Revision: 21587
http://sourceforge.net/p/jmol/code/21587
Author: hansonr
Date: 2017-05-08 20:59:30 +0000 (Mon, 08 May 2017)
Log Message:
-----------
Jmol.___JmolVersion="14.15.3" // 2017-05-08
bug fix: SMARTS search for atropisomeric bond that is in an alicyclic ring
fails (Fred Ziegler)
- used for M/P chirality check
- for example:
load $c1cc2c3-c4c5CC2.c5ccc4C.c3(C)c1
select on smarts("a-a")
calculate chirality
print {*}.chirality.join("")
MM
bug fix: use of the less preferred name of Jmol token that has two optional
forms ("fix" vs "fixed") as a VAR does not assign that variable name
bug fix: set cartoonRibose misses the C1'-O4' and O3'-P(+1) edges
bug fix: JVXL reader not reading Gaussian files with "1" in the third line, 5th
field
bug fix: CIP M/P chirality
test: load "$2,2'-dibromobiphenyl"; calculate chirality; print
{*}.chirality.join("")
bug fix: CIP chirality nearly fully validated on ACD/Labs AY-236 set, with some
unimplemented aspects:
var skip = ({27 229}) || // E/Z only; missing chirality
({95 96 98 99 100 101 102 103 104 108 109 110 111 112 200}) || //
trigonal planar, square planar, or hypervalent
({32 33}) || // helicene
({201 202})|| // spirocyclic central (redundant) atom designation
missing (axial designation option)
({212 213})|| // chiral conformation 1,4-benzene in a ring
({38 84}) || // ignore -- 38: Mancude for cyclopentadienyl; 84:
unknown error with P compound
({203}) || // // chiral bridgehead amine
Issue: Full implementation of the rules requires a slight modification of Rule
1b.
Specifically, aromatic duplicate atoms must reference the sphere of their own
parent, not their
duplicated atom.
Three structures appear to be in error in the IUPAC Blue Book 2013.
,"147":"r,,,R,,,,r,,,S" // r,,,R,,,,r,,,R chiral phosphine -- I think Jmol is
right; disagrees with BB P-93.5.1.1.2 for S vs R
,"227":"SrSEErS" // S,,,,,,,r,S,,,,,,,E,,r,r // -- I think Jmol is right;
disagrees with BB P-93.5.7.2 for S vs. r
,"230":"@2D RrRsR" // r,,,R,,,,s,,,R // p 1282 -- I believe Jmol is correct,
disagrees with BB P-93.6
One structure awaiting full implementation of Rule 4b across all chirality
types, R/S, M/P, and seqCis/seqTrans
,"170":"Spp" // Jmol is missing the S -- mix of R/S and M/P for Rule 4b
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-05-08 20:55:27 UTC
(rev 21586)
+++ trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-05-08 20:59:30 UTC
(rev 21587)
@@ -1253,7 +1253,8 @@
this.massNo = atom.getNominalMass();
atomIndex = atom.getIndex();
bondCount = atom.getCovalentBondCount();
- isTrigonalPyramidal = (bondCount == 3 && !isAlkene && (elemNo > 10 ||
bsAzacyclic != null && bsAzacyclic.get(atomIndex)));
+ isTrigonalPyramidal = (bondCount == 3 && !isAlkene && (elemNo > 10 ||
bsAzacyclic != null
+ && bsAzacyclic.get(atomIndex)));
if (isTrigonalPyramidal)
getLonePair();
canBePseudo = (bondCount == 4 || isTrigonalPyramidal);
@@ -1281,13 +1282,14 @@
// I argue that for aromatic compounds, this introduces a Kekule problem
and that for
// those cases, the rootDistance should be the sphere of the parent, not
the duplicated atom.
// This shows up in AV-360#215.
-
+
if (parent == null) {
// original atom
bsPath.set(atomIndex);
rootDistance = 0;
- } else if (wasDuplicate && bsAromatic != null &&
bsAromatic.get(atomIndex)) {
- rootDistance = parent.rootDistance;
+ } else if (wasDuplicate && bsAromatic != null
+ && bsAromatic.get(atomIndex)) {
+ rootDistance = parent.rootDistance;
} else if (atom == root.atom) {
// pointing to original atom
rootDistance = 0;
@@ -1304,9 +1306,8 @@
}
this.isDuplicate = isDuplicate;
myPath = (parent != null ? parent.myPath + "-" : "") + this;
-
- if (Logger.debugging)
- Logger.info("new CIPAtom " + myPath);
+ if (Logger.debugging)
+ Logger.info("new CIPAtom " + myPath);
isRingDuplicate = (isDuplicate && !wasDuplicate);
return this;
}
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-05-08 20:55:27 UTC
(rev 21586)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-05-08 20:59:30 UTC
(rev 21587)
@@ -55,7 +55,7 @@
# instead of the occupancies I tried to assign in jmol.
-Jmol.___JmolVersion="14.15.3"
+Jmol.___JmolVersion="14.15.3" // 2017-05-08
bug fix: SMARTS search for atropisomeric bond that is in an alicyclic ring
fails (Fred Ziegler)
- used for M/P chirality check
@@ -71,7 +71,7 @@
forms ("fix" vs "fixed") as a VAR does not assign that variable name
bug fix: set cartoonRibose misses the C1'-O4' and O3'-P(+1) edges
bug fix: JVXL reader not reading Gaussian files with "1" in the third line,
5th field
-bug fix: CIP chirality
+bug fix: CIP M/P chirality
test: load "$2,2'-dibromobiphenyl"; calculate chirality; print
{*}.chirality.join("")
bug fix: CIP chirality nearly fully validated on ACD/Labs AY-236 set, with
some unimplemented aspects:
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