Revision: 20963
http://sourceforge.net/p/jmol/code/20963
Author: hansonr
Date: 2016-02-18 04:29:30 +0000 (Thu, 18 Feb 2016)
Log Message:
-----------
Jmol.___JmolVersion="14.4.3_2016.02.17"
bug fix: slab/depth SET do not behave properly
bug fix: select VISIBLE is not properly set based on slab/depth SET
bug fix: _GEOM_BOND reading in CIF files nonfunctional.
-- broken in 13.3.4_dev_2013.08.21
-- result is that between 8/21/2013 and 2/15/2016 the CIF reader
would not recognize _GEOM_BOND and so also not create whole molecules
as it was designed to do when those are present.
-- no impact on states created within this version range
-- no impact on mmCIF reader
-- only impact is upon Materials Studio-generated files such as
http://www.rsc.org/suppdata/cc/c2/c2cc34714h/c2cc34714h.txt
(supplemental mat. for
http://pubs.rsc.org/en/Content/ArticleLanding/2012/CC/c2cc34714h)
See Jmol list discussion:
https://sourceforge.net/p/jmol/mailman/message/31308577/
Modified Paths:
--------------
branches/v14_4/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java
branches/v14_4/Jmol/src/org/jmol/adapter/readers/cif/MMCifReader.java
branches/v14_4/Jmol/src/org/jmol/export/__RayTracerExporter.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/render/SticksRenderer.java
branches/v14_4/Jmol/src/org/jmol/script/ScriptEval.java
branches/v14_4/Jmol/src/org/jmol/scriptext/IsoExt.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/StateCreator.java
branches/v14_4/Jmol/src/org/jmol/viewer/TransformManager.java
branches/v14_4/Jmol/src/org/jmol/viewer/Viewer.java
trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java
trunk/Jmol/src/org/jmol/adapter/readers/cif/MMCifReader.java
trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
trunk/Jmol/src/org/jmol/adapter/smarter/XtalSymmetry.java
trunk/Jmol/src/org/jmol/export/__RayTracerExporter.java
trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
trunk/Jmol/src/org/jmol/render/RepaintManager.java
trunk/Jmol/src/org/jmol/render/SticksRenderer.java
trunk/Jmol/src/org/jmol/script/ScriptEval.java
trunk/Jmol/src/org/jmol/scriptext/IsoExt.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/ShapeManager.java
trunk/Jmol/src/org/jmol/viewer/StateCreator.java
trunk/Jmol/src/org/jmol/viewer/TransformManager.java
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: branches/v14_4/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java
2016-02-15 20:33:16 UTC (rev 20962)
+++ branches/v14_4/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java
2016-02-18 04:29:30 UTC (rev 20963)
@@ -51,8 +51,8 @@
* A true line-free CIF file reader for CIF files.
*
* Subclasses of CIF -- mmCIF/PDBx (pre-initialized) and msCIF (initialized
- * here).
- *
+ * here)
+ *
* Note that a file can be a PDB file without being
*
* Added nonstandard mCIF (magnetic_ tags) 5/2/2014 note that PRELIM keys can
be
@@ -84,7 +84,6 @@
GenericCifDataParser parser;
- private boolean isMolecular;
private boolean filterAssembly;
private boolean allowRotations = true;
private boolean readIdeal = true;
@@ -181,6 +180,8 @@
private boolean readAllData() throws Exception {
if (key.startsWith("data_")) {
isLigand = false;
+ if (asc.atomSetCount == 0)
+ iHaveDesiredModel = false;
if (iHaveDesiredModel)
return false;
if (desiredModelNumber != Integer.MIN_VALUE)
@@ -222,7 +223,7 @@
* tokenizer.getTokenPeeked(); continue; }
*/
if (key.indexOf("_") != 0) {
- Logger.warn("CIF ERROR ? should be an underscore: " + key);
+ Logger.warn("CIF ERROR ? should be an underscore: " + key);
parser.getTokenPeeked();
} else if (!getData()) {
return true;
@@ -243,22 +244,26 @@
processCellParameter();
} else if (key.startsWith("_atom_sites_fract_tran")) {
processUnitCellTransformMatrix();
- } else if (key.equals("_audit_block_code")) {
- auditBlockCode = parser.fullTrim(data).toUpperCase();
- appendLoadNote(auditBlockCode);
- if (htAudit != null && auditBlockCode.contains("_MOD_")) {
- String key = PT.rep(auditBlockCode, "_MOD_", "_REFRNCE_");
- if (asc.setSymmetry((SymmetryInterface) htAudit.get(key)) != null) {
- unitCellParams = asc.getSymmetry().getUnitCellParams();
- iHaveUnitCell = true;
+ } else if (key.startsWith("_audit")) {
+ if (key.equals("_audit_block_code")) {
+ auditBlockCode = parser.fullTrim(data).toUpperCase();
+ appendLoadNote(auditBlockCode);
+ if (htAudit != null && auditBlockCode.contains("_MOD_")) {
+ String key = PT.rep(auditBlockCode, "_MOD_", "_REFRNCE_");
+ if (asc.setSymmetry((SymmetryInterface) htAudit.get(key)) != null)
{
+ unitCellParams = asc.getSymmetry().getUnitCellParams();
+ iHaveUnitCell = true;
+ }
+ } else if (htAudit != null) {
+ if (symops != null)
+ for (int i = 0; i < symops.size(); i++)
+ setSymmetryOperator(symops.get(i));
}
- } else if (htAudit != null) {
- if (symops != null)
- for (int i = 0; i < symops.size(); i++)
- setSymmetryOperator(symops.get(i));
+ if (lastSpaceGroupName != null)
+ setSpaceGroupName(lastSpaceGroupName);
+ } else if (key.equals("_audit_creation_date")) {
+ symmetry = null;
}
- if (lastSpaceGroupName != null)
- setSpaceGroupName(lastSpaceGroupName);
} else if (key.equals(singleAtomID)) {
readSingleAtom();
} else if (key.startsWith("_symmetry_space_group_name_h-m")
@@ -847,7 +852,7 @@
*/
private void processAtomTypeLoopBlock() throws Exception {
parseLoopParameters(atomTypeFields);
- if (!checkAllFieldsPresent(atomTypeFields, false)) {
+ if (!checkAllFieldsPresent(atomTypeFields, -1, false)) {
parser.skipLoop(false);
return;
}
@@ -1519,8 +1524,12 @@
* @throws Exception
*/
private void processGeomBondLoopBlock() throws Exception {
+ // broken in 13.3.4_dev_2013.08.20c
+ // fixed in 14.4.3_2016.02.16
+ boolean bondLoopBug = (stateScriptVersionInt >= 130304 &&
stateScriptVersionInt < 140403
+ || stateScriptVersionInt >= 150000 && stateScriptVersionInt < 150403);
parseLoopParameters(geomBondFields);
- if (!checkAllFieldsPresent(geomBondFields, true)) {
+ if (bondLoopBug || !checkAllFieldsPresent(geomBondFields, 2, true)) {
parser.skipLoop(false);
return;
}
@@ -1556,6 +1565,12 @@
dx = 0.015f;
}
int order = getBondOrder(getField(CCDC_GEOM_BOND_TYPE));
+ // This field is from Materials Studio. See supplemental material for
+ // http://pubs.rsc.org/en/Content/ArticleLanding/2012/CC/c2cc34714h
+ // http://www.rsc.org/suppdata/cc/c2/c2cc34714h/c2cc34714h.txt
+ // Jmol list discussion:
https://sourceforge.net/p/jmol/mailman/message/31308577/
+ // this 5-model file can be read using one model at a time: load
"c2cc34714h.txt" 3
+ // but it is far from perfect, and still the best way is load
"c2cc34714h.txt" 3 packed
bondCount++;
bondTypes.addLast(new Object[] { name1, name2, Float.valueOf(distance),
Float.valueOf(dx), Integer.valueOf(order) });
@@ -1594,12 +1609,12 @@
* (g) set all coordinates as Cartesians (h) remove all unit cell information
*/
