Revision: 21604
http://sourceforge.net/p/jmol/code/21604
Author: hansonr
Date: 2017-05-17 14:10:57 +0000 (Wed, 17 May 2017)
Log Message:
-----------
CIP adds helicene chirality (AY-236.32, AY-236.33); validated using CCDC
HEXHEL02 HEXHEL03 HEXHEL04 ODAGOS ODAHAF
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java
trunk/Jmol/src/org/jmol/symmetry/Symmetry.java
Modified: trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-05-15 03:07:29 UTC
(rev 21603)
+++ trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-05-17 14:10:57 UTC
(rev 21604)
@@ -28,7 +28,7 @@
* Yerin, ACD/Labs (Moscow).
*
* Mikko Vainio also supplied a 64-compound testing suite (MV-64), which is
- * available on SourceForge in the Jmol-datafiles directory.
+ * available on SourceForge in the Jmol-datafiles directory.
* (https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol-datafiles/cip).
*
* Additional thanks to the IUPAC Blue Book Revision project, specifically
@@ -74,33 +74,53 @@
*
* 4/6/17 Introduced in Jmol 14.12.0; validated for Rules 1 and 2 in Jmol
* 14.13.2;
- *
- * E/Z added 14.14.1;
*
- * 4/27/17 Ruled 3-5 preliminary version 14.15.1
+ * E/Z added 14.14.1;
*
+ * 4/27/17 Ruled 3-5 preliminary version 14.15.1
+ *
* 4/28/17 Validated for 146 compounds, including imines and diazines, sulfur,
- * phosphorus
+ * phosphorus
*
- * 4/29/17 validated for 160 compounds, including M/P, m/p (axial
- * chirality for biaryls and odd-number cumulenes)
+ * 4/29/17 validated for 160 compounds, including M/P, m/p (axial chirality for
+ * biaryls and odd-number cumulenes)
*
- * 5/02/17 validated for 161
- * compounds, including M/P, m/p (axial chirality for biaryls and odd-number
- * cumulenes)
+ * 5/02/17 validated for 161 compounds, including M/P, m/p (axial chirality for
+ * biaryls and odd-number cumulenes)
*
* 5/06/16 validated for 236 compound set AY-236.
*
- * 5/13/16 Jmol 14.15.4. algorithm simplified; validated for mixed Rule 4b
systems
- * involving auxiliary R/S, M/P, and seqCis/seqTrans; 959 lines
+ * 5/13/16 Jmol 14.15.4. algorithm simplified; validated for mixed Rule 4b
+ * systems involving auxiliary R/S, M/P, and seqCis/seqTrans; 959 lines
*
- * 5/14/16 Jmol 14.15.5. trimmed up and documented; no need for lone pairs;
948 lines
+ * 5/14/16 Jmol 14.15.5. trimmed up and documented; no need for lone pairs; 948
+ * lines
*
+ * 5/17/16 Jmol 14.15.5. adds helicene M/P chirality; validated using CCDC
+ * structures HEXHEL02 HEXHEL03 HEXHEL04 ODAGOS ODAHAF
+ *
* NOTE! NOTE! NOTE! NOTE! NOTE! NOTE! NOTE! NOTE! NOTE! NOTE! NOTE! NOTE!
NOTE!
*
- * Added logic to Rule 1b: The root distance for a Kekule-ambiguous duplicate
atom is
- * its own sphere, not the sphere of its duplicated atom.
+ * Added logic to Rule 1b: The root distance for a Kekule-ambiguous duplicate
+ * atom is its own sphere, not the sphere of its duplicated atom.
*
+ * Stated more precisely:
+ *
+ * Proposed amended Rule 1:
+ *
+ * (1a) higher atomic number precedes lower;
+ *
+ * (1b) in comparing two duplicate nodes, lower root distance precedes higher
+ * root distance, where "root distance" is defined:
+ *
+ * (i) in the case of a duplicate atom for which the atomic number is averaged
+ * over two or more atoms in applying Rule 1a, the distance from the duplicate
+ * node itself to the root node; and
+ *
+ * (ii) in all other cases, the distance of its corresponding nonduplicated
atom
+ * node to the root node.
