Revision: 18359
http://sourceforge.net/p/jmol/code/18359
Author: hansonr
Date: 2013-06-25 01:43:16 +0000 (Tue, 25 Jun 2013)
Log Message:
-----------
___JmolVersion="13.1.17_dev_2013.06.25"
bug fix: PyMOL movie start frame
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
trunk/Jmol/src/org/jmol/modelset/ModelLoader.java
trunk/Jmol/src/org/jmol/script/T.java
trunk/Jmol/src/org/jmol/viewer/AnimationManager.java
trunk/Jmol/src/org/jmol/viewer/JC.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/StateCreator.java
trunk/Jmol/src/org/jmol/viewer/StateManager.java
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
2013-06-24 22:56:54 UTC (rev 18358)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
2013-06-25 01:43:16 UTC (rev 18359)
@@ -294,8 +294,9 @@
pymolScene.setStateCount(stateCount);
int pymolState = (int) pymolScene.globalSetting(PyMOL.state);
- pymolScene.setFrameObject(T.frame, (allStates ? Integer.valueOf(-1)
- : Integer.valueOf(pymolState - 1)));
+ if (!isMovie)
+ pymolScene.setFrameObject(T.frame, (allStates ? Integer.valueOf(-1)
+ : Integer.valueOf(pymolState - 1)));
appendLoadNote("frame=" + pymolFrame + " state=" + pymolState
+ " all_states=" + allStates);
Modified: trunk/Jmol/src/org/jmol/modelset/ModelLoader.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelLoader.java 2013-06-24 22:56:54 UTC
(rev 18358)
+++ trunk/Jmol/src/org/jmol/modelset/ModelLoader.java 2013-06-25 01:43:16 UTC
(rev 18359)
@@ -740,6 +740,7 @@
int iLast = -1;
boolean isPdbThisModel = false;
boolean addH = false;
+ boolean isLegacyHAddition = false;//viewer.getBoolean(T.legacyhaddition);
JmolAdapterAtomIterator iterAtom =
adapter.getAtomIterator(atomSetCollection);
int nRead = 0;
Model[] models = modelSet.models;
@@ -764,7 +765,7 @@
String group3 = iterAtom.getGroup3();
int chainID = iterAtom.getChainID();
checkNewGroup(adapter, chainID, group3, iterAtom.getSequenceNumber(),
- iterAtom.getInsertionCode(), addH);
+ iterAtom.getInsertionCode(), addH, isLegacyHAddition);
short isotope = iterAtom.getElementNumber();
if (addH && Elements.getElementNumber(isotope) == 1)
jbr.setHaveHsAlready(true);
@@ -794,7 +795,7 @@
);
}
if (groupCount > 0 && addH) {
- jbr.addImplicitHydrogenAtoms(adapter, groupCount - 1, isNewChain ? 1 :
0);
+ jbr.addImplicitHydrogenAtoms(adapter, groupCount - 1, isNewChain &&
!isLegacyHAddition? 1 : 0);
}
iLast = -1;
EnumVdw vdwtypeLast = null;
@@ -849,7 +850,7 @@
private void checkNewGroup(JmolAdapter adapter, int chainID,
String group3, int groupSequenceNumber,
- char groupInsertionCode, boolean addH) {
+ char groupInsertionCode, boolean addH, boolean
isLegacyHAddition) {
String group3i = (group3 == null ? null : group3.intern());
if (chainID != currentChainID) {
currentChainID = chainID;
@@ -863,7 +864,7 @@
|| groupInsertionCode != currentGroupInsertionCode
|| group3i != currentGroup3) {
if (groupCount > 0 && addH) {
- jbr.addImplicitHydrogenAtoms(adapter, groupCount - 1, isNewChain ? 1 :
0);
+ jbr.addImplicitHydrogenAtoms(adapter, groupCount - 1, isNewChain &&
!isLegacyHAddition? 1 : 0);
jbr.setHaveHsAlready(false);
}
currentGroupSequenceNumber = groupSequenceNumber;
Modified: trunk/Jmol/src/org/jmol/script/T.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/T.java 2013-06-24 22:56:54 UTC (rev
18358)
+++ trunk/Jmol/src/org/jmol/script/T.java 2013-06-25 01:43:16 UTC (rev
18359)
@@ -985,26 +985,27 @@
public final static int justifymeasurements = booleanparam | 96;
public final static int languagetranslation = booleanparam | 97;
public final static int legacyautobonding = booleanparam | 98;
- public final static int logcommands = booleanparam | 99;
- public final static int loggestures = booleanparam | 100;
- public final static int measureallmodels = booleanparam | 101;
- public final static int measurementlabels = booleanparam | 102;
- public final static int messagestylechime = booleanparam | 103;
- public final static int minimizationrefresh = booleanparam | 104;
