aiagents4pharma 1.33.0__tar.gz → 1.34.1__tar.gz

{aiagents4pharma-1.33.0 → aiagents4pharma-1.34.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: aiagents4pharma
-Version: 1.33.0
+Version: 1.34.1
 Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D.
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License
@@ -8,7 +8,7 @@ Classifier: Operating System :: OS Independent
 Requires-Python: >=3.12
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: copasi_basico==0.78
+Requires-Dist: copasi_basico==0.84
 Requires-Dist: coverage==7.6.4
 Requires-Dist: einops==0.8.0
 Requires-Dist: gdown==5.2.0

{aiagents4pharma-1.33.0 → aiagents4pharma-1.34.1}/aiagents4pharma/talk2knowledgegraphs/configs/config.yaml

@@ -6,4 +6,6 @@ defaults:
   - tools/graphrag_reasoning: default
   - utils/pubchem_utils: default
   - utils/enrichments/uniprot_proteins: default
+  - utils/enrichments/ols_terms: default
+  - utils/enrichments/reactome_pathways: default
   - app/frontend: default

aiagents4pharma-1.34.1/aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_ols.py

@@ -0,0 +1,62 @@
+#!/usr/bin/env python3
+
+"""
+Test cases for utils/enrichments/ols_terms.py
+"""
+
+import pytest
+from ..utils.enrichments.ols_terms import EnrichmentWithOLS
+
+# In this test, we will consider 5 examples:
+# 1. CL_0000899: T-helper 17 cell (Cell Ontology)
+# 2. GO_0046427: positive regulation of receptor signaling pathway via JAK-STAT (GO)
+# 3. UBERON_0000004: nose (Uberon)
+# 4. HP_0009739: Hypoplasia of the antihelix (Human Phenotype Ontology)
+# 5. MONDO_0005011: Crohn disease (MONDO)
+# 6. XYZ_0000000: Non-existing term (for testing error handling)
+
+# The expected description for each term starts with:
+CL_DESC = "CD4-positive, alpha-beta T cell"
+GO_DESC = "Any process that activates or increases the frequency, rate or extent"
+UBERON_DESC = "The olfactory organ of vertebrates, consisting of nares"
+HP_DESC = "Hypoplasia of the antihelix"
+MONDO_DESC = "A gastrointestinal disorder characterized by chronic inflammation"
+
+# The expected description for the non-existing term is None
+
+@pytest.fixture(name="enrich_obj")
+def fixture_uniprot_config():
+    """Return a dictionary with the configuration for OLS enrichment."""
+    return EnrichmentWithOLS()
+
+def test_enrich_documents(enrich_obj):
+    """Test the enrich_documents method."""
+    ols_terms = ["CL_0000899",
+                 "GO_0046427",
+                 "UBERON_0000004",
+                 "HP_0009739",
+                 "MONDO_0005011",
+                 "XYZ_0000000"]
+    descriptions = enrich_obj.enrich_documents(ols_terms)
+    assert descriptions[0].startswith(CL_DESC)
+    assert descriptions[1].startswith(GO_DESC)
+    assert descriptions[2].startswith(UBERON_DESC)
+    assert descriptions[3].startswith(HP_DESC)
+    assert descriptions[4].startswith(MONDO_DESC)
+    assert descriptions[5] is None
+
+def test_enrich_documents_with_rag(enrich_obj):
+    """Test the enrich_documents_with_rag method."""
+    ols_terms = ["CL_0000899",
+                 "GO_0046427",
+                 "UBERON_0000004",
+                 "HP_0009739",
+                 "MONDO_0005011",
+                 "XYZ_0000000"]
+    descriptions = enrich_obj.enrich_documents_with_rag(ols_terms, None)
+    assert descriptions[0].startswith(CL_DESC)
+    assert descriptions[1].startswith(GO_DESC)
+    assert descriptions[2].startswith(UBERON_DESC)
+    assert descriptions[3].startswith(HP_DESC)
+    assert descriptions[4].startswith(MONDO_DESC)
+    assert descriptions[5] is None

{aiagents4pharma-1.33.0 → aiagents4pharma-1.34.1}/aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_pubchem.py

