Revision: 20884
http://sourceforge.net/p/jmol/code/20884
Author: hansonr
Date: 2015-12-08 16:01:40 +0000 (Tue, 08 Dec 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.4.0_2015.12.07"
bug fix: set selectAllModels not working appropriately
bug fix: set selectAllModels should not be saved in state
JmolVersion="14.4.0_2015.12.05"
bug fix: JmolData.jar does not update atom screen positions upon REFRESH or
select {visible}
bug fix: JmolData.jar -p flag does not work properly
bug fix: model 0 issued when more than one PDB file is open does not execute
model *
Modified Paths:
--------------
branches/v14_4/Jmol/src/org/jmol/api/JmolScriptEvaluator.java
branches/v14_4/Jmol/src/org/jmol/export/__RayTracerExporter.java
branches/v14_4/Jmol/src/org/jmol/io/FileReader.java
branches/v14_4/Jmol/src/org/jmol/io/FilesReader.java
branches/v14_4/Jmol/src/org/jmol/modelset/AtomCollection.java
branches/v14_4/Jmol/src/org/jmol/render/RepaintManager.java
branches/v14_4/Jmol/src/org/jmol/script/SV.java
branches/v14_4/Jmol/src/org/jmol/script/ScriptError.java
branches/v14_4/Jmol/src/org/jmol/script/ScriptEval.java
branches/v14_4/Jmol/src/org/jmol/script/ScriptExpr.java
branches/v14_4/Jmol/src/org/jmol/script/ScriptManager.java
branches/v14_4/Jmol/src/org/jmol/script/ScriptMathProcessor.java
branches/v14_4/Jmol/src/org/jmol/scriptext/CmdExt.java
branches/v14_4/Jmol/src/org/jmol/scriptext/MathExt.java
branches/v14_4/Jmol/src/org/jmol/viewer/AnimationManager.java
branches/v14_4/Jmol/src/org/jmol/viewer/ChimeMessenger.java
branches/v14_4/Jmol/src/org/jmol/viewer/FileManager.java
branches/v14_4/Jmol/src/org/jmol/viewer/GlobalSettings.java
branches/v14_4/Jmol/src/org/jmol/viewer/JC.java
branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties
branches/v14_4/Jmol/src/org/jmol/viewer/ShapeManager.java
branches/v14_4/Jmol/src/org/jmol/viewer/Viewer.java
branches/v14_4/Jmol/src/org/openscience/jmol/app/JmolData.java
Modified: branches/v14_4/Jmol/src/org/jmol/api/JmolScriptEvaluator.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/api/JmolScriptEvaluator.java
2015-12-03 21:31:41 UTC (rev 20883)
+++ branches/v14_4/Jmol/src/org/jmol/api/JmolScriptEvaluator.java
2015-12-08 16:01:40 UTC (rev 20884)
@@ -73,7 +73,7 @@
void runScript(String script) throws ScriptException;
- void runScriptBuffer(String string, SB outputBuffer) throws ScriptException;
+ void runScriptBuffer(String string, SB outputBuffer, boolean isFuncReturn)
throws ScriptException;
float evalFunctionFloat(Object func, Object params, float[] values);
Modified: branches/v14_4/Jmol/src/org/jmol/export/__RayTracerExporter.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/export/__RayTracerExporter.java
2015-12-03 21:31:41 UTC (rev 20883)
+++ branches/v14_4/Jmol/src/org/jmol/export/__RayTracerExporter.java
2015-12-08 16:01:40 UTC (rev 20884)
@@ -61,7 +61,7 @@
if (super.initOutput(vwr, privateKey, g3d, params)) {
vwr.tm.perspectiveDepth = false;
if (wasPerspective)
- vwr.shm.finalizeAtoms(null, null);
+ vwr.shm.finalizeAtoms(false, false);
return true;
}
return false;
Modified: branches/v14_4/Jmol/src/org/jmol/io/FileReader.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/io/FileReader.java 2015-12-03 21:31:41 UTC
(rev 20883)
+++ branches/v14_4/Jmol/src/org/jmol/io/FileReader.java 2015-12-08 16:01:40 UTC
(rev 20884)
@@ -36,6 +36,7 @@
import javajs.api.ZInputStream;
import javajs.util.AU;
import javajs.util.PT;
+import javajs.util.Rdr;
import org.jmol.api.Interface;
import org.jmol.util.Logger;
@@ -78,6 +79,8 @@
vwr.zap(false, true, false);
String errorMessage = null;
Object t = null;
+ if (fullPathNameIn.contains("_CHANGEABLE_"))
+ reader = getChangeableReader(vwr, nameAsGivenIn, fullPathNameIn);
if (reader == null) {
t = fm.getUnzippedReaderOrStreamFromName(fullPathNameIn,
bytes, true, false, false, true, htParams);
@@ -143,6 +146,12 @@
fm.setFileInfo(new String[] { fullPathNameIn, fileNameIn, nameAsGivenIn });
}
+ final static BufferedReader getChangeableReader(Viewer vwr,
+ String nameAsGivenIn, String fullPathNameIn) {
+ Logger.info("caching changeable file " + fullPathNameIn);
+ return Rdr.getBR((String) vwr.getLigandModel(nameAsGivenIn,
fullPathNameIn, "_file", null));
+ }
+
public Object getAtomSetCollection() {
return atomSetCollection;
}
Modified: branches/v14_4/Jmol/src/org/jmol/io/FilesReader.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/io/FilesReader.java 2015-12-03
21:31:41 UTC (rev 20883)
+++ branches/v14_4/Jmol/src/org/jmol/io/FilesReader.java 2015-12-08
16:01:40 UTC (rev 20884)
@@ -95,6 +95,8 @@
subFileList = PT.split(name, "|");
name = subFileList[0];
}
+ if (name.contains("_CHANGEABLE_"))
+ return FileReader.getChangeableReader(vwr, namesAsGivenIn[i], name);
Object t = fm.getUnzippedReaderOrStreamFromName(name, null,
true, forceBinary, false, true, htParams);
if (t instanceof ZipInputStream) {
Modified: branches/v14_4/Jmol/src/org/jmol/modelset/AtomCollection.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/modelset/AtomCollection.java
2015-12-03 21:31:41 UTC (rev 20883)
+++ branches/v14_4/Jmol/src/org/jmol/modelset/AtomCollection.java
2015-12-08 16:01:40 UTC (rev 20884)
@@ -224,8 +224,9 @@
public Lst<P3> getAtomPointVector(BS bs) {
Lst<P3> v = new Lst<P3>();
+ int n = ac;
if (bs != null) {
- for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i+1)) {
+ for (int i = bs.nextSetBit(0); i >= 0 && i < n; i = bs.nextSetBit(i+1)) {
v.addLast(at[i]);
}
}
@@ -2463,8 +2464,10 @@
}
public BS getVisibleSet(boolean forceNew) {
- if (forceNew)
+ if (forceNew) {
vwr.setModelVisibility();
+ vwr.shm.finalizeAtoms(false, true);
+ }
else if (haveBSVisible)
return bsVisible;
bsVisible.clearAll();
Modified: branches/v14_4/Jmol/src/org/jmol/render/RepaintManager.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/render/RepaintManager.java 2015-12-03
21:31:41 UTC (rev 20883)
+++ branches/v14_4/Jmol/src/org/jmol/render/RepaintManager.java 2015-12-08
16:01:40 UTC (rev 20884)
@@ -243,8 +243,7 @@
public String renderExport(GData gdata, ModelSet modelSet,
Map<String, Object> params) {
boolean isOK;
- vwr.finalizeTransformParameters();
- shapeManager.finalizeAtoms(null, null);
+ shapeManager.finalizeAtoms(false, true);
JmolRendererInterface exporter3D = vwr.initializeExporter(params);
isOK = (exporter3D != null);
if (!isOK) {
Modified: branches/v14_4/Jmol/src/org/jmol/script/SV.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/script/SV.java 2015-12-03 21:31:41 UTC
(rev 20883)
