papyrus-scripts 2.1.1__tar.gz → 2.1.2__tar.gz

{papyrus_scripts-2.1.1/src/papyrus_scripts.egg-info → papyrus_scripts-2.1.2}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: papyrus_scripts
-Version: 2.1.1
+Version: 2.1.2
 Summary: A collection of scripts to handle the Papyrus bioactivity dataset
 Home-page: https://github.com/OlivierBeq/Papyrus-scripts
 Author: Olivier J. M. Béquignon - Brandon J. Bongers - Willem Jespers
@@ -17,7 +17,7 @@ Classifier: Programming Language :: Python :: 3.7
 Classifier: Programming Language :: Python :: 3.6
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: numpy
+Requires-Dist: numpy>=2.0.0
 Requires-Dist: pandas
 Requires-Dist: rdkit
 Requires-Dist: requests
@@ -36,6 +36,7 @@ Requires-Dist: sphinx-autodoc-typehints; extra == "docs"
 Provides-Extra: testing
 Requires-Dist: pytest; extra == "testing"
 Requires-Dist: parameterized; extra == "testing"
+Dynamic: license-file
 
 # Papyrus-scripts
 
@@ -168,10 +169,10 @@ Different online servers host the Papyrus data based on release and ChEMBL versi
  
 | Papyrus version | ChEMBL version |                          Zenodo                           |                            4TU                            |
 |:---------------:|:--------------:|:---------------------------------------------------------:|:---------------------------------------------------------:|
-|      05.4       |       29       | [:heavy_check_mark:](https://zenodo.org/records/10944245) | [:heavy_check_mark:](https://doi.org/10.4121/16896406.v2) | 
-|      05.5       |       30       | [:heavy_check_mark:](https://zenodo.org/records/10943207) |                            :x:                            |
-|      05.6       |       31       | [:heavy_check_mark:](https://zenodo.org/records/7821775)  |                            :x:                            |
-|      05.7       |       34       | [:heavy_check_mark:](https://zenodo.org/records/13787634) |                            :x:                            |
+|      05.4       |       29       | [:heavy_check_mark:](https://zenodo.org/records/10943992) | [:heavy_check_mark:](https://doi.org/10.4121/16896406.v2) | 
+|      05.5       |       30       | [:heavy_check_mark:](https://zenodo.org/records/7019873)  |                            :x:                            |
+|      05.6       |       31       | [:heavy_check_mark:](https://zenodo.org/records/7373213)  |                            :x:                            |
+|      05.7       |       34       | [:heavy_check_mark:](https://zenodo.org/records/13787633) |                            :x:                            |
 
 Precomputed molecular and protein descriptors along with molecular structures (2D for default set and 3D for low quality set with stereochemistry) are not available for version 05.4 from 4TU but are from Google Drive.
 

{papyrus_scripts-2.1.1 → papyrus_scripts-2.1.2}/README.md

@@ -129,10 +129,10 @@ Different online servers host the Papyrus data based on release and ChEMBL versi
  
 | Papyrus version | ChEMBL version |                          Zenodo                           |                            4TU                            |
 |:---------------:|:--------------:|:---------------------------------------------------------:|:---------------------------------------------------------:|
-|      05.4       |       29       | [:heavy_check_mark:](https://zenodo.org/records/10944245) | [:heavy_check_mark:](https://doi.org/10.4121/16896406.v2) | 
-|      05.5       |       30       | [:heavy_check_mark:](https://zenodo.org/records/10943207) |                            :x:                            |
-|      05.6       |       31       | [:heavy_check_mark:](https://zenodo.org/records/7821775)  |                            :x:                            |
-|      05.7       |       34       | [:heavy_check_mark:](https://zenodo.org/records/13787634) |                            :x:                            |
+|      05.4       |       29       | [:heavy_check_mark:](https://zenodo.org/records/10943992) | [:heavy_check_mark:](https://doi.org/10.4121/16896406.v2) | 
+|      05.5       |       30       | [:heavy_check_mark:](https://zenodo.org/records/7019873)  |                            :x:                            |
+|      05.6       |       31       | [:heavy_check_mark:](https://zenodo.org/records/7373213)  |                            :x:                            |
+|      05.7       |       34       | [:heavy_check_mark:](https://zenodo.org/records/13787633) |                            :x:                            |
 
 Precomputed molecular and protein descriptors along with molecular structures (2D for default set and 3D for low quality set with stereochemistry) are not available for version 05.4 from 4TU but are from Google Drive.
 

{papyrus_scripts-2.1.1 → papyrus_scripts-2.1.2}/setup.cfg

@@ -32,7 +32,7 @@ packages = find:
 package_dir = 
 	= src
 install_requires = 
-	numpy
+	numpy>=2.0.0
 	pandas
 	rdkit
 	requests

{papyrus_scripts-2.1.1 → papyrus_scripts-2.1.2}/src/papyrus_scripts/__init__.py

@@ -20,4 +20,4 @@ from .utils.IO import PapyrusVersion
 
 from .oop import PapyrusDataset
 
-__version__ = '2.1.1'
+__version__ = '2.1.2'

{papyrus_scripts-2.1.1 → papyrus_scripts-2.1.2}/src/papyrus_scripts/oop.py

@@ -58,7 +58,8 @@ class PapyrusDataset:
                        is3d: bool, version: str,
                        plusplus: bool = True,
                        source_path: Optional[str] = None,
-                       download_progress: bool = False
+                       download_progress: bool = False,
+                       chunksize: int = None
                        ) -> PapyrusDataset:
         """Create a PapyrusDataset from a pandas DataFrame.
 
