Revision: 21584
http://sourceforge.net/p/jmol/code/21584
Author: hansonr
Date: 2017-05-07 00:35:31 +0000 (Sun, 07 May 2017)
Log Message:
-----------
Jmol.___JmolVersion="14.15.3"
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 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
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 2017-05-06 21:50:42 UTC
(rev 21583)
+++ trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-05-07 00:35:31 UTC
(rev 21584)
@@ -1907,14 +1907,16 @@
// resolved as "r" or "s"
// but generally we will want to process this as "R" and "S"
// note that this analysis cannot be done ahead of time
- String aStr = rule4List[ia];
- String bStr = rule4List[ib];
- if (atoms[ia].nextChiralBranch != null)
- aStr += atoms[ia].getMataList(getFirstRef(aStr), isRule5);
- if (atoms[ib].nextChiralBranch != null)
- bStr += atoms[ib].getMataList(getFirstRef(bStr), isRule5);
- aStr = aStr.substring(1);
- bStr = bStr.substring(1);
+ String aStr = rule4List[ia].substring(1);
+ String bStr = rule4List[ib].substring(1);
+ if (atoms[ia].nextChiralBranch != null) {
+ String s = atoms[ia].getMataList(getFirstRef(aStr), isRule5);
+ aStr = (s.indexOf("|") < 0 ? aStr + s : s);
+ }
+ if (atoms[ib].nextChiralBranch != null) {
+ String s = atoms[ib].getMataList(getFirstRef(bStr), isRule5);
+ bStr = (s.indexOf("|") < 0 ? bStr + s : s);
+ }
if (Logger.debugging)
Logger.info(dots() + this + " comparing " + atoms[ia] + " " + aStr + "
to "
+ atoms[ib] + " " + bStr);
@@ -1998,7 +2000,6 @@
if (rule4List[i] != null) {
listA[--j] = rule4List[i];
}
-// Arrays.sort(listA);
if (aref == null) {
aref = getMataRef(isRule5);
} else {
@@ -2099,7 +2100,7 @@
* @return 0 (TIED), -1 (A_WINS), 1 (B_WINS), Integer.MIN_VALUE (IGNORE)
*/
private int compareRule4PairStr(String aStr, String bStr, boolean
isRSTest) {
- if (true || Logger.debugging)
+ if (Logger.debugging)
Logger.info(dots() + this + " Rule 4b comparing " + aStr + " " + bStr);
doCheckPseudo = false;
int n = aStr.length();
@@ -2248,7 +2249,7 @@
isBranch = true;
s = "u";
subRS = "";
-// TODO: Why is this setting of ret to null?
+// TODO: Why is this setting of ret to null?
if (ret != null)
ret[0] = null;
break;
@@ -2362,7 +2363,9 @@
return NOT_RELEVANT; // TODO: ?? this may not be true -- paths with
and without O, N, C for example, that still have stereochemistry
if (rs1.equals(rs2))
return TIED;
- return checkEnantiomer(rs1, rs2, 1, n, " RS");
+
+ System.out.println("testing ~RS here with " + rs1 + " and " + rs2);
+ return checkEnantiomer(rs1, rs2, 1, n, "~RS");
}
private int checkEnantiomer(String rs1, String rs2, int m, int n, String
rs) {
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-05-06 21:50:42 UTC
(rev 21583)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-05-07 00:35:31 UTC
(rev 21584)
@@ -61,9 +61,28 @@
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 may not show M/P for atropisomeric atoms
+bug fix: CIP 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
+ 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
+
JmolVersion="14.15.2" // 4/29/17
bug fix: CIP chirality adds axial chirality (M/P[Ra/Sa], m/p[ra/sa]) for
cumulenes
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