+++ branches/v14_4/Jmol/src/org/jmol/script/SV.java 2015-12-08 16:01:40 UTC
(rev 20884)
@@ -122,7 +122,7 @@
static int sizeOf(T x) {
switch (x == null ? nada : x.tok) {
case bitset:
- return BSUtil.cardinalityOf(bsSelectToken(x));
+ return bsSelectToken(x).cardinality();
case on:
case off:
return -1;
@@ -549,7 +549,7 @@
// case matrix4f:
return (int) fValue(x);
case bitset:
- return BSUtil.cardinalityOf(bsSelectToken(x));
+ return bsSelectToken(x).cardinality();
case barray:
return ((BArray) x.value).data.length;
default:
@@ -816,17 +816,10 @@
return getVariableList(vlist);
}
- static BS bsSelectToken(T x) {
- x = selectItemTok(x, Integer.MIN_VALUE);
- return (BS) x.value;
+ private static BS bsSelectToken(T x) {
+ return (BS) selectItemTok(x, Integer.MIN_VALUE).value;
}
- public static BS bsSelectVar(SV var) {
- if (var.index == Integer.MAX_VALUE)
- var = selectItemVar(var);
- return (BS) var.value;
- }
-
static BS bsSelectRange(T x, int n) {
x = selectItemTok(x, Integer.MIN_VALUE);
x = selectItemTok(x, (n <= 0 ? n : 1));
@@ -835,12 +828,12 @@
}
static SV selectItemVar(SV var) {
- // pass bitsets created by the select() or for() commands
+ // pass bitsets created by the select() or for() inline functions
// and all arrays by reference
- if (var.index != Integer.MAX_VALUE ||
- (var.tok == varray || var.tok == barray) && var.intValue ==
Integer.MAX_VALUE)
- return var;
- return (SV) selectItemTok(var, Integer.MIN_VALUE);
+ return (var.index != Integer.MAX_VALUE
+ || (var.tok == varray || var.tok == barray)
+ && var.intValue == Integer.MAX_VALUE ? var : (SV) selectItemTok(var,
+ Integer.MIN_VALUE));
}
static T selectItemTok(T tokenIn, int i2) {
@@ -881,10 +874,10 @@
if (tokenIn.value instanceof BondSet) {
bs = BondSet.newBS((BS) tokenIn.value,
((BondSet) tokenIn.value).associatedAtoms);
- len = BSUtil.cardinalityOf(bs);
+ len = bs.cardinality();
} else {
bs = BSUtil.copy((BS) tokenIn.value);
- len = (isInputSelected ? 1 : BSUtil.cardinalityOf(bs));
+ len = (isInputSelected ? 1 : bs.cardinality());
}
break;
case barray:
@@ -1307,7 +1300,10 @@
public static BS getBitSet(SV x, boolean allowNull) {
switch (x.tok) {
case bitset:
- return bsSelectVar(x);
+ // selectItemTok is important here because this may come from
setVariable()
+ // in the case of a[1].xyz = ptX1
+ return (BS) (x.index == Integer.MAX_VALUE ? (SV) selectItemTok(x,
+ Integer.MIN_VALUE) : x).value;
case varray:
return unEscapeBitSetArray(x.getList(), allowNull);
default:
Modified: branches/v14_4/Jmol/src/org/jmol/script/ScriptError.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/script/ScriptError.java 2015-12-03
21:31:41 UTC (rev 20883)
+++ branches/v14_4/Jmol/src/org/jmol/script/ScriptError.java 2015-12-08
16:01:40 UTC (rev 20884)
@@ -13,7 +13,7 @@
*/
public abstract class ScriptError implements JmolScriptEvaluator {
- abstract protected void showString(String msg);
+ abstract protected void showStringPrint(String msg, boolean mustDo);
public Viewer vwr;
public boolean chk;
@@ -83,7 +83,7 @@
: errorString(iError, value, more, more2, false));
if (!warningOnly)
evalError(strError, strUntranslated);
- showString(strError);
+ showStringPrint(strError, true);
}
public void evalError(String message, String strUntranslated)
Modified: branches/v14_4/Jmol/src/org/jmol/script/ScriptEval.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/script/ScriptEval.java 2015-12-03
21:31:41 UTC (rev 20883)
+++ branches/v14_4/Jmol/src/org/jmol/script/ScriptEval.java 2015-12-08
16:01:40 UTC (rev 20884)
@@ -233,6 +233,7 @@
private JmolThread scriptDelayThread, fileLoadThread;
public boolean allowJSThreads = true;
+ private boolean isFuncReturn;
@Override
public boolean getAllowJSThreads() {
@@ -420,7 +421,7 @@
vwr.handleError(er, false);
setErrorMessage("" + er + " " + vwr.getShapeErrorState());
errorMessageUntranslated = "" + er;
- report(errorMessage);
+ report(errorMessage, true);
haveError = true;
} catch (ScriptException e) {
if (e instanceof ScriptInterruption && (!isTry || !e.isError)) {
@@ -443,7 +444,7 @@
}
setErrorMessage(e.toString());
errorMessageUntranslated = e.getErrorMessageUntranslated();
- report(errorMessage);
+ report(errorMessage, true);
vwr
.notifyError(
(errorMessage != null
@@ -567,27 +568,30 @@
@Override
public void runScript(String script) throws ScriptException {
if (!vwr.isPreviewOnly)
- runScriptBuffer(script, outputBuffer);
+ runScriptBuffer(script, outputBuffer, false);
}
/**
* runs a script immediately and sends selected output to a provided SB
+ * @param outputBuffer
+ * @param script
*
- * @param script
- * @param outputBuffer
* @throws ScriptException
*/
@Override
- public void runScriptBuffer(String script, SB outputBuffer)
+ public void runScriptBuffer(String script, SB outputBuffer, boolean
isFuncReturn)
throws ScriptException {
pushContext(null, "runScriptBuffer");
contextPath += " >> script() ";
this.outputBuffer = outputBuffer;
allowJSThreads = false;
+ boolean fret = this.isFuncReturn;
+ this.isFuncReturn |= isFuncReturn;
if (compileScript(null, script + JC.SCRIPT_EDITOR_IGNORE
+ JC.REPAINT_IGNORE, false))
dispatchCommands(false, false, false);
popContext(false, false);
+ this.isFuncReturn = fret;
}
/**
@@ -1777,31 +1781,35 @@
//////////////////// showing strings /////////////////
- @Override
public void showString(String str) {
// called by ScriptExt and ScriptError
showStringPrint(str, false);
}
- public void showStringPrint(String str, boolean isPrint) {
- if (chk || str == null)
+ @Override
+ public void showStringPrint(String s, boolean mustDo) {
+ if (chk || s == null)
return;
- if (outputBuffer != null && Logger.isActiveLevel(Logger.LEVEL_WARN))
- outputBuffer.append(str).appendC('\n');
+ if (outputBuffer == null)
+ vwr.showString(s, mustDo);
else
- vwr.showString(str, isPrint);
+ appendBuffer(s, mustDo);
}
- public void report(String s) {
+ public void report(String s, boolean isError) {
if (chk)
return;
- if (outputBuffer != null) {
- outputBuffer.append(s).appendC('\n');
- return;
- }
+ if (outputBuffer == null)
vwr.scriptStatus(s);
+ else
+ appendBuffer(s, isError);
}
+ private void appendBuffer(String str, boolean mustDo) {
+ if (mustDo || isFuncReturn || Logger.isActiveLevel(Logger.LEVEL_INFO))
+ outputBuffer.append(str).appendC('\n');
+ }
+
/*
* ****************************************************************
* =============== command processing checks ===============================
@@ -1860,7 +1868,7 @@
setErrorMessage("" + er);
}
if (error) {
- report(errorMessage);