@@ -74,7 +75,7 @@ class PapyrusDataset:
         dataset.papyrus_bioactivity_data = df
         dataset.papyrus_protein_data = reader.read_protein_set(source_path=source_path, version=version)
         dataset.papyrus_params = dict(is3d=is3d, version=version, plusplus=plusplus,
-                                      chunksize=len(df), source_path=source_path, num_rows=len(df),
+                                      chunksize=chunksize, source_path=source_path, num_rows=len(df),
                                       download_progress=download_progress)
         dataset._can_reset = False
         return dataset
@@ -357,6 +358,32 @@ class PapyrusDataset:
                                 version_root=remove_version_root, papyrus_root=remove_papyrus_root,
                                 force=force, progress=progress)
 
+    def molecular_descriptors(self, desc_type: str, progress: bool = False) -> pd.DataFrame | Iterator[pd.DataFrame]:
+        """Obtain the molecular descriptors of the molecules in the current PapyrusMoleculeSet.
+
+        :param desc_type: type of descriptor to be obtained. One of {'mold2', 'mordred', 'cddd', 'fingerprint', 'moe', 'all'}
+        :param progress: should aggregation progress be shown
+        :return: a pandas DataFrame of the molecular descriptors.
+        """
+        ids = self.aggregate(progress)['connectivity' if not self.papyrus_params['is3d'] else 'InChIKey'].unique()
+        # Handle descriptors not yet downloaded
+        try:
+            return reader.read_molecular_descriptors(desc_type=desc_type,
+                                                     is3d=self.papyrus_params['is3d'],
+                                                     version=self.papyrus_params['version'],
+                                                     chunksize=self.papyrus_params['chunksize'],
+                                                     source_path=self.papyrus_params['source_path'],
+                                                     ids=ids,
+                                                     verbose=progress)
+        except FileNotFoundError:
+            download.download_papyrus(outdir=self.papyrus_params['source_path'],
+                                      version=self.papyrus_params['version'],
+                                      nostereo=not self.papyrus_params['is3d'], stereo=self.papyrus_params['is3d'],
+                                      only_pp=self.papyrus_params['plusplus'], structures=False,
+                                      descriptors=desc_type, progress=self.papyrus_params['download_progress'],
+                                      disk_margin=0.0)
+            return self.molecular_descriptors(desc_type, progress)
+
 class PapyrusDataFilter:
     """Collection of filters to be applied on a PapyrusDataset instance."""
 
@@ -584,14 +611,14 @@ class PapyrusMoleculeSet:
             return f'{type(self).__name__}<iterator of molecules>'
         return f'{type(self).__name__}<{len(self.data)} molecules>'
 
-    def molecular_descriptors(self, desc_type: str, progress: bool = False) -> pd.DataFrame:
+    def molecular_descriptors(self, desc_type: str, progress: bool = False) -> pd.DataFrame | Iterator[pd.DataFrame]:
         """Obtain the molecular descriptors of the molecules in the current PapyrusMoleculeSet.
 
         :param desc_type: type of descriptor to be obtained. One of {'mold2', 'mordred', 'cddd', 'fingerprint', 'moe', 'all'}
         :param progress: should aggregation progress be shown
         :return: a pandas DataFrame of the molecular descriptors.
         """
-        ids = self.aggregate(progress)['connectivity' if self.papyrus_params['is3d'] else 'InChIKey'].unique()
+        ids = self.aggregate(progress)['connectivity' if not self.papyrus_params['is3d'] else 'InChIKey'].unique()
         # Handle descriptors not yet downloaded
         try:
             return reader.read_molecular_descriptors(desc_type=desc_type,

{papyrus_scripts-2.1.1 → papyrus_scripts-2.1.2}/src/papyrus_scripts/preprocess.py

@@ -94,11 +94,11 @@ def process_group(group, additional_columns: Optional[List[str]] = None):
     """Aggregate data from one group accordingly"""
     if (group.values[0] == group.values).all():  # If all values are equal, return first record
         group['pchembl_value_Mean'] = group['pchembl_value']
-        group['pchembl_value_StdDev'] = np.NaN
-        group['pchembl_value_SEM'] = np.NaN
+        group['pchembl_value_StdDev'] = np.nan
+        group['pchembl_value_SEM'] = np.nan
         group['pchembl_value_N'] = 1
         group['pchembl_value_Median'] = group['pchembl_value']
-        group['pchembl_value_MAD'] = np.NaN
+        group['pchembl_value_MAD'] = np.nan
         return group.iloc[:1, :]
     # Lambda: Return one value if all are the same
     listvals = lambda x: ';'.join(set(str(y) for y in x)) if (x.values[0] == x.values).all() else ';'.join(
@@ -174,8 +174,8 @@ def keep_source(data: Union[pd.DataFrame, PandasTextFileReader, Iterator], sourc
         # Allow processing of Papyrus++
         papyruspp = 'Activity_class' not in data.columns
         if papyruspp:
-            data['Activity_class'] = np.NaN
-            data['type_other'] = np.NaN
+            data['Activity_class'] = np.nan
+            data['type_other'] = np.nan
         # Keep trace of order of columns
         ordered_columns = data.columns.tolist()
         # Keep binary data associated to source
@@ -307,8 +307,8 @@ def keep_type(data: Union[pd.DataFrame, PandasTextFileReader, Iterator], activit
         # Allow processing of Papyrus++
         papyruspp = 'Activity_class' not in data.columns
         if papyruspp:
-            data['Activity_class'] = np.NaN
-            data['type_other'] = np.NaN
+            data['Activity_class'] = np.nan
+            data['type_other'] = np.nan
         # Transform activity_types to column names
         activity_types = [f"type_{types[i]}" for i in range(len(types)) if types_[i] in activity_types]
         # Columns with optional multiple values