private void setBondingAndMolecules() {
- Logger.info("CIF creating molecule "
- + (bondTypes.size() > 0 ? " using GEOM_BOND records" : ""));
atoms = asc.atoms;
firstAtom = asc.getLastAtomSetAtomIndex();
int nat = asc.getLastAtomSetAtomCount();
ac = firstAtom + nat;
+ Logger.info("CIF creating molecule for " + nat + " atoms "
+ + (bondTypes.size() > 0 ? " using GEOM_BOND records" : ""));
// get list of sites based on atom names
@@ -1836,8 +1851,8 @@
return doCheckUnitCell;
}
- protected boolean checkAllFieldsPresent(String[] keys, boolean critical) {
- for (int i = keys.length; --i >= 0;)
+ protected boolean checkAllFieldsPresent(String[] keys, int lastKey, boolean
critical) {
+ for (int i = (lastKey < 0 ? keys.length : lastKey); --i >= 0;)
if (key2col[i] == NONE) {
if (critical)
Logger.warn("CIF reader missing property: " + keys[i]);
Modified: branches/v14_4/Jmol/src/org/jmol/adapter/readers/cif/MMCifReader.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/adapter/readers/cif/MMCifReader.java
2016-02-15 20:33:16 UTC (rev 20962)
+++ branches/v14_4/Jmol/src/org/jmol/adapter/readers/cif/MMCifReader.java
2016-02-18 04:29:30 UTC (rev 20963)
@@ -688,7 +688,7 @@
*/
private boolean processStructConfLoopBlock() throws Exception {
parseLoopParametersFor(FAMILY_STRUCTCONF, structConfFields);
- if (!checkAllFieldsPresent(structConfFields, true)) {
+ if (!checkAllFieldsPresent(structConfFields, -1, true)) {
parser.skipLoop(true);
return false;
}
@@ -772,7 +772,7 @@
*/
private boolean processStructSheetRangeLoopBlock() throws Exception {
parseLoopParametersFor(FAMILY_SHEET, structSheetRangeFields);
- if (!checkAllFieldsPresent(structSheetRangeFields, true)) {
+ if (!checkAllFieldsPresent(structSheetRangeFields, -1, true)) {
parser.skipLoop(true);
return false;
}
Modified: branches/v14_4/Jmol/src/org/jmol/export/__RayTracerExporter.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/export/__RayTracerExporter.java
2016-02-15 20:33:16 UTC (rev 20962)
+++ branches/v14_4/Jmol/src/org/jmol/export/__RayTracerExporter.java
2016-02-18 04:29:30 UTC (rev 20963)
@@ -61,7 +61,7 @@
if (super.initOutput(vwr, privateKey, g3d, params)) {
vwr.tm.perspectiveDepth = false;
if (wasPerspective)
- vwr.shm.finalizeAtoms(false, false);
+ vwr.shm.finalizeAtoms(null, false);
return true;
}
return false;
Modified: branches/v14_4/Jmol/src/org/jmol/modelset/AtomCollection.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/modelset/AtomCollection.java
2016-02-15 20:33:16 UTC (rev 20962)
+++ branches/v14_4/Jmol/src/org/jmol/modelset/AtomCollection.java
2016-02-18 04:29:30 UTC (rev 20963)
@@ -2466,14 +2466,16 @@
public BS getVisibleSet(boolean forceNew) {
if (forceNew) {
vwr.setModelVisibility();
- vwr.shm.finalizeAtoms(false, true);
+ vwr.shm.finalizeAtoms(null, true);
+ } else if (haveBSVisible) {
+ return bsVisible;
}
- else if (haveBSVisible)
- return bsVisible;
bsVisible.clearAll();
for (int i = ac; --i >= 0;)
if (at[i].checkVisible())
bsVisible.set(i);
+ if (vwr.shm.bsSlabbedInternal != null)
+ bsVisible.andNot(vwr.shm.bsSlabbedInternal);
haveBSVisible = true;
return bsVisible;
}
Modified: branches/v14_4/Jmol/src/org/jmol/render/RepaintManager.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/render/RepaintManager.java 2016-02-15
20:33:16 UTC (rev 20962)
+++ branches/v14_4/Jmol/src/org/jmol/render/RepaintManager.java 2016-02-18
04:29:30 UTC (rev 20963)
@@ -243,7 +243,7 @@
public String renderExport(GData gdata, ModelSet modelSet,
Map<String, Object> params) {
boolean isOK;
- shapeManager.finalizeAtoms(false, true);
+ shapeManager.finalizeAtoms(null, true);
JmolRendererInterface exporter3D = vwr.initializeExporter(params);
isOK = (exporter3D != null);
if (!isOK) {
Modified: branches/v14_4/Jmol/src/org/jmol/render/SticksRenderer.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/render/SticksRenderer.java 2016-02-15
20:33:16 UTC (rev 20962)
+++ branches/v14_4/Jmol/src/org/jmol/render/SticksRenderer.java 2016-02-18
04:29:30 UTC (rev 20963)
@@ -169,9 +169,9 @@
return false;
if (slabbing) {
- if (vwr.gdata.isClippedZ(a.sZ) && vwr.gdata.isClippedZ(b.sZ)
- || slabByAtom
- && (vwr.gdata.isClippedZ(a.sZ) || vwr.gdata.isClippedZ(b.sZ)))
+ boolean ba = vwr.gdata.isClippedZ(a.sZ);
+ if (ba && vwr.gdata.isClippedZ(b.sZ) || slabByAtom
+ && (ba || vwr.gdata.isClippedZ(b.sZ)))
return false;
}
zA = a.sZ;
@@ -182,14 +182,12 @@
colixB = atomB0.colixAtom;
if (((colix = bond.colix) & C.OPAQUE_MASK) == C.USE_PALETTE) {
colix = (short) (colix & ~C.OPAQUE_MASK);
- colixA = C
- .getColixInherited(
- (short) (colix | vwr.cm.getColixAtomPalette(atomA0, PAL.CPK.id)),
- colixA);
- colixB = C
- .getColixInherited(
- (short) (colix | vwr.cm.getColixAtomPalette(atomB0, PAL.CPK.id)),
- colixB);
+ colixA = C.getColixInherited(
+ (short) (colix | vwr.cm.getColixAtomPalette(atomA0, PAL.CPK.id)),
+ colixA);
+ colixB = C.getColixInherited(
+ (short) (colix | vwr.cm.getColixAtomPalette(atomB0, PAL.CPK.id)),
+ colixB);
} else {
colixA = C.getColixInherited(colix, colixA);
colixB = C.getColixInherited(colix, colixB);
@@ -258,7 +256,6 @@
}
}
-
// set the diameter
xA = a.sX;
Modified: branches/v14_4/Jmol/src/org/jmol/script/ScriptEval.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/script/ScriptEval.java 2016-02-15
20:33:16 UTC (rev 20962)
+++ branches/v14_4/Jmol/src/org/jmol/script/ScriptEval.java 2016-02-18
04:29:30 UTC (rev 20963)
@@ -7508,10 +7508,8 @@
return;
case T.set:
checkLength(2);
- if (chk)
- return;
- vwr.tm.setSlabDepthInternal(isDepth);
- setBooleanProperty("slabEnabled", true);
+ if (!chk)
+ vwr.tm.setSlabDepthInternal(isDepth);
return;
case T.minus:
str = paramAsStr(2);
Modified: branches/v14_4/Jmol/src/org/jmol/scriptext/IsoExt.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/scriptext/IsoExt.java 2016-02-15
20:33:16 UTC (rev 20962)
+++ branches/v14_4/Jmol/src/org/jmol/scriptext/IsoExt.java 2016-02-18
04:29:30 UTC (rev 20963)
@@ -1132,7 +1132,7 @@
boolean isPmesh = (iShape == JC.SHAPE_PMESH);
boolean isPlot3d = (iShape == JC.SHAPE_PLOT3D);
boolean isLcaoCartoon = (iShape == JC.SHAPE_LCAOCARTOON);
- boolean isSilent = (isLcaoCartoon || tokAt(1) == T.delete);
+ boolean isSilent = (isLcaoCartoon || tokAt(1) == T.delete ||
eval.isStateScript);
boolean surfaceObjectSeen = false;
boolean planeSeen = false;
boolean isMapped = false;
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2016-02-15
20:33:16 UTC (rev 20962)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2016-02-18
04:29:30 UTC (rev 20963)
@@ -7,11 +7,22 @@
# see also http://chemapps.stolaf.edu/jmol/zip for daily updates
-Jmol.___JmolVersion="14.4.2_2016.02.15"
+Jmol.___JmolVersion="14.4.3_2016.02.17"
+bug fix: slab/depth SET do not behave properly
+bug fix: select VISIBLE is not properly set based on slab/depth SET
+
bug fix: _GEOM_BOND reading in CIF files nonfunctional.
