transformation between smiles and bsmiles

All chemical molecules can be represented by SMILES notation. But from SMILES notation, can not seperate molecules into fragments directly. Here I create a new notation called BSMILES which is easier to check each fragment.

Example:

SMILES notation: O(=C1CSC(c4ccccn4)N(c2ccc3c(cccc3)c2)1)

BSMILES notation: O{0=C!CSCN!{4c%ccc!c(cccc!)c%}{3c!ccccn!}}

how to convert SMILES to BSMILES

from BSMILES.BSMILES import encode 

 bsmiles = encode(smiles)

how to convert BSMILES back to SMILES

from BSMILES.B_to_smiles import convertB 

smiles = convertB(bsmiles)

how to get fragments from BSMILES notation

1. input one file then got one output file from BSMILES.B_to_smiles import bsmiles_to_frag

inputfile_name ="bsmiles"
outputfile_name="fragment"
bsmiles_to_frag(inputfile_name,outputfile_name)

2. input one bsmiles string return two vectors, the second one contains fragments. from BSMILES.B_to_smiles import getFragments

bsmiles = "any_kind_of_bsmiles"
visited = []#contain all unique fragments from bsmiles
fragments = []#contain all fragments
visited,bsmiles = getFragments(visited,bsmiles)

Installation

pip install BSMILES