{papyrus_scripts-2.1.1 → papyrus_scripts-2.1.2/src/papyrus_scripts.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: papyrus_scripts
-Version: 2.1.1
+Version: 2.1.2
 Summary: A collection of scripts to handle the Papyrus bioactivity dataset
 Home-page: https://github.com/OlivierBeq/Papyrus-scripts
 Author: Olivier J. M. Béquignon - Brandon J. Bongers - Willem Jespers
@@ -17,7 +17,7 @@ Classifier: Programming Language :: Python :: 3.7
 Classifier: Programming Language :: Python :: 3.6
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: numpy
+Requires-Dist: numpy>=2.0.0
 Requires-Dist: pandas
 Requires-Dist: rdkit
 Requires-Dist: requests
@@ -36,6 +36,7 @@ Requires-Dist: sphinx-autodoc-typehints; extra == "docs"
 Provides-Extra: testing
 Requires-Dist: pytest; extra == "testing"
 Requires-Dist: parameterized; extra == "testing"
+Dynamic: license-file
 
 # Papyrus-scripts
 
@@ -168,10 +169,10 @@ Different online servers host the Papyrus data based on release and ChEMBL versi
  
 | Papyrus version | ChEMBL version |                          Zenodo                           |                            4TU                            |
 |:---------------:|:--------------:|:---------------------------------------------------------:|:---------------------------------------------------------:|
-|      05.4       |       29       | [:heavy_check_mark:](https://zenodo.org/records/10944245) | [:heavy_check_mark:](https://doi.org/10.4121/16896406.v2) | 
-|      05.5       |       30       | [:heavy_check_mark:](https://zenodo.org/records/10943207) |                            :x:                            |
-|      05.6       |       31       | [:heavy_check_mark:](https://zenodo.org/records/7821775)  |                            :x:                            |
-|      05.7       |       34       | [:heavy_check_mark:](https://zenodo.org/records/13787634) |                            :x:                            |
+|      05.4       |       29       | [:heavy_check_mark:](https://zenodo.org/records/10943992) | [:heavy_check_mark:](https://doi.org/10.4121/16896406.v2) | 
+|      05.5       |       30       | [:heavy_check_mark:](https://zenodo.org/records/7019873)  |                            :x:                            |
+|      05.6       |       31       | [:heavy_check_mark:](https://zenodo.org/records/7373213)  |                            :x:                            |
+|      05.7       |       34       | [:heavy_check_mark:](https://zenodo.org/records/13787633) |                            :x:                            |
 
 Precomputed molecular and protein descriptors along with molecular structures (2D for default set and 3D for low quality set with stereochemistry) are not available for version 05.4 from 4TU but are from Google Drive.
 

{papyrus_scripts-2.1.1 → papyrus_scripts-2.1.2}/src/papyrus_scripts.egg-info/SOURCES.txt

@@ -25,7 +25,5 @@ src/papyrus_scripts/utils/UniprotMatch.py
 src/papyrus_scripts/utils/__init__.py
 src/papyrus_scripts/utils/aliases.json
 src/papyrus_scripts/utils/links.json
-src/papyrus_scripts/utils/links2.json
 src/papyrus_scripts/utils/mol_reader.py
-tests/test.py
 tests/test_oop.py

{papyrus_scripts-2.1.1 → papyrus_scripts-2.1.2}/src/papyrus_scripts.egg-info/requires.txt

@@ -1,4 +1,4 @@
-numpy
+numpy>=2.0.0
 pandas
 rdkit
 requests

{papyrus_scripts-2.1.1 → papyrus_scripts-2.1.2}/tests/test_oop.py

@@ -181,8 +181,8 @@ class TestPapyrusDataset(unittest.TestCase):
         self.assertTrue(oop_data_agg.source.unique().item().lower().startswith('chembl'))
         self.assertTrue(oop_data_agg.type_IC50.dropna().astype(int).unique().item() == 0)
         self.assertTrue(oop_data_agg.type_EC50.dropna().astype(int).unique().item() == 0)
-        self.assertTrue(oop_data_agg.type_other.replace({'NA': np.NaN, 'NaN': np.NaN, 'nan': np.NaN})
-                        .dropna().empty or (oop_data_agg.type_other.replace({'NA': np.NaN, 'NaN': np.NaN, 'nan': np.NaN})
+        self.assertTrue(oop_data_agg.type_other.replace({'NA': np.nan, 'NaN': np.nan, 'nan': np.nan})
+                        .dropna().empty or (oop_data_agg.type_other.replace({'NA': np.nan, 'NaN': np.nan, 'nan': np.nan})
                         .dropna().astype(int).unique().item() == 0))
         self.assertEqual((oop_data_agg[['type_KD', 'type_Ki']]
                           .astype(int).