- -- broken in 14.3.16_2015.08.11
- -- only affects CCDC file reading, as it requires presence of
_ccdc_geom_bond_type
+ -- broken in 13.3.4_dev_2013.08.21
+ -- result is that between 8/21/2013 and 2/15/2016 the CIF reader
+ would not recognize _GEOM_BOND and so also not create whole molecules
+ as it was designed to do when those are present.
+ -- no impact on states created within this version range
+ -- no impact on mmCIF reader
+ -- only impact is upon Materials Studio-generated files such as
+ http://www.rsc.org/suppdata/cc/c2/c2cc34714h/c2cc34714h.txt
+ (supplemental mat. for
http://pubs.rsc.org/en/Content/ArticleLanding/2012/CC/c2cc34714h)
+ See Jmol list discussion:
https://sourceforge.net/p/jmol/mailman/message/31308577/
JmolVersion="14.4.2_2016.02.14"
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/ShapeManager.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/ShapeManager.java 2016-02-15
20:33:16 UTC (rev 20962)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/ShapeManager.java 2016-02-18
04:29:30 UTC (rev 20963)
@@ -57,6 +57,7 @@
public ShapeManager(Viewer vwr) {
this.vwr = vwr;
bsRenderableAtoms = new BS();
+ bsSlabbedInternal = new BS();
}
/**
@@ -308,10 +309,11 @@
Object getProperty(Object paramInfo) {
if (paramInfo.equals("getShapes"))
return shapes;
+ // could be more here...
return null;
}
- public final BS bsRenderableAtoms;
+ public final BS bsRenderableAtoms, bsSlabbedInternal;
public Shape getShape(int i) {
//RepaintManager
@@ -401,39 +403,43 @@
private final int[] navMinMax = new int[4];
- public int[] finalizeAtoms(boolean checkAtoms, boolean finalizeParams) {
+ public int[] finalizeAtoms(BS bsTranslateSelected, boolean finalizeParams) {
Viewer vwr = this.vwr;
+ TransformManager tm = vwr.tm;
if (finalizeParams)
vwr.finalizeTransformParameters();
- TransformManager tm = vwr.tm;
- BS bs = bsRenderableAtoms;
- BS bsAtoms = (checkAtoms ? tm.bsSelectedAtoms : null);
- if (bsAtoms != null) {
+ if (bsTranslateSelected != null) {
// translateSelected operation
- P3 ptCenter = ms.getAtomSetCenter(bsAtoms);
+ P3 ptCenter = ms.getAtomSetCenter(bsTranslateSelected);
P3 pt = new P3();
tm.transformPt3f(ptCenter, pt);
pt.add(tm.ptOffset);
tm.unTransformPoint(pt, pt);
pt.sub(ptCenter);
- vwr.setAtomCoordsRelative(pt, bsAtoms);
+ vwr.setAtomCoordsRelative(pt, bsTranslateSelected);
tm.ptOffset.set(0, 0, 0);
tm.bsSelectedAtoms = null;
}
- ms.getAtomsInFrame(bs);
+ BS bsOK = bsRenderableAtoms;
+ ms.getAtomsInFrame(bsOK);
Vibration[] vibrationVectors = ms.vibrations;
boolean vibs = (vibrationVectors != null && tm.vibrationOn);
boolean checkOccupancy = (ms.bsModulated != null && ms.occupancies !=
null);
Atom[] atoms = ms.at;
int occ;
boolean haveMods = false;
- for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
+ BS bsSlabbed = bsSlabbedInternal;
+ bsSlabbed.clearAll();
+ for (int i = bsOK.nextSetBit(0); i >= 0; i = bsOK.nextSetBit(i + 1)) {
// note that this vibration business is not compatible with
// PDB objects such as cartoons and traces, which
// use Cartesian coordinates, not screen coordinates
Atom atom = atoms[i];
P3i screen = (vibs && atom.hasVibration() ? tm.transformPtVib(atom,
vibrationVectors[i]) : tm.transformPt(atom));
+ if (screen.z == 1 && tm.internalSlab && tm.xyzIsSlabbedInternal(atom)) {
+ bsSlabbed.set(i);
+ }
atom.sX = screen.x;
atom.sY = screen.y;
atom.sZ = screen.z;
@@ -471,7 +477,7 @@
JmolMolecule m = molecules[i];
int j = 0;
int pt = m.firstAtomIndex;
- if (!bs.get(pt))
+ if (!bsOK.get(pt))
continue;
for (; j < m.ac; j++, pt++)
if (gdata.isClippedZ(atoms[pt].sZ - (atoms[pt].sD >> 1)))
@@ -479,13 +485,13 @@
if (j != m.ac) {
pt = m.firstAtomIndex;
for (int k = 0; k < m.ac; k++) {
- bs.clear(pt);
+ bsOK.clear(pt);
atoms[pt++].sZ = 0;
}
}
}
}
- for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
+ for (int i = bsOK.nextSetBit(0); i >= 0; i = bsOK.nextSetBit(i + 1)) {
Atom atom = atoms[i];
if (gdata.isClippedZ(atom.sZ - (slabByAtom ? atoms[i].sD >> 1 : 0))) {
atom.setClickable(0);
@@ -494,7 +500,7 @@
int r = (slabByAtom ? -1 : 1) * atom.sD / 2;
if (atom.sZ + r < minZ || atom.sZ - r > maxZ
|| !gdata.isInDisplayRange(atom.sX, atom.sY)) {
- bs.clear(i);
+ bsOK.clear(i);
}
}
}
@@ -506,7 +512,7 @@
int maxX = Integer.MIN_VALUE;
int minY = Integer.MAX_VALUE;
int maxY = Integer.MIN_VALUE;
- for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
+ for (int i = bsOK.nextSetBit(0); i >= 0; i = bsOK.nextSetBit(i + 1)) {
Atom atom = atoms[i];
if (atom.sX < minX)
minX = atom.sX;
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/StateCreator.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/StateCreator.java 2016-02-15
20:33:16 UTC (rev 20962)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/StateCreator.java 2016-02-18
04:29:30 UTC (rev 20963)
@@ -233,8 +233,7 @@
}
@Override
- String getModelState(SB sfunc, boolean isAll,
- boolean withProteinStructure) {
+ String getModelState(SB sfunc, boolean isAll, boolean withProteinStructure) {
SB commands = new SB();
if (isAll && sfunc != null) {
sfunc.append(" _setModelState;\n");
@@ -262,22 +261,21 @@
SB sb = new SB();
for (int i = 0; i < ms.bondCount; i++)
if (!models[bonds[i].atom1.mi].isModelKit)
- if (bonds[i].isHydrogen()
- || (bonds[i].order & Edge.BOND_NEW) != 0) {
+ if (bonds[i].isHydrogen() || (bonds[i].order & Edge.BOND_NEW) != 0) {
Bond bond = bonds[i];
int index = bond.atom1.i;
if (bond.atom1.group.isAdded(index))
index = -1 - index;
- sb.appendI(index).appendC('\t').appendI(bond.atom2.i).appendC(
- '\t').appendI(bond.order & ~Edge.BOND_NEW).appendC('\t')
- .appendF(bond.mad / 1000f).appendC('\t').appendF(
- bond.getEnergy()).appendC('\t').append(
- Edge.getBondOrderNameFromOrder(bond.order)).append(
- ";\n");
+ sb.appendI(index).appendC('\t').appendI(bond.atom2.i).appendC('\t')
+ .appendI(bond.order & ~Edge.BOND_NEW).appendC('\t')
+ .appendF(bond.mad / 1000f).appendC('\t')
+ .appendF(bond.getEnergy()).appendC('\t')
+ .append(Edge.getBondOrderNameFromOrder(bond.order))
+ .append(";\n");
}
if (sb.length() > 0)
- commands.append("data \"connect_atoms\"\n").appendSB(sb).append(
- "end \"connect_atoms\";\n");
+ commands.append("data \"connect_atoms\"\n").appendSB(sb)
+ .append("end \"connect_atoms\";\n");
commands.append("\n");
}
@@ -302,12 +300,14 @@
// unnecessary. Removed in 11.5.35 -- oops!
