Merge pull request #95 from talagayev/OpenMMDL_Setup_Simulation_restr…

…ucture

Restructure of OpenMMDL Setup

openmmdl/openmmdl_setup/file_operator.py

@@ -0,0 +1,68 @@
+import tempfile
+import shutil
+from werkzeug.utils import secure_filename
+
+
+class LigandExtractor:
+    @staticmethod
+    def extract_ligand_name(lig_file_name):
+        """
+        Extracts the ligand name from the file name based on its extension.
+
+        This method determines the ligand name by stripping the file extension from the provided ligand
+        file name. It handles files with `.pdb` extensions by removing the extension, while it assigns a
+        default name `"UNL"` to files with `.sdf` extensions.
+
+        Params:
+        -------
+        lig_file_name: str
+            The name of the ligand file, including its extension (e.g., `ligand.pdb` or `ligand.sdf`).
+
+        Returns:
+        --------
+        lig_name: str
+            The extracted ligand name. For `.pdb` files, this is the file name without the `.pdb` extension.
+            For `.sdf` files, it returns a default name `"UNL"`.
+        """
+        if lig_file_name.endswith(".sdf"):
+            lig_name = "UNL"
+        elif lig_file_name.endswith(".pdb"):
+            lig_name = lig_file_name[:-4]
+        else:
+            raise ValueError(
+                "Unsupported file format. Only .sdf and .pdb are supported."
+            )
+
+        return lig_name
+
+
+class FileUploader:
+    """
+    Handles uploading and temporary storage of files.
+    """
+
+    @staticmethod
+    def save_uploaded_files(uploadedFiles, request):
+        """
+        Saves files from the request into temporary storage and updates the given dictionary.
+
+        Parameters
+        ----------
+        uploadedFiles : dict
+            Dictionary to store uploaded files. Keys are field names; values are lists of (temp file, filename) tuples.
+
+        request : object
+            The request object containing uploaded files.
+
+        Returns
+        -------
+        None
+        """
+        uploadedFiles.clear()
+        for key in request.files:
+            filelist = []
+            for file in request.files.getlist(key):
+                temp = tempfile.TemporaryFile()
+                shutil.copyfileobj(file, temp)
+                filelist.append((temp, secure_filename(file.filename)))
+            uploadedFiles[key] = filelist