Revision: 20770
http://sourceforge.net/p/jmol/code/20770
Author: hansonr
Date: 2015-09-10 12:34:16 +0000 (Thu, 10 Sep 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.3.16_2015.09.09"
new feature: SMILES/SMARTS atom designations [C(xxxx)]
-- allows pointing to the same atom without connection numbers
-- (xxxx) may be anything, including just ()
-- definition may be anywhere in bracketed atom specification
-- any additional primitives in referring expression will be ignored
-- involves only a very simple addition to parser code
-- Jmol is not currently creating these strings, just interpreting them
-- rationale:
One basic aspect of SMILES is that it efficiently uses numbers to
indicate connectivity using a process of "opening" bonds and "closing"
them.
Along with radical (.) notation, this is totally sufficient for describing
any connected network of atoms, including situations where the ordering
of connections is critical (e.g., in describing stereochemistry).
Basically,
one can simply list all the atoms in an arbitrary order as single-atom
components (separated by "."), then assign bonds as desired, in whatever
order is desired.
The problem comes when attempting to indicate stereochemistry for
centers with more than six substituents or with geometries that are
outside the standard set of AL, TH, TP, SP, and OH. In such cases,
there may arise situations where the ordering of unbonded substituents
will be critical. An example is crystal structures of metals and metal
alloys. In this situation there are no covalent bonds. The need is to
be able to compare two such crystal structures.
The solution is to create SMARTS and SMILES strings for complex
"atomic environments" consisting of a central atom and any number of
nearby atoms, using a cutoff radius rather than a bonding pattern.
One possibility is to create a "pseudobond" that connects the central
atom to all of its connected atoms, but this is not really necessary and
slows processing significantly. Instead, the [@PHn] syntax proposed here
allows the polyhedral environment to be specified only for the polyhedron
itself, exclusive of the central atom.
By providing a means of referring to a specific previously defined atom
in a
SMILES or SMARTS string, we can allow an atom in such an arrangement
to be part of two different polyhedra.
Thus, although isolated polySMARTS can be implemented without atom
referents,
extending that to more complex multi-atom polySMARTS searches requires
them.
-- example, simple branched organic
$ load $t-butylmethylether
$ select on search("[O][C(a)H0].[C(a)]C")
5 atoms selected
same as
$ select on search("[O][CH0](C)")
-- note that [C(2)] and [O(2)] are not sensible and may be disallowed.
code: javajs.util reconciled with swingjs project
bug fix: polyhedra.stereoSmiles --> polyhedra.polySmiles
new feature: polyhedron.polySmiles adds central atom
-- example:
load SF6.smol -1
polyhedra
calculate symmetry polyhedra
x = {polyhedra}.polyhedra.polySmiles
print x
//* S1 #1 *// [S@PH6].
//* F6 #7 *// [F]1234.
//* F2 #3 *// [F]5672.
//* F3 #4 *// [F]849%10.
//* F4 #5 *// [F]%11%10%126.
//* F1 #2 *// [F]937%12.
//* F5 #6 *// [F]8%1151
print polyhedron(x).atomname
S1
JmolVersion="14.3.16_2015.09.08"
code: Efficient JSON parser javajs.util.JSONParser
-- requires object being parsed to be an object (bounded by "{" and "}")
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-09-10 12:32:35 UTC
(rev 20769)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-09-10 12:34:16 UTC
(rev 20770)
@@ -64,7 +64,9 @@
-- allows pointing to the same atom without connection numbers
-- (xxxx) may be anything, including just ()
-- definition may be anywhere in bracketed atom specification
- -- any additional primitives in referring expression will be ignored
+ -- any additional primitives in referring expression will be ignored
+ -- involves only a very simple addition to parser code
+ -- Jmol is not currently creating these strings, just interpreting them
-- rationale:
One basic aspect of SMILES is that it efficiently uses numbers to
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