@@ -13,7 +13,9 @@ from ..utils.enrichments.pubchem_strings import EnrichmentWithPubChem
 # The expected SMILES representation for the first PubChem ID is:
 SMILES_FIRST = 'C[C@@H]1C[C@H]2[C@@H]3[C@@H](CC4=CC(=O)C=C[C@@]'
 SMILES_FIRST += '4([C@H]3[C@H](C[C@@]2([C@]1(C(=O)CO)O)C)O)C)Cl'
-# The expected SMILES representation for the second PubChem ID is None.
+# The expected description for the first PubChem ID starts with:
+DESCRIPTION_FIRST = "Alclometasone is a prednisolone compound having an alpha-chloro substituent"
+# The expected SMILES representation and description for the second PubChem ID is None.
 
 @pytest.fixture(name="enrich_obj")
 def fixture_pubchem_config():
@@ -23,11 +25,16 @@ def fixture_pubchem_config():
 def test_enrich_documents(enrich_obj):
     """Test the enrich_documents method."""
     pubchem_ids = ["5311000", "1X"]
-    enriched_strings = enrich_obj.enrich_documents(pubchem_ids)
+    enriched_descriptions, enriched_strings = enrich_obj.enrich_documents(pubchem_ids)
     assert enriched_strings == [SMILES_FIRST, None]
+    assert enriched_descriptions[0].startswith(DESCRIPTION_FIRST)
+    assert enriched_descriptions[1] is None
 
 def test_enrich_documents_with_rag(enrich_obj):
     """Test the enrich_documents_with_rag method."""
     pubchem_ids = ["5311000", "1X"]
-    enriched_strings = enrich_obj.enrich_documents_with_rag(pubchem_ids, None)
+    enriched_descriptions, enriched_strings = enrich_obj.enrich_documents_with_rag(pubchem_ids,
+                                                                                   None)
     assert enriched_strings == [SMILES_FIRST, None]
+    assert enriched_descriptions[0].startswith(DESCRIPTION_FIRST)
+    assert enriched_descriptions[1] is None

aiagents4pharma-1.34.1/aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_reactome.py

@@ -0,0 +1,44 @@
+#!/usr/bin/env python3
+
+"""
+Test cases for utils/enrichments/reactome_pathways.py
+"""
+
+import pytest
+from ..utils.enrichments.reactome_pathways import EnrichmentWithReactome
+
+# In this test, we will consider 2 examples:
+# 1. R-HSA-3244647: cGAS binds cytosolic DNA
+# 2. R-HSA-9905952: ATP binds P2RX7 in P2RX7 trimer:PANX1 heptamer
+# 3. R-HSA-1234567: Fake pathway
+
+# The expected description of pathway R-HSA-3244647 startswith:
+FIRST_PATHWAY = "Cyclic GMP-AMP (cGAMP) synthase (cGAS) was identified as a cytosolic DNA"
+# The expected description of pathway R-HSA-9905952 startswith:
+SECOND_PATHWAY = "The P2RX7 (P2X7, P2Z) trimer binds ATP,"
+# The expected description of pathway R-HSA-1234567 is None.
+
+@pytest.fixture(name="enrich_obj")
+def fixture_uniprot_config():
+    """Return a dictionary with the configuration for Reactome enrichment."""
+    return EnrichmentWithReactome()
+
+def test_enrich_documents(enrich_obj):
+    """Test the enrich_documents method."""
+    reactome_pathways = ["R-HSA-3244647",
+                         "R-HSA-9905952",
+                         "R-HSA-1234567"]
+    descriptions = enrich_obj.enrich_documents(reactome_pathways)
+    assert descriptions[0].startswith(FIRST_PATHWAY)
+    assert descriptions[1].startswith(SECOND_PATHWAY)
+    assert descriptions[2] is None
+
+def test_enrich_documents_with_rag(enrich_obj):
+    """Test the enrich_documents_with_rag method."""
+    reactome_pathways = ["R-HSA-3244647",
+                         "R-HSA-9905952",
+                         "R-HSA-1234567"]
+    descriptions = enrich_obj.enrich_documents_with_rag(reactome_pathways, None)
+    assert descriptions[0].startswith(FIRST_PATHWAY)
+    assert descriptions[1].startswith(SECOND_PATHWAY)
+    assert descriptions[2] is None

aiagents4pharma-1.34.1/aiagents4pharma/talk2knowledgegraphs/tests/test_utils_pubchem_utils.py