+ report(errorMessage, true);
setErrorMessage(null);
}
restoreScriptContext(scSave, true, false, false);
@@ -2105,7 +2113,7 @@
return true;
String script = vwr.getInsertedCommand();
if (!"".equals(script))
- runScriptBuffer(script, null);
+ runScriptBuffer(script, null, false);
else if (isSpt && debugScript && vwr.getBoolean(T.messagestylechime))
vwr.getChimeMessenger().update(null);
if (!mustResumeEval && !allowJSInterrupt || fromFunc)
@@ -3252,7 +3260,7 @@
if (slen == 4 && optParameterAsString(2).equals("saved") && slen == 4) {
vwr.stm.deleteSaved(optParameterAsString(3));
if (doReport())
- report(GT.o(GT._("show saved: {0}"), vwr.stm.listSavedStates()));
+ report(GT.o(GT._("show saved: {0}"), vwr.stm.listSavedStates()),
false);
return;
}
setObjectProperty();
@@ -3266,7 +3274,7 @@
bs = vwr.getAllAtoms();
int nDeleted = vwr.deleteAtoms(bs, false);
if (doReport())
- report(GT.i(GT._("{0} atoms deleted"), nDeleted));
+ report(GT.i(GT._("{0} atoms deleted"), nDeleted), false);
}
private void cmdDisplay(boolean isDisplay) throws ScriptException {
@@ -3484,8 +3492,8 @@
SV vl = what.get(0);
switch (inTok = vl.tok) {
case T.bitset:
- bsOrList = SV.getBitSet(vl, false);
- isOK = (((BS) bsOrList).nextSetBit(0) >= 0);
+ bsOrList = vl.value;
+ isOK = !((BS) bsOrList).isEmpty();
break;
case T.varray:
Lst<SV> v = vl.getList();
@@ -3984,7 +3992,7 @@
if (chk)
return;
int n = vwr.autoHbond(null, null, false);
- report(GT.i(GT._("{0} hydrogen bonds"), Math.abs(n)));
+ report(GT.i(GT._("{0} hydrogen bonds"), Math.abs(n)), false);
return;
}
if (slen == 2 && getToken(1).tok == T.delete) {
@@ -4687,7 +4695,7 @@
if (debugHigh)
report("Successfully loaded:"
- + (filenames == null ? htParams.get("fullPathName") : modelName));
+ + (filenames == null ? htParams.get("fullPathName") : modelName),
false);
finalizeLoad(isAppend, appendNew, isConcat, doOrient, nFiles, ac0,
modelCount0);
@@ -4920,10 +4928,10 @@
if (chk)
return;
String s = Txt.formatText(vwr, text);
- if (outputBuffer == null)
- vwr.warn(s);
+ if (outputBuffer == null && !vwr.isPrintOnly)
+ Logger.warn(s);
if (!s.startsWith("_"))
- report(s);
+ report(s, false);
}
/**
@@ -7650,7 +7658,7 @@
if (pt == 2) {
saveContext(info);
if (doReport())
- report(GT.o(GT._("to resume, enter: &{0}"), info));
+ report(GT.o(GT._("to resume, enter: &{0}"), info), false);
throw new ScriptInterruption(this, info, Integer.MIN_VALUE);
}
evalError(info, null);
@@ -7943,7 +7951,7 @@
int nDeleted = vwr.deleteAtoms(bs, true);
boolean isQuiet = !doReport();
if (!isQuiet)
- report(GT.i(GT._("{0} atoms deleted"), nDeleted));
+ report(GT.i(GT._("{0} atoms deleted"), nDeleted), false);
vwr.select(null, false, 0, isQuiet);
}
Modified: branches/v14_4/Jmol/src/org/jmol/script/ScriptExpr.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/script/ScriptExpr.java 2015-12-03
21:31:41 UTC (rev 20883)
+++ branches/v14_4/Jmol/src/org/jmol/script/ScriptExpr.java 2015-12-08
16:01:40 UTC (rev 20884)
@@ -2166,7 +2166,7 @@
}
break;
case T.bitset:
- bs = SV.getBitSet(t, true);
+ bs = SV.getBitSet(t, false);
int nAtoms = vwr.ms.ac;
int nbs = bs.cardinality();
propertyName = sel.asString();
Modified: branches/v14_4/Jmol/src/org/jmol/script/ScriptManager.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/script/ScriptManager.java 2015-12-03
21:31:41 UTC (rev 20883)
+++ branches/v14_4/Jmol/src/org/jmol/script/ScriptManager.java 2015-12-08
16:01:40 UTC (rev 20884)
@@ -677,7 +677,7 @@
.append(" ").appendF(pts[i].z).append(" - - - - ").appendI(++atomno)
.appendC('\n');
vwr.openStringInlineParamsAppend(sb.toString(), null, true);
- eval.runScriptBuffer(sbConnect.toString(), null);
+ eval.runScriptBuffer(sbConnect.toString(), null, false);
BS bsB = vwr.getModelUndeletedAtomsBitSet(modelIndex);
bsB.andNot(bsA);
return bsB;
Modified: branches/v14_4/Jmol/src/org/jmol/script/ScriptMathProcessor.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/script/ScriptMathProcessor.java
2015-12-03 21:31:41 UTC (rev 20883)
+++ branches/v14_4/Jmol/src/org/jmol/script/ScriptMathProcessor.java
2015-12-08 16:01:40 UTC (rev 20884)
@@ -941,7 +941,7 @@
m4.transpose();
return addXM4(m4);
case T.bitset:
- return addXBs(BSUtil.copyInvert(SV.bsSelectVar(x2),
+ return addXBs(BSUtil.copyInvert((BS) x2.value,
(x2.value instanceof BondSet ? vwr.ms.bondCount : vwr.ms.ac)));
}
return addXFloat(-x2.asFloat());
@@ -958,7 +958,7 @@
case T.matrix4f:
return addXM4(M4.newM4((M4) x2.value).invert());
case T.bitset:
- return addXBs(BSUtil.copyInvert(SV.bsSelectVar(x2),
+ return addXBs(BSUtil.copyInvert((BS) x2.value,
(x2.value instanceof BondSet ? vwr.ms.bondCount : vwr.ms.ac)));
default:
return addXBool(!x2.asBoolean());
@@ -1074,14 +1074,14 @@
case T.opAnd:
switch (x1.tok) {
case T.bitset:
- BS bs = SV.bsSelectVar(x1);
+ BS bs = (BS) x1.value;
switch (x2.tok) {
case T.integer:
int x = x2.asInt();
return (addXBool(x < 0 ? false : bs.get(x)));
case T.bitset:
bs = BSUtil.copy(bs);
- bs.and(SV.bsSelectVar(x2));
+ bs.and((BS) x2.value);
return addXBs(bs);
}
break;
@@ -1090,10 +1090,10 @@
case T.opOr:
switch (x1.tok) {
case T.bitset:
- BS bs = BSUtil.copy(SV.bsSelectVar(x1));
+ BS bs = BSUtil.copy((BS) x1.value);
switch (x2.tok) {
case T.bitset:
- bs.or(SV.bsSelectVar(x2));
+ bs.or((BS) x2.value);
return addXBs(bs);
case T.integer:
int x = x2.asInt();
@@ -1117,8 +1117,8 @@
return addXBool(x1.asBoolean() || x2.asBoolean());
case T.opXor:
if (x1.tok == T.bitset && x2.tok == T.bitset) {
- BS bs = BSUtil.copy(SV.bsSelectVar(x1));
- bs.xor(SV.bsSelectVar(x2));
+ BS bs = BSUtil.copy((BS) x1.value);
+ bs.xor((BS) x2.value);
return addXBs(bs);
}
boolean a = x1.asBoolean();
@@ -1127,8 +1127,8 @@
case T.opToggle:
if (x1.tok != T.bitset || x2.tok != T.bitset)
return false;
- return addXBs(BSUtil.toggleInPlace(BSUtil.copy(SV.bsSelectVar(x1)),
- SV.bsSelectVar(x2)));
+ return addXBs(BSUtil.toggleInPlace(BSUtil.copy((BS) x1.value),
+ (BS) x2.value));
case T.opLE:
return addXBool(x1.asFloat() <= x2.asFloat());
case T.opGE:
@@ -1543,8 +1543,8 @@
case T.point3f:
return (P3) x.value;
case T.bitset:
- BS bs = SV.bsSelectVar(x);
- if (bs.nextSetBit(0) < 0)
+ BS bs = (BS) x.value;
+ if (bs.isEmpty())
break;
return (P3) eval.getBitsetProperty(bs, T.xyz, null, null,
x.value, null, false, Integer.MAX_VALUE, false);
@@ -1603,7 +1603,7 @@
private boolean getAllProperties(SV x2, String abbr)
throws ScriptException {
- BS bs = SV.bsSelectVar(x2);
+ BS bs = (BS) x2.value;
Lst<T> tokens;
int n = bs.cardinality();
if (n == 0 || !abbr.endsWith("?")
