Revision: 20968
http://sourceforge.net/p/jmol/code/20968
Author: hansonr
Date: 2016-02-28 01:43:05 +0000 (Sun, 28 Feb 2016)
Log Message:
-----------
Jmol.___JmolVersion="14.4.3_2016.02.28"
bug fix: cyclic peptides do not complete loop for cartoons, backbone, etc.
Modified Paths:
--------------
branches/v14_4/Jmol/src/org/jmol/modelsetbio/BioPolymer.java
branches/v14_4/Jmol/src/org/jmol/renderbio/BackboneRenderer.java
branches/v14_4/Jmol/src/org/jmol/renderbio/BioShapeRenderer.java
branches/v14_4/Jmol/src/org/jmol/shapebio/Backbone.java
branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java
trunk/Jmol/src/org/jmol/renderbio/BackboneRenderer.java
trunk/Jmol/src/org/jmol/renderbio/BioShapeRenderer.java
trunk/Jmol/src/org/jmol/shapebio/Backbone.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: branches/v14_4/Jmol/src/org/jmol/modelsetbio/BioPolymer.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/modelsetbio/BioPolymer.java
2016-02-27 20:23:18 UTC (rev 20967)
+++ branches/v14_4/Jmol/src/org/jmol/modelsetbio/BioPolymer.java
2016-02-28 01:43:05 UTC (rev 20968)
@@ -81,6 +81,8 @@
protected final static int TYPE_NUCLEIC = 2;
protected final static int TYPE_CARBOHYDRATE = 3;
+ public int cyclicFlag;
+
protected void set(Monomer[] monomers) {
this.monomers = monomers;
monomerCount = monomers.length;
@@ -483,4 +485,9 @@
return type;
}
+ public boolean isCyclic() { // Jmol 14.5.3
+ return ((cyclicFlag == 0 ? (cyclicFlag = (monomerCount >= 4 && monomers[0]
+ .isConnectedAfter(monomers[monomerCount - 1])) ? 1 : -1) : cyclicFlag)
== 1);
+ }
+
}
Modified: branches/v14_4/Jmol/src/org/jmol/renderbio/BackboneRenderer.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/renderbio/BackboneRenderer.java
2016-02-27 20:23:18 UTC (rev 20967)
+++ branches/v14_4/Jmol/src/org/jmol/renderbio/BackboneRenderer.java
2016-02-28 01:43:05 UTC (rev 20968)
@@ -45,12 +45,15 @@
boolean showSteps = vwr.getBoolean(T.backbonesteps)
&& bioShape.bioPolymer.isNucleic();
isDataFrame = vwr.ms.isJmolDataFrameForModel(bioShape.modelIndex);
+ int n = monomerCount;
+ Atom[] atoms = ms.at;
for (int i = bsVisible.nextSetBit(0); i >= 0; i = bsVisible
.nextSetBit(i + 1)) {
- Atom atomA = ms.at[leadAtomIndices[i]];
+ Atom atomA = atoms[leadAtomIndices[i]];
short cA = colixes[i];
mad = mads[i];
- drawSegment(atomA, ms.at[leadAtomIndices[i + 1]], cA, colixes[i + 1],
100, checkPass2);
+ int i1 = (i + 1) % n;
+ drawSegment(atomA, atoms[leadAtomIndices[i1]], cA, colixes[i1], 100,
checkPass2);
if (showSteps) {
NucleicMonomer g = (NucleicMonomer) monomers[i];
Lst<BasePair> bps = g.getBasePairs();
@@ -58,7 +61,7 @@
for (int j = bps.size(); --j >= 0;) {
int iAtom = bps.get(j).getPartnerAtom(g);
if (iAtom > i)
- drawSegment(atomA, ms.at[iAtom], cA, cA, 1000, checkPass2);
+ drawSegment(atomA, atoms[iAtom], cA, cA, 1000, checkPass2);
}
}
}
Modified: branches/v14_4/Jmol/src/org/jmol/renderbio/BioShapeRenderer.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/renderbio/BioShapeRenderer.java
2016-02-27 20:23:18 UTC (rev 20967)
+++ branches/v14_4/Jmol/src/org/jmol/renderbio/BioShapeRenderer.java
2016-02-28 01:43:05 UTC (rev 20968)
@@ -85,6 +85,7 @@
protected boolean wireframeOnly;
private boolean needTranslucent;
JmolBioMeshRenderer meshRenderer;
+ BioShape bioShape;
protected abstract void renderBioShape(BioShape bioShape);
@@ -161,12 +162,13 @@
BioShapeCollection mps = (BioShapeCollection) shape;
for (int c = mps.bioShapes.length; --c >= 0;) {
- BioShape bioShape = mps.getBioShape(c);
+ bioShape = mps.getBioShape(c);
if ((bioShape.modelVisibilityFlags & myVisibilityFlag) == 0)
continue;
if (bioShape.monomerCount >= 2 && initializePolymer(bioShape)) {
