Is it possible to search for a fragment that is not a valid structure itself, but part of a structure?
Problem: "Given a structure, and a decomposition of the structure, highlight each part with a different color" The decomposition is always in the form of 1 SMILES and n SMILES FRAGMENTS The "smiles fragments" are noted with an asterisk in the "connection bonds". For example: mol: CCC=C decomposition: C* CC *=C For a human it takes nothing to spot "who is who", but how would you approach it? - I cannot match the SMARTS "C=": it's not a valid SMARTS - I cannot match it without the broken bonds: I would lose the difference between C* and C=* - I cannot match it like it is: the asterisks will match the first atom of the other fragment. (Maybe is there a way to get which part matched with who? In that case I could remove the atom matching the asterisk...) Maybe there is an easy way to represent this pattern 'C=' in SMARTS, but the daylight manual is not clear about it. Or maybe I'm just too lazy to get it.... In other words: is it possible to write n SMARTS that together match the whole structure (all the atoms and all the bonds, with no overlapping and no gaps)? Because if the SMARTS must be a complete structure (without "unbonded" bonds), that's actually not possible. Thank you
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