Hi,
I am looking for a way or function in R programming language to edit the molecule in mol format. For my purpose, I am following following steps
1. Read the smiles from a file by line operation.
2. Parse the smiles into SDF/ mol using fuction from ChemminR
3. look for a specific SMART pattern in the read molecule using function from rcdk package.
4. Now I want to delete a specific bond based on the above pattern match, but don't know how to do it in R.
Someone please help me.
Thanks!
@Sharad. Thanks for interest.
Entire code is rather not much helpful. Here is what i am trying to do.
1.Read smiles
con
ChemmineR seems to have a bondblock() function (http://www.bioconductor.org/packages/release/bioc/manuals/ChemmineR/man/ChemmineR.pdf) that can be used to replace one bond matrix with another, so you could change the matrix to get rid of the bond. I don't know how easy it will be to work with indices in your specific case and identify the appropriate bond matrix row and column. As an alternative, you could write the molecule out in SDF format, edit the resulting text file accordingly (maybe with PerlMol - http://www.perlmol.org/pod/PerlMol.html which has a $bond->delete method) and then read it back.
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