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This set of essential and valuable microservices is designed to be accessed via API calls to support cheminformatics.

Home Page: https://docs.api.naturalproducts.net

License: MIT License

Python 97.93% Dockerfile 0.50% HTML 0.23% CSS 0.39% Shell 0.95%

cheminformatics chemistry docker fastapi-boilerplate microservices-architecture

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jcheminform jonasschaub thwic-autoqspr

cheminformatics-microservice's Issues

When calling all descriptors the order is getting shuffled

Error parsing smiles for 2D Depiction

URL:
https://api.naturalproducts.net/chem/depict?smiles=C[C@H](CC[C@H](C(C)(C)O)O)[C@H]1C[C@H]([C@H]2[C@H]3[C@H](CC[C@]12C[R])[C@@]4(C)CC[C@@H](C[C@@H]4CC3=O)O)O

504 Gateway Time-out

Images with a lot of structures will need more time for processing. Increase the time out to allow this and avoid 504 timeout errors.

Example

POST: https://api.naturalproducts.net/chem/process

{"reference":"chem_instance_11","path":"https://media.springernature.com/lw685/springer-static/image/art%3A10.1186%2Fs13321-021-00538-8/MediaObjects/13321_2021_538_Fig9_HTML.png"}

Add Aromatic Ring descriptor using CDK

java code block from @JonasSchaub

SmilesParser tmpSmiPar = new SmilesParser(DefaultChemObjectBuilder.getInstance());
IAtomContainer tmpMolecule = tmpSmiPar.parseSmiles("C1=CC=CC=C1");

//arguments might need to be changed to be in accordance with RDKit method
Aromaticity tmpAromaticity = new Aromaticity(ElectronDonation.daylight(), Cycles.cdkAromaticSet());

tmpAromaticity.apply(tmpMolecule);

//also, the cycle finder used here is debatable
IRingSet tmpMCBRings = Cycles.mcb(tmpMolecule).toRingSet();
int tmpNumberOfAromaticRings = 0;
for (IAtomContainer tmpRingContainer: tmpMCBRings.atomContainers()) {
    boolean tmpAreAllRingBondsAromatic = true;
    for (IBond tmpBond: tmpRingContainer.bonds()) {
        if (!tmpBond.isAromatic()) {
            tmpAreAllRingBondsAromatic = false;
            break;
        }
    }
    if (tmpAreAllRingBondsAromatic) {
        tmpNumberOfAromaticRings++;
    }
}
System.out.println(tmpNumberOfAromaticRings);

Format CDK2D to display nicely

Provide description to workflows and move test job before creating a release.

Create COCONUT Descriptors using CDK

Get Images depicted using CDK

Suggested by Chris.
@CS76 Maybe we can have a separate endpoint?

Add NP Likeness score to the coconut descriptors end point

Fix the mol block display

Currently a mol block is being displayed like this:

"\n  CDK     03232309132D\n\n 14 15  0  0  0  0  0  0  0  0999 V2000\n    2.6838    2.4465    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    2.2200    1.0200    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n    3.1000   -0.1900    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    2.2200   -1.4000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n    0.8000   -0.9400    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.8000    0.5600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.5000    1.3100    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.5000    2.8100    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.8000    0.5600    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.8000   -0.9400    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -3.0989   -1.6902    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.5000   -1.6900    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.5000   -3.1900    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -3.0989    1.3102    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  1  0  0  0  0\n  2  3  1  0  0  0  0\n  3  4  2  0  0  0  0\n  4  5  1  0  0  0  0\n  5  6  2  0  0  0  0\n  2  6  1  0  0  0  0\n  6  7  1  0  0  0  0\n  7  8  2  0  0  0  0\n  7  9  1  0  0  0  0\n  9 10  1  0  0  0  0\n 10 11  2  0  0  0  0\n 10 12  1  0  0  0  0\n  5 12  1  0  0  0  0\n 12 13  1  0  0  0  0\n  9 14  1  0  0  0  0\nM  END\n$$$$\n"

It should be displayed like this:

  CDK     03232309152D

 14 15  0  0  0  0  0  0  0  0999 V2000
    2.6838    2.4465    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2200    1.0200    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.1000   -0.1900    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2200   -1.4000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8000   -0.9400    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8000    0.5600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5000    1.3100    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5000    2.8100    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8000    0.5600    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8000   -0.9400    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0989   -1.6902    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5000   -1.6900    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5000   -3.1900    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0989    1.3102    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  2  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
  5 12  1  0  0  0  0
 12 13  1  0  0  0  0
  9 14  1  0  0  0  0
M  END
$$$$

return original and standardized SMILES together as a dictionary

Create ChEMBL Standarizer function for SMILES input

Swagger POST request body input missing

Bi-annual major release with minor and patches

Enable manual major releases bi-annually with conventional commits-based versioning in between.

#167

API to serve fragments and fragments with sugar

Expose API to generate fragments and fragments with sugar for a given set of smiles

Change logP to calculated logP

Distribute docker image of microservice on docker hub

Create a docker hub organisation for Steinbeck lab and publish the docker images to the hub

DECIMER process endpoint optional parameters

{ "path": "string", "reference": "string", "img": "string" }

Path needs to be optional if img src is provided

Descriptor values should be of type number (int or float) not array

Provide descriptor values as number (int or float) not as an array

Move all path parameter based smiles input to query

Example: SMILES to mol conversion

Current URL pattern (path-based)
GET: https://api.naturalproducts.net/chem/CCC%28C%29C%28C%29c1ccccc1/mol

Update to
GET: https://api.naturalproducts.net/chem/mol?smiles=CCC%28C%29C%28C%29c1ccccc1
GET: https://api.naturalproducts.net/chem/mol?inchi=<>

Support multi molecules input in case of certain end points

Descriptor calculation
Conversion etc.

Create HTML descriptor preview

Implement RDKit RegistrationHash

Documentation:
https://rdkit.org/docs/source/rdkit.Chem.RegistrationHash.html

put info in the Swagger API what the license is of the return output

For example, consider state that all calculated output is CCZero. But I can imagine where you return database content, the license will be different. This should be communicated well.

Document API endpoints on postman

Parse SDF to autofill a predefined template

When a post request is made to the API services, can we loop through the structures and fill in the following fields from the SDF properties/structure details and respond back with the following JSON structure?

{
	"standard_inchi": null,
	"cannonical_smiles": null,
	"name": null,
	"cas": null,
	"synonyms": [],
	"iupac_name": null,
	"sdf": null,
	"properties": {
		"found_in_databases": []
	},
	"citations": [{
			"doi": null,
			"type": "publication"
		}/
		{
			"href": null,
			"identifier": null,
			"source": null,
			"type": "database"
		}
	]
}

Failing depiction

Coconut ID: CNP0436856

https://dev.api.naturalproducts.net/chem/depict?smiles=N=1C=C(OC)C=2C=3C=CC=CC3NC2C1C4CCCC5C=6NC=7C=CC=CC7C6C(OC)=C[NH+]45&height=300&width=300

Create an end point for all possible descriptors using CDK and RDKit

Standardize naming conventions across all end points

3D depiction crashes when SMILES with R group are parsed

Create ChEMBL molecule issue checker

Create docker-compose file

Creat kekule SMILES when generating SMILES

Chem.MolToSmiles(mol, kekuleSmiles=True)

Create end point for all descriptors

Add function to return Tanimoto similarity indices

Tanimoto similarity index comparing two SMILES
Create functions for CDK and RDKit
Process via chem
Default, for now, could be CDK= PubChem fingerprint, RDKit= Morgan Fingerprints

Display CDK's Aromatic Ring Count

500 internal server error

https://pubs.acs.org/doi/10.1021/acs.jnatprod.2c01087

Add missing description to all end points and correct issues

Implement NPLikeness score - RDKit and CDK and expose via API

CIP annotations for CDK Depict

Missing CIP annotations

Choose different endpoint to the convert API

Return type to be MOL instead of SDF

When structure-related operations are performed, the return mol format should be MOL instead of SDF. In terms of descriptor calculation, if the return format is SDF, the calculated descriptors should be added as properties to the SDF format and returned.