fix: format doc strings

.pre-commit-config.yaml

@@ -7,6 +7,10 @@ repos:
     -   id: check-yaml
     -   id: debug-statements
     -   id: requirements-txt-fixer
+-   repo: https://github.com/DanielNoord/pydocstringformatter
+    rev: v0.7.3
+    hooks:
+    -   id: pydocstringformatter
 -   repo: https://github.com/psf/black
     rev: 22.6.0
     hooks:

app/main.py

@@ -104,7 +104,8 @@ async def root():
 )
 def get_health() -> HealthCheck:
     """
-    ## Perform a Health Check
+    ## Perform a Health Check.
+
     Endpoint to perform a health check on. This endpoint can primarily be used by Docker
     to ensure a robust container orchestration and management are in place. Other
     services that rely on the proper functioning of the API service will not deploy if this

app/modules/all_descriptors.py

@@ -22,6 +22,7 @@
 def get_all_rdkit_descriptors(molecule: any) -> Union[tuple, str]:
     """
     Calculate a selected set of molecular descriptors using RDKit.
+
     This function takes an input SMILES string and calculates various molecular descriptors
     using RDKit.
 
@@ -80,6 +81,7 @@ def get_all_rdkit_descriptors(molecule: any) -> Union[tuple, str]:
 def get_all_cdk_descriptors(molecule: any) -> Union[tuple, str]:
     """
     Calculate a set of molecular descriptors using the CDK.
+
     This function takes a SMILES string as input and calculates various molecular descriptors
     using the CDK. The calculated descriptors are returned as a tuple.
 

app/modules/classyfire.py

@@ -7,7 +7,8 @@
 
 async def classify(smiles: str) -> dict:
     """
-    This function queries the ClassyFire API to classify a chemical compound
+    This function queries the ClassyFire API to classify a chemical compound.
+
     represented by a SMILES string.
 
     Args:

app/modules/coconut/preprocess.py

@@ -21,7 +21,6 @@ def get_mol_block(input_text: str) -> str:
 
     Raises:
         ValueError: If input_text is not a valid Mol or SMILES.
-
     """
     check = rdkitmodules.is_valid_molecule(input_text)
 
@@ -47,7 +46,6 @@ def get_molecule_hash(molecule: any) -> dict:
 
     Returns:
         dict: Dictionary containing Formula, Isomeric SMILES, and Canonical SMILES.
-
     """
     if molecule:
         Formula = Chem.rdMolDescriptors.CalcMolFormula(molecule)
@@ -75,7 +73,6 @@ def get_representations(molecule: any) -> dict:
 
     Returns:
         dict: Dictionary containing InChI, InChi Key, and Murko framework.
-
     """
     if molecule:
         InChI = Chem.inchi.MolToInchi(molecule)
@@ -96,7 +93,6 @@ def get_COCONUT_preprocessing(input_text: str) -> dict:
 
     Returns:
         dict: COCONUT preprocessed data.
-
     """
     original_mol = get_mol_block(input_text)
     standarised_mol_block = standardizer.standardize_molblock(original_mol)

app/modules/depiction.py

@@ -19,7 +19,8 @@ def get_cdk_depiction(
     unicolor=False,
 ):
     """
-    This function takes the user input SMILES and Depicts it
+    This function takes the user input SMILES and Depicts it.
+
     using the CDK Depiction Generator.
 
     Args:

app/modules/toolkits/cdk_wrapper.py

@@ -84,7 +84,8 @@ def get_CDK_IAtomContainer(smiles: str):
 
 def get_CDK_SDG(molecule: any):
     """
-    This function takes the input IAtomContainer and Creates a
+    This function takes the input IAtomContainer and Creates a.
+
     Structure Diagram Layout using the CDK.
 
     Args:
@@ -125,7 +126,8 @@ def get_CDK_SDG_mol(molecule: any, V3000=False) -> str:
 
 def get_murko_framework(molecule: any) -> str:
     """
-    This function takes the user input SMILES and returns
+    This function takes the user input SMILES and returns.
+
     the Murko framework
 
     Args:
@@ -198,7 +200,8 @@ def get_vander_waals_volume(molecule: any) -> float:
 
 def get_CDK_descriptors(molecule: any) -> Union[tuple, str]:
     """
-    Take an input SMILES and generate a selected set of molecular
+    Take an input SMILES and generate a selected set of molecular.
+
     descriptors generated using CDK as a list.
 
