lucinamay / biosynfoni Goto Github PK

🌿 a biosynformatic molecular fingerprint tailored to natural product chem- and bioinformatic research 🌿 ________________________________________________________________________________________

bi·o·syn·for·ma·tic
/ˌbaɪ oʊ sɪn fərˈ mæt ɪk/
adjective Computers, Biochemistry

relating to biosynthetic information and biochemical logic.
as a concatenation of biosynthetic and bioinformatics, it was coined
during the creation of BioSynFoni.

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install the package by downloading the repository and in it run pip install . (requires python > 3.9 )
(you can do this inside your desired conda environment if you want)
then it's ready to use!
you can call the biosynfoni by name as a stand-alone command-line program or import it as a package in your python scripts.
most basic command line usage example:

• biosynfoni "<SMILES>" -> prints default biosynfoni version of the molecule
• biosynfoni "<InChI>" -> prints default biosynfoni version of the molecule
• biosynfoni <molecule_supplier.sdf> -> writes the biosynfonies of all the supplier's molecule to csv file

to explore other options, type biosynfoni -h or biosynfoni --help

* for imports into jupyter notebook from a conda environment, you might need to additionally run
%pip install biosynfoni in the notebook before it can import biosynfoni.
if it does not work like that either, you might want to check your notebook's sys.path and
add <path>/<to>/condaenv/<path>/<to>/<site-packages>

current 'default version' == 'strictphenyl_1016' | no amino acids, no >6C rings
default setting for blocking : block (change with flags: see biosynfoni -h or biosynfoni --help for more info
newer versions not yet set as default version
rest of info: under construction...\

converture | (c)O(n)VERTure | converts file of InChI's or SMILES into a RDKit Chem.Mol object sdf file
concerto_fp | Convert Chemical E-Representation TO fingerprint | converts RDKit Chem.Mol objects into their respective biosynfoni fingerprints
def_biosynfoni | contains the definitions of biosynfoni (versions of each substructure key,
versions of collections of substructure keys) as dictionaries
inoutput | collection of input and output handling functions that are reused between codes\

other files (e.g. in 'experiments') were used in collection and curation of data, and are written for specific scopes.
reuse at own discretion.

We welcome your feedback. For a streamlined feedback process, please open a new issue on github.com/biosynfoni if you cannot find your issue among existing ones. Please also make sure to add the appropriate subject in the title for clarity as follows, for easier understanding and faster help:

• SMARTS representation of a specific existing substructure
  • [SMARTS] <issue title>
• adding/removing/merging substructures within current biosynfoni
  • [SUBSTRUCTURE] <issue title>
• new substructure collection for specific application
  • [COLLECTION] <issue title>
• detection algorithm of the substructures within the molecule
  • [DETECTION] <issue title>
• output options
  • [OUTPUT] <issue title>
• other feedback
  • [<1-keyword summary of feedback topic>] <issue title>

In addition, please explain any reasoning behind your feedback to help us speed up decisions on if and how to implement changes within the biosynfoni tool.

findability & accessability:
-URL to the repository/code: https://github.com/lucinamay/biosynfoni\ interoperability:
-dependencies: rdkit, numpy,tqdm, python>=3.9\ - experiment dependencies: scikit-learn>=1.3, umap, matplotlib, seaborn -related data: - natural product database https://coconut.naturalproducts.net | https://doi.org/10.1186/s13321-020-00478-9, -synthetic products were filtered out from zinc.: https://zinc.docking.org | https://pubs.acs.org/doi/10.1021/acs.jcim.0c00675
-related software: n.a.
reusability
-licence: MIT (see LICENCE file)\

badge of FAIRness: