName (capitalize first letters of words), subroutine_name, variable_name
-
-ClassName, function_name: keep acronyms in their original case: GetPDB, get_PDB
-
- 
-
+---
+title: SoluProtMut
+emoji: 🔬
+colorFrom: red
+colorTo: blue
+sdk: gradio
+sdk_version: 4.44.1
+app_file: app.py
+pinned: false
+---
+
+## Installation
+
+Clone the repository `???`.  
+Then, extract the [FoldX](https://foldxsuite.crg.eu/products#foldx) distribution for your operating system into `external/foldx` in the cloned project folder, _make sure_ the binary is named `foldx`.  
+Finally, install the dependencies and check the installation works:  
+```bash
+pip install -r requirements.in
+python -m tests.inference
+```
+
+If the installation *fails*, or the application *crashes*, try to install *pinned dependencies* instead: `pip install -r requirements.txt`. Also check the table below.
+
+#### Tested configurations:
+
+| OS    | Python | PyTorch | Engine    | Project version                |
+|-------|--------|---------|-----------|--------------------------------|
+| Win 10 | 3.8.18 | 2.1.2   | CPU       | January 16, 2024               |
+| Linux | 3.9.19 | 2.1.2   | CPU       | January 16, 2024               | 
+| Linux | 3.8.13 | 1.10.0  | CUDA 11.3 | January 16, 2024                               | 
+
+### Usage
+
+```
+wrapper.py [-h] [-v] pdb-code [chain] wild-type location mutation
+
+Solubility change preditor:
+  Predicts the change in the solubility of a given protein variant
+
+positional arguments:
+  pdb-code       PDB code
+  chain          target chain          character; default=A
+  wild-type      wild-type residue(s)  amino-acid[n]
+  location       mutated position(s)   integer[n]
+  mutation       1 or n substituents   amino-acid|amino-acid[n]
+
+optional arguments:
+  -h, --help     show this help message and exit
+  -v, --verbose
+
+Amino acids can be specified by both 1- or 3-letter code.
+```
+
+Example usage (double-point mutant in [erythropoietin](https://www.rcsb.org/sequence/1EER))`and its outpus:
+```bash
+./wrapper.py 1EER F,R 48,150 D --verbose
+```
+
+```
+Predicted solubility change: 5.000398e-01 (solubilizing)
+```
+
+## Development
+
+### Reproducible environment
+
+`requirements.in` – project (direct) dependencies required for *inference*. Keep the PyTorch version specified here in sync with the link for the *pyg* wheels specified ibidem.
+
+`requirements.txt` – _resolved_ and _pinned_ dependencies based on the file above, a result of `pip install -r requirements.in && pip freeze` in a fresh Python environment.  
+note: `pip-compile` of pip-tools does not seem to work with complex PyTorch ecosystem 
+
+### Style guide
+#### Indentation
+Use tabs `\t` for an indentation, spaces (after tabs) for an alignment ([reasoning](https://stackoverflow.com/a/5048130/1908192), [reasoning2](https://www.reddit.com/r/javascript/comments/c8drjo/nobody_talks_about_the_real_reason_to_use_tabs/
+))
+
+#### Naming conventions (PEP8-based)
+module_name, CONSTANT_NAME, ClassName (capitalize first letters of words), subroutine_name, variable_name
+
+ClassName, function_name: keep acronyms in their original case: GetPDB, get_PDB
+
+ 
+