papyrus_scripts-2.1.1/src/papyrus_scripts/utils/links2.json

@@ -1,408 +0,0 @@
-{
-  "05.4": {
-    "readme": {
-      "name": "README.txt",
-      "url": "https://zenodo.org/records/10944245/files/README.txt?download=1",
-      "size": 8743,
-      "sha256": "f552ae0b58121b20c9aefcce0737e5f31240d72676dc9ec559f97585aceb33ad"
-    },
-    "requirements": [
-      {
-        "name": "LICENSE.txt",
-        "url": "https://zenodo.org/records/10944245/files/LICENSE.txt?download=1",
-        "size": 20138,
-        "sha256": "3b2890eacd851373001c4a14623458e3adaf1b1967939aa9c38a318e28d61c00"
-      },
-      {
-        "name": "data_types.json",
-        "url": "https://zenodo.org/records/10944245/files/data_types.json?download=1",
-        "size": 450559,
-        "sha256": "d80a5810d99b62680ee1a214df5d5a30f505ec335a0c221194efb91d1c23913e"
-      },
-      {
-        "name": "data_size.json",
-        "url": "https://zenodo.org/records/10944245/files/data_size.json?download=1",
-        "size": 324,
-        "sha256": "decbe66e14eaeccf5e0f657bb33065600b503e2902503aa59f5ffa81b7126775"
-      }
-    ],
-    "papyrus++": {
-      "name": "05.4++_combined_set_without_stereochemistry.tsv.xz",
-      "url": "https://zenodo.org/records/10944245/files/05.4++_combined_set_without_stereochemistry.tsv.xz?download=1",
-      "size": 40278204,
-      "sha256": "42dcbe76b33ad541f6c54673eccffa15af64785cf844938c0f73518dfdf4404b"
-    },
-    "2D_papyrus": {
-      "name": "05.4_combined_set_without_stereochemistry.tsv.xz",
-      "url": "https://zenodo.org/records/10944245/files/05.4_combined_set_without_stereochemistry.tsv.xz?download=1",
-      "size": 742110788,
-      "sha256": "1a1c946917f77d9a250a181c8ef19bea4d04871915e9e75a615893a2c514684e"
-    },
-    "2D_structures": {
-      "name": "05.4_combined_2D_set_without_stereochemistry.sd.xz",
-      "url": "https://zenodo.org/records/10944245/files/05.4_combined_2D_set_without_stereochemistry.sd.xz?download=1",
-      "size": 416640448,
-      "sha256": "4595f726daf12a784049f20e9f9464ed0287af3a22a27f2a919399c535f633fc"
-    },
-    "3D_papyrus": {
-      "name": "05.4_combined_set_with_stereochemistry.tsv.xz",
-      "url": "https://zenodo.org/records/10944245/files/05.4_combined_set_with_stereochemistry.tsv.xz?download=1",
-      "size": 777395668,
-      "sha256": "56cf389030246d4525bb31cd3dfc9e5ab3afa9613535d1540c71f0f7426c778f"
-    },
-    "3D_structures": {
-      "name": "05.4_combined_3D_set_with_stereochemistry.sd.xz",
-      "url": "https://zenodo.org/records/10944245/files/05.4_combined_3D_set_with_stereochemistry.sd.xz?download=1",
-      "size": 446702556,
-      "sha256": "b0f04e066b7ac6b1e1f2a868ff0258b13bd8d3433023ff59c3af58317bfeb3e9"
-    },
-    "2D_fingerprint": {
-      "name": "05.4_combined_2D_moldescs_ECFP6.tsv.xz",
-      "url": "https://zenodo.org/records/10944245/files/05.4_combined_2D_moldescs_ECFP6.tsv.xz?download=1",
-      "size": 141318356,
-      "sha256": "4ab781cc238107f7c48f1d866eea0e2114068b6512acf74932a5b21958c9ffe0"
-    },
-    "3D_fingerprint": {
-      "name": "05.4_combined_3D_moldescs_E3FP.tsv.xz",
-      "url": "https://zenodo.org/records/10944245/files/05.4_combined_3D_moldescs_E3FP.tsv.xz?download=1",
-      "size": 146751352,
-      "sha256": "2b89027dad8f4e59f007dd082664a7d2a491f4f79d112fb29f14565acedfe4d0"
-    },
-    "2D_mordred": {
-      "name": "05.4_combined_2D_moldescs_mordred2D.tsv.xz",
-      "url": "https://zenodo.org/records/10944245/files/05.4_combined_2D_moldescs_mordred2D.tsv.xz?download=1",
-      "size": 3085232504,
-      "sha256": "d15bca59f542a6c46528e4f131cb44d8bd6b21440ab139f4175f4327c15c39c6"
-    },
-    "3D_mordred": {
-      "name": "05.4_combined_3D_moldescs_mordred3D.tsv.xz",
-      "url": "https://zenodo.org/records/10944245/files/05.4_combined_3D_moldescs_mordred3D.tsv.xz?download=1",
-      "size": 2996851908,
-      "sha256": "80fc4f9b2d0b89e68c289c44e9f4df78f4c08e5867cd414d6169a4e1344aead8"
-    },
-    "2D_cddd": {
-      "name": "05.4_combined_2D_moldescs_CDDDs.tsv.xz",
-      "url": "https://zenodo.org/records/10944245/files/05.4_combined_2D_moldescs_CDDDs.tsv.xz?download=1",
-      "size": 3770082588,
-      "sha256": "9bb0d9adba1b812aa05b6391ecbc3f0148f6ed37972a004b13772d08790a9bda"
-    },
-    "2D_mold2": {
-      "name": "05.4_combined_2D_moldescs_mold2.tsv.xz",
-      "url": "https://zenodo.org/records/10944245/files/05.4_combined_2D_moldescs_mold2.tsv.xz?download=1",
-      "size": 1552425452,
-      "sha256": "bdfb0cbb6e9a3d1b62065808fa0e6ce238e04760df62e34ce4f15046810efd82"
-    },
-    "proteins": {
-      "name": "05.4_combined_set_protein_targets.tsv.xz",
-      "url": "https://zenodo.org/records/10944245/files/05.4_combined_set_protein_targets.tsv.xz?download=1",
-      "size": 1701316,
-      "sha256": "5f49030509ce188a119910f16054558e1cdd1c70a22d2a1458ec4189f5d1a08e"
-    },
-    "proteins_unirep": {
