TMAP of COCONUT database

The script and data used in SIDERITE paper to generate TMAP picture (Figure S3 in supplementart material).

Requirement: tmap

You can install tmap by conda.

conda create -n tmap python=3.7

conda activate tmap

conda install -c tmap tmap

pip install faerun

pip install matplotlib

conda install scipy

conda install -c rdkit rdkit

conda install -c conda-forge mhfp

Usage: python plot_COCONUT.py

Then it will use  COCONUT.csv to generate  index.html and index.js. Open index.html to see result.

Other large input files

Tanimoto_COCONUT_SIDERITE.xlsx is the input file in SIDERITE/predicted_new/Clustering_coconut.m at main · RuolinHe/SIDERITE.

Sid_structure_output3.xlsx is used in SIDERITE/statistics/Figure1.m at main · RuolinHe/SIDERITE, SIDERITE/TAMP/tmap_code.m at main · RuolinHe/SIDERITE and SIDERITE/siderophore_process/Sid_process_code.m at main · RuolinHe/SIDERITE.

COCONUT4MetFrag_Canonical.xlsx is the input file in SIDERITE/TAMP/tmap_code.m at main · RuolinHe/SIDERITE.

COCONUT_r.txt is the output file in SIDERITE/TAMP/tmap_code.m at main · RuolinHe/SIDERITE. and the input file in SIDERITE/predicted_new/isSiderophore1.py at main · RuolinHe/SIDERITE.

COCONUT4MetFrag.xlsx is the input file in SIDERITE/TAMP/CheckSMILES2.py at main · RuolinHe/SIDERITE.