     Args (str):
@@ -366,6 +369,7 @@ def get_tanimoto_similarity_PubChem_CDK(mol1: any, mol2: any) -> str:
 def get_tanimoto_similarity_ECFP_CDK(mol1: any, mol2: any, ECFP: int = 2) -> str:
     """
     Calculate the Tanimoto similarity index between two molecules using CircularFingerprinter fingerprints.
+
     https://cdk.github.io/cdk/2.8/docs/api/org/openscience/cdk/fingerprint/CircularFingerprinter.html
 
     Args:
@@ -447,7 +451,6 @@ def get_cip_annotation(molecule: any) -> str:
 
     Returns:
         str: A CIP annotated molecule block.
-
     """
     SDGMol = get_CDK_SDG(molecule)
     centres_base = "com.simolecule.centres"

app/modules/toolkits/helpers.py

@@ -30,7 +30,9 @@ def parse_input(input: str, framework: str = "rdkit", standardize: bool = False)
 
 def parse_SMILES(smiles: str, framework: str = "rdkit", standardize: bool = False):
     """
-    Check whether the input SMILES string is valid. If not, attempt to standardize
+    Check whether the input SMILES string is valid.
+
+    If not, attempt to standardize
     the molecule using the ChEMBL standardization pipeline.
 
     Args:

app/modules/toolkits/rdkit_wrapper.py

@@ -109,7 +109,6 @@ def get_3d_conformers(molecule: any, depict=True) -> Chem.Mol:
     Returns:
         str or rdkit.Chem.rdchem.Mol: If `depict` is True, returns the 3D structure in MolBlock format.
             Otherwise, returns an RDKit Mol object.
-
     """
     if molecule:
         molecule = Chem.AddHs(molecule)
@@ -192,6 +191,7 @@ def get_tanimoto_similarity_rdkit(
 async def get_rdkit_HOSE_codes(molecule: any, noOfSpheres: int) -> List[str]:
     """
     Calculate and retrieve RDKit HOSE codes for a given SMILES string.
+
     This function takes a SMILES string as input and returns the calculated HOSE codes.
 
     Args:
@@ -361,7 +361,8 @@ def get_sas_score(molecule: any) -> float:
 
 def get_PAINS(molecule: any) -> Union[bool, Tuple[str, str]]:
     """
-    Check if a molecule contains a PAINS (Pan Assay INterference compoundS)
+    Check if a molecule contains a PAINS (Pan Assay INterference compoundS).
+
     substructure.
 
     Parameters:
@@ -481,7 +482,6 @@ def get_REOSFilter(molecule: any) -> bool:
 
     Returns:
         bool: True if the molecule passes the REOS filter, False otherwise.
-
     """
     MW = Descriptors.ExactMolWt(molecule)
     logP = Descriptors.MolLogP(molecule)
@@ -523,7 +523,6 @@ def get_RuleofThree(molecule: any) -> bool:
 
     Returns:
         bool: True if the molecule meets the Rule of Three criteria, False otherwise.
-
     """
     MW = Descriptors.ExactMolWt(molecule)
     logP = Descriptors.MolLogP(molecule)
@@ -539,7 +538,8 @@ def get_RuleofThree(molecule: any) -> bool:
 
 def get_ertl_functional_groups(molecule: any) -> list:
     """
-    This function takes an organic molecule as input and uses the algorithm proposed by Peter Ertl to
+    This function takes an organic molecule as input and uses the algorithm proposed by Peter Ertl to.
+
     identify functional groups within the molecule. The identification is based on the analysis of
     chemical fragments present in the molecular structure.
 
@@ -556,7 +556,6 @@ def get_ertl_functional_groups(molecule: any) -> list:
 
     If no functional groups are found, the function returns a list with a single element:
     [{'None': 'No fragments found'}]
-
     """
     if molecule:
         fragments = ifg.identify_functional_groups(molecule)

app/modules/tools/sugar_removal.py

@@ -6,6 +6,7 @@
 def get_sugar_info(molecule: any) -> tuple:
     """
     Analyzes a molecule represented by a SMILES string to determine if it contains sugars.
+
     This function utilizes the Sugar Removal Utility to check for the presence of circular or linear sugars.
 
     Args:
@@ -36,7 +37,8 @@ def get_sugar_info(molecule: any) -> tuple:
 
 def remove_linear_sugar(molecule: any) -> str:
     """
-    Detects and removes linear sugars from a given SMILES string using the CDK-based
+    Detects and removes linear sugars from a given SMILES string using the CDK-based.
+
     sugar removal utility.
 
     Args:
@@ -119,14 +121,14 @@ def remove_circular_sugar(molecule: any) -> str:
 
 
 def remove_linear_and_circular_sugar(molecule: any):
-    """This fucntion detects and removes linear and circular sugars from a give
+    """This fucntion detects and removes linear and circular sugars from a give.
+
     SMILES string. Uses the CDK based sugar removal utility.
 
