Revision: 20476
http://sourceforge.net/p/jmol/code/20476
Author: hansonr
Date: 2015-05-03 18:46:39 +0000 (Sun, 03 May 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.3.13_2015.05.03"
new feature: for msCIF (modulated structure files), setting modulation or using
vibration ON
now also indicates occupancy changes
Modified Paths:
--------------
trunk/Jmol/src/javajs/util/CifDataParser.java
trunk/Jmol/src/org/jmol/adapter/readers/cif/MSRdr.java
trunk/Jmol/src/org/jmol/modelset/Atom.java
trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
trunk/Jmol/src/org/jmol/modelset/ModelLoader.java
trunk/Jmol/src/org/jmol/render/HalosRenderer.java
trunk/Jmol/src/org/jmol/render/ShapeRenderer.java
trunk/Jmol/src/org/jmol/render/SticksRenderer.java
trunk/Jmol/src/org/jmol/renderspecial/VectorsRenderer.java
trunk/Jmol/src/org/jmol/script/T.java
trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
trunk/Jmol/src/org/jmol/shape/Labels.java
trunk/Jmol/src/org/jmol/shapespecial/Dots.java
trunk/Jmol/src/org/jmol/util/Modulation.java
trunk/Jmol/src/org/jmol/util/ModulationSet.java
trunk/Jmol/src/org/jmol/util/Vibration.java
trunk/Jmol/src/org/jmol/viewer/GlobalSettings.java
trunk/Jmol/src/org/jmol/viewer/JC.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/ShapeManager.java
trunk/Jmol/src/org/jmol/viewer/TransformManager.java
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: trunk/Jmol/src/javajs/util/CifDataParser.java
===================================================================
--- trunk/Jmol/src/javajs/util/CifDataParser.java 2015-05-02 17:47:14 UTC
(rev 20475)
+++ trunk/Jmol/src/javajs/util/CifDataParser.java 2015-05-03 18:46:39 UTC
(rev 20476)
@@ -280,13 +280,14 @@
while ((str = peekToken()) != null && str.charAt(0) == '_') {
if (ret != null)
ret.append(str).append("\n");
- getTokenPeeked();
- n++;
+ getTokenPeeked();
+ n++;
}
int m = 0;
while ((str = getNextDataToken()) != null) {
- if (ret != null)
- ret.append(str).append(" ");
+ if (ret == null)
+ continue;
+ ret.append(str).append(" ");
if ((++m % n) == 0)
ret.append("\n");
}
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cif/MSRdr.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cif/MSRdr.java 2015-05-02
17:47:14 UTC (rev 20475)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cif/MSRdr.java 2015-05-03
18:46:39 UTC (rev 20476)
@@ -350,8 +350,7 @@
if (modTUV != null)
cr.appendLoadNote("modTUV=" + modTUV);
cr.asc.setInfo("modulationOn", modTUV == null ? Boolean.TRUE : modTUV);
- cr.addJmolScript((haveOccupancy && !isCommensurate ? ";display occupancy
>= 0.5"
- : ""));
+ cr.addJmolScript("set modulateOccupancy " + (haveOccupancy &&
!isCommensurate ? true: false));
}
finalized = true;
}
@@ -857,8 +856,8 @@
// because we are going to repurpose that.
ModulationSet ms = new ModulationSet().setMod(a.index + " " + a.atomName,
getAtomR0(cr.asc.atoms[a.atomSite]), getAtomR0(a),
- modDim, list, gammaE, getMatrices(a), iop, getSymmetry(a),
- a.vib instanceof Vibration ? (Vibration) a.vib : null);
+ modDim, list, gammaE, getMatrices(a), getSymmetry(a), nOps, iop,
+ a.vib instanceof Vibration ? (Vibration) a.vib : null, isCommensurate);
ms.calculate(modTUV, false);
@@ -866,30 +865,8 @@
// vibrations, and anisotropy tensors.
