Merge pull request #145 from PyEED/fixes_standard_numbering

Fixes standard numbering and addtions mutation detection

Author: haeussma

.gitignore

@@ -3,6 +3,11 @@ __pycache__/
 *.py[cod]
 *$py.class
 
+# AlphaFold output
+docs/resources/alphafold/output/*
+src/pyeed/tools/alphafold2.py
+docs/usage/alphafold.ipynb
+
 # C extensions
 *.so
 .vscode/

docs/usage/basics.ipynb

@@ -189,7 +189,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "pyeed",
+   "display_name": "pyeed_niklas",
    "language": "python",
    "name": "python3"
   },
@@ -203,7 +203,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.5"
+   "version": "3.12.8"
   }
  },
  "nbformat": 4,

docs/usage/embeddings_analysis.ipynb

@@ -18,7 +18,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 67,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -31,7 +31,7 @@
     "from pyeed.analysis.embedding_analysis import EmbeddingTool\n",
     "\n",
     "logger.remove()\n",
-    "level = logger.add(sys.stderr, level=\"WARNING\")"
+    "level = logger.add(sys.stderr, level=\"INFO\")"
    ]
   },
   {
@@ -47,60 +47,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 69,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "📡 Connected to database.\n",
-      "All data has been wiped from the database.\n",
-      "Connecting to bolt://neo4j:12345678@129.69.129.130:7687\n",
-      "Dropping constraints...\n",
-      " - Dropping unique constraint and index on label CatalyticActivity with property catalytic_id.\n",
-      " - Dropping unique constraint and index on label DNA with property accession_id.\n",
-      " - Dropping unique constraint and index on label GOAnnotation with property go_id.\n",
-      " - Dropping unique constraint and index on label OntologyObject with property name.\n",
-      " - Dropping unique constraint and index on label Organism with property taxonomy_id.\n",
-      " - Dropping unique constraint and index on label Protein with property accession_id.\n",
-      " - Dropping unique constraint and index on label Region with property region_id.\n",
-      " - Dropping unique constraint and index on label Site with property site_id.\n",
-      "\n",
-      "Dropping indexes...\n",
-      " - Dropping index on labels DNA with properties embedding.\n",
-      " - Dropping index on labels Protein with properties embedding.\n",
-      "\n",
-      "All constraints and indexes have been removed from the database.\n",
-      "the connection url is bolt://neo4j:12345678@129.69.129.130:7687\n",
-      "Loaded /home/nab/Niklas/pyeed/src/pyeed/model.py\n",
-      "Connecting to bolt://neo4j:12345678@129.69.129.130:7687\n",
-      "Setting up indexes and constraints...\n",
-      "\n",
-      "Found model.StrictStructuredNode\n",
-      " ! Skipping class model.StrictStructuredNode is abstract\n",
-      "Found model.Organism\n",
-      " + Creating node unique constraint for taxonomy_id on label Organism for class model.Organism\n",
-      "Found model.Site\n",
-      " + Creating node unique constraint for site_id on label Site for class model.Site\n",
-      "Found model.Region\n",
-      " + Creating node unique constraint for region_id on label Region for class model.Region\n",
-      "Found model.CatalyticActivity\n",
-      " + Creating node unique constraint for catalytic_id on label CatalyticActivity for class model.CatalyticActivity\n",
-      "Found model.StandardNumbering\n",
-      "Found model.GOAnnotation\n",
-      " + Creating node unique constraint for go_id on label GOAnnotation for class model.GOAnnotation\n",
-      "Found model.Protein\n",
-      " + Creating node unique constraint for accession_id on label Protein for class model.Protein\n",
-      " + Creating vector index for embedding on label Protein for class model.Protein\n",
-      "Found model.DNA\n",
-      " + Creating node unique constraint for accession_id on label DNA for class model.DNA\n",
-      " + Creating vector index for embedding on label DNA for class model.DNA\n",
-      "Found model.OntologyObject\n",
-      " + Creating node unique constraint for name on label OntologyObject for class model.OntologyObject\n",
-      "\n",
-      "Finished 10 classes.\n",
-      "✅ Databse constraints and indexes set up according to Pyeed Graph Object Model.\n"
+      "📡 Connected to database.\n"
      ]
     }
    ],
@@ -1269,7 +1223,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "pyeed",
+   "display_name": "pyeed_niklas",
    "language": "python",
    "name": "python3"
   },
@@ -1283,7 +1237,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.5"
+   "version": "3.12.8"
   }
  },
  "nbformat": 4,