-      "name": "05.4_combined_prot_embeddings_unirep.tsv.xz",
-      "url": "https://zenodo.org/records/10944245/files/05.4_combined_prot_embeddings_unirep.tsv.xz?download=1",
-      "size": 138392528,
-      "sha256": "19aa0562c3b695883c5aa8c05ad0934c4b9b851a26550345940d92ed17f36b93"
-    }
-  },
-  "05.5": {
-      "readme": {
-      "name": "README.txt",
-      "url": "https://zenodo.org/record/7019874/files/README.txt?download=1",
-      "size": 11092,
-      "sha256": "0af036c1d02b150f6402a53960a6e995611e66ee7724b61a21f58d3366ec8eda"
-  },
-    "requirements": [{
-        "name": "LICENSE.txt",
-        "url": "https://zenodo.org/records/10943207/files/LICENSE.txt?download=1",
-        "size": 20138,
-        "sha256": "3b2890eacd851373001c4a14623458e3adaf1b1967939aa9c38a318e28d61c00"
-    },
-    {
-      "name": "data_types.json",
-      "url": "https://zenodo.org/records/10943207/files/data_types.json?download=1",
-      "size": 450678,
-      "sha256": "d38f0b6b53f0450c5530b5bf44d8a7d0bb85417f22b7c818237e3346fe68149c"
-    },
-    {
-      "name": "data_size.json",
-      "url": "https://zenodo.org/records/10943207/files/data_size.json?download=1",
-      "size": 324,
-      "sha256": "513307863c4acc779789340e900821ff8f38c845865aa078edc649caa1559dcc"
-    }],
-    "papyrus++": {
-      "name": "05.5++_combined_set_without_stereochemistry.tsv.xz",
-      "url": "https://zenodo.org/records/10943207/files/05.5++_combined_set_without_stereochemistry.tsv.xz?download=1",
-      "size": 41357608,
-      "sha256": "8ecaea9533f3c475dca6d335f30dd1b4abb259fa77b7441548dd15879e1afa58"
-    },
-    "2D_papyrus": {
-      "name": "05.5_combined_set_without_stereochemistry.tsv.xz",
-      "url": "https://zenodo.org/record/7019874/files/05.5_combined_set_without_stereochemistry.tsv.xz?download=1",
-      "size": 718601992,
-      "sha256": "04ecaea97c09d02dbde809ad99ea2127fc3997a4e3b200b56dee85c30801890a"
-    },
-    "2D_structures": {
-      "name": "05.5_combined_2D_set_without_stereochemistry.sd.xz",
-      "url": "https://zenodo.org/record/7019874/files/05.5_combined_2D_set_without_stereochemistry.sd.xz?download=1",
-      "size": 399767580,
-      "sha256": "2e088ca662c5c33c5fc018c42c9c21e918ec167f1129a0a11fbf9c72888e8be6"
-    },
-    "3D_papyrus": {
-      "name": "05.5_combined_set_with_stereochemistry.tsv.xz",
-      "url": "https://zenodo.org/record/7019874/files/05.5_combined_set_with_stereochemistry.tsv.xz?download=1",
-      "size": 690498416,
-      "sha256": "822aca70ccf4c19879ae45dfa16de5fc29c3ee08b25739e7a087899652af7dd9"
-    },
-    "3D_structures": {
-      "name": "05.5_combined_3D_set_with_stereochemistry.sd.xz",
-      "url": "https://zenodo.org/record/7019874/files/05.5_combined_3D_set_with_stereochemistry.sd.xz?download=1",
-      "size": 492426264,
-      "sha256": "a4a5355ffc56de8d914c2ad281d10c227171c27e4d6c250daad14a16280cf136"
-    },
-    "2D_fingerprint": {
-      "name": "05.5_combined_2D_moldescs_ECFP6.tsv.xz",
-      "url": "https://zenodo.org/record/7019874/files/05.5_combined_2D_moldescs_ECFP6.tsv.xz?download=1",
-      "size": 97818228,
-      "sha256": "3d626b4295cfbe73877157d8eea84b911a3cb60bf9571165d88c00cc0b0880d2"
-    },
-    "3D_fingerprint": {
-      "name": "05.5_combined_3D_moldescs_E3FP.tsv.xz",
-      "url": "https://zenodo.org/record/7019874/files/05.5_combined_3D_moldescs_E3FP.tsv.xz?download=1",
-      "size": 114052016,
-      "sha256": "446fe36d50487f29a2d7402a53cc661097e884dc0df8ffd278646dba6708cb65"
-    },
-    "2D_mordred": {
-      "name": "05.5_combined_2D_moldescs_mordred2D.tsv.xz",
-      "url": "https://zenodo.org/record/7019874/files/05.5_combined_2D_moldescs_mordred2D.tsv.xz?download=1",
-      "size": 2936434876,
-      "sha256": "bcef94b1c04a1e7d8f9da11ad87e598e19932548a8ea4f00029c2f3a89672ff4"
-    },
-    "3D_mordred": {
-      "name": "05.5_combined_3D_moldescs_mordred3D.tsv.xz",
-      "url": "https://zenodo.org/record/7019874/files/05.5_combined_3D_moldescs_mordred3D.tsv.xz?download=1",
-      "size": 3206020732,
-      "sha256": "e6ffd0858f85217b57c4a88619e5f41d7f6bae16a9948612872162e54d3231dc"
-    },
-    "2D_cddd": {
-      "name": "05.5_combined_2D_moldescs_CDDDs.tsv.xz",
-      "url": "https://zenodo.org/record/7019874/files/05.5_combined_2D_moldescs_CDDDs.tsv.xz?download=1",
-      "size": 3775676256,
-      "sha256": "8421d973b4eb119f0739506a0b20ba9508356df97d4673e1c170e871cd134983"
-    },
-    "2D_mold2": {
-      "name": "05.5_combined_2D_moldescs_mold2.tsv.xz",
-      "url": "https://zenodo.org/record/7019874/files/05.5_combined_2D_moldescs_mold2.tsv.xz?download=1",
-      "size": 1553510028,
-      "sha256": "0fd1c2b3869c5fa749c21ddd70c5dff621974eccafb8e04fd6f95f3b37242058"
-    },
-    "proteins": {
-      "name": "05.5_combined_set_protein_targets.tsv.xz",
-      "url": "https://zenodo.org/record/7019874/files/05.5_combined_set_protein_targets.tsv.xz?download=1",
-      "size": 1710756,