@@ -1636,7 +1636,7 @@
private boolean getBoundBox(SV x2) {
if (x2.tok != T.bitset)
return false;
- BoxInfo b = vwr.ms.getBoxInfo(SV.bsSelectVar(x2), 1);
+ BoxInfo b = vwr.ms.getBoxInfo((BS) x2.value, 1);
P3[] pts = b.getBoundBoxPoints(true);
Lst<P3> list = new Lst<P3>();
for (int i = 0; i < 4; i++)
@@ -1739,7 +1739,7 @@
boolean isAtoms = (op.intValue != T.bonds);
if (!isAtoms && x2.value instanceof BondSet)
return addX(x2);
- BS bs = SV.bsSelectVar(x2);
+ BS bs = (BS) x2.value;
if (isAtoms && bs.cardinality() == 1 && (op.intValue & T.minmaxmask) ==
0)
op.intValue |= T.min;
Object val = eval.getBitsetProperty(bs, op.intValue, null, null,
Modified: branches/v14_4/Jmol/src/org/jmol/scriptext/CmdExt.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/scriptext/CmdExt.java 2015-12-03
21:31:41 UTC (rev 20883)
+++ branches/v14_4/Jmol/src/org/jmol/scriptext/CmdExt.java 2015-12-08
16:01:40 UTC (rev 20884)
@@ -276,7 +276,7 @@
LabelToken[] tokens = (asIdentity ? null : isAtoms ? labeler.compile(
vwr, label, '\0', null) : labeler.compile(vwr, label, '\1',
htValues));
- int nmax = (haveIndex ? 1 : BSUtil.cardinalityOf(bs));
+ int nmax = (haveIndex ? 1 : bs.cardinality());
String[] sout = new String[nmax];
P3 ptTemp = new P3();
for (int j = (haveIndex ? index : bs.nextSetBit(0)); j >= 0; j = bs
@@ -640,7 +640,7 @@
return;
n = vwr.autoHbond(bs1, bs2, false);
if (n != Integer.MIN_VALUE)
- eval.report(GT.i(GT._("{0} hydrogen bonds"), Math.abs(n)));
+ eval.report(GT.i(GT._("{0} hydrogen bonds"), Math.abs(n)), false);
return;
case T.hydrogen:
boolean andBond = (tokAt(2) == T.on);
@@ -1869,7 +1869,7 @@
boolean report = eval.doReport();
if (isDelete) {
if (report)
- eval.report(GT.i(GT._("{0} connections deleted"), nModified));
+ eval.report(GT.i(GT._("{0} connections deleted"), nModified), false);
return;
}
if (isColorOrRadius) {
@@ -1882,7 +1882,7 @@
}
if (report)
eval.report(GT.o(GT._("{0} new bonds; {1} modified"),
- new Object[] { Integer.valueOf(nNew), Integer.valueOf(nModified) }));
+ new Object[] { Integer.valueOf(nNew), Integer.valueOf(nModified) }),
false);
}
private void console() throws ScriptException {
@@ -3775,9 +3775,10 @@
if (timeMsg)
showString(Logger.getTimerMsg("export", 0));
if (msg != null) {
- if (!msg.startsWith("OK"))
+ boolean isError = !msg.startsWith("OK");
+ if (isError)
eval.evalError(msg, null);
- eval.report(data);
+ eval.report(data, isError);
}
return "";
}
@@ -3994,7 +3995,8 @@
private String writeMsg(String msg) throws ScriptException {
if (chk || msg == null)
return "";
- if (!msg.startsWith("OK")) {
+ boolean isError = !msg.startsWith("OK");
+ if (isError) {
e.evalError(msg, null);
/**
* @j2sNative
@@ -4004,7 +4006,7 @@
{
}
}
- e.report(msg);
+ e.report(msg, isError);
return msg;
}
@@ -4738,7 +4740,7 @@
switch (tokAt(++i)) {
case T.bitset:
case T.expressionBegin:
- pt = P3.newP(vwr.ms.getAtomSetCenter(atomExpressionAt(i)));
+ pt = vwr.ms.getAtomSetCenter(atomExpressionAt(i));
vwr.toFractional(pt, true);
i = eval.iToken;
break;
Modified: branches/v14_4/Jmol/src/org/jmol/scriptext/MathExt.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/scriptext/MathExt.java 2015-12-03
21:31:41 UTC (rev 20883)
+++ branches/v14_4/Jmol/src/org/jmol/scriptext/MathExt.java 2015-12-08
16:01:40 UTC (rev 20884)
@@ -757,10 +757,10 @@
return mp.addXBs(data[2] == null ? new BS() : (BS) data[2]);
case T.bondcount:
SV x1 = mp.getX();
- if (x1.tok != T.bitset)
+ if (x1.tok != T.bitset || args.length != 1 || args[0].tok != T.bitset)
return false;
- atoms1 = SV.bsSelectVar(x1);
- atoms2 = SV.bsSelectVar(args[0]);
+ atoms1 = (BS) x1.value;
+ atoms2 = (BS) args[0].value;
Lst<Integer> list = new Lst<Integer>();
Atom[] atoms = vwr.ms.at;
for (int i = atoms1.nextSetBit(0); i >= 0; i = atoms1.nextSetBit(i + 1))
{
@@ -781,9 +781,9 @@
if (isBonds && atoms1 != null)
return false;
if (atoms1 == null)
- atoms1 = SV.bsSelectVar(var);
+ atoms1 = (BS) var.value;
else if (atoms2 == null)
- atoms2 = SV.bsSelectVar(var);
+ atoms2 = (BS) var.value;
else
return false;
break;
@@ -858,8 +858,8 @@
}
if (i == args.length || !(args[i].value instanceof BS))
return false;
- BS bsA = BSUtil.copy(SV.bsSelectVar(args[i++]));
- BS bsB = (i < args.length ? BSUtil.copy(SV.bsSelectVar(args[i])) : null);
+ BS bsA = BSUtil.copy((BS) args[i++].value);
+ BS bsB = (i < args.length ? BSUtil.copy((BS) args[i].value) : null);
RadiusData rd = new RadiusData(null, (distance > 10 ? distance / 100
: distance), (distance > 10 ? EnumType.FACTOR : EnumType.OFFSET),
VDW.AUTO);
@@ -1021,12 +1021,12 @@
boolean isAll = minMax == T.minmaxmask;
switch (x1.tok) {
case T.bitset:
- BS bs = SV.bsSelectVar(x1);
+ BS bs = (BS) x1.value;
BS bs2 = null;
boolean returnAtom = (isMinMax && x3 != null && x3.asBoolean());
switch (x2.tok) {
case T.bitset:
- bs2 = (x2.tok == T.bitset ? SV.bsSelectVar(x2) : null);
+ bs2 = (x2.tok == T.bitset ? (BS) x2.value : null);
//$FALL-THROUGH$
case T.point3f:
Atom[] atoms = vwr.ms.at;
@@ -1200,8 +1200,7 @@
boolean isON = !isList && (argLast.tok == T.on);
try {
if (isChemical) {
- String data = (x1.tok == T.bitset ? vwr.getSmiles(SV.getBitSet(x1,
- false)) : SV.sValue(x1));
+ String data = (x1.tok == T.bitset ? vwr.getSmiles((BS) x1.value) :
SV.sValue(x1));
data = data.length() == 0 ? "" : vwr.getChemicalInfo(data,
args.length > 1 ? T.getTokenFromName(flags.toLowerCase()) : null);
if (data.endsWith("\n"))
@@ -1483,11 +1482,11 @@
} else if (args.length > pt) {
switch (args[pt].tok) {
case T.bitset:
- propertyValue = SV.bsSelectVar(args[pt++]);
+ propertyValue = args[pt++].value;
if (propertyName.equalsIgnoreCase("bondInfo") && args.length > pt
&& args[pt].tok == T.bitset)
propertyValue = new BS[] { (BS) propertyValue,
- SV.bsSelectVar(args[pt]) };
+ (BS) args[pt].value };
break;
case T.hash:
case T.string:
@@ -1497,7 +1496,7 @@
}
}
if (isAtomProperty) {
- BS bs = SV.bsSelectVar(x);
+ BS bs = (BS) x.value;
int iAtom = bs.nextSetBit(0);
if (iAtom < 0)
return mp.addXStr("");
@@ -1568,7 +1567,7 @@
return mp.addXList(listOut);
}
- BS bs = SV.getBitSet(x1, true);
+ BS bs = (x1.tok == T.bitset ? (BS) x1.value : null);
boolean asArray = T.tokAttr(intValue, T.minmaxmask); // "all"
return mp.addXObj(format == null ? "" : bs == null ?
