transformation between smiles and bsmiles
Project description
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
- 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)
- 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)
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BSMILES-0.0.1.tar.gz
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