Revision: 21173
http://sourceforge.net/p/jmol/code/21173
Author: hansonr
Date: 2016-07-12 03:28:38 +0000 (Tue, 12 Jul 2016)
Log Message:
-----------
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/smiles/package.html
Modified: trunk/Jmol/src/org/jmol/smiles/package.html
===================================================================
--- trunk/Jmol/src/org/jmol/smiles/package.html 2016-07-11 23:24:40 UTC (rev
21172)
+++ trunk/Jmol/src/org/jmol/smiles/package.html 2016-07-12 03:28:38 UTC (rev
21173)
@@ -293,19 +293,19 @@
<tr><td>$n(pattern)</td><td>A specific number of occurances of <b>pattern</b>.
For example, <b>C[$3(C=C)]C</b> is synonymous with <b>CC=CC=CC=CC</b>.</td></tr>
<tr><td>$min-max(pattern)</td><td>A variable number of occurances of
<b>pattern</b>.
For example: <b>A[$0-2(C:G)]A</b> is synonymous with <b>AA</b> or
<b>AC(:G)A</b> or <b>AC(:G)C(:G)A</b>.</td></tr>
-<tr><td>residueName#resno.atomName#atomicNumber</b> </td><td>
-Both #resno and #atomicNumber are optional. This primitive may appear with
other primitives provided (a) it is first, and (b) it is followed by an
operator ("," ,"&", or ";").
+<tr><td>residueName#resno^insCode.atomName#atomicNumber</b> </td><td>
+All five fields are optional; only the period itself is required.
+This primitive may appear with other primitives provided (a) it is first, and
(b) it is followed by an operator ("," ,"&", or ";").
This allows searching a bioSMILES string using SMARTS patterns that only
involve standard atom types. In the above example,
notice that the connecting atoms to protein chains within the non-bioSEQUENCE
component indicates the
connections to the protein using this extended notation. Thus, both the actual
3D model and the bioSMARTS string for 1d66
can be searched using the SMARTS search "[Cd][S]" as well as the more specific
search "Cd[*.SG]".
-Wild cards provide additional options: [ALA.*], [*.*], [*.CA]. The special
-designation "0" for an atom name, as in <b>[GLY.0]</b>, indicates the "lead
atom" -- the alpha carbon for proteins,
+Wild cards provide additional options: [*#35.], [ALA.*], [*#*^A.] [*.*],
[*.CA]; however, their presence is optional: [#35.], [ALA.], [^A.] [.], [.CA].
+The special designation "0" for an atom name, as in <b>[GLY.0]</b>, indicates
the "lead atom" -- the alpha carbon for proteins,
the phosphorus atom in nucleic acids, or the anomeric carbon in carbohydrates.
</td></tr>
-
</table>
<br>
<br>
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