SV.sprintf(PT.formatCheck(format), x1) : e
.getCmdExt().getBitsetIdent(bs, format, x1.value, true, x1.index,
@@ -2082,7 +2081,8 @@
}
if (t456 == null && t < 1e6)
t456 = P3.new3(t, t, t);
- BS bs = SV.getBitSet(mp.getX(), false);
+ SV x = mp.getX();
+ BS bs = (x.tok == T.bitset ? (BS) x.value : new BS());
return mp.addXList(vwr.ms.getModulationList(bs,
(type + "D").toUpperCase().charAt(0), t456));
}
@@ -2109,7 +2109,7 @@
switch (args.length) {
case 1:
if (args[0].tok == T.bitset) {
- BS bs = SV.getBitSet(args[0], false);
+ BS bs = (BS) args[0].value;
if (bs.cardinality() == 3) {
Lst<P3> pts = vwr.ms.getAtomPointVector(bs);
return mp.addXPt4(Measure.getPlaneThroughPoints(pts.get(0),
pts.get(1), pts.get(2),
@@ -2282,7 +2282,7 @@
pt3 = P3.newP((T3) args[0].value);
break;
case T.bitset:
- pt3 = vwr.ms.getAtomSetCenter(SV.bsSelectVar(args[0]));
+ pt3 = vwr.ms.getAtomSetCenter((BS) args[0].value);
break;
default:
return false;
@@ -2649,6 +2649,7 @@
private boolean evaluateScript(ScriptMathProcessor mp, SV[] args, int tok)
throws ScriptException {
+ // eval(cmd)
// javascript(cmd)
// script(cmd)
// script(cmd, syncTarget)
@@ -2668,10 +2669,10 @@
if (!appID.equals("."))
sb.append(vwr.jsEval(appID + "\1" + s));
if (appID.equals(".") || appID.equals("*"))
- e.runScriptBuffer(s, sb);
+ e.runScriptBuffer(s, sb, true);
break;
case T.show:
- e.runScriptBuffer("show " + s, sb);
+ e.runScriptBuffer("show " + s, sb, true);
break;
case T.javascript:
sb.append(vwr.jsEval(s));
@@ -2779,7 +2780,7 @@
switch (tok) {
case T.split:
if (x.tok == T.bitset) {
- BS bsSelected = SV.bsSelectVar(x);
+ BS bsSelected = (BS) x.value;
int modelCount = vwr.ms.mc;
Lst<SV> lst = new Lst<SV>();
for (int i = 0; i < modelCount; i++) {
@@ -2818,9 +2819,8 @@
String pattern = SV.sValue(args[0]);
if (pattern.length() > 0)
try {
- BS bsSelected = (isSelector ? SV.bsSelectVar(mp.getX())
- : args.length == 2 && args[1].tok == T.bitset ? SV
- .bsSelectVar(args[1]) : null);
+ BS bsSelected = (isSelector ? (BS) mp.getX().value
+ : args.length == 2 && args[1].tok == T.bitset ? (BS)
args[1].value : null);
bs = vwr.getSmilesMatcher().getSubstructureSet(pattern, vwr.ms.at,
vwr.ms.ac, bsSelected,
(tok == T.smiles ? JC.SMILES_TYPE_SMILES : JC.SMILES_TYPE_SMARTS));
@@ -2909,9 +2909,10 @@
// {*}.tensor("isc") // only within this atom set
// {atomindex=1}.tensor("isc") // all to this atom
// {*}.tensor("efg","eigenvalues")
- if (args.length > 2)
+ SV x = mp.getX();
+ if (args.length > 2 || x.tok != T.bitset)
return false;
- BS bs = SV.getBitSet(mp.getX(), false);
+ BS bs = (BS) x.value;
String tensorType = (args.length == 0 ? null : SV.sValue(args[0])
.toLowerCase());
JmolNMRInterface calc = vwr.getNMRCalculation();
@@ -2949,7 +2950,7 @@
}
if (isSelector) {
return mp
- .addXObj(e.getBitsetProperty(SV.bsSelectVar(x1), tok, null, null,
+ .addXObj(e.getBitsetProperty((BS) x1.value, tok, null, null,
x1.value, new Object[] { name, params }, false, x1.index,
false));
}
SV var = e.getUserFunctionResult(name, params, null);
@@ -3134,9 +3135,10 @@
plane = e.getHklPlane(pt);
break;
case T.varray:
- if (last != 2)
+ pt = (last == 2 ? SV.ptValue(args[1]) : last == 1 ? P3.new3(Float.NaN, 0,
+ 0) : null);
+ if (pt == null)
return false;
- pt = SV.ptValue(args[1]);
break;
}
if (last > 0 && plane == null && pt == null
@@ -3146,7 +3148,7 @@
if (plane != null)
return mp.addXBs(ms.getAtomsNearPlane(distance, plane));
- bs = (args[last].tok == T.bitset ? SV.bsSelectVar(args[last]) : null);
+ bs = (args[last].tok == T.bitset ? (BS) args[last].value : null);
if (tok == T.unitcell) {
boolean asMap = isWithinModelSet;
return mp
@@ -3220,7 +3222,7 @@
private BS getAtomsNearPts(float distance, T3[] points, BS bsInclude) {
BS bsResult = new BS();
- if (points.length == 0 || bsInclude != null && bsInclude.cardinality() ==
0)
+ if (points.length == 0 || bsInclude != null && bsInclude.isEmpty())
return bsResult;
if (bsInclude == null)
bsInclude = BSUtil.setAll(points.length);
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/AnimationManager.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/AnimationManager.java
2015-12-03 21:31:41 UTC (rev 20883)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/AnimationManager.java
2015-12-08 16:01:40 UTC (rev 20884)
@@ -173,7 +173,7 @@
}
void setDisplay(BS bs) {
- bsDisplay = (bs == null || bs.cardinality() == 0? null : BSUtil.copy(bs));
+ bsDisplay = (bs == null || bs.isEmpty() ? null : BSUtil.copy(bs));
