BSMILES 0.0.1

transformation between smiles and bsmiles

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)