if (withProteinStructure)
- commands.append(ms.getProteinStructureState(null, isAll ? T.all :
T.state));
+ commands.append(ms
+ .getProteinStructureState(null, isAll ? T.all : T.state));
// introduced in 14.4.2
for (int i = 0; i < modelCount; i++)
if (models[i].mat4 != null)
- commands.append(" frame orientation " + ms.getModelNumberDotted(i) +
Escape.matrixToScript(models[i].mat4) + ";\n");
+ commands.append(" frame orientation " + ms.getModelNumberDotted(i)
+ + Escape.matrixToScript(models[i].mat4) + ";\n");
getShapeState(commands, isAll, Integer.MAX_VALUE);
@@ -319,33 +319,31 @@
break;
}
SB sb = new SB();
- for (int i = 0; i < modelCount; i++) {
+ for (int i = 0; i < modelCount; i++) {
Model m = models[i];
sb.setLength(0);
String s = (String) ms.getInfo(i, "modelID");
- if (s != null
- && !s.equals(ms.getInfo(i, "modelID0")))
- sb.append(" frame ID ").append(PT.esc(s))
- .append(";\n");
+ if (s != null && !s.equals(ms.getInfo(i, "modelID0")))
+ sb.append(" frame ID ").append(PT.esc(s)).append(";\n");
String t = ms.frameTitles[i];
if (t != null && t.length() > 0)
- sb.append(" frame title ").append(PT.esc(t))
- .append(";\n");
+ sb.append(" frame title ").append(PT.esc(t)).append(";\n");
if (needOrientations && m.orientation != null
&& !ms.isTrajectorySubFrame(i))
- sb.append(" ").append(
- m.orientation.getMoveToText(false)).append(";\n");
+ sb.append(" ").append(m.orientation.getMoveToText(false))
+ .append(";\n");
if (m.frameDelay != 0 && !ms.isTrajectorySubFrame(i))
- sb.append(" frame delay ").appendF(
- m.frameDelay / 1000f).append(";\n");
+ sb.append(" frame delay ").appendF(m.frameDelay / 1000f)
+ .append(";\n");
if (m.simpleCage != null) {
- sb.append(" unitcell ").append(
- Escape.eAP(m.simpleCage.getUnitCellVectors())).append(
- ";\n");
+ sb.append(" unitcell ")
+ .append(Escape.eAP(m.simpleCage.getUnitCellVectors()))
+ .append(";\n");
getShapeState(sb, isAll, JC.SHAPE_UCCAGE);
}
if (sb.length() > 0)
- commands.append(" frame " + ms.getModelNumberDotted(i) +
";\n").appendSB(sb);
+ commands.append(" frame " + ms.getModelNumberDotted(i) + ";\n")
+ .appendSB(sb);
}
boolean loadUC = false;
@@ -358,9 +356,8 @@
sb.setLength(0);
if (symmetry.getState(sb)) {
loadUC = true;
- commands.append(" frame ")
- .append(ms.getModelNumberDotted(i))
- .appendSB(sb).append(";\n");
+ commands.append(" frame ").append(ms.getModelNumberDotted(i))
+ .appendSB(sb).append(";\n");
}
haveModulation |= (vwr.ms.getLastVibrationVector(i, T.modulation) >=
0);
}
@@ -383,8 +380,8 @@
}
commands.append(" set fontScaling " + vwr.getBoolean(T.fontscaling)
+ ";\n");
-// if (vwr.getBoolean(T.modelkitmode))
- // commands.append(" set modelKitMode true;\n");
+ // if (vwr.getBoolean(T.modelkitmode))
+ // commands.append(" set modelKitMode true;\n");
}
if (sfunc != null)
commands.append("\n}\n\n");
@@ -811,11 +808,12 @@
if (vwr.ms.modelSetHasVibrationVectors() && tm.vibrationOn)
app(commands, "set vibrationPeriod " + tm.vibrationPeriod
+ ";vibration on");
+ boolean slabInternal = (tm.depthPlane != null || tm.slabPlane != null);
if (navigating) {
commands.append(tm.getNavigationState());
- if (tm.depthPlane != null || tm.slabPlane != null)
- commands.append(" slab on;\n");
- }
+ }
+ if (!tm.slabEnabled && slabInternal)
+ commands.append(" slab off;\n");
if (sfunc != null)
commands.append("}\n\n");
return commands.toString();
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/TransformManager.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/TransformManager.java
2016-02-15 20:33:16 UTC (rev 20962)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/TransformManager.java
2016-02-18 04:29:30 UTC (rev 20963)
@@ -831,7 +831,7 @@
public boolean slabEnabled;
public boolean zShadeEnabled;
- boolean internalSlab;
+ public boolean internalSlab;
int slabPercentSetting;
int depthPercentSetting;
@@ -851,8 +851,7 @@
}
void setSlabEnabled(boolean slabEnabled) {
- this.slabEnabled = slabEnabled;
- vwr.g.setB("slabEnabled", slabEnabled);
+ vwr.g.setB("slabEnabled", this.slabEnabled = slabEnabled);
}
void setZShadeEnabled(boolean zShadeEnabled) {
@@ -922,15 +921,16 @@
}
public void slabToPercent(int percentSlab) {
+ slabPlane = null;
vwr.setFloatProperty("slabRange", 0);
slabPercentSetting = percentSlab;
- slabPlane = null;
if (depthPercentSetting >= slabPercentSetting)
depthPercentSetting = slabPercentSetting - 1;
slabDepthChanged();
}
public void depthToPercent(int percentDepth) {
+ depthPlane = null;
vwr.g.setI("depth", percentDepth);
depthPercentSetting = percentDepth;
if (slabPercentSetting <= depthPercentSetting)
@@ -972,23 +972,24 @@
depthPlane = null;
else
slabPlane = null;
+ finalizeTransformParameters();
slabInternal(getSlabDepthPlane(isDepth), isDepth);
}
private P4 getSlabDepthPlane(boolean isDepth) {
// the third row of the matrix defines the Z coordinate, which is all we
need
// and, in fact, it defines the plane. How convenient!