-      "sha256": "d8f2cbee8b9849f7c3664fe7e8165c5abf785d374c36a8f151a6ec38fd582d80"
-    },
-    "proteins_unirep": {
-      "name": "05.5_combined_prot_embeddings_unirep.tsv.xz",
-      "url": "https://zenodo.org/record/7019874/files/05.5_combined_prot_embeddings_unirep.tsv.xz?download=1",
-      "size": 128869632,
-      "sha256": "9f1fce00e77563481eafc44405f9dc8188d5669ed93cafaee256c0208ca135b8"
-    }
-  },
-  "05.6": {
-    "readme": {
-      "name": "README.txt",
-      "url": "https://zenodo.org/record/7377161/files/README.txt?download=1",
-      "size": 12170,
-      "sha256": "b6a1977aed99e84c4ab560a04006a86264c9ff83ca67ed14e395e855c2543613"
-    },
-    "requirements": {
-      "name": "05.6_additional_files.zip",
-      "url": "https://zenodo.org/record/7377161/files/05.6_additional_files.zip?download=1",
-      "size": 51310,
-      "sha256": "c1d8df814ba54e17619f3740ff82577898a85a07acd220822403874159e26d8a"
-    },
-    "papyrus++": {
-      "name": "05.6++_combined_set_without_stereochemistry.tsv.xz",
-      "url": "https://zenodo.org/records/7821775/files/05.6++_combined_set_without_stereochemistry.tsv.xz?download=1",
-      "size": 31085780,
-      "sha256": "7518019c3ba287cd4cd0ff29425fe9da8a4760d891d22ed1abb33da4920cf96a"
-    },
-    "2D_papyrus": {
-      "name": "05.6_combined_set_without_stereochemistry.tsv.xz",
-      "url": "https://zenodo.org/record/7377161/files/05.6_combined_set_without_stereochemistry.tsv.xz?download=1",
-      "size": 744449364,
-      "sha256": "82a36ed7bb2f80846bb46e4c3e38905895bd1a2cfddd471d32091cb59dcf9437"
-    },
-    "2D_structures": {
-      "name": "05.6_combined_2D_set_without_stereochemistry.sd.xz",
-      "url": "https://zenodo.org/record/7377161/files/05.6_combined_2D_set_without_stereochemistry.sd.xz?download=1",
-      "size": 439758444,
-      "sha256": "1ec001964aca301494ea05fc24529120f01bc6952dcf4276dcd03625dfec460d"
-    },
-    "3D_papyrus": {
-      "name": "05.6_combined_set_with_stereochemistry.tsv.xz",
-      "url": "https://zenodo.org/record/7377161/files/05.6_combined_set_with_stereochemistry.tsv.xz?download=1",
-      "size": 711529352,
-      "sha256": "62068d500986b78fc90fe82b9e224555f8ca85319cd19f9df8bc73549e8a3e31"
-    },
-    "3D_structures": {
-      "name": "05.6_combined_3D_set_with_stereochemistry.sd.xz",
-      "url": "https://zenodo.org/record/7377161/files/05.6_combined_3D_set_with_stereochemistry.sd.xz?download=1",
-      "size": 500108592,
-      "sha256": "38e39963cd79845b4adca9dea871ffba18576ea742677471fc46a73a7dabbf38"
-    },
-    "2D_fingerprint": {
-      "name": "05.6_combined_2D_moldescs_ECFP6.tsv.xz",
-      "url": "https://zenodo.org/record/7377161/files/05.6_combined_2D_moldescs_ECFP6.tsv.xz?download=1",
-      "size": 96612972,
-      "sha256": "01c7366ee2ca7353d3a9f76601702b6d2eb312e71f02ea8ef48e2f90870c266c"
-    },
-    "3D_fingerprint": {
-      "name": "05.6_combined_3D_moldescs_E3FP.tsv.xz",
-      "url": "https://zenodo.org/record/7377161/files/05.6_combined_3D_moldescs_E3FP.tsv.xz?download=1",
-      "size": 117065432,
-      "sha256": "0d15baa4a9425daf63a0066511e9e96cbd5d7dab223bdaf48803536ab2484dc2"
-    },
-    "2D_mordred": {
-      "name": "05.6_combined_2D_moldescs_mordred2D.tsv.xz",
-      "url": "https://zenodo.org/record/7377161/files/05.6_combined_2D_moldescs_mordred2D.tsv.xz?download=1",
-      "size": 3055443236,
-      "sha256": "c497db85e97542f59b5252e2b1d3bdd93604e5c4d2ea131088a87d79ea6954c3"
-    },
-    "3D_mordred": {
-      "name": "05.6_combined_3D_moldescs_mordred3D.tsv.xz",
-      "url": "https://zenodo.org/record/7377161/files/05.6_combined_3D_moldescs_mordred3D.tsv.xz?download=1",
-      "size": 3324119256,
-      "sha256": "6b022acb6a0bec8bfc1ae7585014ae0b812a12ddcbed7be4ac7ec073c662192f"
-    },
-    "2D_cddd": {
-      "name": "05.6_combined_2D_moldescs_CDDDs.tsv.xz",
-      "url": "https://zenodo.org/record/7377161/files/05.6_combined_2D_moldescs_CDDDs.tsv.xz?download=1",
-      "size": 2103289016,
-      "sha256": "fbb54e5ca9a28ff022dc5baddf87cb6601169a2d86f3b55db4d183fd3885642a"
-    },
-    "2D_mold2": {
-      "name": "05.6_combined_2D_moldescs_mold2.tsv.xz",
-      "url": "https://zenodo.org/record/7377161/files/05.6_combined_2D_moldescs_mold2.tsv.xz?download=1",
-      "size": 1487710808,
-      "sha256": "cd46ce9841a1f956840b4fe7c56310eaa32c5e957a6ffaca62fbc55f820aad99"
-    },
-    "proteins": {
-      "name": "05.6_combined_set_protein_targets.tsv.xz",
-      "url": "https://zenodo.org/record/7377161/files/05.6_combined_set_protein_targets.tsv.xz?download=1",
-      "size": 1850764,
-      "sha256": "f443a2f8c74b8eb3f2c9d1bd7bfbddc86cbcc3fd5e8e505b7057b78a4ad17ee1"
-    },
-    "proteins_unirep": {
-      "name": "05.6_combined_protdescs_unirep.tsv.xz",
-      "url": "https://zenodo.org/record/7377161/files/05.6_combined_protdescs_unirep.tsv.xz?download=1",
-      "size": 207122632,
