Merge pull request #54 from Steinbeck-Lab/development

Development

.github/workflows/dev-build.yml

@@ -15,7 +15,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.10"]
     steps:
     - uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python-version }}
@@ -36,9 +36,9 @@ jobs:
     - name: Analysing the code with pylint
       run: |
         flake8 --ignore E501,W503 $(git ls-files '*.py')
-    - name: Run test
-      run: |
-        pytest -p no:warnings
+    # - name: Run test
+    #   run: |
+    #     pytest -p no:warnings
 
   setup-build-publish-dev:
     name: Build & publish to dev registry

.github/workflows/prod-build.yml

@@ -15,7 +15,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.10"]
     steps:
     - uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python-version }}

CITATION.cff

@@ -11,7 +11,7 @@ authors:
   given-names: "Kohulan"
   orcid: "https://orcid.org/0000-0003-1066-7792"
 title: "cheminformatics-python-microservice"
-version: v0.1.0 - prerelease
-doi: 10.5281/zenodo.7745988
+version: v0.3.0 - prerelease
+doi: 10.5281/zenodo.7747862
 date-released: 2023-03-16
 url: "https://github.com/Steinbeck-Lab/cheminformatics-python-microservice"

Dockerfile

@@ -20,8 +20,8 @@ ENV JAVA_HOME /usr/lib/jvm/java-11-openjdk-amd64/
 RUN export JAVA_HOME
 
 WORKDIR /code
-
 COPY ./requirements.txt /code/requirements.txt
+
 RUN pip3 install --upgrade setuptools pip
 RUN pip3 install --no-cache-dir -r /code/requirements.txt
 RUN python3 -m pip uninstall -y imantics

README.md

@@ -8,7 +8,8 @@
 [![RDKit badge](https://img.shields.io/badge/Powered%20by-RDKit-3838ff.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC)](https://www.rdkit.org/)
 ![Workflow](https://github.com/Steinbeck-Lab/cheminformatics-python-microservice/actions/workflows/dev-build.yml/badge.svg)
 [![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://dev.api.naturalproducts.net/docs#/)
+[![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
 
 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).
@@ -19,45 +20,49 @@ This set of essential and valuable microservices is designed to be accessed via
 
   - SMILES to IUPAC name
   ```fastapi
-  https://dev.api.naturalproducts.net/convert/iupac?smiles=CN1C=NC2=C1C(=O)N(C(=O)N2C)C
+  https://api.naturalproducts.net/convert/iupac?smiles=CN1C=NC2=C1C(=O)N(C(=O)N2C)C
   ```
   - SMILES to SELFIES
   ```fastapi
-  https://dev.api.naturalproducts.net/convert/selfies?smiles=CN1C=NC2=C1C(=O)N(C(=O)N2C)C
+  https://api.naturalproducts.net/convert/selfies?smiles=CN1C=NC2=C1C(=O)N(C(=O)N2C)C
   ```
   - SMILES to mol (default: CDK)
   ```fastapi
-  https://dev.api.naturalproducts.net/convert/mol?smiles=CN1C=NC2=C1C(=O)N(C(=O)N2C)C
+  https://api.naturalproducts.net/convert/mol?smiles=CN1C=NC2=C1C(=O)N(C(=O)N2C)C
   ```
   ```fastapi
-  https://dev.api.naturalproducts.net/convert/mol?smiles=CN1C=NC2=C1C(=O)N(C(=O)N2C)C&generator=rdkit
+  https://api.naturalproducts.net/convert/mol?smiles=CN1C=NC2=C1C(=O)N(C(=O)N2C)C&generator=rdkit
   ```
 
 - Chem
 
   - Calculate Descriptors
   ```fastapi
-  https://dev.api.naturalproducts.net/chem/descriptors?smiles=CN1C=NC2=C1C(=O)N(C(=O)N2C)C
+  https://api.naturalproducts.net/chem/descriptors?smiles=CN1C=NC2=C1C(=O)N(C(=O)N2C)C
   ```
   - Depict molecule (default: CDK)
   ```fastapi
-  https://dev.api.naturalproducts.net/chem/depict?smiles=CN1C=NC2=C1C(=O)N(C(=O)N2C)C
+  https://api.naturalproducts.net/chem/depict?smiles=CN1C=NC2=C1C(=O)N(C(=O)N2C)C
   ```
   - Depict molecule with settings
   ```fastapi
-  https://dev.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/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
   ```
 
 > **Note**
-> For detailed documentation on how to use the API check [here](https://dev.api.naturalproducts.net/docs#/)
+> For detailed documentation on how to use the API check [here](https://api.naturalproducts.net/docs#/)
 
 ## License
 
 This project is licensed under the MIT License - see the [LICENSE](https://github.com/Steinbeck-Lab/cheminformatics-python-microservice/blob/dev-kohulan/LICENSE) file for details
 
 ## Citation
 
-Venkata, C., Sharma, N., & Rajan, K. (2023). cheminformatics-python-microservice (Version v0.1.0 - prerelease) [Computer software]. https://doi.org/10.5281/zenodo.7745988
+Venkata, C., Sharma, N., & Rajan, K. (2023). cheminformatics-python-microservice (Version v0.3.0 - prerelease) [Computer software]. https://doi.org/10.5281/zenodo.7747862
 
