Merge pull request #269 from Steinbeck-Lab/development

Development

.gitignore

@@ -131,5 +131,8 @@ docs/.vitepress/cache
 docs/.vitepress/cache/*
 node_modules
 
+# Sphinx documentation
+docs/_build/
+
 #grafana
 grafana_data/

.readthedocs.yml

@@ -0,0 +1,29 @@
+# Read the Docs configuration file for Sphinx projects
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+   configuration: docs/conf.py
+
+# Optionally build your docs in additional formats such as PDF and ePub
+formats:
+    - epub
+
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+  install:
+    - requirements: docs/requirements.txt
+    - requirements: docs/extra-requirements.txt
+      ignore_dependencies: true

CITATION.cff

@@ -11,7 +11,7 @@ authors:
   given-names: "Kohulan"
   orcid: "https://orcid.org/0000-0003-1066-7792"
 title: "cheminformatics-python-microservice"
-version: v0.3.0 - prerelease
-doi: 10.5281/zenodo.7747862
+version: V1.0.0
+doi: 10.5281/zenodo.8112749
 date-released: 2023-03-16
 url: "https://github.com/Steinbeck-Lab/cheminformatics-python-microservice"

README.md

@@ -12,7 +12,8 @@
 ![Workflow](https://github.com/Steinbeck-Lab/cheminformatics-python-microservice/actions/workflows/release-please.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://api.naturalproducts.net/v1/docs#/)
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7747862.svg)](https://doi.org/10.5281/zenodo.7747862)
+[![Documentation Status](https://readthedocs.org/projects/cheminformatics-python-microservice/badge/?version=latest)](https://cheminformatics-python-microservice.readthedocs.io/en/latest/?badge=latest)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.8112749.svg)](https://doi.org/10.5281/zenodo.8112749)
 ## Overview of Cheminformatics Python Microservice
 
 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).
@@ -33,7 +34,7 @@ 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 v0.9.0 - prerelease) [Computer software]. https://doi.org/10.5281/zenodo.7747862
+Venkata, C., Sharma, N., & Rajan, K. (2023). Cheminformatics Python Microservice (Version V1.0.0) [Computer software]. https://doi.org/10.5281/zenodo.7747862
 
 ## Maintained by
 

app/modules/coconut/preprocess.py

@@ -7,9 +7,13 @@
 def getMolBlock(input_text: str):
     """
     This function generates a molblock from the
-    input text.
-    Args (str): Input text (mol / SMILES)
-    returns (str): molblock
+    input text using CDK.
+
+    Args (str):
+        Input text (mol / SMILES)
+    Returns (str):
+        molblock
+
     """
     check = rdkitmodules.is_valid_molecule(input_text)
 
@@ -25,8 +29,12 @@ def getMolBlock(input_text: str):
 def getMolculeHash(smiles: str):
     """
     This function returns a set of molecule hashes defined.
-    Args (str): SMILES string (strandardised is preferred).
-    Returns (dict): molecule_hash
+
+    Args (str):
+        SMILES string (strandardised is preferred).
+    Returns (dict):
+        molecule_hash
+
     """
     mol = Chem.MolFromSmiles(smiles)
     if mol:
@@ -46,8 +54,12 @@ def getRepresentations(smiles: str):
     """
     This functions returns COCONUT representations.
     InChI, InChi key and Murko framework.
-    Args (str): SMILES string.
-    Returns (dict): dictionary of InChI, InChi key and Murko framework.
+
+    Args (str):
+        SMILES string.
+    Returns (dict):
+        dictionary of InChI, InChi key and Murko framework.
+
     """
     mol = Chem.MolFromSmiles(smiles)
     if mol:
@@ -57,11 +69,15 @@ def getRepresentations(smiles: str):
         return {"InChI": InChI, "InChI_Key": InChI_Key, "Murko": Murko}
 
 
-def COCONUTpreprocessing(input_text: str):
+def getCOCONUTpreprocessing(input_text: str):
     """
     This function takes a user input text and returns a dictionary for COCONUT input.
-    Args (str): input_text (mol/str).
-    Returns (dict): COCONUT preprocessed data.
+
+    Args (str):
+        input_text (mol/str).
+    Returns (dict):
+        COCONUT preprocessed data.
+
     """
     original_mol = getMolBlock(input_text)
     standarised_mol_block = rdkitmodules.standardizer.standardize_molblock(original_mol)

app/modules/decimer.py

@@ -7,6 +7,7 @@
 
 def convert_image(path: str):
     """Takes an image filepath of GIF image and returns Hi Res PNG image.
+
     Args:
         input_path (str): path of an image.
 
@@ -31,6 +32,7 @@ def convert_image(path: str):
 
 def get_segments(path: str):
     """Takes an image filepath and returns a set of paths and image name of segmented images.
+
     Args:
         input_path (str): path of an image.
 
