Revision: 21566
http://sourceforge.net/p/jmol/code/21566
Author: hansonr
Date: 2017-04-28 00:45:28 +0000 (Fri, 28 Apr 2017)
Log Message:
-----------
Jmol.___JmolVersion="14.15.1" // 4/28/17
new feature: x.split(true)
-- does a white-space token split of the string value of x
new feature: MOL/SDF reader reads M ISO lines for isotopes
new feature: CIP chirality adds P, S, As, Se, Sb, Te, Bi, Po trigonal pyramidal
and tetrahedral
new feature: CIP chirality adds imine and diazine E/Z chirality
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
bug fix: write MO broken
bug fix: set cartoonBlockHeight (for DSSR nucleic acid rendering) fails
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 Paths:
--------------
trunk/Jmol/src/org/jmol/renderbio/NucleicRenderer.java
trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/renderbio/NucleicRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/renderbio/NucleicRenderer.java 2017-04-28
00:02:43 UTC (rev 21565)
+++ trunk/Jmol/src/org/jmol/renderbio/NucleicRenderer.java 2017-04-28
00:45:28 UTC (rev 21566)
@@ -67,6 +67,7 @@
private P3[] rScr, rScr5;
private P3 basePt, backbonePt;
private P3 baseScreen, backboneScreen;
+ private P3 ptTemp;
private Viewer vwr;
private TransformManager tm;
private JmolRendererInterface g3d;
@@ -259,6 +260,7 @@
boolean isPurine = g.isPurine();
if (box == null || lastHeight != blockHeight) {
g.dssrBoxHeight = blockHeight;
+ System.out.println("nucleic "+ blockHeight);
if (box == null) {
box = new P3[8];
for (int j = 8; --j >= 0;)
@@ -266,8 +268,12 @@
g.dssrBox = box;
}
SymmetryInterface uc = vwr.getSymTemp().getUnitCell(oxyz, false, null);
- uc.toFractional(oxyz[0], true);
- uc.setOffsetPt(P3.new3(oxyz[0].x - 2.25f, oxyz[0].y + 5f, oxyz[0].z
+ System.out.println(uc.getUnitCellState());
+ if (ptTemp == null)
+ ptTemp = new P3();
+ ptTemp.setT(oxyz[0]);
+ uc.toFractional(ptTemp, true);
+ uc.setOffsetPt(P3.new3(ptTemp.x - 2.25f, ptTemp.y + 5f, ptTemp.z
- blockHeight / 2));
float x = 4.5f;
float y = (isPurine ? -4.5f : -3f);
Modified: trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-04-28 00:02:43 UTC
(rev 21565)
+++ trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-04-28 00:45:28 UTC
(rev 21566)
@@ -600,6 +600,7 @@
*
* @param atom
* @param allBonds true to do all bonds to these atoms from other atoms, not
just among them
+ * @param ruleMax
* @param lstEZ
* @param bsToDo
*/
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-04-28 00:02:43 UTC
(rev 21565)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-04-28 00:45:28 UTC
(rev 21566)
@@ -63,6 +63,7 @@
bug fix: values not saved in state for cartoonBlockHeight, cartoonBlocks, and
cartoonSteps
bug fix: write MO broken
+bug fix: set cartoonBlockHeight (for DSSR nucleic acid rendering) fails
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/
This was sent by the SourceForge.net collaborative development platform, the
world's largest Open Source development site.
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Jmol-commits mailing list
Jmol-commits@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-commits
