ps - there is information about Jmol and SMARTS here:
[1] http://chemapps.stolaf.edu/jmol/docs/?search=SMARTS#jmolsmarts/smiles
A full discussion of Jmol SMARTS notation is at
[2]
sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol/src/org/jmol/smiles/package.html?format=raw
The key is that SMARTS is designed for searching substructures, while
SMILES is for distinquishing full compounds. In many ways they are
indistinguishable. For example, CCCC means "normal-butane" in SMILES and
"four consecutive aliphatic carbons" in SMARTS.
But SMARTS is far more elaborate, particularly in having wild cards and
specialized [...] notation, as well as variables.
Jmol's implementation of SMARTS a nearly complete version of Daylight
SMARTS, as described here:
http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html
Jmol's version includes several additional features, such as conformational
searches, including bond distance, angle, and dihedral ranges, more
ring-checking methods, and {...} notation to select specific atoms in a
SMARTS search result.
,
I can see I need to write this up in an article somewhere.
The Jmol documentation shows several contexts where SMARTS can be used. For
selection, the easiest thing is to use the SEARCH() function, here with
SELECT ON to highlight the atoms:
*load $THF*
*select on search("{[C&v4]}[O&r5]{[C&v4]}") # flanking carbons of an
aliphatic cyclic ether*
but because the notation evolved, you can also do this:
*load $THF; select within(SMARTS,"{[C&v4]}[O&r5]{[C&v4]}")*
and to assign a variable, you can use the FIND() function:
*x = {*}.find("SMARTS","{[C&v4]}[O&r5]{[C&v4]}")print x*
({0 3})
#which, like all variables, can be used in a select command:
*select x*
Overall, the SMARTS searching in Jmol is very powerful and definitely the
way to go for anything remotely complex.
Bob
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