Revision: 21564
http://sourceforge.net/p/jmol/code/21564
Author: hansonr
Date: 2017-04-27 20:58:32 +0000 (Thu, 27 Apr 2017)
Log Message:
-----------
CIP alkene + RS
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java
trunk/Jmol/src/org/jmol/viewer/GlobalSettings.java
trunk/Jmol/src/org/jmol/viewer/JC.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-04-27 19:00:54 UTC
(rev 21563)
+++ trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-04-27 20:58:32 UTC
(rev 21564)
@@ -353,7 +353,7 @@
// using BSAtoms here because we need the entire graph, even starting
with an H atom.
getSmallRings(atoms[bsAtoms.nextSetBit(0)]);
for (int i = bsToDo.nextSetBit(0); i >= 0; i = bsToDo.nextSetBit(i + 1))
- getAtomBondChirality(atoms[i], false, lstEZ, bsToDo);
+ getAtomBondChirality(atoms[i], false, RULE_3, lstEZ, bsToDo);
}
@@ -366,6 +366,13 @@
a.setCIPChirality(getAtomChiralityLimited(a, null, null, 5));
}
+ if (haveAlkenes) {
+ for (int i = bsToDo.nextSetBit(0); i >= 0; i = bsToDo.nextSetBit(i + 1))
+ getAtomBondChirality(atoms[i], false, RULE_5, lstEZ, bsToDo);
+ }
+
+
+
// Finally, remove any E/Z indications in small rings
if (lstSmallRings.size() > 0 && lstEZ.size() > 0)
@@ -597,7 +604,7 @@
* @param bsToDo
*/
- private void getAtomBondChirality(Node atom, boolean allBonds,
Lst<int[]>lstEZ, BS bsToDo) {
+ private void getAtomBondChirality(Node atom, boolean allBonds, int ruleMax,
Lst<int[]>lstEZ, BS bsToDo) {
Edge[] bonds = atom.getEdges();
int index = atom.getIndex();
for (int j = bonds.length; --j >= 0;) {
@@ -605,10 +612,10 @@
if (bond.getCovalentOrder() == 2) {
int index2 = bond.getOtherAtomNode(atom).getIndex();
if ((allBonds || index2 > index)
- && getBondChiralityLimited(bond, RULE_3) != NO_CHIRALITY) {
+ && getBondChiralityLimited(bond, ruleMax) != NO_CHIRALITY) {
lstEZ.addLast(new int[] {index, index2});
- bsToDo.clear(index);
- bsToDo.clear(index2);
+ //bsToDo.clear(index);
+ //bsToDo.clear(index2);
}
}
}
Modified: trunk/Jmol/src/org/jmol/viewer/GlobalSettings.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/GlobalSettings.java 2017-04-27 19:00:54 UTC
(rev 21563)
+++ trunk/Jmol/src/org/jmol/viewer/GlobalSettings.java 2017-04-27 20:58:32 UTC
(rev 21564)
@@ -202,9 +202,9 @@
setF("axesScale", axesScale);
setF("axesOffset", axesOffset);
setB("axesOrientationRasmol", axesOrientationRasmol);
- setF("backboneBlock", backboneBlockWidth);
- setB("backboneBlocks", backboneBlocks);
- setB("backboneSteps", backboneSteps);
+ setF("cartoonBlockHeight", cartoonBlockHeight);
+ setB("cartoonBlocks", cartoonBlocks);
+ setB("cartoonSteps", cartoonSteps);
setB("bondModeOr", bondModeOr);
setB("bondPicking", bondPicking);
setI("bondRadiusMilliAngstroms", bondRadiusMilliAngstroms);
@@ -544,9 +544,9 @@
boolean cartoonBaseEdges = false;
boolean cartoonRockets = false;
- float backboneBlockWidth = 0.5f;
- boolean backboneBlocks = false;
- boolean backboneSteps = false;
+ float cartoonBlockHeight = 0.5f;
+ boolean cartoonBlocks = false;
+ boolean cartoonSteps = false;
boolean cartoonFancy = false;
boolean cartoonLadders = false;
boolean cartoonRibose = false;
Modified: trunk/Jmol/src/org/jmol/viewer/JC.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/JC.java 2017-04-27 19:00:54 UTC (rev
21563)
+++ trunk/Jmol/src/org/jmol/viewer/JC.java 2017-04-27 20:58:32 UTC (rev
21564)
@@ -52,8 +52,8 @@
public final static int CIP_CHIRALITY_r_FLAG = 5;
public final static int CIP_CHIRALITY_s_FLAG = 6;
public final static int CIP_CHIRALITY_CANTDETERMINE = 7;
- public final static int CIP_CHIRALITY_Z_FLAG = 8;
- public final static int CIP_CHIRALITY_E_FLAG = 0x10; // Z|E is "no chirality"
+ public final static int CIP_CHIRALITY_Z_FLAG = 1 << 3;
+ public final static int CIP_CHIRALITY_E_FLAG = 2 << 3; // Z|E is "no
chirality"
public static String getCIPChiralityName(int flags) {
switch (flags) {
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-04-27 19:00:54 UTC
(rev 21563)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-04-27 20:58:32 UTC
(rev 21564)
@@ -61,6 +61,8 @@
bug fix: CIP chirality broken for carbonyl groups
bug fix: CIP chirality E/Z should not be indicated for rings of size < 8
+bug fix: values not saved in state for cartoonBlockHeight, cartoonBlocks, and
cartoonSteps
+
code: CIPChirality.java 779 lines Rules 1-5 validated on 145 compounds
- see https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol-datafiles/cip/
code: CIP optimizations
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2017-04-27 19:00:54 UTC (rev
21563)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2017-04-27 20:58:32 UTC (rev
21564)
@@ -5142,9 +5142,9 @@
case T.axesorientationrasmol:
return g.axesOrientationRasmol;
case T.cartoonsteps:
- return g.backboneSteps;
+ return g.cartoonSteps;
case T.cartoonblocks:
- return g.backboneBlocks;
+ return g.cartoonBlocks;
case T.bondmodeor:
return g.bondModeOr;
case T.cartoonbaseedges:
@@ -5381,7 +5381,7 @@
return g.vibrationPeriod;
case T.cartoonblockheight:
// 14.11.0
- return g.backboneBlockWidth;
+ return g.cartoonBlockHeight;
}
Logger.error("viewer.getFloat(" + T.nameOf(tok) + ") - not listed");
return 0;
@@ -5648,7 +5648,7 @@
switch (tok) {
case T.cartoonblockheight:
// 14.11.0
- g.backboneBlockWidth = value;
+ g.cartoonBlockHeight = value;
break;
case T.modulationscale:
// 14.0.1
@@ -6126,11 +6126,11 @@
break;
case T.cartoonblocks:
// 14.11.0
- g.backboneBlocks = value;
+ g.cartoonBlocks = value;
break;
case T.cartoonsteps:
// 14.1.14
- g.backboneSteps = value;
+ g.cartoonSteps = value;
break;
case T.cartoonribose:
// 14.1.8
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