+ *
+ *
* Rationale: Giving the distance of the duplicated atom introduces a Kekule
* bias, which is not acceptable.
*
@@ -333,7 +353,8 @@
Lst<BS> lstSmallRings = new Lst<BS>();
/**
- * don't do this atom again (atropisomer)
+ * the aromatic atoms connected by a nonaromatic single bond
+ * smarts("a-a")
*
*/
BS bsAtropisomeric;
@@ -381,8 +402,10 @@
* bit set of all atoms to process
* @param bsAtropisomeric
* bit set of all biphenyl-like connections
+ * @param bsHelixM aromatic atoms at the end of a negative helical turn;
smarts("A{a}(.t:-10,-40)a(.t:-10,-40)aaa")
+ * @param bsHelixP aromatic atoms at the end of a positive helical turn;
smarts("A{a}(.t:10,40)a(.t:10,40)aaa")
*/
- public void getChiralityForAtoms(Node[] atoms, BS bsAtoms, BS
bsAtropisomeric) {
+ public void getChiralityForAtoms(Node[] atoms, BS bsAtoms, BS
bsAtropisomeric, BS bsHelixM, BS bsHelixP) {
if (bsAtoms.isEmpty())
return;
init();
@@ -419,7 +442,22 @@
if (lstSmallRings.size() > 0 && lstEZ.size() > 0)
clearSmallRingEZ(atoms, lstEZ);
}
+
+ // add helical chiralities
+ if (bsHelixM != null)
+ for (int i = bsHelixM.nextSetBit(0); i >= 0; i = bsHelixM.nextSetBit(i +
1))
+ atoms[i].setCIPChirality(STEREO_M);
+
+
+ if (bsHelixM != null)
+ for (int i = bsHelixM.nextSetBit(0); i >= 0; i = bsHelixM.nextSetBit(i +
1))
+ atoms[i].setCIPChirality(STEREO_M);
+
+ if (bsHelixP != null)
+ for (int i = bsHelixP.nextSetBit(0); i >= 0; i = bsHelixP.nextSetBit(i +
1))
+ atoms[i].setCIPChirality(STEREO_P);
+
if (Logger.debugging) {
Logger.info("sp2-aromatic = " + bsKekuleAmbiguous);
Logger.info("smallRings = " + PT.toJSON(null,lstSmallRings));
Modified: trunk/Jmol/src/org/jmol/symmetry/Symmetry.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/Symmetry.java 2017-05-15 03:07:29 UTC
(rev 21603)
+++ trunk/Jmol/src/org/jmol/symmetry/Symmetry.java 2017-05-17 14:10:57 UTC
(rev 21604)
@@ -795,8 +795,15 @@
@Override
public void calculateCIPChiralityForAtoms(Viewer vwr, BS bsAtoms) {
CIPChirality cip = getCIPChirality(vwr);
- BS bsAtropisomer = vwr.getAtomBitSet("smarts('a-a')");
- cip.getChiralityForAtoms(vwr.ms.at, bsAtoms, bsAtropisomer);
+ BS bsAtropisomer = null, bsHelixM = null, bsHelixP = null;
+ try {
+ bsAtropisomer = vwr.getSmartsMatch("a-a", bsAtoms);
+ bsHelixM = vwr.getSmartsMatch("A{a}(.t:-10,-40)a(.t:-10,-40)aaa",
bsAtoms);
+ bsHelixP = vwr.getSmartsMatch("A{a}(.t:10,40)a(.t:10,40)aaa", bsAtoms);
+ } catch (Exception e) {
+ // ignore
+ }
+ cip.getChiralityForAtoms(vwr.ms.at, bsAtoms, bsAtropisomer, bsHelixM,
bsHelixP);
}
CIPChirality cip;
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