backend layout

proteinshake/database.py

@@ -8,9 +8,119 @@ class Database:
 
     def __init__(self, storage: Path) -> None:
         pass
+
+    def adapter(self, adapter):
+        """
+        Adds adapter to the database.
+        """
+        pass
 
-    def update(self) -> None:
+    def sync(self) -> None:
+        """
+        Syncs all adapters.
+        """
         pass
 
     def query(self, query: str):
+        """
+        Queries the database and returns a protein collection with metadata and assets.
+        """
+        pass
+
+class AssetStorage:
+    """
+    A mapping of Asset-IDs to locations on the filesystem.
+    """
+
+class Adapter:
+    """
+    Provides an API to an online database.
+    """
+
+    def __init__(self) -> None:
+        pass
+
+    def sync(self):
+        pass
+
+
+class StructureStorage:
+    """
+    Stores residue and atoms coordinates with meta data. Provides access by Structure-IDs.
+    Structures are stored as contiguous arrays of coordinates and other residue/atom level information, in shards.
+    An index file maintains the mapping from ID to shard and start/end positions.
+    """
+
+    def __init__(self) -> None:
+        pass
+
+class StructureFileProcessor:
+    """
+    Converts a pdb/mmcif file to a more efficient Atoms & Residue format. Implements QC.
+    Applies transforms to clean and polish the structure, e.g. energy minimization.
+    Also computes and annotates quality scores which can be used for later filtering.
+    """
+
+    def __init__(self) -> None:
+        pass
+
+class Protein:
+    """
+    A dictionary-type data structure for a protein. Contains the PS-ID, other database IDs, sequences, protein-level information, and links to assets and structures.
+    """
+
+    def __init__(self) -> None:
+        pass
+
+
+class Atoms:
+    """
+    A array-type data structure for the atom-level information and coordinates of a protein structure.
+    """
+
+    def __init__(self) -> None:
+        pass
+
+class Residues:
+    """
+    A array-type data structure for the residue-level information of a protein structure.
+    """
+
+    def __init__(self) -> None:
+        pass
+
+class Collection:
+    """
+    A set of Proteins as a result of a Database query. Provides methods to store and load to the filesystem.
+    Stores files as tar bundles with sharded structures, a protein-level info file, metadata, and assets.
+    Loads files as an iterator with associated metadata and assets.
+    """
+
+    def __init__(self) -> None:
         pass
+
+class ProteinIterator:
+    """
+    An iterator class extending the Python class capabilities to store additional data.
+    """
+
+    def __init__(self) -> None:
+        pass
+
+class CollectionTransform:
+    """
+    Transforms a Collection. May be used to precompute splits or filter proteins.
+    Can be applied before or after write to the filesystem, i.e. can be applied before hosting or at the user-end when loading a Task.
+    """
+
+    def __init__(self) -> None:
+        pass
+
+class Dataset:
+    """
+    Abstract class to define a Database query and a file path. Used to create and load a dataset.
+    Provides the means to download a precomputed Collection from a server or filesystem.
+    """
+
+    def __init__(self) -> None:
+        pass