- // eval "slab set"
+ // eval "slab set"
if (isDepth) {
if (depthPlane != null)
return depthPlane;
- } else {
- if (slabPlane != null)
+ } else if (slabPlane != null) {
return slabPlane;
}
M4 m = matrixTransform;
- return P4.new4(-m.m20, -m.m21, -m.m22, -m.m23
+ P4 plane = P4.new4(-m.m20, -m.m21, -m.m22, -m.m23
+ (isDepth ? depthValue : slabValue));
+ return plane;
}
/* ***************************************************************
@@ -1446,7 +1447,6 @@
// don't care
}
}
-
vwr.g.setO("_slabPlane", Escape.eP4(getSlabDepthPlane(false)));
vwr.g.setO("_depthPlane", Escape.eP4(getSlabDepthPlane(true)));
if (slabEnabled)
@@ -1508,9 +1508,16 @@
public void transformPtScrT3(T3 ptXYZ, T3 pointScreen) {
transformPt(ptXYZ);
+ // note that this point may be returned as z=1 if the point is
+ // past the camera or slabbed internally
pointScreen.setT(fScrPt);
}
+ public void transformPt3f(T3 ptXYZ, P3 screen) {
+ applyPerspective(ptXYZ, ptXYZ);
+ screen.setT(fScrPt);
+ }
+
public void transformPtNoClip(T3 ptXYZ, T3 pointScreen) {
applyPerspective(ptXYZ, null);
pointScreen.setT(fScrPt);
@@ -1548,11 +1555,6 @@
(Float.isNaN(scale) ? vibrationScale : scale), vwr.g.modulationScale);
}
- public void transformPt3f(T3 ptXYZ, P3 screen) {
- applyPerspective(ptXYZ, ptXYZ);
- screen.setT(fScrPt);
- }
-
public synchronized P3i transformPt2D(T3 ptXyp) {
// axes position [50 50]
// just does the processing for [x y] and [x y %]
@@ -1650,16 +1652,19 @@
iScrPt.set((int) fScrPt.x, (int) fScrPt.y,
(int) fScrPt.z);
- if (ptRef != null
- && (slabPlane != null
- && ptRef.x * slabPlane.x + ptRef.y * slabPlane.y + ptRef.z
- * slabPlane.z + slabPlane.w > 0 || depthPlane != null
- && ptRef.x * depthPlane.x + ptRef.y * depthPlane.y + ptRef.z
- * depthPlane.z + depthPlane.w < 0))
+ if (ptRef != null && xyzIsSlabbedInternal(ptRef))
fScrPt.z = iScrPt.z = 1;
return iScrPt;
}
+ public boolean xyzIsSlabbedInternal(T3 ptRef) {
+ return (slabPlane != null
+ && ptRef.x * slabPlane.x + ptRef.y * slabPlane.y + ptRef.z
+ * slabPlane.z + slabPlane.w > 0 || depthPlane != null
+ && ptRef.x * depthPlane.x + ptRef.y * depthPlane.y + ptRef.z
+ * depthPlane.z + depthPlane.w < 0);
+ }
+
final protected P3 untransformedPoint = new P3();
/* ***************************************************************
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/Viewer.java 2016-02-15 20:33:16 UTC
(rev 20962)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/Viewer.java 2016-02-18 04:29:30 UTC
(rev 20963)
@@ -3346,7 +3346,7 @@
return;
if (!haveDisplay) {
setModelVisibility();
- shm.finalizeAtoms(false, true);
+ shm.finalizeAtoms(null, true);
return;
}
rm.requestRepaintAndWait(why);
@@ -3630,7 +3630,7 @@
|| rm == null)
return;
boolean antialias2 = antialiased && g.antialiasTranslucent;
- int[] navMinMax = shm.finalizeAtoms(true, true);
+ int[] navMinMax = shm.finalizeAtoms(tm.bsSelectedAtoms, true);
if (isWebGL) {
rm.renderExport(gdata, ms, jsParams);
notifyViewerRepaintDone();
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java 2016-02-15
20:33:16 UTC (rev 20962)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java 2016-02-18
04:29:30 UTC (rev 20963)
@@ -51,8 +51,8 @@
* A true line-free CIF file reader for CIF files.
*
* Subclasses of CIF -- mmCIF/PDBx (pre-initialized) and msCIF (initialized
- * here).
- *
+ * here)
+ *
* Note that a file can be a PDB file without being
*
* Added nonstandard mCIF (magnetic_ tags) 5/2/2014 note that PRELIM keys can
be
@@ -84,7 +84,6 @@
GenericCifDataParser parser;
- private boolean isMolecular;
private boolean filterAssembly;
private boolean allowRotations = true;
private boolean readIdeal = true;
@@ -181,6 +180,8 @@
private boolean readAllData() throws Exception {
if (key.startsWith("data_")) {
isLigand = false;
+ if (asc.atomSetCount == 0)
+ iHaveDesiredModel = false;
if (iHaveDesiredModel)
return false;
if (desiredModelNumber != Integer.MIN_VALUE)
@@ -222,7 +223,7 @@
* tokenizer.getTokenPeeked(); continue; }
*/
if (key.indexOf("_") != 0) {
- Logger.warn("CIF ERROR ? should be an underscore: " + key);
+ Logger.warn("CIF ERROR ? should be an underscore: " + key);
parser.getTokenPeeked();
} else if (!getData()) {
return true;
@@ -243,22 +244,26 @@
processCellParameter();
} else if (key.startsWith("_atom_sites_fract_tran")) {
processUnitCellTransformMatrix();
- } else if (key.equals("_audit_block_code")) {
- auditBlockCode = parser.fullTrim(data).toUpperCase();
- appendLoadNote(auditBlockCode);
- if (htAudit != null && auditBlockCode.contains("_MOD_")) {
- String key = PT.rep(auditBlockCode, "_MOD_", "_REFRNCE_");
- if (asc.setSymmetry((SymmetryInterface) htAudit.get(key)) != null) {
- unitCellParams = asc.getSymmetry().getUnitCellParams();
- iHaveUnitCell = true;
+ } else if (key.startsWith("_audit")) {
+ if (key.equals("_audit_block_code")) {
+ auditBlockCode = parser.fullTrim(data).toUpperCase();
+ appendLoadNote(auditBlockCode);
+ if (htAudit != null && auditBlockCode.contains("_MOD_")) {
+ String key = PT.rep(auditBlockCode, "_MOD_", "_REFRNCE_");
+ if (asc.setSymmetry((SymmetryInterface) htAudit.get(key)) != null)
{
+ unitCellParams = asc.getSymmetry().getUnitCellParams();
+ iHaveUnitCell = true;
+ }
+ } else if (htAudit != null) {
+ if (symops != null)
+ for (int i = 0; i < symops.size(); i++)
+ setSymmetryOperator(symops.get(i));
}
- } else if (htAudit != null) {
- if (symops != null)
- for (int i = 0; i < symops.size(); i++)
- setSymmetryOperator(symops.get(i));
+ if (lastSpaceGroupName != null)
+ setSpaceGroupName(lastSpaceGroupName);
+ } else if (key.equals("_audit_creation_date")) {
+ symmetry = null;
}
- if (lastSpaceGroupName != null)
- setSpaceGroupName(lastSpaceGroupName);
} else if (key.equals(singleAtomID)) {
readSingleAtom();
} else if (key.startsWith("_symmetry_space_group_name_h-m")
@@ -847,7 +852,7 @@
*/
private void processAtomTypeLoopBlock() throws Exception {
parseLoopParameters(atomTypeFields);
- if (!checkAllFieldsPresent(atomTypeFields, false)) {
+ if (!checkAllFieldsPresent(atomTypeFields, -1, false)) {
parser.skipLoop(false);
return;
}
@@ -1519,8 +1524,12 @@
* @throws Exception
*/
private void processGeomBondLoopBlock() throws Exception {
+ // broken in 13.3.4_dev_2013.08.20c
+ // fixed in 14.4.3_2016.02.16
+ boolean bondLoopBug = (stateScriptVersionInt >= 130304 &&
stateScriptVersionInt < 140403
+ || stateScriptVersionInt >= 150000 && stateScriptVersionInt < 150403);