- public final static int minimizationsilent = booleanparam | 105;
- public final static int modelkitmode = booleanparam | 106;
// 12.0.RC15
- public final static int monitorenergy = booleanparam | 107;
- public final static int multiprocessor = booleanparam | 108;
- public final static int navigatesurface = booleanparam | 109;
- public final static int navigationmode = booleanparam | 110;
- public final static int navigationperiodic = booleanparam | 111;
- public final static int partialdots = booleanparam | 112;
// 12.1.46
- public final static int pdbaddhydrogens = booleanparam | 113;
- public final static int pdbgetheader = booleanparam | 114;
- public final static int pdbsequential = booleanparam | 115;
- public final static int perspectivedepth = booleanparam | 116;
- public final static int preservestate = booleanparam | 117;
- public final static int rangeselected = booleanparam | 118;
+ public final static int legacyhaddition = booleanparam | 99;
+ public final static int logcommands = booleanparam | 100;
+ public final static int loggestures = booleanparam | 101;
+ public final static int measureallmodels = booleanparam | 102;
+ public final static int measurementlabels = booleanparam | 103;
+ public final static int messagestylechime = booleanparam | 104;
+ public final static int minimizationrefresh = booleanparam | 105;
+ public final static int minimizationsilent = booleanparam | 106;
+ public final static int modelkitmode = booleanparam | 107;
// 12.0.RC15
+ public final static int monitorenergy = booleanparam | 108;
+ public final static int multiprocessor = booleanparam | 109;
+ public final static int navigatesurface = booleanparam | 110;
+ public final static int navigationmode = booleanparam | 111;
+ public final static int navigationperiodic = booleanparam | 112;
+ public final static int partialdots = booleanparam | 113;
// 12.1.46
+ public final static int pdbaddhydrogens = booleanparam | 114;
+ public final static int pdbgetheader = booleanparam | 115;
+ public final static int pdbsequential = booleanparam | 116;
+ public final static int perspectivedepth = booleanparam | 117;
+ public final static int preservestate = booleanparam | 118;
+ public final static int rangeselected = booleanparam | 119;
public final static int refreshing = booleanparam | 120;
public final static int ribbonborder = booleanparam | 122;
public final static int rocketbarrels = booleanparam | 124;
Modified: trunk/Jmol/src/org/jmol/viewer/AnimationManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/AnimationManager.java 2013-06-24
22:56:54 UTC (rev 18358)
+++ trunk/Jmol/src/org/jmol/viewer/AnimationManager.java 2013-06-25
01:43:16 UTC (rev 18359)
@@ -363,8 +363,8 @@
currentAnimationFrame = ((Integer)
info.get("currentFrame")).intValue();
if (currentAnimationFrame < 0 || currentAnimationFrame >=
animationFrames.length)
currentAnimationFrame = 0;
- //movie = info;
}
+ setFrame(currentAnimationFrame);
}
if (!isMovie) {
//movie = null;
Modified: trunk/Jmol/src/org/jmol/viewer/JC.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/JC.java 2013-06-24 22:56:54 UTC (rev
18358)
+++ trunk/Jmol/src/org/jmol/viewer/JC.java 2013-06-25 01:43:16 UTC (rev
18359)
@@ -896,10 +896,13 @@
return (pt < 0 || pt >= pdbHydrogenCount.length ? -1 :
pdbHydrogenCount[pt]);
}
- public static String[][] getPdbBondInfo(int pt) {
+ public static String[][] getPdbBondInfo(int pt, boolean isLegacy) {
if (pt < 0 || pt > pdbBondInfo.length)
return null;
String s = pdbBondInfo[pt];
+ // unfortunately, this change is not backward compatible.
+ if (isLegacy && (pt = s.indexOf("O3'")) >= 0)
+ s = s.substring(0, pt);
String[] temp = Parser.getTokens(s);
String[][] info = new String[temp.length / 2][];
for (int i = 0, p = 0; i < info.length; i++) {
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-06-24 22:56:54 UTC
(rev 18358)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-06-25 01:43:16 UTC
(rev 18359)
