Merge pull request #439 from Steinbeck-Lab/dev-nisha

Upgrade versions of RDKit, CDK and OB.

Dockerfile

@@ -1,8 +1,8 @@
 FROM continuumio/miniconda3 AS cheminf-python-ms
 
 ENV PYTHON_VERSION=3.10
-ENV RDKIT_VERSION=2023.03.1
-ENV OPENBABEL_VERSION=v3.1
+ENV RDKIT_VERSION=2023.09.4
+ENV OPENBABEL_VERSION=v3.1.1
 
 # Install runtime dependencies
 RUN apt-get update && \
@@ -17,7 +17,7 @@ RUN chmod +x surge
 RUN mv surge /usr/bin
 
 RUN conda install -c conda-forge python>=PYTHON_VERSION
-#RUN conda install -c conda-forge rdkit==RDKIT_VERSION
+RUN conda install -c conda-forge rdkit==RDKIT_VERSION
 RUN conda install -c conda-forge openbabel>=OPENBABEL_VERSION
 
 RUN python3 -m pip install -U pip
@@ -32,7 +32,7 @@ RUN pip3 install --upgrade setuptools pip
 RUN pip3 install --no-cache-dir -r /code/requirements.txt
 RUN python3 -m pip uninstall -y imantics
 RUN pip3 install imantics==0.1.12
-RUN pip3 install rdkit
+#RUN pip3 install rdkit
 RUN pip3 install --no-deps decimer-segmentation==1.1.3
 RUN pip3 install --no-deps decimer==2.3.0
 RUN pip3 install --no-deps STOUT-pypi>=2.0.5

app/modules/toolkits/cdk_wrapper.py

@@ -23,14 +23,14 @@
     )
     jvmPath = "Define/path/or/set/JAVA_HOME/variable/properly"
 if not isJVMStarted():
-    cdk_path = "https://github.com/cdk/cdk/releases/download/cdk-2.8/cdk-2.8.jar"
+    cdk_path = "https://github.com/cdk/cdk/releases/download/cdk-2.9/cdk-2.9.jar"
     sru_path = "https://github.com/JonasSchaub/SugarRemoval/releases/download/v1.3.2/SugarRemovalUtility-jar-with-dependencies.jar"
     centres_path = (
         "https://github.com/SiMolecule/centres/releases/download/1.0/centres.jar"
     )
     opsin_path = "https://github.com/dan2097/opsin/releases/download/2.8.0/opsin-cli-2.8.0-jar-with-dependencies.jar"
 
-    cdkjar_path = str(pystow.join("STOUT-V2")) + "/cdk-2.8.jar"
+    cdkjar_path = str(pystow.join("STOUT-V2")) + "/cdk-2.9.jar"
     srujar_path = (
         str(pystow.join("STOUT-V2")) + "/SugarRemovalUtility-jar-with-dependencies.jar"
     )

docs/versions.md

@@ -19,9 +19,9 @@ The Cheminformatics Microservice, framework is developed using Python and [FastA
 
 | Toolkits    | Version     |
 |-------------|-------------|
-| RDKit <sup>1</sup>    | 2023.03.1  |
-| CDK <sup>2</sup>      | 2.8.0       |
-| Open Babel <sup>3</sup> | 3.1.0       |
+| RDKit <sup>1</sup>    | 2023.09.4  |
+| CDK <sup>2</sup>      | 2.9.0       |
+| Open Babel <sup>3</sup> | 3.1.1       |
 
 
 **External Tools Versions**

ops/docker-compose-dev.yml

@@ -64,4 +64,4 @@ volumes:
   postgres_data:
 networks:
   default:
-    name: cm_fastapi
+    name: cm_fastapi