aiondata - pypi Package Compare versions

Comparing version 0.4.6 to 0.5.0

aiondata/__init__.py

@@ -1,2 +0,2 @@
-from .bindingdb import BindingDB
+from .bindingdb import BindingDB, BindingAffinity
 from .protein_structure import (
@@ -3,0 +3,0 @@ FoldswitchProteinsTableS1A,

aiondata/bindingdb.py

@@ -1,11 +0,9 @@
-from collections import OrderedDict
 import io
 from typing import Optional, Generator, Union, Tuple
 import urllib.request
-from rdkit import Chem
-from rdkit import RDLogger
+from rdkit import Chem, RDLogger
 from tqdm.auto import tqdm
 import zipfile
 
-from .datasets import GeneratedDataset
+from .datasets import GeneratedDataset, CachedDataset
 import polars as pl
@@ -235,1 +233,34 @@
         RDLogger.EnableLog("rdApp.warning")
+
+
+class BindingAffinity(CachedDataset):
+    def __init__(self, fd: Optional[io.BufferedReader] = None):
+        """
+        Initializes a BindingAffinity instance.
+
+        Args:
+            fd (Optional[io.BufferedReader]): The file-like object containing the BindingDB content.
+                If `fd` is not provided, the dataset content will be fetched from the default source.
+        """
+        self.bindingdb = BindingDB(fd)
+
+    def get_df(self) -> pl.DataFrame:
+        bdb_df = self.bindingdb.to_df()
+        ba_df = bdb_df.select(
+            [
+                "SMILES",
+                "BindingDB Target Chain Sequence",
+                "Ki (nM)",
+                "IC50 (nM)",
+                "Kd (nM)",
+                "EC50 (nM)",
+                "kon (M-1-s-1)",
+                "koff (s-1)",
+            ]
+        )
+        ba_df = ba_df.rename({"BindingDB Target Chain Sequence": "Sequence"})
+
+        # Remove spaces from BindingDB Target Chain Sequence column
+        ba_df = ba_df.with_columns(pl.col("Sequence").str.replace_all(" ", ""))
+
+        return ba_df

PKG-INFO

 Metadata-Version: 2.1
 Name: aiondata
-Version: 0.4.6
+Version: 0.5.0
 Summary: A common data access layer for AI-driven drug discovery.
@@ -5,0 +5,0 @@ Home-page: https://www.github.com/aion-labs/aiondata

pyproject.toml

 [tool.poetry]
 name = "aiondata"
-version = "0.4.6"
+version = "0.5.0"
 description = "A common data access layer for AI-driven drug discovery."
@@ -5,0 +5,0 @@ authors = ["JJ Ben-Joseph <[e-mail]>"]

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Improved metrics

Total package byte prevSize

54945

1.97%

Lines of code

680

3.82%