Wang¶
- autoFragment(inchi, radius, dGPredictorPath, canonicalise, cacheName, printLevel)[source]¶
given one or more inchi, automatically fragment it into a set of smiles each centered around an atom with radius specifying the number of bonds to neighbouring atoms
INPUT inchi n x 1 cell array of molecules each specified by InChI strings
or a single InChI string as a char
OPTIONAL INPUT radius number of bonds around each central smiles atom dGPredictorPath path to the folder containg a git clone of https://github.com/maranasgroup/dGPredictor
path must be the full absolute path without ~/
cacheName fileName of cache to load (if it exists) or save to (if it does not exist)
OUTPUT fragmentedMol n x 1 structure with the following fields for each inchi: *.inchi inchi string *.smilesCount Map structure
Each Key is a canonical smiles string (not canonical smiles if canonicalise==0) Each value is the incidence of each smiles string in a molecule
decomposableBool n x 1 logical vector, true if inchi is decomposable
EXTERNAL DEPENDENCIES Python, see: [pyEnvironment,pySearchPath]=initPythonEnvironment(environmentName,reset)
rdkit, e.g., installed in an Anaconda environment https://www.rdkit.org https://www.rdkit.org/docs/Install.html#introduction-to-anaconda
dGPredictor https://github.com/maranasgroup/dGPredictor Wang L, Upadhyay V, Maranas CD (2021) dGPredictor: Automated fragmentation method for metabolic reaction free energy prediction and de novo pathway design. PLOS Computational Biology 17(9): e1009448. https://doi.org/10.1371/journal.pcbi.1009448