@@ -0,0 +1,38 @@
+"""
+Test cases for utils/pubchem_utils.py
+"""
+
+from ..utils import pubchem_utils
+
+def test_external_id2pubchem_cid():
+    """
+    Test the external_id2pubchem_cid function.
+
+    The DrugBank ID for Alclometasone is DB00240.
+    The PubChem CID for Alclometasone is 5311000.
+
+    The CTD ID for Butylated Hydroxyanisole is D002083
+    The PubChem CID for Butylated Hydroxyanisole is 24667.
+    """
+    drugbank_id = "DB00240"
+    pubchem_cid = pubchem_utils.external_id2pubchem_cid('drugbank', drugbank_id)
+    assert pubchem_cid == 5311000
+
+    ctd_id = "D002083"
+    pubchem_cid = pubchem_utils.external_id2pubchem_cid(
+                    'comparative toxicogenomics database',
+                    ctd_id)
+    assert pubchem_cid == 24667
+
+def test_pubchem_cid_description():
+    """
+    Test the pubchem_cid_description function.
+
+    The PubChem CID for Alclometasone is 5311000.
+    The description for Alclometasone starts with 
+        "Alclometasone is a prednisolone compound having an alpha-chloro substituent".
+    """
+    pubchem_cid = 5311000
+    description = pubchem_utils.pubchem_cid_description(pubchem_cid)
+    assert description.startswith(
+        "Alclometasone is a prednisolone compound having an alpha-chloro substituent")

{aiagents4pharma-1.33.0 → aiagents4pharma-1.34.1}/aiagents4pharma/talk2knowledgegraphs/utils/enrichments/__init__.py

@@ -5,3 +5,5 @@ from . import enrichments
 from . import ollama
 from . import pubchem_strings
 from . import uniprot_proteins
+from . import reactome_pathways
+from . import ols_terms

aiagents4pharma-1.34.1/aiagents4pharma/talk2knowledgegraphs/utils/enrichments/ols_terms.py

@@ -0,0 +1,76 @@
+#!/usr/bin/env python3
+
+"""
+Enrichment class for enriching OLS terms with textual descriptions
+"""
+
+from typing import List
+import logging
+import json
+import hydra
+import requests
+from .enrichments import Enrichments
+
+# Initialize logger
+logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger(__name__)
+
+class EnrichmentWithOLS(Enrichments):
+    """
+    Enrichment class using OLS terms
+    """
+    def enrich_documents(self, texts: List[str]) -> List[str]:
+        """
+        Enrich a list of input OLS terms
+
+        Args:
+            texts: The list of OLS terms to be enriched.
+
+        Returns:
+            The list of enriched descriptions
+        """
+
+        ols_ids = texts
+
+        logger.log(logging.INFO,
+                   "Load Hydra configuration for OLS enrichments.")
+        with hydra.initialize(version_base=None, config_path="../../configs"):
+            cfg = hydra.compose(config_name='config',
+                                overrides=['utils/enrichments/ols_terms=default'])
+            cfg = cfg.utils.enrichments.ols_terms
+
+        descriptions = []
+        for ols_id in ols_ids:
+            params = {
+                'short_form': ols_id
+            }
+            r = requests.get(cfg.base_url,
+                             headers={ "Accept" : "application/json"},
+                             params=params,
+                             timeout=cfg.timeout)
+            response_body = json.loads(r.text)
+            # if the response body is empty
+            if '_embedded' not in response_body:
+                descriptions.append(None)
+                continue
+            # Add the description to the list
+            description = response_body['_embedded']['terms'][0]['description']
+            # Add synonyms to the description
+            description += response_body['_embedded']['terms'][0]['synonyms']
+            # Add the label to the description
+            # Label is not provided as list, so we need to convert it to a list
+            description += [response_body['_embedded']['terms'][0]['label']]
+            descriptions.append('\n'.join(description))
+        return descriptions
+
+    def enrich_documents_with_rag(self, texts, docs):
+        """
+        Enrich a list of input OLS terms
+
+        Args:
+            texts: The list of OLS to be enriched.
+
+        Returns:
+            The list of enriched descriptions
+        """
+        return self.enrich_documents(texts)

