Thank you, Brian!
Actually what I expected as output:
S=c1c([*:1])c(Cl)[nH]c([*:3])c1[*:2]
S=c1c([*:1])c(Cl)[nH]c([*:2])c1[*:3]
S=c1c([*:2])c(Cl)[nH]c([*:1])c1[*:3]
and so on
You gave me the right direction. I can store old-new maps in a dict and
after relabeling and producing of canonical
Pavel, this isn't exactly trivial so I went ahead and made an example. The
basics are that atomMaps are canonicalized, i.e. their value is used in the
generation of smiles.
To solve this problem:
1) backup the atom maps and remove them
2) canonicalize *without* atom maps but figure out the order
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