@@ -9,8 +9,9 @@
# The quotes above look odd for a parameter file, but they are
# important for the JavaScript version of Jmol.
-___JmolVersion="13.1.17_dev_2013.06.24"
+___JmolVersion="13.1.17_dev_2013.06.25"
+bug fix: PyMOL movie start frame
bug fix: PyMOL putty broken
bug fix: pdbAddHydrogens may miss O3' or O5' H atoms at end of DNA strands
bug fix: pdbAddHydrogens may miss H in first group of a chain
Modified: trunk/Jmol/src/org/jmol/viewer/StateCreator.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/StateCreator.java 2013-06-24 22:56:54 UTC
(rev 18358)
+++ trunk/Jmol/src/org/jmol/viewer/StateCreator.java 2013-06-25 01:43:16 UTC
(rev 18359)
@@ -1138,7 +1138,6 @@
}
public String getShapeState(Shape shape) {
- clearTemp();
String s;
switch (shape.shapeID) {
case JC.SHAPE_ECHO:
@@ -1171,6 +1170,7 @@
hs.translucentAllowed) + ";\n";
break;
case JC.SHAPE_HOVER:
+ clearTemp();
Hover h = (Hover) shape;
if (h.atomFormats != null)
for (int i = viewer.getAtomCount(); --i >= 0;)
@@ -1180,8 +1180,10 @@
s = "\n hover "
+ Escape.eS((h.labelFormat == null ? "" : h.labelFormat))
+ ";\n" + getCommands(temp, null, "select");
+ clearTemp();
break;
case JC.SHAPE_LABELS:
+ clearTemp();
Labels l = (Labels) shape;
for (int i = l.bsSizeSet.nextSetBit(0); i >= 0; i = l.bsSizeSet
.nextSetBit(i + 1)) {
@@ -1237,8 +1239,10 @@
s = getCommands(temp, temp2, "select")
+ getCommands(null, temp3, "select");
temp3.clear();
+ clearTemp();
break;
case JC.SHAPE_BALLS:
+ clearTemp();
int atomCount = viewer.getAtomCount();
Atom[] atoms = viewer.modelSet.atoms;
Balls balls = (Balls) shape;
@@ -1263,11 +1267,11 @@
}
}
s = getCommands(temp, temp2, "select");
+ clearTemp();
break;
default:
s = "";
}
- clearTemp();
return s;
}
@@ -1409,6 +1413,7 @@
// if (autoLoadOrientation)
// appendCmd(str, "set autoLoadOrientation true");
appendCmd(str, "set legacyAutoBonding " + g.legacyAutoBonding);
+ appendCmd(str, "set legacyHAddition " + g.legacyHAddition);
appendCmd(str, "set minBondDistance " + g.minBondDistance);
// these next two might be part of a 2D->3D operation
appendCmd(str, "set minimizationCriterion " + g.minimizationCriterion);
Modified: trunk/Jmol/src/org/jmol/viewer/StateManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/StateManager.java 2013-06-24 22:56:54 UTC
(rev 18358)
+++ trunk/Jmol/src/org/jmol/viewer/StateManager.java 2013-06-25 01:43:16 UTC
(rev 18359)
@@ -559,7 +559,7 @@
+
";axis3color;backgroundcolor;backgroundmodel;bondsymmetryatoms;boundboxcolor;cameradepth"
+
";debug;debugscript;defaultlatttice;defaults;defaultdropscript;diffusepercent;exportdrivers"
+
";_filecaching;_filecache;fontcaching;fontscaling;forcefield;language"
- + ";legacyautobonding"
+ + ";legacyautobonding;legacyhaddition"
+ ";loglevel;logfile;loggestures;logcommands;measurestylechime"
+
";loadformat;loadligandformat;smilesurlformat;pubchemformat;nihresolverformat;edsurlformat;edsurlcutoff;multiprocessor;navigationmode;"
+
";pathforallfiles;perspectivedepth;phongexponent;perspectivemodel;preservestate;refreshing;repaintwaitms;rotationradius"
@@ -677,6 +677,7 @@
allowMultiTouch = g.allowMultiTouch;
allowKeyStrokes = g.allowKeyStrokes;
legacyAutoBonding = g.legacyAutoBonding;
+ legacyHAddition = g.legacyHAddition;
useScriptQueue = g.useScriptQueue;
useArcBall = g.useArcBall;
databases = g.databases;
@@ -886,6 +887,7 @@
setI("isosurfacePropertySmoothingPower",
isosurfacePropertySmoothingPower);
setB("justifyMeasurements", justifyMeasurements);
setB("legacyAutoBonding", legacyAutoBonding);
+ setB("legacyHAddition", legacyHAddition);
setF("loadAtomDataTolerance", loadAtomDataTolerance);
setS("loadFormat", loadFormat);
setS("loadLigandFormat", loadLigandFormat);
@@ -1049,6 +1051,7 @@
boolean smartAromatic = true;
boolean zeroBasedXyzRasmol = false;
boolean legacyAutoBonding = false;
+ boolean legacyHAddition = false;
void setDefaultLattice(P3 ptLattice) {
ptDefaultLattice.setT(ptLattice);
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2013-06-24 22:56:54 UTC (rev
18358)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2013-06-25 01:43:16 UTC (rev
18359)
@@ -5728,6 +5728,9 @@
// wrong bonds.
// reset after a state script is read
return global.legacyAutoBonding;
+ case T.legacyhaddition:
+ // aargh -- Some atoms missed before Jmol 13.1.17
+ return global.legacyHAddition;
case T.loggestures:
return global.logGestures;
case T.measureallmodels:
@@ -9567,6 +9570,7 @@
stateScriptVersionInt = main * 10000 + sub * 100 + minor;
// here's why:
global.legacyAutoBonding = (stateScriptVersionInt < 110924);
+ global.legacyHAddition = (stateScriptVersionInt < 130117);
return;
}
} catch (Exception e) {
@@ -9652,7 +9656,7 @@
String[][] info = htPdbBondInfo.get(group3);
if (info != null)
return info;
- info = JC.getPdbBondInfo(Group.lookupGroupID(group3));
+ info = JC.getPdbBondInfo(Group.lookupGroupID(group3),
global.legacyHAddition);
htPdbBondInfo.put(group3, info);
return info;
}
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