     Args:
         molecule (IAtomContainer): CDK molecule object.
     Returns:
         smiles (str): SMILES string without linear and circular sugars.
-
     """
     cdk_base = "org.openscience.cdk"
     SCOB = cdk.JClass(cdk_base + ".silent.SilentChemObjectBuilder")

app/modules/tools/surge.py

@@ -15,7 +15,6 @@ def get_heavy_atom_count(formula: str) -> int:
 
     Returns:
         count (int): The number of heavy atoms in the molecule.
-
     """
 
     elements = re.findall(r"[A-Z][a-z]*\d*", formula)

app/routers/chem.py

@@ -90,7 +90,8 @@
 )
 def get_health() -> HealthCheck:
     """
-    ## Perform a Health Check
+    ## Perform a Health Check.
+
     Endpoint to perform a health check on. This endpoint can primarily be used by Docker
     to ensure a robust container orchestration and management are in place. Other
     services that rely on the proper functioning of the API service will not deploy if this
@@ -131,7 +132,7 @@ async def get_stereoisomers(
     ),
 ):
     """
-    For a given SMILES string this function enumerates all possible stereoisomers
+    For a given SMILES string this function enumerates all possible stereoisomers.
 
     Parameters:
     - **SMILES**: required (query parameter): The SMILES string to be enumerated.
@@ -141,7 +142,6 @@ async def get_stereoisomers(
 
     Raises:
     - ValueError: If the SMILES string is not provided or is invalid.
-
     """
     mol = parse_input(smiles, "rdkit", False)
     if mol:
@@ -205,7 +205,6 @@ async def get_descriptors(
 
     Raises:
     - None
-
     """
     data = get_COCONUT_descriptors(smiles, toolkit)
     if format == "html":
@@ -293,7 +292,6 @@ async def get_multiple_descriptors(
 
     - Request: GET /descriptors/multiple?smiles=CCC
       Response: "Error invalid SMILES"
-
     """
     molecules = [m.strip() for m in smiles.split(",")]
 
@@ -376,7 +374,6 @@ async def hose_codes(
 
     Raises:
     - ValueError: If the SMILES string is not provided or is invalid.
-
     """
     if toolkit == "cdk":
         mol = parse_input(smiles, "cdk", False)
@@ -428,7 +425,8 @@ async def standardize_mol(
     ],
 ):
     """
-    Standardize molblock using the ChEMBL curation pipeline
+    Standardize molblock using the ChEMBL curation pipeline.
+
     and return the standardized molecule, SMILES, InChI, and InCHI-Key.
 
     Parameters:
@@ -443,7 +441,6 @@ async def standardize_mol(
 
     Raises:
     - ValueError: If the SMILES string is not provided or is invalid.
-
     """
     try:
         if data:
@@ -534,7 +531,6 @@ async def check_errors(
     Notes:
     - If the SMILES string contains spaces, they will be replaced with "+" characters before processing.
     - If the SMILES string cannot be read, the function returns the string "Error reading SMILES string, check again."
-
     """
     mol = Chem.MolFromSmiles(smiles, sanitize=False)
     if mol:
@@ -609,7 +605,6 @@ async def np_likeness_score(
 
     Raises:
     - ValueError: If the SMILES string is not provided or is invalid.
-
     """
     mol = parse_input(smiles, "rdkit", False)
     try:
@@ -777,7 +772,6 @@ async def coconut_preprocessing(
 
     Raises:
     - HTTPException: If there is an error reading the SMILES string.
-
     """
     try:
         data = get_COCONUT_preprocessing(smiles)
@@ -839,7 +833,6 @@ async def classyfire_classify(
     Note:
     - ClassyFire is a chemical taxonomy classification tool that predicts the chemical class and subclass of a compound based on its structural features.
     - This service pings the http://classyfire.wishartlab.com server for information retrieval.
-
     """
     mol = parse_input(smiles, "rdkit", False)
     if mol:
@@ -864,6 +857,7 @@ async def classyfire_classify(
 async def classyfire_result(jobid: str):
     """
     Retrieve the ClassyFire classification results based on the provided Job ID.
+
     To obtain the results from ClassyFire, please initiate a new request and obtain a unique job ID.
     Once you have the job ID, you need to submit another request using this ID in order to retrieve the desired outcome.
 
@@ -876,7 +870,6 @@ async def classyfire_result(jobid: str):
 
     Returns:
     - The ClassyFire classification results as JSON.
-
     """
 
     if jobid:
@@ -1076,7 +1069,7 @@ async def get_functional_groups(
     ),
 ):
     """
-    For a given SMILES string this function generates a list of identified functional groups
+    For a given SMILES string this function generates a list of identified functional groups.
 
     Parameters:
     - **SMILES**: required (query parameter): The SMILES string to be checked for functional groups.
@@ -1086,7 +1079,6 @@ async def get_functional_groups(
 
     Raises:
     - ValueError: If the SMILES string is not provided or is invalid.
-
     """
     mol = parse_input(smiles, "rdkit", False)
     if mol: