Merge pull request #152 from Steinbeck-Lab/development

New Developments
Steinbeck-Lab · Jun 5, 2023 · 75b201c · 75b201c
2 parents dd124b2 + 2c361a8
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diff --git a/Dockerfile b/Dockerfile
@@ -1,22 +1,20 @@
-FROM debian:buster-20230227-slim AS cheminf-python-ms
+FROM continuumio/miniconda3 AS cheminf-python-ms
+
+ENV PYTHON_VERSION=3.10
+ENV RDKIT_VERSION=2023.03.1
 
 ARG RELEASE_VERSION
 ENV RELEASE_VERSION=${RELEASE_VERSION}
 
 # Install runtime dependencies
-RUN apt-get update \
- && apt-get upgrade -y \
- && apt-get install -y --no-install-recommends \
-    python3 \
-    python3-pip \
- && apt-get clean \
- && rm -rf /var/lib/apt/lists/*
-
 RUN apt-get update && \
     apt-get install -y software-properties-common && \
     apt-get update -y && \
     apt-get install -y openjdk-11-jre
 
+RUN conda install -c conda-forge python>=$PYTHON_VERSION
+RUN conda install -c conda-forge rdkit>=RDKIT_VERSION
+
 RUN python3 -m pip install -U pip
 
 ENV JAVA_HOME /usr/lib/jvm/java-11-openjdk-amd64/

diff --git a/README.md b/README.md
@@ -13,7 +13,7 @@
 [![framework](https://img.shields.io/badge/Framework-FastAPI-blue?style)](https://fastapi.tiangolo.com/)
 [![FastAPI Documentation](https://img.shields.io/badge/docs-fastapi-blue)](https://api.naturalproducts.net/docs#/)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7747862.svg)](https://doi.org/10.5281/zenodo.7747862)
-## Overview of Cheminformatics Micro Services
+## Overview of Cheminformatics Python Microservices
 
 This set of essential and valuable microservices is designed to be accessed via API calls to support cheminformatics. Generally, it is designed to work with SMILES-based inputs and could be used to translate between different machine-readable representations, get Natural Product (NP) likeliness scores, visualize chemical structures, and generate descriptors. In addition, the microservices also host an instance of [STOUT](https://github.com/Kohulan/Smiles-TO-iUpac-Translator) and another instance of [DECIMER](https://github.com/Kohulan/DECIMER-Image_Transformer) (two deep learning models for IUPAC name generation and optical chemical structure recognition, respectively).
 
@@ -23,37 +23,37 @@ This set of essential and valuable microservices is designed to be accessed via
 
   - SMILES to IUPAC name
   ```fastapi
-  https://api.naturalproducts.net/convert/iupac?smiles=CN1C=NC2=C1C(=O)N(C(=O)N2C)C
+  https://api.naturalproducts.net/v1/convert/iupac?smiles=CN1C=NC2=C1C(=O)N(C(=O)N2C)C
   ```
   - SMILES to SELFIES
   ```fastapi
-  https://api.naturalproducts.net/convert/selfies?smiles=CN1C=NC2=C1C(=O)N(C(=O)N2C)C
+  https://api.naturalproducts.net/v1/convert/selfies?smiles=CN1C=NC2=C1C(=O)N(C(=O)N2C)C
   ```
   - SMILES to mol (default: CDK)
   ```fastapi
-  https://api.naturalproducts.net/convert/mol?smiles=CN1C=NC2=C1C(=O)N(C(=O)N2C)C
+  https://api.naturalproducts.net/v1/convert/mol?smiles=CN1C=NC2=C1C(=O)N(C(=O)N2C)C
   ```
   ```fastapi
-  https://api.naturalproducts.net/convert/mol?smiles=CN1C=NC2=C1C(=O)N(C(=O)N2C)C&generator=rdkit
+  https://api.naturalproducts.net/v1/convert/mol?smiles=CN1C=NC2=C1C(=O)N(C(=O)N2C)C&generator=rdkit
   ```
 