if (!Float.isNaN(ms.vOcc)) {
- double[] pt = getMod("J_O#0;" + a.atomName);
- float occ0 = ms.vOcc0;
- double occ;
- if (Float.isNaN(occ0)) {
- // Crenel
- occ = ms.vOcc;
- } else if (pt == null) {
- // cif Fourier
- // _atom_site_occupancy + SUM
- occ = a.foccupancy + ms.vOcc;
- } else if (a.vib != null) {
- // cif with m40 Fourier
- // occ_site * (occ_0 + SUM)
- double site_mult = a.vib.x;
- double o_site = a.foccupancy * site_mult / nOps / pt[1];
- occ = o_site * (pt[1] + ms.vOcc);
- } else {
- // m40 Fourier
- // occ_site * (occ_0 + SUM)
- occ = pt[0] * (pt[1] + ms.vOcc);
- }
- // 49/50 is an important range for cutoffs -- we let this range be void
- a.foccupancy = (occ > 0.49 && occ < 0.50 ? 0.489f : (float) Math.min(1,
- Math.max(0, occ)));
+ // a.vib may be used to temporarily store an M40 site multiplicity
+ a.foccupancy = ms.setOccupancy(getMod("J_O#0;" + a.atomName),
a.foccupancy, (a.vib == null ? 0 : a.vib.x));
//Logger.info("atom " + a.atomName + " occupancy = " + a.foccupancy);
}
if (ms.htUij != null) {
Modified: trunk/Jmol/src/org/jmol/modelset/Atom.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/Atom.java 2015-05-02 17:47:14 UTC (rev
20475)
+++ trunk/Jmol/src/org/jmol/modelset/Atom.java 2015-05-03 18:46:39 UTC (rev
20476)
@@ -56,6 +56,18 @@
public class Atom extends Point3fi implements BNode {
+ // ATOM_IN_FRAME simply associates an atom with the current model
+ // but doesn't necessarily mean it is visible
+ // ATOM_VIS_SET and ATOM_VISIBLE are checked once only for each atom per
rendering
+
+ public final static int ATOM_INFRAME = 1;
+ public final static int ATOM_VISSET = 2; // have carried out
checkVisible()
+ public final static int ATOM_VISIBLE = 4; // set from checkVisible()
+ public final static int ATOM_NOTHIDDEN = 8;
+ public final static int ATOM_NOFLAGS = ~63; // all of the above, plus
balls and sticks
+ public final static int ATOM_INFRAME_NOTHIDDEN = ATOM_INFRAME |
ATOM_NOTHIDDEN;
+ public final static int ATOM_SHAPE_VIS_MASK = ~ATOM_INFRAME_NOTHIDDEN;
+
private final static byte VIBRATION_VECTOR_FLAG = 1;
private final static byte IS_HETERO_FLAG = 2;
private final static byte FLAG_MASK = 3;
@@ -376,9 +388,15 @@
// a percentage value in the range 0-100
public int getOccupancy100() {
float[] occupancies = group.chain.model.ms.occupancies;
- return occupancies == null ? 100 : Math.round(occupancies[i]);
+ return (occupancies == null ? 100 : Math.round(occupancies[i]));
}
+ // a percentage value in the range 0-100
+ public boolean isOccupied() {
+ float[] occupancies = group.chain.model.ms.occupancies;
+ return (occupancies == null || occupancies[i] >= 50);
+ }
+
// This is called bfactor100 because it is stored as an integer
// 100 times the bfactor(temperature) value
public int getBfactor100() {
@@ -947,9 +965,9 @@
}
public boolean checkVisible() {
- if (isVisible(JC.ATOM_VISSET))
- return isVisible(JC.ATOM_VISIBLE);
- boolean isVis = isVisible(JC.ATOM_INFRAME_NOTHIDDEN);
+ if (isVisible(ATOM_VISSET))
+ return isVisible(ATOM_VISIBLE);
+ boolean isVis = isVisible(ATOM_INFRAME_NOTHIDDEN);
if (isVis) {
int flags = shapeVisibilityFlags;
// Is its PDB group visible in any way (cartoon, e.g.)?
@@ -963,16 +981,16 @@
// We know that (flags & AIM), so now we must remove that flag
// and check to see if any others are remaining.
// Only then is the atom considered visible.
- flags &= JC.ATOM_SHAPE_VIS_MASK;
+ flags &= ATOM_SHAPE_VIS_MASK;
// problem with display of bond-only when not clickable.