{aiagents4pharma-1.33.0 → aiagents4pharma-1.34.1}/aiagents4pharma/talk2knowledgegraphs/utils/enrichments/pubchem_strings.py

@@ -1,12 +1,13 @@
 #!/usr/bin/env python3
 
 """
-Enrichment class for enriching PubChem IDs with their STRINGS representation.
+Enrichment class for enriching PubChem IDs with their STRINGS representation and descriptions.
 """
 
 from typing import List
 import pubchempy as pcp
 from .enrichments import Enrichments
+from ..pubchem_utils import pubchem_cid_description
 
 class EnrichmentWithPubChem(Enrichments):
     """
@@ -20,20 +21,24 @@ class EnrichmentWithPubChem(Enrichments):
             texts: The list of pubchem IDs to be enriched.
 
         Returns:
-            The list of enriched STRINGS
+            The list of enriched STRINGS and their descriptions.
         """
 
-        enriched_pubchem_ids = []
+        enriched_pubchem_ids_smiles = []
+        enriched_pubchem_ids_descriptions = []
+
         pubchem_cids = texts
         for pubchem_cid in pubchem_cids:
             try:
                 c = pcp.Compound.from_cid(pubchem_cid)
             except pcp.BadRequestError:
-                enriched_pubchem_ids.append(None)
+                enriched_pubchem_ids_smiles.append(None)
+                enriched_pubchem_ids_descriptions.append(None)
                 continue
-            enriched_pubchem_ids.append(c.isomeric_smiles)
+            enriched_pubchem_ids_smiles.append(c.isomeric_smiles)
+            enriched_pubchem_ids_descriptions.append(pubchem_cid_description(pubchem_cid))
 
-        return enriched_pubchem_ids
+        return enriched_pubchem_ids_descriptions, enriched_pubchem_ids_smiles
 
     def enrich_documents_with_rag(self, texts, docs):
         """

aiagents4pharma-1.34.1/aiagents4pharma/talk2knowledgegraphs/utils/enrichments/reactome_pathways.py

@@ -0,0 +1,65 @@
+#!/usr/bin/env python3
+
+"""
+Enrichment class for enriching Reactome pathways with textual descriptions
+"""
+
+from typing import List
+import logging
+import hydra
+import requests
+from .enrichments import Enrichments
+
+# Initialize logger
+logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger(__name__)
+
+class EnrichmentWithReactome(Enrichments):
+    """
+    Enrichment class using Reactome pathways
+    """
+    def enrich_documents(self, texts: List[str]) -> List[str]:
+        """
+        Enrich a list of input Reactome pathways
+
+        Args:
+            texts: The list of Reactome pathways to be enriched.
+
+        Returns:
+            The list of enriched descriptions
+        """
+
+        reactome_pathways_ids = texts
+
+        logger.log(logging.INFO,
+                   "Load Hydra configuration for reactome enrichment")
+        with hydra.initialize(version_base=None, config_path="../../configs"):
+            cfg = hydra.compose(config_name='config',
+                                overrides=['utils/enrichments/reactome_pathways=default'])
+            cfg = cfg.utils.enrichments.reactome_pathways
+
+        descriptions = []
+        for reactome_pathway_id in reactome_pathways_ids:
+            r = requests.get(cfg.base_url + reactome_pathway_id + '/summation',
+                             headers={ "Accept" : "text/plain"},
+                             timeout=cfg.timeout)
+            # if the response is not ok
+            if not r.ok:
+                descriptions.append(None)
+                continue
+            response_body = r.text
+            # if the response is ok
+            descriptions.append(response_body.split('\t')[1])
+        return descriptions
+
+    def enrich_documents_with_rag(self, texts, docs):
+        """
+        Enrich a list of input Reactome pathways
+
+        Args:
+            texts: The list of Reactome pathways to be enriched.
+
+        Returns:
+            The list of enriched descriptions
+        """
+        return self.enrich_documents(texts)

aiagents4pharma-1.34.1/aiagents4pharma/talk2knowledgegraphs/utils/pubchem_utils.py

