I have a molecule with a SMILES string as given below.
smi='c1ccccc1OCCOC(=O)CC'
I want to obtain BRICS based fragments which I did as follows.
frag=BRICS.BRICSDecompose(Chem.MolFromSmiles('c1ccccc1OCCOC(=O)CC'))
I obtain the following fragments.
{'[1*]C(=O)CC', '[16*]c1ccccc1', '[3*]O[3*]', '[4*]CC[4*]'}
How to interpret [1*], [16*], [3*] ,[4*] ? What does these number with brackets and stars means with each fragment?
Cutting a molecule (expressed with SMILES strings) into fragments yields sub-structures. Typically these fragments can't be considered as molecules for their open, non-bonding valencies. Derived from SMILES, it is then the SMARTS notation which is used to represent them, or to search with this notation of sub-structures in databases, e.g. in bioinformatics.
Open Babel supports the display of SMARTS-encoded fragments with branching points marked by an asterisk. The phenyl group, [16*]c1ccccc1 thus is shown as:
Consequently, bidental fragments are represented with two asterisks, e.g., [4*]CC[4*]:
[16*]c1ccccc1, according to the Daylight documentation, the * is a placeholder / wild card for any atom. As for the integer, I do not know the answer. The conversion of the SMARTS string into a .png, the program openbabel does no yield a visual difference in the output for using either [16*]c1ccccc1, or [5*]c1ccccc1, or even [*]c1ccccc1 (no integer at all); a weak evidence that it has have little for this type of processing the input. Perhaps Geoff Hutchison (chemistry.stackexchange.com/users/5017/geoff-hutchison) may help here.
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Commented
Aug 24, 2020 at 14:46
Please see the original paper for the interpretations.
Briefly, the numbers correspond to the chemical environment of the BRICS fragments. e.g. the number 16 in [16*]c1ccccc1 indicates that the fragment is an all-carbon aromatic ring system. Below is the illustration of fragment prototypes and their numbers taken from the original paper by Degen et al.