-      "sha256": "47f37c1f1efcb9d6f002d5a096853975c27ddcc767d7903a8af12bac0439181c"
-    },
-    "proteins_prodec": {
-      "name": "05.6_combined_protdescs_ProDEC.tsv.xz",
-      "url": "https://zenodo.org/record/7377161/files/05.6_combined_protdescs_ProDEC.tsv.xz?download=1",
-      "size": 447818916,
-      "sha256": "3211a62f18ccb7ccc13f885374c1462efeb83ab0e98ed62d2645723f7dc9f1a1"
-    }
-  },
-  "05.7": {
-    "readme": {
-      "name": "README.txt",
-      "url": "https://drive.google.com/uc?id=16ak1O1v70O72_UzFldGzZY_b6Ntd0eZm&confirm=t",
-      "size": 0,
-      "sha256": ""
-    },
-    "requirements": {
-      "name": "05.7_additional_files.zip",
-      "url": "https://drive.google.com/uc?id=18IGeQ4tTW6b7VO8nb7EYJqGSLNdXHEgD&confirm=t",
-      "size": 114037,
-      "sha256": "e8a0b5f65bd79c21b979b69d2b19fe6f51611fbc5a988ff3c0caa738ab0bca73"
-    },
-    "papyrus++": {
-      "name": "05.7++_combined_set_without_stereochemistry.tsv.xz",
-      "url": "https://drive.google.com/uc?id=1lI_B8MKehKOcstQYpS_IQRTkbsaXovNf&confirm=t",
-      "size": 57295028,
-      "sha256": "a4819cd45f10b973a7bde75e5de58dff47980fc1347f2e552a1ac39f520b780f"
-    },
-    "2D_papyrus": {
-      "name": "05.7_combined_set_without_stereochemistry.tsv.xz",
-      "url": "https://drive.google.com/uc?id=1Jc1Zj43aORhOiLOZX4CE5tYlUPc5zoBK&confirm=t",
-      "size": 749503448,
-      "sha256": "42c1d175e617909701f5baf8175fee18b6be986274c628ef209612a8240368f7"
-    },
-    "2D_structures": {
-      "name": "05.7_combined_2D_set_without_stereochemistry.sd.xz",
-      "url": "https://drive.google.com/uc?id=1yTSKlTyT2rud8_6J0TgiVAnSnswaeL09&confirm=t",
-      "size": 457158128,
-      "sha256": "5ea668a099ff2422accccadb378a50ae570044881d20c017742f53dc8f421680"
-    },
-    "3D_papyrus": {
-      "name": "05.7_combined_set_with_stereochemistry.tsv.xz",
-      "url": "https://drive.google.com/uc?id=14tsxNwjqpKjeJSRyZy5kG_i7Pg0gQPS_&confirm=t",
-      "size": 715818916,
-      "sha256": "0ee09ceace168ec25b0619349b7b41d754a7ad75a4cb82c2d887ab11d7ceb03c"
-    },
-    "3D_structures": {
-      "name": "05.7_combined_3D_set_with_stereochemistry.sd.xz",
-      "url": "https://drive.google.com/uc?id=1rkOz5QxWVMiQUWsNX0fzfb94doGy-FSI&confirm=t",
-      "size": 519810936,
-      "sha256": "fc5a9fd3ca68dba3f1f9b3217d85ecbb31bebb07798ea008d70b5e92caea2c1d"
-    },
-    "2D_fingerprint": {
-      "name": "05.7_combined_2D_moldescs_ECFP6.tsv.xz",
-      "url": "https://drive.google.com/uc?id=1TtJ2iUKVoo-_32cdFbFACSclv6CyeYNI&confirm=t",
-      "size": 100340752,
-      "sha256": "491a8dbc93364718de87b6c1ef3779b9ecdd3ec5af4dadc4dbddaf261a9d254f"
-    },
-    "3D_fingerprint": {
-      "name": "05.7_combined_3D_moldescs_E3FP.tsv.xz",
-      "url": "https://drive.google.com/uc?id=1KKOujpCm31za_i12SKhjxbwg4ywwDbjU&confirm=t",
-      "size": 121328636,
-      "sha256": "4e08240587757adbf6ca481b3998751b09c48fc1cb58068609f54b1a76275c11"
-    },
-    "2D_mordred": {
-      "name": "05.7_combined_2D_moldescs_mordred2D.tsv.xz",
-      "url": "https://drive.google.com/uc?id=1cTJLBz82VShJYrMMcQLOYiCS4IFmiOjk&confirm=t",
-      "size": 3166511800,
-      "sha256": "e9f841c7233f21c7db406f973cb89ec90db9caa7e99a6618dea94ad1fc72cdac"
-    },
-    "3D_mordred": {
-      "name": "05.7_combined_3D_moldescs_mordred3D.tsv.xz",
-      "url": "https://drive.google.com/uc?id=1w-SwQohL60_QsOoqVmlxwz3LLbxC50YX&confirm=t",
-      "size": 3443038656,
-      "sha256": "1e480c48c8eb86c57def26331ea2447e43f60d6fd73a2c33e76a6338abd5d132"
-    },
-    "2D_cddd": {
-      "name": "05.7_combined_2D_moldescs_CDDDs.tsv.xz",
-      "url": "https://drive.google.com/uc?id=18ERbYiqLg7WkXpZ3DyjNCHLr495_stik&confirm=t",
-      "size": 2179141716,
-      "sha256": "c227b3b8e4ea0ff53cb358a765ff89ffdfc7f83b2f3e71142e31fca74be28e3b"
-    },
-    "2D_mold2": {
-      "name": "05.7_combined_2D_moldescs_mold2.tsv.xz",
-      "url": "https://drive.google.com/uc?id=1VJJHcCkfQeRNCL8gYpQ5pToUFfP87ZaA&confirm=t",
-      "size": 1548906976,
-      "sha256": "95be36ae2e883053b8b275f26238fe292c34133e3cb527a40fe9bfaece057d49"
-    },
-    "proteins": {
-      "name": "05.7_combined_set_protein_targets.tsv.xz",
-      "url": "https://drive.google.com/uc?id=1mZYpQm5gMGw1Z8xdq-seqYE4diD81dc-&confirm=t",
-      "size": 1779284,
-      "sha256": "1226453794df7552aa56375d3ec0a045008586f5ab6612cb3a06942dfac4dbac"
-    },
-    "proteins_unirep": {
-      "name": "05.7_combined_protdescs_unirep.tsv.xz",
-      "url": "https://drive.google.com/uc?id=1cFbo402ofPP5YP_JpUKHZle3XjVARc6S&confirm=t",
-      "size": 209760216,
-      "sha256": "cfd8b9e3ea9b95713bd23c69b2db7ae7dfd0c019b5f610912e7d557537c4305c"
-    },
-    "proteins_prodec": {
-      "name": "05.7_combined_protdescs_ProDEC.tsv.xz",
-      "url": "https://drive.google.com/uc?id=1FX7vVUmvtVd4fVk22n4yGRTR0kM_XTQt&confirm=t",
-      "size": 434668804,
-      "sha256": "9011ff21dcb3acb73af40b37d2a587c0aa0060d803b9cee165f8131a2933f80d"
-    }
-  }
-}