}
public void setMorphCount(int n) {
@@ -439,7 +439,7 @@
setFrameRangeVisible();
vwr.setStatusFrameChanged(false, false);
if (vwr.ms != null && !vwr.g.selectAllModels)
- vwr.slm.setSelectionSubset(vwr.getModelUndeletedAtomsBitSet(cmi));
+
vwr.slm.setSelectionSubset(vwr.ms.getModelAtomBitSetIncludingDeleted(cmi,
true));
}
private void setFrameRangeVisible() {
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/ChimeMessenger.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/ChimeMessenger.java 2015-12-03
21:31:41 UTC (rev 20883)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/ChimeMessenger.java 2015-12-08
16:01:40 UTC (rev 20884)
@@ -33,6 +33,7 @@
import org.jmol.modelset.Group;
import org.jmol.modelset.Model;
import org.jmol.modelset.ModelSet;
+import org.jmol.util.Logger;
/**
*
@@ -86,7 +87,8 @@
if (s == null)
return;
if (outputBuffer == null) {
- vwr.warn(s);
+ if (!vwr.isPrintOnly)
+ Logger.warn(s);
vwr.scriptStatus(s);
} else {
outputBuffer.append(s).appendC('\n');
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/FileManager.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/FileManager.java 2015-12-03
21:31:41 UTC (rev 20883)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/FileManager.java 2015-12-08
16:01:40 UTC (rev 20884)
@@ -595,6 +595,7 @@
}
if (bytes == null && (bytes = getCachedPngjBytes(name)) != null &&
htParams != null)
htParams.put("sourcePNGJ", Boolean.TRUE);
+ name = name.replace("_CHANGEABLE_", "");
String fullName = name;
String[] subFileList = null;
if (name.indexOf("|") >= 0) {
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/GlobalSettings.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/GlobalSettings.java 2015-12-03
21:31:41 UTC (rev 20883)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/GlobalSettings.java 2015-12-08
16:01:40 UTC (rev 20884)
@@ -75,8 +75,9 @@
getDataBaseList(JC.databases);
getDataBaseList(userDatabases);
}
- loadFormat = databases.get("pdb");
- loadLigandFormat = databases.get("ligand");
+ loadFormat = pdbLoadFormat = databases.get("pdb");
+ pdbLoadFormat0 = databases.get("pdb0");
+ pdbLoadLigandFormat = databases.get("ligand");
nmrUrlFormat = databases.get("nmr");
nmrPredictFormat = databases.get("nmrdb");
smilesUrlFormat = databases.get("nci") + "/file?format=sdf&get3d=True";
@@ -283,7 +284,7 @@
setB("legacyJavaFloat", legacyJavaFloat);
setF("loadAtomDataTolerance", loadAtomDataTolerance);
setO("loadFormat", loadFormat);
- setO("loadLigandFormat", loadLigandFormat);
+ setO("loadLigandFormat", pdbLoadLigandFormat);
setB("logCommands", logCommands);
setB("logGestures", logGestures);
setB("measureAllModels", measureAllModels);
@@ -440,7 +441,7 @@
boolean forceAutoBond = false;
boolean fractionalRelative = true;// true: {1/2 1/2 1/2} relative to
current (possibly offset) unit cell
char inlineNewlineChar = '|'; //pseudo static
- String loadFormat, loadLigandFormat, nmrUrlFormat, nmrPredictFormat,
smilesUrlFormat, nihResolverFormat, pubChemFormat;
+ String loadFormat, pdbLoadFormat, pdbLoadFormat0, pdbLoadLigandFormat,
nmrUrlFormat, nmrPredictFormat, smilesUrlFormat, nihResolverFormat,
pubChemFormat;
String edsUrlFormat =
"http://eds.bmc.uu.se/eds/dfs/%LC13/%LCFILE/%LCFILE.omap";;
String edsUrlFormatDiff =
"http://eds.bmc.uu.se/eds/dfs/%LC13/%LCFILE/%LCFILE_diff.omap";;
@@ -888,16 +889,30 @@
return structureList;
}
- String resolveDataBase(String database, String id) {
- String format = databases.get(database.toLowerCase());
- if (format == null)
+ String resolveDataBase(String database, String id, String format) {
+ if (format == null) {
+ if ((format = databases.get(database.toLowerCase())) == null)
return null;
- if (id.indexOf("/") < 0) {
+ int pt = id.indexOf("/");
+ if (pt < 0) {
if (database.equals("pubchem"))
id = "name/" + id;
else if (database.equals("nci"))
id += "/file?format=sdf&get3d=True";
}
+ if (format.startsWith("'")) {
+ // needs evaluation
+ // xxxx.n means "the nth item"
+ pt = id.indexOf(".");
+ int n = (pt > 0 ? PT.parseInt(id.substring(pt + 1)) : 0);
+ if (pt > 0)
+ id = id.substring(0, pt);
+ format = PT.rep(format, "%n", "" + n);
+ }
+ } else if (id.indexOf(".") >= 0 && format.indexOf("%FILE.") >= 0) {
+ // replace RCSB format extension when a file extension is made explicit
+ format = format.substring(0, format.indexOf("%FILE"));
+ }
try {
while (format.indexOf("%c") >= 0)
for (int i = 1; i < 10; i++) {
@@ -906,8 +921,9 @@
} catch (Exception e) {
// too bad.