@@ -50,6 +52,7 @@ def get_segments(path: str):
 
 def getPredictedSegments(path: str):
     """Takes an image filepath and returns predicted SMILES for segmented images.
+
     Args:
         input_path (str): path of an image.
 

app/modules/toolkits/cdk_wrapper.py

@@ -43,10 +43,11 @@
 def getCDKSDG(smiles: str):
     """This function takes the user input SMILES and Creates a
        Structure Diagram Layout using the CDK.
+
     Args:
-            smiles (string): SMILES string given by the user.
+        smiles (string): SMILES string given by the user.
     Returns:
-            mol object : mol object with CDK SDG.
+        mol object : mol object with CDK SDG.
     """
     if any(char.isspace() for char in smiles):
         smiles = smiles.replace(" ", "+")
@@ -63,10 +64,11 @@ def getCDKSDG(smiles: str):
 def getMurkoFramework(smiles: str):
     """This function takes the user input SMILES and returns
     the Murko framework
+
     Args:
-            smiles (string): SMILES string given by the user.
+        smiles (string): SMILES string given by the user.
     Returns:
-            smiles (string) : Murko Framework as SMILES.
+        smiles (string) : Murko Framework as SMILES.
     """
     if any(char.isspace() for char in smiles):
         smiles = smiles.replace(" ", "+")
@@ -84,11 +86,13 @@ def getMurkoFramework(smiles: str):
 def getCDKSDGMol(smiles: str, V3000=False):
     """This function takes the user input SMILES and returns a mol
        block as a string with Structure Diagram Layout.
+
     Args:
-            smiles (string): SMILES string given by the user.
-            V3000 (boolean): Gives an option to return V3000 mol.
+        smiles (string): SMILES string given by the user.
+        V3000 (boolean): Gives an option to return V3000 mol.
     Returns:
-            mol object (string): CDK Structure Diagram Layout mol block.
+        mol object (string): CDK Structure Diagram Layout mol block.
+
     """
     if any(char.isspace() for char in smiles):
         smiles = smiles.replace(" ", "+")
@@ -107,8 +111,12 @@ def getAromaticRingCount(mol):
     """This function is adapted from CDK to
     calculate the number of Aromatic Rings
     present in a given molecule.
-    Args (mol): CDK mol object as input.
-    Returns (int): Number if aromatic rings present
+
+    Args (mol):
+        CDK mol object as input.
+    Returns (int):
+        Number if aromatic rings present.
+
     """
     Cycles = JClass(cdk_base + ".graph.Cycles")
     ElectronDonation = JClass(cdk_base + ".aromaticity.ElectronDonation")
@@ -133,8 +141,12 @@ def getAromaticRingCount(mol):
 def getCDKDescriptors(smiles: str):
     """Take an input SMILES and generate a selected set of molecular
     descriptors generated using CDK as a list.
-    Args (str): SMILES string
-    Returns (list): a list of calculated descriptors
+
+    Args (str):
+        SMILES string.
+    Returns (list):
+        A list of calculated descriptors.
+
     """
     Mol = getCDKSDG(smiles)
     if Mol:
@@ -229,8 +241,11 @@ def getTanimotoSimilarityCDK(smiles1: str, smiles2: str):
     Take two SMILES strings and calculate
     Tanimoto similarity index using Pubchem
     Fingerprints.
-    Args (str,str): SMILES strings.
-    Returns (float): Tanimoto similarity.
+
+    Args (str,str):
+        SMILES strings.
+    Returns (float):
+        Tanimoto similarity.
     """
     Tanimoto = JClass(cdk_base + ".similarity.Tanimoto")
     SCOB = JClass(cdk_base + ".silent.SilentChemObjectBuilder")
@@ -289,8 +304,12 @@ def getCIPAnnotation(smiles: str):
     """
     The function return the CIP annotations using the CDK
     CIP toolkit.
-    Args: mol block
-    Returns: CIP annotated mol block
+
+    Args (str):
+        SMILES string as input.
+    Returns (str):
+        CIP annotated mol block.
+
     """
     mol = getCDKSDG(smiles)
     centres_base = "com.simolecule.centres"
@@ -392,10 +411,11 @@ def getCIPAnnotation(smiles: str):
 def getCXSMILES(smiles: str):
     """This function takes the user input SMILES and creates a
     CXSMILES string with 2D atom coordinates
+
     Args:
-            smiles (string): SMILES string given by the user.
+        smiles (str): SMILES string given by the user.
     Returns:
-            smiles (string): CXSMILES string.
+        smiles (str): CXSMILES string.
 
     """
     moleculeSDG = getCDKSDG(smiles)
@@ -410,10 +430,11 @@ def getCXSMILES(smiles: str):
 def getCanonSMILES(smiles: str):
     """This function takes the user input SMILES and creates a
     Canonical SMILES string with 2D atom coordinates
+
     Args:
-            smiles (string): SMILES string given by the user.
+        smiles (str): SMILES string given by the user.
     Returns:
-            smiles (string): Canonical SMILES string.
+        smiles (str): Canonical SMILES string.
 
     """
     moleculeSDG = getCDKSDG(smiles)
@@ -426,10 +447,11 @@ def getCanonSMILES(smiles: str):
 def getInChI(smiles: str, InChIKey=False):
     """This function takes the user input SMILES and creates a
     InChI string
+
     Args:
-            smiles (string): SMILES string given by the user.
+        smiles (str): SMILES string given by the user.
     Returns:
-            smiles (string): InChI/InChIKey string.
+        smiles (str): InChI/InChIKey string.
 
     """
     moleculeSDG = getCDKSDG(smiles)
@@ -450,10 +472,12 @@ def getInChI(smiles: str, InChIKey=False):
 async def getCDKHOSECodes(smiles: str, noOfSpheres: int, ringsize: bool):
     """This function takes the user input SMILES and returns a mol
        block as a string with Structure Diagram Layout.
+
     Args:
-            smiles(str), noOfSpheres(int), ringsize(bool): SMILES string, No of Spheres and the ringsize given by the user.
+        smiles(str), noOfSpheres(int), ringsize(bool): SMILES string, No of Spheres and the ringsize given by the user.
     Returns:
-            HOSECodes (string): CDK generted HOSECodes.
+        HOSECodes (str): CDK generted HOSECodes.
+
     """
     if any(char.isspace() for char in smiles):
         smiles = smiles.replace(" ", "+")