if (meshRenderer != null)
meshRenderer.initBS();
+ isCyclic = bioShape.bioPolymer.isCyclic();
renderBioShape(bioShape);
if (meshRenderer != null)
meshRenderer.renderMeshes();
@@ -304,12 +306,21 @@
short madBeg, madMid, madEnd;
short colixBack;
private BS reversed;
+ private boolean isCyclic;
void setNeighbors(int i) {
- iPrev = Math.max(i - 1, 0);
- iNext = Math.min(i + 1, monomerCount);
- iNext2 = Math.min(i + 2, monomerCount);
- iNext3 = Math.min(i + 3, monomerCount);
+ if (isCyclic) {
+ i += monomerCount;
+ iPrev = (i - 1) % monomerCount;
+ iNext = (i + 1) % monomerCount;
+ iNext2 = (i + 2) % monomerCount;
+ iNext3 = (i + 3) % monomerCount;
+ } else {
+ iPrev = Math.max(i - 1, 0);
+ iNext = Math.min(i + 1, monomerCount);
+ iNext2 = Math.min(i + 2, monomerCount);
+ iNext3 = Math.min(i + 3, monomerCount);
+ }
}
protected boolean setColix(short colix) {
Modified: branches/v14_4/Jmol/src/org/jmol/shapebio/Backbone.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/shapebio/Backbone.java 2016-02-27
20:23:18 UTC (rev 20967)
+++ branches/v14_4/Jmol/src/org/jmol/shapebio/Backbone.java 2016-02-28
01:43:05 UTC (rev 20968)
@@ -73,9 +73,10 @@
if (bioShape.bsSizeSet == null)
bioShape.bsSizeSet = new BS();
bioShape.isActive = true;
- for (int i = bioShape.monomerCount - 1; --i >= 0;) {
+ int n = bioShape.monomerCount;
+ for (int i = n - (bioShape.bioPolymer.isCyclic() ? 0 : 1); --i >= 0;) {
int index1 = atomIndices[i];
- int index2 = atomIndices[i + 1];
+ int index2 = atomIndices[(i + 1) % n];
boolean isAtom1 = bsSelected.get(index1);
boolean isAtom2 = bsSelected.get(index2);
if (isAtom1 && isAtom2
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2016-02-27
20:23:18 UTC (rev 20967)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2016-02-28
01:43:05 UTC (rev 20968)
@@ -8,7 +8,11 @@
# see also http://chemapps.stolaf.edu/jmol/zip for daily updates
-Jmol.___JmolVersion="14.4.3_2016.02.27"
+Jmol.___JmolVersion="14.4.3_2016.02.28"
+
+bug fix: cyclic peptides do not complete loop for cartoons, backbone, etc.
+
+JmolVersion="14.4.3_2016.02.27"
released
bug fix: [function:"yyy",Function:"zzz"] fails to retain key capitalization
after first entry for special names
Modified: trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java 2016-02-27 20:23:18 UTC
(rev 20967)
+++ trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java 2016-02-28 01:43:05 UTC
(rev 20968)
@@ -81,6 +81,8 @@
protected final static int TYPE_NUCLEIC = 2;
protected final static int TYPE_CARBOHYDRATE = 3;
+ public int cyclicFlag;
+
protected void set(Monomer[] monomers) {
this.monomers = monomers;
monomerCount = monomers.length;
@@ -483,4 +485,9 @@
return type;
}
+ public boolean isCyclic() { // Jmol 14.5.3
+ return ((cyclicFlag == 0 ? (cyclicFlag = (monomerCount >= 4 && monomers[0]
+ .isConnectedAfter(monomers[monomerCount - 1])) ? 1 : -1) : cyclicFlag)
== 1);
+ }
+
}
Modified: trunk/Jmol/src/org/jmol/renderbio/BackboneRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/renderbio/BackboneRenderer.java 2016-02-27
20:23:18 UTC (rev 20967)
+++ trunk/Jmol/src/org/jmol/renderbio/BackboneRenderer.java 2016-02-28
01:43:05 UTC (rev 20968)
@@ -45,12 +45,15 @@
boolean showSteps = vwr.getBoolean(T.backbonesteps)
&& bioShape.bioPolymer.isNucleic();
isDataFrame = vwr.ms.isJmolDataFrameForModel(bioShape.modelIndex);
+ int n = monomerCount;
+ Atom[] atoms = ms.at;
for (int i = bsVisible.nextSetBit(0); i >= 0; i = bsVisible
.nextSetBit(i + 1)) {
- Atom atomA = ms.at[leadAtomIndices[i]];
+ Atom atomA = atoms[leadAtomIndices[i]];
short cA = colixes[i];
mad = mads[i];
- drawSegment(atomA, ms.at[leadAtomIndices[i + 1]], cA, colixes[i + 1],