@@ -0,0 +1,72 @@
+#!/usr/bin/env python3
+
+"""
+Enrichment class for enriching PubChem IDs with their STRINGS representation.
+"""
+
+import logging
+import requests
+import hydra
+
+# Initialize logger
+logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger(__name__)
+
+def external_id2pubchem_cid(db, db_id):
+    """
+    Convert external DB ID to PubChem CID.
+    Please refer to the following URL for more information
+    on data sources:
+    https://pubchem.ncbi.nlm.nih.gov/sources/
+
+    Args:
+        db: The database name.
+        db_id: The database ID of the drug.
+
+    Returns:
+        The PubChem CID of the drug.
+    """
+    logger.log(logging.INFO, "Load Hydra configuration for PubChem ID conversion.")
+    with hydra.initialize(version_base=None, config_path="../configs"):
+        cfg = hydra.compose(config_name='config',
+                            overrides=['utils/pubchem_utils=default'])
+        cfg = cfg.utils.pubchem_utils
+    # Prepare the URL
+    pubchem_url_for_drug = f"{cfg.pubchem_cid_base_url}/{db}/{db_id}/JSON"
+    # Get the data
+    response = requests.get(pubchem_url_for_drug, timeout=60)
+    data = response.json()
+    # Extract the PubChem CID
+    cid = None
+    for substance in data.get("PC_Substances", []):
+        for compound in substance.get("compound", []):
+            if "id" in compound and "type" in compound["id"] and compound["id"]["type"] == 1:
+                cid = compound["id"].get("id", {}).get("cid")
+                break
+    return cid
+
+def pubchem_cid_description(cid):
+    """
+    Get the description of a PubChem CID.
+
+    Args:
+        cid: The PubChem CID of the drug.
+
+    Returns:
+        The description of the PubChem CID.
+    """
+    logger.log(logging.INFO, "Load Hydra configuration for PubChem CID description.")
+    with hydra.initialize(version_base=None, config_path="../configs"):
+        cfg = hydra.compose(config_name='config',
+                            overrides=['utils/pubchem_utils=default'])
+        cfg = cfg.utils.pubchem_utils
+    # Prepare the URL
+    pubchem_url_for_descpription = f"{cfg.pubchem_cid_description_url}/{cid}/description/JSON"
+    # Get the data
+    response = requests.get(pubchem_url_for_descpription, timeout=60)
+    data = response.json()
+    # Extract the PubChem CID description
+    description = ''
+    for information in data["InformationList"]['Information']:
+        description += information.get("Description", '')
+    return description

{aiagents4pharma-1.33.0 → aiagents4pharma-1.34.1}/aiagents4pharma.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: aiagents4pharma
-Version: 1.33.0
+Version: 1.34.1
 Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D.
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License
@@ -8,7 +8,7 @@ Classifier: Operating System :: OS Independent
 Requires-Python: >=3.12
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: copasi_basico==0.78
+Requires-Dist: copasi_basico==0.84
 Requires-Dist: coverage==7.6.4
 Requires-Dist: einops==0.8.0
 Requires-Dist: gdown==5.2.0

{aiagents4pharma-1.33.0 → aiagents4pharma-1.34.1}/aiagents4pharma.egg-info/SOURCES.txt

@@ -120,7 +120,9 @@ aiagents4pharma/talk2knowledgegraphs/tests/test_utils_embeddings_ollama.py
 aiagents4pharma/talk2knowledgegraphs/tests/test_utils_embeddings_sentencetransformer.py
 aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_enrichments.py
 aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_ollama.py
+aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_ols.py
 aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_pubchem.py
+aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_reactome.py
 aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_uniprot.py
 aiagents4pharma/talk2knowledgegraphs/tests/test_utils_kg_utils.py
 aiagents4pharma/talk2knowledgegraphs/tests/test_utils_pubchem_utils.py
@@ -141,7 +143,9 @@ aiagents4pharma/talk2knowledgegraphs/utils/embeddings/sentence_transformer.py
 aiagents4pharma/talk2knowledgegraphs/utils/enrichments/__init__.py
 aiagents4pharma/talk2knowledgegraphs/utils/enrichments/enrichments.py
 aiagents4pharma/talk2knowledgegraphs/utils/enrichments/ollama.py
+aiagents4pharma/talk2knowledgegraphs/utils/enrichments/ols_terms.py
 aiagents4pharma/talk2knowledgegraphs/utils/enrichments/pubchem_strings.py
+aiagents4pharma/talk2knowledgegraphs/utils/enrichments/reactome_pathways.py
 aiagents4pharma/talk2knowledgegraphs/utils/enrichments/uniprot_proteins.py
 aiagents4pharma/talk2knowledgegraphs/utils/extractions/__init__.py
 aiagents4pharma/talk2knowledgegraphs/utils/extractions/pcst.py

{aiagents4pharma-1.33.0 → aiagents4pharma-1.34.1}/aiagents4pharma.egg-info/requires.txt

@@ -1,4 +1,4 @@
-copasi_basico==0.78
+copasi_basico==0.84
 coverage==7.6.4
 einops==0.8.0
 gdown==5.2.0

{aiagents4pharma-1.33.0 → aiagents4pharma-1.34.1}/pyproject.toml

@@ -13,7 +13,7 @@ classifiers = [
   "Operating System :: OS Independent",
 ]
 dependencies = [
-  "copasi_basico==0.78",
+  "copasi_basico==0.84",
   "coverage==7.6.4",
   "einops==0.8.0",
   "gdown==5.2.0",

aiagents4pharma-1.34.1/release_version.txt

@@ -0,0 +1 @@
+v1.34.1

aiagents4pharma-1.33.0/aiagents4pharma/talk2knowledgegraphs/tests/test_utils_pubchem_utils.py

@@ -1,16 +0,0 @@
-"""
-Test cases for utils/pubchem_utils.py
-"""
-
-from ..utils import pubchem_utils
-
-def test_drugbank_id2pubchem_cid():
-    """
-    Test the drugbank_id2pubchem_cid method.
-
-    The DrugBank ID for Alclometasone is DB00240.
-    The PubChem CID for Alclometasone is 5311000.
-    """
-    drugbank_id = "DB00240"
-    pubchem_cid = pubchem_utils.drugbank_id2pubchem_cid(drugbank_id)
-    assert pubchem_cid == 5311000

aiagents4pharma-1.33.0/aiagents4pharma/talk2knowledgegraphs/utils/pubchem_utils.py

@@ -1,42 +0,0 @@
-#!/usr/bin/env python3
-
-"""
-Enrichment class for enriching PubChem IDs with their STRINGS representation.
-"""
-
-import logging
-import requests
-import hydra
-
-# Initialize logger
-logging.basicConfig(level=logging.INFO)
-logger = logging.getLogger(__name__)
-
-def drugbank_id2pubchem_cid(drugbank_id):
-    """
-    Convert DrugBank ID to PubChem CID.
-
-    Args:
-        drugbank_id: The DrugBank ID of the drug.
-
-    Returns:
-        The PubChem CID of the drug.
-    """
-    logger.log(logging.INFO, "Load Hydra configuration for PubChem ID conversion.")
-    with hydra.initialize(version_base=None, config_path="../configs"):
-        cfg = hydra.compose(config_name='config',
-                            overrides=['utils/pubchem_utils=default'])
-        cfg = cfg.utils.pubchem_utils
-    # Prepare the URL
-    pubchem_url_for_drug = cfg.drugbank_id_to_pubchem_cid_url + drugbank_id + '/JSON'
-    # Get the data
-    response = requests.get(pubchem_url_for_drug, timeout=60)
-    data = response.json()
-    # Extract the PubChem CID
-    cid = None
-    for substance in data.get("PC_Substances", []):
-        for compound in substance.get("compound", []):
-            if "id" in compound and "type" in compound["id"] and compound["id"]["type"] == 1:
-                cid = compound["id"].get("id", {}).get("cid")
-                break
-    return cid

aiagents4pharma-1.33.0/release_version.txt

@@ -1 +0,0 @@
-v1.33.0