// bit of a kludge here.
if (flags == JC.VIS_BOND_FLAG && clickabilityFlags == 0)
flags = 0;
isVis = (flags != 0);
if (isVis)
- shapeVisibilityFlags |= JC.ATOM_VISIBLE;
+ shapeVisibilityFlags |= ATOM_VISIBLE;
}
- shapeVisibilityFlags |= JC.ATOM_VISSET;
+ shapeVisibilityFlags |= ATOM_VISSET;
return isVis;
}
Modified: trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2015-05-02
17:47:14 UTC (rev 20475)
+++ trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2015-05-03
18:46:39 UTC (rev 20476)
@@ -96,7 +96,7 @@
int[] atomResnos;
int[] atomSeqIDs;
public Vibration[] vibrations;
- float[] occupancies;
+ public float[] occupancies;
short[] bfactor100s;
float[] partialCharges;
float[] bondingRadii;
@@ -2443,11 +2443,11 @@
haveBSClickable = false;
}
- public void getRenderable(BS bsAtoms) {
+ public void getAtomsInFrame(BS bsAtoms) {
clearVisibleSets();
bsAtoms.clearAll();
for (int i = ac; --i >= 0;)
- if (at[i].isVisible(JC.ATOM_INFRAME))
+ if (at[i].isVisible(Atom.ATOM_INFRAME))
bsAtoms.set(i);
}
Modified: trunk/Jmol/src/org/jmol/modelset/ModelLoader.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelLoader.java 2015-05-02 17:47:14 UTC
(rev 20475)
+++ trunk/Jmol/src/org/jmol/modelset/ModelLoader.java 2015-05-03 18:46:39 UTC
(rev 20476)
@@ -1069,7 +1069,7 @@
int modelIndex = -1;
SymmetryInterface c = null;
boolean isFractional = false;
- boolean roundCoords = !vwr.getBoolean(T.legacyjavafloat);
+ boolean roundCoords = !vwr.g.legacyJavaFloat;
for (int i = baseAtomIndex; i < ms.ac; i++) {
if (atoms[i].mi != modelIndex) {
modelIndex = atoms[i].mi;
Modified: trunk/Jmol/src/org/jmol/render/HalosRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/render/HalosRenderer.java 2015-05-02 17:47:14 UTC
(rev 20475)
+++ trunk/Jmol/src/org/jmol/render/HalosRenderer.java 2015-05-03 18:46:39 UTC
(rev 20476)
@@ -40,8 +40,7 @@
protected boolean render() {
Halos halos = (Halos) shape;
boolean showOnce = vwr.getShowSelectedOnce();
- boolean selectDisplayTrue = vwr.getSelectionHalosEnabled() || showOnce;
- System.out.println(showOnce + " testhalos");
+ boolean selectDisplayTrue = (vwr.getSelectionHalosEnabled() || showOnce);
boolean showHiddenSelections = (selectDisplayTrue &&
vwr.getBoolean(T.showhiddenselectionhalos));
if (halos.mads == null && halos.bsHighlight == null && !selectDisplayTrue)
return false;
@@ -53,7 +52,7 @@
g3d.addRenderer(T.circle);
for (int i = ms.ac; --i >= 0;) {
Atom atom = atoms[i];
- if ((atom.shapeVisibilityFlags & JC.ATOM_INFRAME) == 0)
+ if ((atom.shapeVisibilityFlags & Atom.ATOM_INFRAME) == 0)
continue;
boolean isHidden = ms.isAtomHidden(i);
mad = (halos.mads == null ? 0 : halos.mads[i]);
Modified: trunk/Jmol/src/org/jmol/render/ShapeRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/render/ShapeRenderer.java 2015-05-02 17:47:14 UTC
(rev 20475)
+++ trunk/Jmol/src/org/jmol/render/ShapeRenderer.java 2015-05-03 18:46:39 UTC
(rev 20476)
@@ -85,7 +85,7 @@
}
protected boolean isVisibleForMe(Atom a) {
- return a.isVisible(myVisibilityFlag | JC.ATOM_INFRAME_NOTHIDDEN);
+ return a.isVisible(myVisibilityFlag | Atom.ATOM_INFRAME_NOTHIDDEN);
}
Modified: trunk/Jmol/src/org/jmol/render/SticksRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/render/SticksRenderer.java 2015-05-02 17:47:14 UTC
(rev 20475)
+++ trunk/Jmol/src/org/jmol/render/SticksRenderer.java 2015-05-03 18:46:39 UTC
(rev 20476)
@@ -154,8 +154,8 @@
}
}
if (!isPass2
- && (!a.isVisible(JC.ATOM_INFRAME_NOTHIDDEN)
- || !b.isVisible(JC.ATOM_INFRAME_NOTHIDDEN)
+ && (!a.isVisible(Atom.ATOM_INFRAME_NOTHIDDEN)
+ || !b.isVisible(Atom.ATOM_INFRAME_NOTHIDDEN)
|| !g3d.isInDisplayRange(a.sX, a.sY) || !g3d.isInDisplayRange(b.sX,
b.sY)))
return false;
Modified: trunk/Jmol/src/org/jmol/renderspecial/VectorsRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/renderspecial/VectorsRenderer.java 2015-05-02
17:47:14 UTC (rev 20475)
+++ trunk/Jmol/src/org/jmol/renderspecial/VectorsRenderer.java 2015-05-03
18:46:39 UTC (rev 20476)
@@ -33,6 +33,7 @@
import org.jmol.shape.Shape;
import org.jmol.shapespecial.Vectors;
import org.jmol.util.GData;
+import org.jmol.util.Point3fi;
import javajs.util.P3;
import javajs.util.P3i;
@@ -43,8 +44,8 @@
private final static float arrowHeadOffset = -0.2f;
private final P3 pointVectorStart = new P3();
- private final P3 ptTemp = new P3();
- private final P3 pointVectorEnd = new P3();
+ private final Point3fi ptTemp = new Point3fi();
+ private final Point3fi pointVectorEnd = new Point3fi();
private final P3 pointArrowHead = new P3();
private final P3i screenVectorStart = new P3i();
private final P3i screenVectorEnd = new P3i();
Modified: trunk/Jmol/src/org/jmol/script/T.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/T.java 2015-05-02 17:47:14 UTC (rev
20475)
+++ trunk/Jmol/src/org/jmol/script/T.java 2015-05-03 18:46:39 UTC (rev
20476)
@@ -1043,19 +1043,20 @@
public final static int minimizationrefresh = booleanparam | 105;
public final static int minimizationsilent = booleanparam | 106;
public final static int modelkitmode = booleanparam | 107;
// 12.0.RC15
- public final static int monitorenergy = booleanparam | 108;
- public final static int multiprocessor = booleanparam | 109;
- public final static int navigatesurface = booleanparam | 110;
- public final static int navigationmode = booleanparam | 111;
- public final static int navigationperiodic = booleanparam | 112;
- public final static int partialdots = booleanparam | 113;
// 12.1.46
- public final static int pdbaddhydrogens = booleanparam | 114;
- public final static int pdbgetheader = booleanparam | 115;
- public final static int pdbsequential = booleanparam | 116;
- public final static int perspectivedepth = booleanparam | 117;
- public final static int preservestate = booleanparam | 118;
- public final static int rangeselected = booleanparam | 119;
- public final static int refreshing = booleanparam | 120;
+ public final static int modulateoccupancy = booleanparam | 108;
// 14.3.13
+ public final static int monitorenergy = booleanparam | 109;
+ public final static int multiprocessor = booleanparam | 110;
+ public final static int navigatesurface = booleanparam | 111;
+ public final static int navigationmode = booleanparam | 112;
+ public final static int navigationperiodic = booleanparam | 113;
+ public final static int partialdots = booleanparam | 114;
// 12.1.46
+ public final static int pdbaddhydrogens = booleanparam | 115;
+ public final static int pdbgetheader = booleanparam | 116;
+ public final static int pdbsequential = booleanparam | 117;
+ public final static int perspectivedepth = booleanparam | 118;
+ public final static int preservestate = booleanparam | 119;
+ public final static int rangeselected = booleanparam | 120;
+ public final static int refreshing = booleanparam | 121;
public final static int ribbonborder = booleanparam | 122;
public final static int rocketbarrels = booleanparam | 124;
public final static int saveproteinstructurestate = booleanparam | 126;
@@ -2562,6 +2563,7 @@
"minimizationRefresh",
"minimizationSilent",
"modelkitMode",
+ "modulateOccupancy",
"monitorEnergy",
"multipleBondRadiusFactor",
"multipleBondSpacing",
@@ -3586,6 +3588,7 @@
minimizationrefresh, // "minimizationRefresh"
minimizationsilent, // "minimizationSilent"
modelkitmode, // "modelkitMode"
+ modulateoccupancy,
monitorenergy, // "monitorEnergy"
multiplebondradiusfactor, //
"multipleBondRadiusFactor"
multiplebondspacing, // "multipleBondSpacing"
Modified: trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2015-05-02 17:47:14 UTC
(rev 20475)
+++ trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2015-05-03 18:46:39 UTC
(rev 20476)
@@ -1402,7 +1402,7 @@
BS bsExclude = new BS();
vwr.ms.setPdbConectBonding(0, 0, bsExclude);
if (isAuto) {
- boolean isLegacy = eval.isStateScript && vwr.g.legacyAutoBonding;
+ boolean isLegacy = eval.isStateScript &&
vwr.getBoolean(T.legacyautobonding);
vwr.ms.autoBondBs4(null, null, bsExclude, null, vwr.getMadBond(),
isLegacy);
vwr.addStateScript(
(isLegacy ? "set legacyAutoBonding TRUE;connect PDB AUTO;set
legacyAutoBonding FALSE;"
Modified: trunk/Jmol/src/org/jmol/shape/Labels.java
===================================================================
--- trunk/Jmol/src/org/jmol/shape/Labels.java 2015-05-02 17:47:14 UTC (rev
20475)
+++ trunk/Jmol/src/org/jmol/shape/Labels.java 2015-05-03 18:46:39 UTC (rev
20476)
@@ -684,7 +684,7 @@
int imin = -1;
float zmin = Float.MAX_VALUE;
for (Map.Entry<Integer, float[]> entry : labelBoxes.entrySet()) {
- if (!atoms[entry.getKey().intValue()].isVisible(vf |
JC.ATOM_INFRAME_NOTHIDDEN))
+ if (!atoms[entry.getKey().intValue()].isVisible(vf |
Atom.ATOM_INFRAME_NOTHIDDEN))
continue;
float[] boxXY = entry.getValue();
float dx = x - boxXY[0];
Modified: trunk/Jmol/src/org/jmol/shapespecial/Dots.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapespecial/Dots.java 2015-05-02 17:47:14 UTC
(rev 20475)
+++ trunk/Jmol/src/org/jmol/shapespecial/Dots.java 2015-05-03 18:46:39 UTC
(rev 20476)
@@ -131,7 +131,7 @@
ec.setMads(null);
mads = new short[ac];
for (int i = 0; i < ac; i++)
- if (atoms[i].isVisible(JC.ATOM_INFRAME | vf))
+ if (atoms[i].isVisible(Atom.ATOM_INFRAME | vf))
// was there a reason we were not checking for hidden?