100, checkPass2);
+ int i1 = (i + 1) % n;
+ drawSegment(atomA, atoms[leadAtomIndices[i1]], cA, colixes[i1], 100,
checkPass2);
if (showSteps) {
NucleicMonomer g = (NucleicMonomer) monomers[i];
Lst<BasePair> bps = g.getBasePairs();
@@ -58,7 +61,7 @@
for (int j = bps.size(); --j >= 0;) {
int iAtom = bps.get(j).getPartnerAtom(g);
if (iAtom > i)
- drawSegment(atomA, ms.at[iAtom], cA, cA, 1000, checkPass2);
+ drawSegment(atomA, atoms[iAtom], cA, cA, 1000, checkPass2);
}
}
}
Modified: trunk/Jmol/src/org/jmol/renderbio/BioShapeRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/renderbio/BioShapeRenderer.java 2016-02-27
20:23:18 UTC (rev 20967)
+++ trunk/Jmol/src/org/jmol/renderbio/BioShapeRenderer.java 2016-02-28
01:43:05 UTC (rev 20968)
@@ -85,6 +85,7 @@
protected boolean wireframeOnly;
private boolean needTranslucent;
JmolBioMeshRenderer meshRenderer;
+ BioShape bioShape;
protected abstract void renderBioShape(BioShape bioShape);
@@ -161,12 +162,13 @@
BioShapeCollection mps = (BioShapeCollection) shape;
for (int c = mps.bioShapes.length; --c >= 0;) {
- BioShape bioShape = mps.getBioShape(c);
+ bioShape = mps.getBioShape(c);
if ((bioShape.modelVisibilityFlags & myVisibilityFlag) == 0)
continue;
if (bioShape.monomerCount >= 2 && initializePolymer(bioShape)) {
if (meshRenderer != null)
meshRenderer.initBS();
+ isCyclic = bioShape.bioPolymer.isCyclic();
renderBioShape(bioShape);
if (meshRenderer != null)
meshRenderer.renderMeshes();
@@ -304,12 +306,21 @@
short madBeg, madMid, madEnd;
short colixBack;
private BS reversed;
+ private boolean isCyclic;
void setNeighbors(int i) {
- iPrev = Math.max(i - 1, 0);
- iNext = Math.min(i + 1, monomerCount);
- iNext2 = Math.min(i + 2, monomerCount);
- iNext3 = Math.min(i + 3, monomerCount);
+ if (isCyclic) {
+ i += monomerCount;
+ iPrev = (i - 1) % monomerCount;
+ iNext = (i + 1) % monomerCount;
+ iNext2 = (i + 2) % monomerCount;
+ iNext3 = (i + 3) % monomerCount;
+ } else {
+ iPrev = Math.max(i - 1, 0);
+ iNext = Math.min(i + 1, monomerCount);
+ iNext2 = Math.min(i + 2, monomerCount);
+ iNext3 = Math.min(i + 3, monomerCount);
+ }
}
protected boolean setColix(short colix) {
Modified: trunk/Jmol/src/org/jmol/shapebio/Backbone.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapebio/Backbone.java 2016-02-27 20:23:18 UTC
(rev 20967)
+++ trunk/Jmol/src/org/jmol/shapebio/Backbone.java 2016-02-28 01:43:05 UTC
(rev 20968)
@@ -73,9 +73,10 @@
if (bioShape.bsSizeSet == null)
bioShape.bsSizeSet = new BS();
bioShape.isActive = true;
- for (int i = bioShape.monomerCount - 1; --i >= 0;) {
+ int n = bioShape.monomerCount;
+ for (int i = n - (bioShape.bioPolymer.isCyclic() ? 0 : 1); --i >= 0;) {
int index1 = atomIndices[i];
- int index2 = atomIndices[i + 1];
+ int index2 = atomIndices[(i + 1) % n];
boolean isAtom1 = bsSelected.get(index1);
boolean isAtom2 = bsSelected.get(index2);
if (isAtom1 && isAtom2
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2016-02-27 20:23:18 UTC
(rev 20967)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2016-02-28 01:43:05 UTC
(rev 20968)
@@ -65,8 +65,12 @@
TODO: isosurface molecular has an issue with 2gb1
TODO: slab SET will not be rendered correctly when exported because
tm.transformPoint
-Jmol.___JmolVersion="14.5.3_2016.02.27"
+Jmol.___JmolVersion="14.5.3_2016.02.28"
+bug fix: cyclic peptides do not complete loop for cartoons, backbone, etc.
+
+JmolVersion="14.5.3_2016.02.27"
+
bug fix: [function:"yyy",Function:"zzz"] fails to retain key capitalization
after first entry for special names
bug fix: (JavaScript only) polyhedra not saved in state
bug fix: (Applet) broken image in coverImage
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