parseLoopParameters(geomBondFields);
- if (!checkAllFieldsPresent(geomBondFields, true)) {
+ if (bondLoopBug || !checkAllFieldsPresent(geomBondFields, 2, true)) {
parser.skipLoop(false);
return;
}
@@ -1556,6 +1565,12 @@
dx = 0.015f;
}
int order = getBondOrder(getField(CCDC_GEOM_BOND_TYPE));
+ // This field is from Materials Studio. See supplemental material for
+ // http://pubs.rsc.org/en/Content/ArticleLanding/2012/CC/c2cc34714h
+ // http://www.rsc.org/suppdata/cc/c2/c2cc34714h/c2cc34714h.txt
+ // Jmol list discussion:
https://sourceforge.net/p/jmol/mailman/message/31308577/
+ // this 5-model file can be read using one model at a time: load
"c2cc34714h.txt" 3
+ // but it is far from perfect, and still the best way is load
"c2cc34714h.txt" 3 packed
bondCount++;
bondTypes.addLast(new Object[] { name1, name2, Float.valueOf(distance),
Float.valueOf(dx), Integer.valueOf(order) });
@@ -1594,12 +1609,12 @@
* (g) set all coordinates as Cartesians (h) remove all unit cell information
*/
private void setBondingAndMolecules() {
- Logger.info("CIF creating molecule "
- + (bondTypes.size() > 0 ? " using GEOM_BOND records" : ""));
atoms = asc.atoms;
firstAtom = asc.getLastAtomSetAtomIndex();
int nat = asc.getLastAtomSetAtomCount();
ac = firstAtom + nat;
+ Logger.info("CIF creating molecule for " + nat + " atoms "
+ + (bondTypes.size() > 0 ? " using GEOM_BOND records" : ""));
// get list of sites based on atom names
@@ -1836,8 +1851,8 @@
return doCheckUnitCell;
}
- protected boolean checkAllFieldsPresent(String[] keys, boolean critical) {
- for (int i = keys.length; --i >= 0;)
+ protected boolean checkAllFieldsPresent(String[] keys, int lastKey, boolean
critical) {
+ for (int i = (lastKey < 0 ? keys.length : lastKey); --i >= 0;)
if (key2col[i] == NONE) {
if (critical)
Logger.warn("CIF reader missing property: " + keys[i]);
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cif/MMCifReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cif/MMCifReader.java
2016-02-15 20:33:16 UTC (rev 20962)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cif/MMCifReader.java
2016-02-18 04:29:30 UTC (rev 20963)
@@ -688,7 +688,7 @@
*/
private boolean processStructConfLoopBlock() throws Exception {
parseLoopParametersFor(FAMILY_STRUCTCONF, structConfFields);
- if (!checkAllFieldsPresent(structConfFields, true)) {
+ if (!checkAllFieldsPresent(structConfFields, -1, true)) {
parser.skipLoop(true);
return false;
}
@@ -772,7 +772,7 @@
*/
private boolean processStructSheetRangeLoopBlock() throws Exception {
parseLoopParametersFor(FAMILY_SHEET, structSheetRangeFields);
- if (!checkAllFieldsPresent(structSheetRangeFields, true)) {
+ if (!checkAllFieldsPresent(structSheetRangeFields, -1, true)) {
parser.skipLoop(true);
return false;
}
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
2016-02-15 20:33:16 UTC (rev 20962)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
2016-02-18 04:29:30 UTC (rev 20963)
@@ -173,6 +173,7 @@
protected boolean doCheckUnitCell;
protected boolean getHeader;
protected boolean isSequential;
+ public boolean isMolecular; // only for CIF so that it can read multiple
unit cells
protected int templateAtomCount;
public int modelNumber;
protected int vibrationNumber;
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/XtalSymmetry.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/XtalSymmetry.java 2016-02-15
20:33:16 UTC (rev 20962)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/XtalSymmetry.java 2016-02-18
04:29:30 UTC (rev 20963)
@@ -779,7 +779,7 @@
boolean checkSymmetryRange = (checkRangeNoSymmetry || checkRange111);
boolean checkDistances = (checkSpecial || checkSymmetryRange);
boolean addCartesian = (checkSpecial || checkSymmetryMinMax);
-
+ BS bsAtoms = (acr.isMolecular ? null : asc.bsAtoms);
SymmetryInterface symmetry = this.symmetry;
if (checkRangeNoSymmetry)
baseCount = noSymmetryCount;
@@ -809,7 +809,7 @@
Atom a = asc.atoms[i];
if (a.ignoreSymmetry)
continue;
- if (asc.bsAtoms != null && !asc.bsAtoms.get(i))
+ if (bsAtoms != null && !bsAtoms.get(i))
continue;
if (ms == null) {
Modified: trunk/Jmol/src/org/jmol/export/__RayTracerExporter.java
===================================================================
--- trunk/Jmol/src/org/jmol/export/__RayTracerExporter.java 2016-02-15
20:33:16 UTC (rev 20962)
+++ trunk/Jmol/src/org/jmol/export/__RayTracerExporter.java 2016-02-18
04:29:30 UTC (rev 20963)
@@ -61,7 +61,7 @@
if (super.initOutput(vwr, privateKey, g3d, params)) {
vwr.tm.perspectiveDepth = false;
if (wasPerspective)
- vwr.shm.finalizeAtoms(false, false);
+ vwr.shm.finalizeAtoms(null, false);
return true;
}
return false;
Modified: trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2016-02-15
20:33:16 UTC (rev 20962)
+++ trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2016-02-18
04:29:30 UTC (rev 20963)
@@ -2466,14 +2466,16 @@
public BS getVisibleSet(boolean forceNew) {
if (forceNew) {
vwr.setModelVisibility();
- vwr.shm.finalizeAtoms(false, true);
+ vwr.shm.finalizeAtoms(null, true);
+ } else if (haveBSVisible) {
+ return bsVisible;
}
- else if (haveBSVisible)
- return bsVisible;
bsVisible.clearAll();
for (int i = ac; --i >= 0;)
if (at[i].checkVisible())
bsVisible.set(i);
+ if (vwr.shm.bsSlabbedInternal != null)
+ bsVisible.andNot(vwr.shm.bsSlabbedInternal);
haveBSVisible = true;
return bsVisible;
}
Modified: trunk/Jmol/src/org/jmol/render/RepaintManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/render/RepaintManager.java 2016-02-15 20:33:16 UTC
(rev 20962)
+++ trunk/Jmol/src/org/jmol/render/RepaintManager.java 2016-02-18 04:29:30 UTC
(rev 20963)
@@ -243,7 +243,7 @@
public String renderExport(GData gdata, ModelSet modelSet,
Map<String, Object> params) {
boolean isOK;
- shapeManager.finalizeAtoms(false, true);
+ shapeManager.finalizeAtoms(null, true);
JmolRendererInterface exporter3D = vwr.initializeExporter(params);
isOK = (exporter3D != null);
if (!isOK) {
Modified: trunk/Jmol/src/org/jmol/render/SticksRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/render/SticksRenderer.java 2016-02-15 20:33:16 UTC
(rev 20962)
+++ trunk/Jmol/src/org/jmol/render/SticksRenderer.java 2016-02-18 04:29:30 UTC
(rev 20963)
@@ -169,9 +169,9 @@
return false;
if (slabbing) {
- if (vwr.gdata.isClippedZ(a.sZ) && vwr.gdata.isClippedZ(b.sZ)
- || slabByAtom
- && (vwr.gdata.isClippedZ(a.sZ) || vwr.gdata.isClippedZ(b.sZ)))
+ boolean ba = vwr.gdata.isClippedZ(a.sZ);