}
- return (format.indexOf("%FILE") < 0 ? format + id : PT.formatStringS(
- format, "FILE", id));
+ return (format.indexOf("%FILE") >= 0 ? PT.formatStringS(format, "FILE", id)
+ : format.indexOf("%file") >= 0 ? PT.formatStringS(format, "file",
+ id.toLowerCase()) : format + id);
}
static boolean doReportProperty(String name) {
@@ -1018,7 +1034,7 @@
app(str, "set forceAutoBond " + forceAutoBond);
app(str, "#set defaultDirectory " + PT.esc(defaultDirectory));
app(str, "#set loadFormat " + PT.esc(loadFormat));
- app(str, "#set loadLigandFormat " + PT.esc(loadLigandFormat));
+ app(str, "#set loadLigandFormat " + PT.esc(pdbLoadLigandFormat));
app(str, "#set smilesUrlFormat " + PT.esc(smilesUrlFormat));
app(str, "#set nihResolverFormat " + PT.esc(nihResolverFormat));
app(str, "#set pubChemFormat " + PT.esc(pubChemFormat));
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/JC.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/JC.java 2015-12-03 21:31:41 UTC
(rev 20883)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/JC.java 2015-12-08 16:01:40 UTC
(rev 20884)
@@ -66,7 +66,10 @@
"pubchem",
"http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/%FILE/SDF?record_type=3d";,
"map",
"http://www.ebi.ac.uk/pdbe/api/%TYPE/%FILE?pretty=false&metadata=true";,
"rna3d", "http://rna.bgsu.edu/rna3dhub/%TYPE/download/%FILE";,
- "aflow",
"http://aflowlib.mems.duke.edu/users/jmolers/binary_new/%FILE.aflow_binary";
+ "aflow",
"http://aflowlib.mems.duke.edu/users/jmolers/binary_new/%FILE.aflow_binary";,
+ // _CHANGEABLE_ flag indicates that the loaded file should be saved in any
state in full
+ "ams",
"http://rruff.geo.arizona.edu/AMS/viewJmol.php?_CHANGEABLE_&mineral=%file&action=showcif";,
+ "am",
"'http://rruff.geo.arizona.edu/AMS/CIF_text_files/'+load('http://rruff.geo.arizona.edu/AMS/minerals/%FILE').split(\"viewJmol('\")[(%n
== 0 ? 0 : %n + 1)].split(\"'\")[1]+'_cif.txt'"
};
public static String[] macros = {
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2015-12-03
21:31:41 UTC (rev 20883)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2015-12-08
16:01:40 UTC (rev 20884)
@@ -8,10 +8,21 @@
# see also http://chemapps.stolaf.edu/jmol/zip for daily updates
-Jmol.___JmolVersion="14.4.0_2015.12.03"
+Jmol.___JmolVersion="14.4.0_2015.12.07"
+bug fix: set selectAllModels not working appropriately
+bug fix: set selectAllModels should not be saved in state
+
+JmolVersion="14.4.0_2015.12.05"
+
+bug fix: JmolData.jar does not update atom screen positions upon REFRESH or
select {visible}
+bug fix: JmolData.jar -p flag does not work properly
bug fix: model 0 issued when more than one PDB file is open does not execute
model *
+JmolVersion="14.4.0_2015.12.03"
+
+bug fix: model 0 issued when more than one PDB file is open does not execute
model *
+
JmolVersion="14.4.0_2015.12.02"
bug fix: PDB reader broken for filter "biomolecule n"
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/ShapeManager.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/ShapeManager.java 2015-12-03
21:31:41 UTC (rev 20883)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/ShapeManager.java 2015-12-08
16:01:40 UTC (rev 20884)
@@ -401,20 +401,24 @@
private final int[] navMinMax = new int[4];
- public int[] finalizeAtoms(BS bsAtoms, P3 ptOffset) {
+ public int[] finalizeAtoms(boolean checkAtoms, boolean finalizeParams) {
Viewer vwr = this.vwr;
+ if (finalizeParams)
+ vwr.finalizeTransformParameters();
TransformManager tm = vwr.tm;
BS bs = bsRenderableAtoms;
+ BS bsAtoms = (checkAtoms ? tm.bsSelectedAtoms : null);
if (bsAtoms != null) {
// translateSelected operation
P3 ptCenter = ms.getAtomSetCenter(bsAtoms);
P3 pt = new P3();
tm.transformPt3f(ptCenter, pt);
- pt.add(ptOffset);
+ pt.add(tm.ptOffset);
tm.unTransformPoint(pt, pt);
pt.sub(ptCenter);
vwr.setAtomCoordsRelative(pt, bsAtoms);
- ptOffset.set(0, 0, 0);
+ tm.ptOffset.set(0, 0, 0);
+ tm.bsSelectedAtoms = null;
}
ms.getAtomsInFrame(bs);
Vibration[] vibrationVectors = ms.vibrations;
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/Viewer.java 2015-12-03 21:31:41 UTC
(rev 20883)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/Viewer.java 2015-12-08 16:01:40 UTC
(rev 20884)
@@ -265,7 +265,7 @@
String logFilePath = "";
private boolean allowScripting;
- private boolean isPrintOnly = false;
+ public boolean isPrintOnly = false;
public boolean isSignedApplet = false;
private boolean isSignedAppletLocal = false;
private boolean isSilent;
@@ -477,15 +477,15 @@
apiPlatform = (GenericPlatform) o;
display = info.get("display");
isSingleThreaded = apiPlatform.isSingleThreaded();
- noGraphicsAllowed = checkOption2("noGraphics", "-n");
- System.out.println("nographics " + noGraphicsAllowed);
+ noGraphicsAllowed = checkOption2("noDisplay", "-n");
+ //System.out.println("nographics " + noGraphicsAllowed);
headless = apiPlatform.isHeadless();
haveDisplay = (isWebGL || display != null && !noGraphicsAllowed
&& !headless && !dataOnly);
noGraphicsAllowed &= (display == null);
- System.out.println("nographics " + noGraphicsAllowed);
+ //System.out.println("nographics " + noGraphicsAllowed);
headless |= noGraphicsAllowed;
- System.out.println("headless " + headless + commandOptions);
+ //System.out.println("headless " + headless + commandOptions);
if (haveDisplay) {
mustRender = true;
multiTouch = checkOption2("multiTouch", "-multitouch");
@@ -777,8 +777,7 @@
public void initialize(boolean clearUserVariables) {
g = new GlobalSettings(this, g, clearUserVariables);
setStartupBooleans();
- g.setI("_width", dimScreen.width);
- g.setI("_height", dimScreen.height);
+ setWidthHeightVar();
if (haveDisplay) {
g.setB("_is2D", isJS && !isWebGL);
g.setB("_multiTouchClient", acm.isMTClient());
@@ -800,6 +799,11 @@
tm.setDefaultPerspective();
}
+ public void setWidthHeightVar() {
+ g.setI("_width", dimScreen.width);
+ g.setI("_height", dimScreen.height);
+ }
+
void saveModelOrientation() {
ms.saveModelOrientation(am.cmi, stm.getOrientation());
}
@@ -1769,6 +1773,7 @@
}
return null;
}
+ id = id.replace('\\', '/');
boolean isLigand = prefix.equals("ligand_");
id = (isLigand ? id.toUpperCase() : id.substring(id.lastIndexOf("/") + 1));
if (ligandModelSet == null)
@@ -1863,7 +1868,7 @@
boolean haveFileData = (htParams.containsKey("fileData"));
if (fileName.indexOf('$') == 0)
htParams.put("smilesString", fileName.substring(1));
- boolean isString = (fileName.equalsIgnoreCase("string") || fileName
+ boolean isString = (fileName.equals("string") || fileName
.equals(JC.MODELKIT_ZAP_TITLE));
String strModel = null;
if (haveFileData) {
@@ -3333,8 +3338,13 @@
// called by AnimationThread run()
// called by TransformationManager move and moveTo
// called by TransformationManager11 navigate, navigateTo
- if (!haveDisplay || rm == null)
+ if (rm == null)
return;
+ if (!haveDisplay) {
+ setModelVisibility();
+ shm.finalizeAtoms(false, true);
+ return;
+ }
rm.requestRepaintAndWait(why);
setSync();
}
@@ -3616,9 +3626,7 @@
|| rm == null)
return;
boolean antialias2 = antialiased && g.antialiasTranslucent;
- finalizeTransformParameters();
- int[] navMinMax = shm.finalizeAtoms(tm.bsSelectedAtoms, tm.ptOffset);
