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haddocking · Apr 22, 2024 · 456c25d · 456c25d
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diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
@@ -19,4 +19,4 @@
       ]
     }
   }
-}
+}
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -3,7 +3,6 @@ name: ci
 on:
   push:
 
-
 jobs:
   test:
     runs-on: ubuntu-latest

diff --git a/INSTALLATION.md b/INSTALLATION.md
@@ -19,9 +19,9 @@ To install Whiscy, follow these steps:
 
 - Clone the repository:
 
-    ```bash
-    git clone https://github.com/haddocking/whiscy && cd whiscy
-    ```
+  ```bash
+  git clone https://github.com/haddocking/whiscy && cd whiscy
+  ```
 
 - Install the scripts
 
@@ -33,23 +33,23 @@ To install Whiscy, follow these steps:
 
 - Check the installation
 
-    ```text
-    $ whiscy -h
-    usage: whiscy [-h] [-o output_file] [--version]
-                  surface_list conversion_table alignment_file distance_file
-
-    positional arguments:
-      surface_list          Surface list
-      conversion_table      Conversion table
-      alignment_file        Alignment file
-      distance_file         Distance file
-
-    options:
-      -h, --help            show this help message and exit
-      -o output_file, --output output_file
-                            If set, output prediction to this file
-      --version             show program's version number and exit
-    ```
+  ```text
+  $ whiscy -h
+  usage: whiscy [-h] [-o output_file] [--version]
+                surface_list conversion_table alignment_file distance_file
+
+  positional arguments:
+    surface_list          Surface list
+    conversion_table      Conversion table
+    alignment_file        Alignment file
+    distance_file         Distance file
+
+  options:
+    -h, --help            show this help message and exit
+    -o output_file, --output output_file
+                          If set, output prediction to this file
+    --version             show program's version number and exit
+  ```
 
 ### Troubleshooting
 

diff --git a/USAGE.md b/USAGE.md
@@ -10,9 +10,9 @@ Below we will give an example of how to use WHISCY to predict the binding site o
 
 Download the PDB file of the protein 1PPE from the [RCSB PDB](https://www.rcsb.org/structure/1PPE) website.
 
-  ```bash
-  wget https://files.rcsb.org/download/1PPE.pdb
-  ```
+```bash
+wget https://files.rcsb.org/download/1PPE.pdb
+```
 
 ### Setup the prediction
 
@@ -32,26 +32,26 @@ $ whiscy_setup 1PPE.pdb E
   2024-04-22 11:44:44,046 cli_setup:319 INFO - Protdist calculated
   2024-04-22 11:44:44,054 cli_setup:326 INFO - Conversion table file generated
   2024-04-22 11:44:44,054 cli_setup:328 INFO - Whiscy setup finished
-  ```
+```
 
 This script will generate a set of files needed for the prediction step with `whiscy`. Here it is a list of the generated files in our 1PPE complex.
 
 > Follow the links to see a set of pre-generated files for the 1PPE protein.
 
-| File name                                 |    Explanation                                                 |
-| ----------------------------------------- |----------------------------------------------------------------|
-| [1ppe.hssp](example/1ppe.hssp)           | Multiple sequence alignment download from the HSSP database     |
-| [1ppe.hssp.bz2](example/1ppe.hssp.bz2)   | HSSP MSA file compressed                                        |
-| [1ppe.pdb](example/1ppe.pdb)             | PDB file download from the Protein Data Bank                    |
-| [1ppe_E.pdb](example/1ppe_E.pdb)         | 1ppe.pdb parsed to select only the given `chain_id`             |
-| [1ppe_E.rsa](example/1ppe_E.rsa)         | SASA output of `freesasa` in `NACCESS` format of `1ppe_E.pdb` file|
-| [1ppe_E.fasta](example/1ppe_E.fasta)     | Sequence of 1ppe_E.pdb. Alternative residues have been removed  |
-| [1ppe_E.phylseq](example/1ppe_E.phylseq) | MSA file translated from HSSP to PHYLIP format                  |
-| [1ppe_E.conv](example/1ppe_E.conv)       | PDB residue numeration to FASTA sequence numeration             |
-| [1ppe_E.out](example/1ppe_E.out)         | Output of the `protdist` software on 1ppe_E.pdb                 |
-| [1ppe_E.sur](example/1ppe_E.sur)         | >15 % surface residue list according to `sa_pred_cutoff` cutoff |
-| [1ppe_E.suract](example/1ppe_E.suract)   | >40 % surface residue list according to `sa_act_cutoff` cutoff  |
-| [1ppe_E.lac](example/1ppe_E.lac)         | 0-15 % accessible residue list                                  |
+| File name                                | Explanation                                                        |
+| ---------------------------------------- | ------------------------------------------------------------------ |
+| [1ppe.hssp](example/1ppe.hssp)           | Multiple sequence alignment download from the HSSP database        |
+| [1ppe.hssp.bz2](example/1ppe.hssp.bz2)   | HSSP MSA file compressed                                           |
+| [1ppe.pdb](example/1ppe.pdb)             | PDB file download from the Protein Data Bank                       |
+| [1ppe_E.pdb](example/1ppe_E.pdb)         | 1ppe.pdb parsed to select only the given `chain_id`                |
+| [1ppe_E.rsa](example/1ppe_E.rsa)         | SASA output of `freesasa` in `NACCESS` format of `1ppe_E.pdb` file |
+| [1ppe_E.fasta](example/1ppe_E.fasta)     | Sequence of 1ppe_E.pdb. Alternative residues have been removed     |
+| [1ppe_E.phylseq](example/1ppe_E.phylseq) | MSA file translated from HSSP to PHYLIP format                     |
+| [1ppe_E.conv](example/1ppe_E.conv)       | PDB residue numeration to FASTA sequence numeration                |
+| [1ppe_E.out](example/1ppe_E.out)         | Output of the `protdist` software on 1ppe_E.pdb                    |
+| [1ppe_E.sur](example/1ppe_E.sur)         | >15 % surface residue list according to `sa_pred_cutoff` cutoff    |
+| [1ppe_E.suract](example/1ppe_E.suract)   | >40 % surface residue list according to `sa_act_cutoff` cutoff     |
+| [1ppe_E.lac](example/1ppe_E.lac)         | 0-15 % accessible residue list                                     |
 
 ### Make the interface prediction
 

diff --git a/media/1ppe_whiscy.png b/media/1ppe_whiscy.png
diff --git a/media/loch_haddock.png b/media/loch_haddock.png
diff --git a/media/whiscy_logo.png b/media/whiscy_logo.png
diff --git a/media/whiscy_logo.svg b/media/whiscy_logo.svg
diff --git a/src/whiscy/cli_consadjust.py b/src/whiscy/cli_consadjust.py
@@ -84,7 +84,7 @@ def main():
             neg = True
 
         index = np.argmax(z_values < currz)
-        upperz = z_values[index]
+        z_values[index]
 
         if index >= 24999:
             pscore = 0.5

diff --git a/src/whiscy/cli_setup.py b/src/whiscy/cli_setup.py
@@ -226,7 +226,7 @@ def main():
                     hssp_file = hssp_file.replace("hssp", "hssp3")
                 hssp.decompress_bz2(compressed_hssp_file, hssp_file)
                 logger.info("HSSP alignment stored to {0}".format(hssp_file))
-            except Exception as err:
+            except Exception:
                 logger.warning("HSSP file could not be downloaded")
         try:
             if "hssp3" in hssp_file:
-Original file line number
+Diff line change
@@ Expand Up / @@ -19,4 +19,4 @@ @@
           ]
         }
       }
-    }
+    }