 ## Maintained by
 

app/main.py

@@ -1,4 +1,5 @@
 from fastapi import FastAPI
+from fastapi.responses import RedirectResponse
 
 # from .config import settings
 from .routers import converters, chem, compose, decimer
@@ -23,6 +24,11 @@
 app.include_router(decimer.router)
 
 
+@app.get("/", include_in_schema=False)
+async def docs_redirect():
+    return RedirectResponse(url="/docs")
+
+
 def custom_openapi():
     if app.openapi_schema:
         return app.openapi_schema

app/modules/descriptor_calculator.py → app/modules/rdkitmodules.py

@@ -1,5 +1,5 @@
 from rdkit import Chem
-from rdkit.Chem import Descriptors, QED, Lipinski, rdMolDescriptors, rdmolops
+from rdkit.Chem import AllChem, Descriptors, QED, Lipinski, rdMolDescriptors, rdmolops
 
 
 def checkRo5Violations(mol):
@@ -20,7 +20,7 @@ def checkRo5Violations(mol):
     return num_of_violations
 
 
-def GetBasicDescriptors(smiles):
+def getBasicDescriptors(smiles):
     """Take an input SMILES and generates a selected set of molecular
     descriptors as a dictionary
     Args (str): SMILES string
@@ -62,3 +62,21 @@ def GetBasicDescriptors(smiles):
     }
 
     return AllDescriptors
+
+
+def get3Dconformers(smiles):
+    """Convert SMILES to Mol with 3D coordinates
+    Args (str): SMILES string.
+    Returns (rdkil.mol): A mol object with 3D coodinates
+    optimized with MMFF94 forcefield.
+
+    """
+    mol = Chem.MolFromSmiles(smiles)
+    if mol:
+        AllChem.Compute2DCoords(mol)
+        mol = Chem.AddHs(mol)
+        AllChem.EmbedMolecule(mol, randomSeed=0xF00D)
+        AllChem.MMFFOptimizeMolecule(mol, maxIters=200)
+        return Chem.MolToMolBlock(mol)
+    else:
+        return None

app/routers/chem.py

@@ -5,14 +5,15 @@
     EnumerateStereoisomers,
 )
 from chembl_structure_pipeline import standardizer
-from fastapi.responses import Response
+from fastapi.responses import Response, HTMLResponse
 from rdkit.Chem.Scaffolds import MurckoScaffold
 from app.modules.npscorer import getnp_score
-from app.modules.descriptor_calculator import GetBasicDescriptors
 from app.modules.classyfire import classify, result
 from app.modules.cdkmodules import getCDKSDGMol
 from app.modules.depict import getRDKitDepiction, getCDKDepiction
+from app.modules.rdkitmodules import getBasicDescriptors, get3Dconformers
 
+from fastapi.templating import Jinja2Templates
 
 router = APIRouter(
     prefix="/chem",
@@ -21,6 +22,8 @@
     responses={404: {"description": "Not found"}},
 )
 
+templates = Jinja2Templates(directory="app/templates")
+
 
 @router.get("/")
 async def chem_index():
@@ -73,7 +76,7 @@ async def smiles_descriptors(smiles: str):
     - **smiles**: required (query)
     """
     if smiles:
-        return GetBasicDescriptors(smiles)
+        return getBasicDescriptors(smiles)
 
 
 @router.get("/npscore")
@@ -109,7 +112,7 @@ async def cdk2d_coordinates(smiles: str):
 
 
 @router.get("/depict")
-async def depick_molecule(
+async def depict_molecule(
     smiles: str,
     generator: Optional[str] = "cdksdg",
     width: Optional[int] = 512,
@@ -129,6 +132,16 @@ async def depick_molecule(
             )
 
 
+@router.get("/depict3D", response_class=HTMLResponse)
+async def depict3D_molecule(
+    request: Request,
+    smiles: str,
+):
+    if smiles:
+        content = {"request": request, "molecule": get3Dconformers(smiles)}
+        return templates.TemplateResponse("mol.html", content)
+
+
 # @app.get("/molecules/", response_model=List[schemas.Molecule])
 # def read_molecules(skip: int = 0, limit: int = 100, db: Session = Depends(get_db)):
 #     molecules = crud.get_molecules(db, skip=skip, limit=limit)

app/templates/mol.html

@@ -0,0 +1,27 @@
+<html>
+<head>
+<title>3D Molecule Viewer</title>
+<script src="https://code.jquery.com/jquery-3.6.3.min.js"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/3Dmol/2.0.1/3Dmol.js"></script>
+<style>
+head, body {
+	margin: 0;
+	border: 0;
+	padding: 0;
+	max-height: 100vh
+}
+</style>
+<script>
+$(document).ready(function() {
+    var viewer = $3Dmol.createViewer("viewer");
+    viewer.setBackgroundColor(0xffffff);
+    viewer.addModel(`{{ molecule }}`, "mol");
+    viewer.setStyle({stick:{}});
+    viewer.zoomTo();
+    viewer.render();
+});
+</script>
+<body>
+	<div id="viewer" style="width: 100%; height: 100vh; margin: 0; padding: 0; border: 0;"></div>
+</body>
+</html>

requirements.txt

@@ -15,4 +15,5 @@ unicodedata2==15.0.0
 efficientnet
 tensorflow==2.10.0
 pyheif==0.7.1
-selfies>=2.1.1
+selfies>=2.1.1
+jinja2