+ if (ba && vwr.gdata.isClippedZ(b.sZ) || slabByAtom
+ && (ba || vwr.gdata.isClippedZ(b.sZ)))
return false;
}
zA = a.sZ;
@@ -182,14 +182,12 @@
colixB = atomB0.colixAtom;
if (((colix = bond.colix) & C.OPAQUE_MASK) == C.USE_PALETTE) {
colix = (short) (colix & ~C.OPAQUE_MASK);
- colixA = C
- .getColixInherited(
- (short) (colix | vwr.cm.getColixAtomPalette(atomA0, PAL.CPK.id)),
- colixA);
- colixB = C
- .getColixInherited(
- (short) (colix | vwr.cm.getColixAtomPalette(atomB0, PAL.CPK.id)),
- colixB);
+ colixA = C.getColixInherited(
+ (short) (colix | vwr.cm.getColixAtomPalette(atomA0, PAL.CPK.id)),
+ colixA);
+ colixB = C.getColixInherited(
+ (short) (colix | vwr.cm.getColixAtomPalette(atomB0, PAL.CPK.id)),
+ colixB);
} else {
colixA = C.getColixInherited(colix, colixA);
colixB = C.getColixInherited(colix, colixB);
@@ -258,7 +256,6 @@
}
}
-
// set the diameter
xA = a.sX;
Modified: trunk/Jmol/src/org/jmol/script/ScriptEval.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEval.java 2016-02-15 20:33:16 UTC
(rev 20962)
+++ trunk/Jmol/src/org/jmol/script/ScriptEval.java 2016-02-18 04:29:30 UTC
(rev 20963)
@@ -7492,8 +7492,7 @@
vwr.tm.slabToPercent(percent);
return;
case T.on:
- checkLength(2);
- TF = true;
+ TF = true;
//$FALL-THROUGH$
case T.off:
checkLength(2);
@@ -7508,10 +7507,8 @@
return;
case T.set:
checkLength(2);
- if (chk)
- return;
- vwr.tm.setSlabDepthInternal(isDepth);
- setBooleanProperty("slabEnabled", true);
+ if (!chk)
+ vwr.tm.setSlabDepthInternal(isDepth);
return;
case T.minus:
str = paramAsStr(2);
Modified: trunk/Jmol/src/org/jmol/scriptext/IsoExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/IsoExt.java 2016-02-15 20:33:16 UTC
(rev 20962)
+++ trunk/Jmol/src/org/jmol/scriptext/IsoExt.java 2016-02-18 04:29:30 UTC
(rev 20963)
@@ -78,7 +78,7 @@
@Override
public String dispatch(int iTok, boolean b, T[] st) throws ScriptException {
- chk = e.chk;
+ chk = e.chk;
slen = e.slen;
this.st = st;
@@ -1132,7 +1132,7 @@
boolean isPmesh = (iShape == JC.SHAPE_PMESH);
boolean isPlot3d = (iShape == JC.SHAPE_PLOT3D);
boolean isLcaoCartoon = (iShape == JC.SHAPE_LCAOCARTOON);
- boolean isSilent = (isLcaoCartoon || tokAt(1) == T.delete);
+ boolean isSilent = (isLcaoCartoon || tokAt(1) == T.delete ||
eval.isStateScript);
boolean surfaceObjectSeen = false;
boolean planeSeen = false;
boolean isMapped = false;
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2016-02-15 20:33:16 UTC
(rev 20962)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2016-02-18 04:29:30 UTC
(rev 20963)
@@ -63,12 +63,25 @@
TODO: consider if models with no atoms will cause issues in relation to
model.firstAtomIndex
TODO: isosurface molecular has an issue with 2gb1
+TODO: slab SET will not be rendered correctly when exported because
tm.transformPoint
-Jmol.___JmolVersion="14.5.2_2016.02.15"
+Jmol.___JmolVersion="14.5.3_2016.02.17"
+bug fix: slab/depth SET do not behave properly
+bug fix: select VISIBLE is not properly set based on slab/depth SET
+
bug fix: _GEOM_BOND reading in CIF files nonfunctional.
- -- broken in 14.3.16_2015.08.11
- -- only affects CCDC file reading, as it requires presence of
_ccdc_geom_bond_type
+ -- broken in 13.3.4_dev_2013.08.21
+ -- result is that between 8/21/2013 and 2/15/2016 the CIF reader
+ would not recognize _GEOM_BOND and so also not create whole molecules
+ as it was designed to do when those are present.
+ -- no impact on states created within this version range
+ -- no impact on mmCIF reader
+ -- only impact is upon Materials Studio-generated files such as
+ http://www.rsc.org/suppdata/cc/c2/c2cc34714h/c2cc34714h.txt
+ (supplemental mat. for
http://pubs.rsc.org/en/Content/ArticleLanding/2012/CC/c2cc34714h)
+ See Jmol list discussion:
https://sourceforge.net/p/jmol/mailman/message/31308577/
+
JmolVersion="14.5.2_2016.02.14"
Modified: trunk/Jmol/src/org/jmol/viewer/ShapeManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/ShapeManager.java 2016-02-15 20:33:16 UTC
(rev 20962)
+++ trunk/Jmol/src/org/jmol/viewer/ShapeManager.java 2016-02-18 04:29:30 UTC
(rev 20963)
@@ -57,6 +57,7 @@
public ShapeManager(Viewer vwr) {
this.vwr = vwr;
bsRenderableAtoms = new BS();
+ bsSlabbedInternal = new BS();
}
/**
@@ -308,10 +309,11 @@
Object getProperty(Object paramInfo) {
if (paramInfo.equals("getShapes"))
return shapes;
+ // could be more here...
return null;
}
- public final BS bsRenderableAtoms;
+ public final BS bsRenderableAtoms, bsSlabbedInternal;
public Shape getShape(int i) {
//RepaintManager
@@ -401,39 +403,43 @@
private final int[] navMinMax = new int[4];
- public int[] finalizeAtoms(boolean checkAtoms, boolean finalizeParams) {
+ public int[] finalizeAtoms(BS bsTranslateSelected, boolean finalizeParams) {
Viewer vwr = this.vwr;
+ TransformManager tm = vwr.tm;
if (finalizeParams)
vwr.finalizeTransformParameters();
- TransformManager tm = vwr.tm;
- BS bs = bsRenderableAtoms;
- BS bsAtoms = (checkAtoms ? tm.bsSelectedAtoms : null);
- if (bsAtoms != null) {
+ if (bsTranslateSelected != null) {
// translateSelected operation
- P3 ptCenter = ms.getAtomSetCenter(bsAtoms);
+ P3 ptCenter = ms.getAtomSetCenter(bsTranslateSelected);
P3 pt = new P3();
tm.transformPt3f(ptCenter, pt);
pt.add(tm.ptOffset);
tm.unTransformPoint(pt, pt);
pt.sub(ptCenter);
- vwr.setAtomCoordsRelative(pt, bsAtoms);
+ vwr.setAtomCoordsRelative(pt, bsTranslateSelected);
tm.ptOffset.set(0, 0, 0);
tm.bsSelectedAtoms = null;
}
- ms.getAtomsInFrame(bs);
+ BS bsOK = bsRenderableAtoms;
+ ms.getAtomsInFrame(bsOK);
Vibration[] vibrationVectors = ms.vibrations;
boolean vibs = (vibrationVectors != null && tm.vibrationOn);
boolean checkOccupancy = (ms.bsModulated != null && ms.occupancies !=
null);
Atom[] atoms = ms.at;
int occ;
boolean haveMods = false;
- for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
+ BS bsSlabbed = bsSlabbedInternal;
+ bsSlabbed.clearAll();
+ for (int i = bsOK.nextSetBit(0); i >= 0; i = bsOK.nextSetBit(i + 1)) {
// note that this vibration business is not compatible with
// PDB objects such as cartoons and traces, which
// use Cartesian coordinates, not screen coordinates
Atom atom = atoms[i];
P3i screen = (vibs && atom.hasVibration() ? tm.transformPtVib(atom,
vibrationVectors[i]) : tm.transformPt(atom));
+ if (screen.z == 1 && tm.internalSlab && tm.xyzIsSlabbedInternal(atom)) {
+ bsSlabbed.set(i);
+ }
atom.sX = screen.x;
atom.sY = screen.y;
atom.sZ = screen.z;
@@ -471,7 +477,7 @@