- tm.bsSelectedAtoms = null;
+ int[] navMinMax = shm.finalizeAtoms(true, true);
if (isWebGL) {
rm.renderExport(gdata, ms, jsParams);
notifyViewerRepaintDone();
@@ -3893,7 +3901,7 @@
* @return String or String[]
*/
public Object setLoadFormat(String name, char type, boolean withPrefix) {
- String format;
+ String format = null;
String f = name.substring(1);
switch (type) {
case '=':
@@ -3905,18 +3913,26 @@
try {
int pt = f.indexOf("/");
String database = f.substring(0, pt);
- f = g.resolveDataBase(database, f.substring(pt + 1));
- return (f == null ? name : f);
+ f = g.resolveDataBase(database, f.substring(pt + 1), null);
+ if (f != null && f.startsWith("'"))
+ f = evaluateExpression(f).toString();
+ return (f == null || f.length() == 0 ? name : f);
} catch (Exception e) {
return name;
}
+ } else {
+ format = (
+ // following is temporary, until issues are resolved for AJAX asych
+ isJS && g.loadFormat.equals(g.pdbLoadFormat) ? g.pdbLoadFormat0
+ : g.loadFormat);
}
//$FALL-THROUGH$
case '#': // ligand
- String s = (type == '=' ? g.loadFormat : g.loadLigandFormat);
- if (f.indexOf(".") > 0 && s.indexOf("%FILE.") >= 0)
- s = s.substring(0, s.indexOf("%FILE") + 5);
- return PT.formatStringS(s, "FILE", f);
+ if (format == null)
+ format = g.pdbLoadLigandFormat;
+ if (f.indexOf(".") >= 0 && format.equals(g.pdbLoadFormat))
+ format = g.pdbLoadFormat0; // older version for =1crn.cif or
=1crn.pdb
+ return g.resolveDataBase(null, f, format);
case '*':
// European Bioinformatics Institute
int pt = name.lastIndexOf("/");
@@ -3924,23 +3940,23 @@
// *dom/.../.../.../xxxx
f = name.substring(pt + 1);
format = (pt > 4 ? name.substring(5) : "mappings");
- return PT.rep(g.resolveDataBase("map", f), "%TYPE", format);
+ return PT.rep(g.resolveDataBase("map", f, null), "%TYPE", format);
} else if (name.startsWith("*val/")) {
// *val/.../.../.../xxxx
f = name.substring(pt + 1);
format = (pt > 4 ? name.substring(5) : "validation/outliers/all");
- return PT.rep(g.resolveDataBase("map", f), "%TYPE", format);
+ return PT.rep(g.resolveDataBase("map", f, null), "%TYPE", format);
} else if (name.startsWith("*rna3d/")) {
// *rna3d/.../.../.../xxxx
f = name.substring(pt + 1);
format = (pt > 6 ? name.substring(6) : "loops");
- return PT.rep(g.resolveDataBase("rna3d", f), "%TYPE", format);
+ return PT.rep(g.resolveDataBase("rna3d", f, null), "%TYPE", format);
} else if (name.startsWith("*dssr/")) {
f = name.substring(pt + 1);
- return g.resolveDataBase("dssr", f);
+ return g.resolveDataBase("dssr", f, null);
} else if (name.startsWith("*dssr1/")) {
f = name.substring(pt + 1);
- return g.resolveDataBase("dssr1", f);
+ return g.resolveDataBase("dssr1", f, null);
}
// these are processed in SmarterJmolAdapter
String pdbe = "pdbe";
@@ -3948,7 +3964,7 @@
pdbe = "pdbe2";
f = f.substring(0, 4);
}
- return g.resolveDataBase(pdbe, f);
+ return g.resolveDataBase(pdbe, f, null);
case ':': // PubChem
format = g.pubChemFormat;
if (f.equals("")) {
@@ -5365,7 +5381,7 @@
return;
case T.loadligandformat:
// /12.1.51//
- g.loadLigandFormat = value;
+ g.pdbLoadLigandFormat = value;
break;
// 12.1.50
case T.defaultlabelpdb:
@@ -6195,6 +6211,10 @@
case T.selectallmodels:
// 11.5.52
g.selectAllModels = value;
+ if (value)
+ slm.setSelectionSubset(null);
+ else
+ slm.setSelectionSubset(ms.getModelAtomBitSetIncludingDeleted(am.cmi,
true));
break;
case T.messagestylechime:
// 11.5.39
@@ -7375,7 +7395,7 @@
}
public void setAtomCoords(BS bs, int tokType, Object xyzValues) {
- if (bs.cardinality() == 0)
+ if (bs.isEmpty())
return;
ms.setAtomCoords(bs, tokType, xyzValues);
checkMinimization();
@@ -7386,7 +7406,7 @@
// Eval
if (bs == null)
bs = bsA();
- if (bs.cardinality() == 0)
+ if (bs.isEmpty())
return;
ms.setAtomCoordsRelative(offset, bs);
checkMinimization();
@@ -7409,7 +7429,7 @@
public void invertSelected(P3 pt, P4 plane, int iAtom, BS invAtoms) {
// Eval
BS bs = bsA();
- if (bs.cardinality() == 0)
+ if (bs.isEmpty())
return;
ms.invertSelected(pt, plane, iAtom, invAtoms, bs);
checkMinimization();
@@ -7419,7 +7439,7 @@
public void moveAtoms(M4 m4, M3 mNew, M3 rotation, V3 translation, P3 center,
boolean isInternal, BS bsAtoms, boolean
translationOnly) {
// from TransformManager exclusively
- if (bsAtoms.cardinality() == 0)
+ if (bsAtoms.isEmpty())
return;
ms.moveAtoms(m4, mNew, rotation, translation, bsAtoms, center, isInternal,
translationOnly);
@@ -7464,7 +7484,7 @@
actionRotateBond(deltaX, deltaY, x, y);
} else {
bsSelected = setMovableBitSet(bsSelected, !asAtoms);
- if (bsSelected.cardinality() != 0) {
+ if (!bsSelected.isEmpty()) {
if (isTranslation) {
P3 ptCenter = ms.getAtomSetCenter(bsSelected);
tm.finalizeTransformParameters();
@@ -8260,11 +8280,6 @@
return getStateCreator().getFunctionCalls(selectedFunction);
}
- public void warn(String s) {
- if (!isPrintOnly)
- Logger.warn(s);
- }
-
/**
* Simple method to ensure that the image creator (which writes files) was in
* fact opened by this vwr and not by some manipulation of the applet. When
@@ -8815,7 +8830,7 @@
try {
if (getScriptManager() == null)
return null;
- eval.runScriptBuffer(script, outputBuffer);
+ eval.runScriptBuffer(script, outputBuffer, false);
} catch (Exception e) {
return eval.getErrorMessage();
}
@@ -8866,7 +8881,7 @@
}
public void calculatePartialCharges(BS bsSelected) throws JmolAsyncException
{
- if (bsSelected == null || bsSelected.cardinality() == 0)
+ if (bsSelected == null || bsSelected.isEmpty())
bsSelected = getModelUndeletedAtomsBitSetBs(getVisibleFramesBitSet());
int pt = bsSelected.nextSetBit(0);
if (pt < 0)
@@ -9003,7 +9018,7 @@
if (bsAtoms == null)
bsAtoms = getModelUndeletedAtomsBitSet(getVisibleFramesBitSet().length()
- 1);
BS bsB = new BS();
- if (bsAtoms.cardinality() == 0)
+ if (bsAtoms.isEmpty())
return bsB;
int modelIndex = ms.at[bsAtoms.nextSetBit(0)].mi;
if (modelIndex != ms.mc - 1)
@@ -9318,7 +9333,7 @@
void dragMinimizeAtom(int iAtom) {
stopMinimization();
- BS bs = (getMotionFixedAtoms().cardinality() == 0 ? ms.getAtoms(
+ BS bs = (getMotionFixedAtoms().isEmpty() ? ms.getAtoms(
(ms.isAtomPDB(iAtom) ? T.group : T.molecule),
BSUtil.newAndSetBit(iAtom)) : BSUtil.setAll(ms.ac));
try {
Modified: branches/v14_4/Jmol/src/org/openscience/jmol/app/JmolData.java
===================================================================
--- branches/v14_4/Jmol/src/org/openscience/jmol/app/JmolData.java
2015-12-03 21:31:41 UTC (rev 20883)
+++ branches/v14_4/Jmol/src/org/openscience/jmol/app/JmolData.java
2015-12-08 16:01:40 UTC (rev 20884)
@@ -25,7 +25,6 @@
import javajs.util.PT;
-import org.jmol.api.JmolViewer;
import org.jmol.util.Escape;
import org.jmol.viewer.Viewer;
@@ -42,7 +41,7 @@
*/
public JmolApp jmolApp;
- public JmolViewer vwr;
+ public Viewer vwr;
public static JmolData getJmol(int width, int height, String commandOptions)
{
JmolApp jmolApp = new JmolApp();
@@ -82,6 +81,7 @@
this.jmolApp = jmolApp;
vwr = new Viewer(jmolApp.info);
vwr.setScreenDimension(jmolApp.startupWidth, jmolApp.startupHeight);
+ vwr.setWidthHeightVar();
jmolApp.startViewer(vwr, null, true);
}
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