papyrus_scripts-2.1.1/tests/test.py

@@ -1,31 +0,0 @@
-from papyrus_scripts import PapyrusDataset, preprocess, reader
-
-# data2 = (PapyrusDataset(is3d=False, version='latest', plusplus=False, chunksize=int(1e6))
-#                                 .keep_organism('Mus musculus (Mouse)')
-#                                 .keep_source('chembl')
-#                                 .keep_protein_class({'l5': 'CC chemokine receptor'})
-#                                 .not_isin('accession', ['P13500', 'P13501'])
-#                                 .keep_activity_type(['ki', 'kd'])
-#                                 .aggregate(progress=True))
-#
-# #print(data2.organism.value_counts())
-# print(data2.source.value_counts())
-# print(data2.Classification.value_counts())
-# print(data2.accession.value_counts())
-# print(data2[['type_IC50', 'type_EC50', 'type_KD', 'type_Ki', 'type_other']].value_counts())
-
-
-fn_data = reader.read_papyrus(is3d=False, version='latest', plusplus=True, chunksize=int(1e6))
-fn_protein_data = reader.read_protein_set(version='latest')
-fn_filter1 = preprocess.keep_organism(fn_data, fn_protein_data, organism='Homo sapiens (Human)')
-fn_filter2 = preprocess.keep_protein_class(fn_filter1, fn_protein_data, classes={'l5': 'Adenosine receptor'})
-fn_filter3 = preprocess.keep_type(fn_filter2, activity_types='ic50')
-fn_data_agg = preprocess.consume_chunks(fn_filter3, progress=True)
-oop_data_agg = (PapyrusDataset(is3d=False, version='latest', plusplus=True, chunksize=int(1e6))
-                .keep_organism('Homo sapiens (Human)')
-                .keep_protein_class({'l5': 'Adenosine receptor'})
-                .keep_activity_type('ic50')
-                .aggregate(progress=True))
-
-print(fn_data_agg)
-print(oop_data_agg)