JmolMolecule m = molecules[i];
int j = 0;
int pt = m.firstAtomIndex;
- if (!bs.get(pt))
+ if (!bsOK.get(pt))
continue;
for (; j < m.ac; j++, pt++)
if (gdata.isClippedZ(atoms[pt].sZ - (atoms[pt].sD >> 1)))
@@ -479,13 +485,13 @@
if (j != m.ac) {
pt = m.firstAtomIndex;
for (int k = 0; k < m.ac; k++) {
- bs.clear(pt);
+ bsOK.clear(pt);
atoms[pt++].sZ = 0;
}
}
}
}
- for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
+ for (int i = bsOK.nextSetBit(0); i >= 0; i = bsOK.nextSetBit(i + 1)) {
Atom atom = atoms[i];
if (gdata.isClippedZ(atom.sZ - (slabByAtom ? atoms[i].sD >> 1 : 0))) {
atom.setClickable(0);
@@ -494,7 +500,7 @@
int r = (slabByAtom ? -1 : 1) * atom.sD / 2;
if (atom.sZ + r < minZ || atom.sZ - r > maxZ
|| !gdata.isInDisplayRange(atom.sX, atom.sY)) {
- bs.clear(i);
+ bsOK.clear(i);
}
}
}
@@ -506,7 +512,7 @@
int maxX = Integer.MIN_VALUE;
int minY = Integer.MAX_VALUE;
int maxY = Integer.MIN_VALUE;
- for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
+ for (int i = bsOK.nextSetBit(0); i >= 0; i = bsOK.nextSetBit(i + 1)) {
Atom atom = atoms[i];
if (atom.sX < minX)
minX = atom.sX;
Modified: trunk/Jmol/src/org/jmol/viewer/StateCreator.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/StateCreator.java 2016-02-15 20:33:16 UTC
(rev 20962)
+++ trunk/Jmol/src/org/jmol/viewer/StateCreator.java 2016-02-18 04:29:30 UTC
(rev 20963)
@@ -808,11 +808,12 @@
if (vwr.ms.modelSetHasVibrationVectors() && tm.vibrationOn)
app(commands, "set vibrationPeriod " + tm.vibrationPeriod
+ ";vibration on");
+ boolean slabInternal = (tm.depthPlane != null || tm.slabPlane != null);
if (navigating) {
commands.append(tm.getNavigationState());
- if (tm.depthPlane != null || tm.slabPlane != null)
- commands.append(" slab on;\n");
- }
+ }
+ if (!tm.slabEnabled && slabInternal)
+ commands.append(" slab off;\n");
if (sfunc != null)
commands.append("}\n\n");
return commands.toString();
Modified: trunk/Jmol/src/org/jmol/viewer/TransformManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/TransformManager.java 2016-02-15
20:33:16 UTC (rev 20962)
+++ trunk/Jmol/src/org/jmol/viewer/TransformManager.java 2016-02-18
04:29:30 UTC (rev 20963)
@@ -831,7 +831,7 @@
public boolean slabEnabled;
public boolean zShadeEnabled;
- boolean internalSlab;
+ public boolean internalSlab;
int slabPercentSetting;
int depthPercentSetting;
@@ -851,8 +851,7 @@
}
void setSlabEnabled(boolean slabEnabled) {
- this.slabEnabled = slabEnabled;
- vwr.g.setB("slabEnabled", slabEnabled);
+ vwr.g.setB("slabEnabled", this.slabEnabled = slabEnabled);
}
void setZShadeEnabled(boolean zShadeEnabled) {
@@ -922,15 +921,16 @@
}
public void slabToPercent(int percentSlab) {
+ slabPlane = null;
vwr.setFloatProperty("slabRange", 0);
slabPercentSetting = percentSlab;
- slabPlane = null;
if (depthPercentSetting >= slabPercentSetting)
depthPercentSetting = slabPercentSetting - 1;
slabDepthChanged();
}
public void depthToPercent(int percentDepth) {
+ depthPlane = null;
vwr.g.setI("depth", percentDepth);
depthPercentSetting = percentDepth;
if (slabPercentSetting <= depthPercentSetting)
@@ -972,23 +972,24 @@
depthPlane = null;
else
slabPlane = null;
+ finalizeTransformParameters();
slabInternal(getSlabDepthPlane(isDepth), isDepth);
}
private P4 getSlabDepthPlane(boolean isDepth) {
// the third row of the matrix defines the Z coordinate, which is all we
need
// and, in fact, it defines the plane. How convenient!
- // eval "slab set"
+ // eval "slab set"
if (isDepth) {
if (depthPlane != null)
return depthPlane;
- } else {
- if (slabPlane != null)
+ } else if (slabPlane != null) {
return slabPlane;
}
M4 m = matrixTransform;
- return P4.new4(-m.m20, -m.m21, -m.m22, -m.m23
+ P4 plane = P4.new4(-m.m20, -m.m21, -m.m22, -m.m23
+ (isDepth ? depthValue : slabValue));
+ return plane;
}
/* ***************************************************************
@@ -1446,7 +1447,6 @@
// don't care
}
}
-
vwr.g.setO("_slabPlane", Escape.eP4(getSlabDepthPlane(false)));
vwr.g.setO("_depthPlane", Escape.eP4(getSlabDepthPlane(true)));
if (slabEnabled)
@@ -1508,9 +1508,16 @@
public void transformPtScrT3(T3 ptXYZ, T3 pointScreen) {
transformPt(ptXYZ);
+ // note that this point may be returned as z=1 if the point is
+ // past the camera or slabbed internally
pointScreen.setT(fScrPt);
}
+ public void transformPt3f(T3 ptXYZ, P3 screen) {
+ applyPerspective(ptXYZ, ptXYZ);
+ screen.setT(fScrPt);
+ }
+
public void transformPtNoClip(T3 ptXYZ, T3 pointScreen) {
applyPerspective(ptXYZ, null);
pointScreen.setT(fScrPt);
@@ -1548,11 +1555,6 @@
(Float.isNaN(scale) ? vibrationScale : scale), vwr.g.modulationScale);
}
- public void transformPt3f(T3 ptXYZ, P3 screen) {
- applyPerspective(ptXYZ, ptXYZ);
- screen.setT(fScrPt);
- }
-
public synchronized P3i transformPt2D(T3 ptXyp) {
// axes position [50 50]
// just does the processing for [x y] and [x y %]
@@ -1650,16 +1652,19 @@
iScrPt.set((int) fScrPt.x, (int) fScrPt.y,
(int) fScrPt.z);
- if (ptRef != null
- && (slabPlane != null
- && ptRef.x * slabPlane.x + ptRef.y * slabPlane.y + ptRef.z
- * slabPlane.z + slabPlane.w > 0 || depthPlane != null
- && ptRef.x * depthPlane.x + ptRef.y * depthPlane.y + ptRef.z
- * depthPlane.z + depthPlane.w < 0))
+ if (ptRef != null && xyzIsSlabbedInternal(ptRef))
fScrPt.z = iScrPt.z = 1;
return iScrPt;
}
+ public boolean xyzIsSlabbedInternal(T3 ptRef) {
+ return (slabPlane != null
+ && ptRef.x * slabPlane.x + ptRef.y * slabPlane.y + ptRef.z
+ * slabPlane.z + slabPlane.w > 0 || depthPlane != null
+ && ptRef.x * depthPlane.x + ptRef.y * depthPlane.y + ptRef.z
+ * depthPlane.z + depthPlane.w < 0);
+ }
+
final protected P3 untransformedPoint = new P3();
/* ***************************************************************
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2016-02-15 20:33:16 UTC (rev
20962)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2016-02-18 04:29:30 UTC (rev
20963)
@@ -3346,7 +3346,7 @@
return;
if (!haveDisplay) {
setModelVisibility();
- shm.finalizeAtoms(false, true);
+ shm.finalizeAtoms(null, true);
return;
}
rm.requestRepaintAndWait(why);
@@ -3630,7 +3630,7 @@
|| rm == null)
return;
boolean antialias2 = antialiased && g.antialiasTranslucent;
- int[] navMinMax = shm.finalizeAtoms(true, true);
+ int[] navMinMax = shm.finalizeAtoms(tm.bsSelectedAtoms, true);
if (isWebGL) {
rm.renderExport(gdata, ms, jsParams);
notifyViewerRepaintDone();
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