 - Chem
 
   - Calculate Descriptors
   ```fastapi
-  https://api.naturalproducts.net/chem/descriptors?smiles=CN1C=NC2=C1C(=O)N(C(=O)N2C)C
+  https://api.naturalproducts.net/v1/chem/descriptors?smiles=CN1C=NC2=C1C(=O)N(C(=O)N2C)C
   ```
   - Depict molecule (default: CDK)
   ```fastapi
-  https://api.naturalproducts.net/chem/depict?smiles=CN1C=NC2=C1C(=O)N(C(=O)N2C)C
+  https://api.naturalproducts.net/v1/chem/depict?smiles=CN1C=NC2=C1C(=O)N(C(=O)N2C)C
   ```
   - Depict molecule with settings
   ```fastapi
-  https://api.naturalproducts.net/chem/depict?smiles=CN1C=NC2=C1C(=O)N(C(=O)N2C)C&generator=rdkit&width=256&height=256&rotate=75
+  https://api.naturalproducts.net/v1/chem/depict?smiles=CN1C=NC2=C1C(=O)N(C(=O)N2C)C&generator=rdkit&width=256&height=256&rotate=75
   ```
   - Visualize molecule in 3D
   ```fastapi
-  https://api.naturalproducts.net/chem/depict3D?smiles=CN1C=NC2=C1C(=O)N(C(=O)N2C)C
+  https://api.naturalproducts.net/v1/chem/depict3D?smiles=CN1C=NC2=C1C(=O)N(C(=O)N2C)C
   ```
 
 > **Note**
@@ -65,10 +65,28 @@ This project is licensed under the MIT License - see the [LICENSE](https://githu
 
 ## Citation
 
-Venkata, C., Sharma, N., & Rajan, K. (2023). cheminformatics-python-microservice (Version v0.3.0 - prerelease) [Computer software]. https://doi.org/10.5281/zenodo.7747862
+Venkata, C., Sharma, N., & Rajan, K. (2023). Cheminformatics Python Microservice (Version v0.8.0 - prerelease) [Computer software]. https://doi.org/10.5281/zenodo.7747862
+
+## Version information
+<p align="center">
+  <b>Cheminformatics Python Microservice: V0.8.0</b>
+</p>
+
+<p align="center">
+
+| Tools      | Version   |
+|------------|-----------|
+| RDKit      | 2023.03.1 |
+| CDK        | 2.8.0     |
+| STOUT      | 2.0.0     |
+| DECIMER    | 2.2.0     |
+
+</p>
+
+
 
 ## Maintained by
 
-Cheminformatics Micro Services and [Natural Products Online](https://naturalproducts.net) are developed and maintained by the [Steinbeck group](https://cheminf.uni-jena.de) at the [Friedrich Schiller University](https://www.uni-jena.de/en/) Jena, Germany. 
+Cheminformatics Python Microservice and [Natural Products Online](https://naturalproducts.net) are developed and maintained by the [Steinbeck group](https://cheminf.uni-jena.de) at the [Friedrich Schiller University](https://www.uni-jena.de/en/) Jena, Germany. 
 The code for this web application is released under the [MIT license](https://opensource.org/licenses/MIT). Copyright © CC-BY-SA 2023
 <p align="center"><a href="https://cheminf.uni-jena.de/" target="_blank"><img src="https://github.com/Kohulan/DECIMER-Image-to-SMILES/blob/master/assets/CheminfGit.png" width="800" alt="cheminf Logo"></a></p>
diff --git a/app/__init__.py b/app/__init__.py
@@ -0,0 +1,12 @@
+# -*- coding: utf-8 -*-
+
+"""
+Cheminformatics Micro Services Python Modules.
+
+This set of essential and valuable microservices is designed to be accessed via API calls to support cheminformatics. Generally, it is designed to work with SMILES-based inputs and could be used to translate between different machine-readable representations, get Natural Product (NP) likeliness scores, visualize chemical structures, and generate descriptors. In addition, the microservices also host an instance of STOUT and another instance of DECIMER (two deep learning models for IUPAC name generation and optical chemical structure recognition, respectively).
+
+For comments, bug reports or feature requests,
+please raise a issue on our Github repository.
+"""
+
+__version__ = "0.8.0"
diff --git a/app/config.py b/app/config.py
diff --git a/app/main.py b/app/main.py
@@ -1,13 +1,25 @@
 from fastapi import FastAPI
 from fastapi.responses import RedirectResponse
+from fastapi_versioning import VersionedFastAPI
 
 # from .config import settings
-from .routers import chem, converters, compose, decimer
+from .routers import chem, converters, decimer
 from fastapi.middleware.cors import CORSMiddleware
-from fastapi.openapi.utils import get_openapi
-import os
 
-app = FastAPI()
+app = FastAPI(
+    title="Cheminf Micro Services",
+    description="This set of essential and valuable microservices is designed to be accessed via API calls to support cheminformatics. Generally, it is designed to work with SMILES-based inputs and could be used to translate between different machine-readable representations, get Natural Product (NP) likeliness scores, visualize chemical structures, and generate descriptors. In addition, the microservices also host an instance of STOUT and another instance of DECIMER (two deep learning models for IUPAC name generation and optical chemical structure recognition, respectively).",
+    terms_of_service="https://github.com/Steinbeck-Lab",
+    contact={
+        "name": "Steinbeck Lab",
+        "url": "https://cheminf.uni-jena.de/",
+        "email": "caffeine@listserv.uni-jena.de",
+    },
+    license_info={
+        "name": "CC BY 4.0",
+        "url": "https://creativecommons.org/licenses/by/4.0/",
+    },
+)
 
 origins = ["*"]
 
@@ -21,7 +33,6 @@
 
 app.include_router(chem.router)
 app.include_router(converters.router)
-app.include_router(compose.router)
 app.include_router(decimer.router)
 
 
@@ -30,20 +41,18 @@ async def docs_redirect():
     return RedirectResponse(url="/docs")
 
 
-def custom_openapi():
-    if app.openapi_schema:
-        return app.openapi_schema
-    openapi_schema = get_openapi(
-        title="Cheminf Micro Services",
-        version=os.getenv("RELEASE_VERSION", "latest"),
-        description="This set of essential and valuable microservices is designed to be accessed via API calls to support cheminformatics. Generally, it is designed to work with SMILES-based inputs and could be used to translate between different machine-readable representations, get Natural Product (NP) likeliness scores, visualize chemical structures, and generate descriptors. In addition, the microservices also host an instance of STOUT and another instance of DECIMER (two deep learning models for IUPAC name generation and optical chemical structure recognition, respectively).",
-        routes=app.routes,
-    )
-    openapi_schema["info"]["x-logo"] = {
-        "url": "https://github.com/Steinbeck-Lab/cheminformatics-python-microservice/raw/main/public/img/logo.png"
-    }
-    app.openapi_schema = openapi_schema
-    return app.openapi_schema
-
-
-app.openapi = custom_openapi
+app = VersionedFastAPI(
+    app,
+    version_format="{major}",
+    prefix_format="/v{major}",
+    terms_of_service="https://github.com/Steinbeck-Lab",
+    contact={
+        "name": "Steinbeck Lab",
+        "url": "https://cheminf.uni-jena.de/",
+        "email": "caffeine@listserv.uni-jena.de",
+    },
+    license_info={
+        "name": "CC BY 4.0",
+        "url": "https://creativecommons.org/licenses/by/4.0/",
+    },
+)
diff --git a/app/modules/alldescriptors.py b/app/modules/alldescriptors.py
@@ -175,7 +175,7 @@ def getCDKRDKitcombinedDescriptors(smiles: str):
         "Heavy atom count",
         "Molecular weight",
         "Exact molecular weight",
-        "ALogP",
+        "Calculated LogP",
         "Rotatable bond count",
         "Topological polar surface area",
         "Hydrogen bond acceptors",