try {
mads[i] = (short) (ec.getAppropriateRadius(i) * 1000);
Modified: trunk/Jmol/src/org/jmol/util/Modulation.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Modulation.java 2015-05-02 17:47:14 UTC
(rev 20475)
+++ trunk/Jmol/src/org/jmol/util/Modulation.java 2015-05-03 18:46:39 UTC
(rev 20476)
@@ -147,10 +147,12 @@
case TYPE_U_LEGENDRE:
// not implemented in reader, but all set here
case TYPE_DISP_LEGENDRE:
- ms.vOcc0 = Float.NaN; // absolute
+ ms.occAbsolute = true;
nt -= Math.floor(nt);
- if (!range(nt))
+ if (!range(nt)) {
+ ms.vOcc = 0;
return;
+ }
ms.vOcc = 1;
// normalize to [-1,1]
double x = (nt - center) / delta2;
@@ -175,15 +177,15 @@
// p(x4)=1 if x4 belongs to the interval [c-w/2,c+w/2]
// p(x4)=0 if x4 is outside the interval [c-w/2,c+w/2],
+ ms.occAbsolute = true;
ms.vOcc = (range(nt - Math.floor(nt)) ? 1 : 0);
- ms.vOcc0 = Float.NaN; // absolute
- //System.out.println("MOD " + ms.r + " " + ms.delta + " " + ms.epsilon
+ " " + ms.id + " " + ms.v + " l=" + left + " x=" + x4 + " r=" + right);
+ //System.out.println("MOD " + ms.id + " v=" + ms.vOcc + " l=" + left + "
x=" + nt + " r=" + right);
return;
case TYPE_SPIN_SAWTOOTH:
isSpin = true;
//$FALL-THROUGH$
case TYPE_DISP_SAWTOOTH:
-
+ ms.occAbsolute = true;
// _atom_site_displace_special_func_sawtooth_ items are the
// adjustable parameters of a sawtooth function. A displacive sawtooth
// function along the internal space is defined as follows:
@@ -199,8 +201,11 @@
// here we have set a1 = 2a_xyz/w
nt -= Math.floor(nt);
- if (!range(nt))
+ if (!range(nt)) {
+ ms.vOcc = 0;
return;
+ }
+ ms.vOcc = 1;
// x < L < c
//
@@ -261,7 +266,7 @@
}
if (isSpin) {
- float[] f = ms.getAxesLengths();
+ float[] f = ms.axesLengths;
switch (axis) {
case 'x':
ms.mxyz.x += v / f[0];
Modified: trunk/Jmol/src/org/jmol/util/ModulationSet.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/ModulationSet.java 2015-05-02 17:47:14 UTC
(rev 20475)
+++ trunk/Jmol/src/org/jmol/util/ModulationSet.java 2015-05-03 18:46:39 UTC
(rev 20476)
@@ -24,55 +24,165 @@
public class ModulationSet extends Vibration implements JmolModulationSet {
- public float vOcc = Float.NaN;
- public Map<String, Float> htUij;
- public float vOcc0;
-
+ /**
+ * an identifier for this modulation
+ *
+ */
String id;
+
+ /**
+ * the unmodulated original position of this atom;
+ * note that x,y,z extended from Vibration(V3) is the current displacement
modulation itself
+ *
+ */
+ private P3 r0;
- private Lst<Modulation> mods;
+
+ /**
+ * the space group appropriate to this atom
+ *
+ */
+ private SymmetryInterface symmetry;
+
+ /**
+ * unit cell axes -- used in Modulation for calculating magnetic modulations
+ */
+ float[] axesLengths;
+
+ /**
+ * the number of operators in this space group -- needed for occupancy
calculation
+ */
+ private int nOps;
+
+ /**
+ * the symmetry operation used to generate this atom
+ */
private int iop;
- private P3 r0;
+
/**
+ * a string description of the atom's symmetry operator
+ */
+ private String strop;
+
+ /**
+ * the spin operation for this atom: +1/0/-1
+ */
+ private float spinOp;
+
+ /**
+ * the matrix representation for this atom's symmetry operation
+ *
+ */
+ private Matrix rsvs;
+
+ /**
* vib is a spin vector when the model has modulation; otherwise an
* unmodulated vibration.
*
*/
public Vibration vib;
- public V3 mxyz;
+
+ /**
+ * the list of all modulations associated with this atom
+ */
+ private Lst<Modulation> mods;
+
+ /**
+ * subsystems can deliver their own unique unit cell;
+ * they are commensurate
+ *
+ */
+ private boolean isSubsystem;
+
+ @Override
+ public SymmetryInterface getSubSystemUnitCell() {
+ return (isSubsystem ? symmetry : null);
+ }
- private SymmetryInterface symmetry;
- private M3 gammaE;
- private Matrix gammaIinv;
- private Matrix sigma;
- private Matrix tau;
+ /**
+ * commensurate modulations cannot be "undone"
+ * and they cannot be turned off
+ *
+ */
+ private boolean isCommensurate;
- private boolean enabled;
- private float scale = 1;
+ // parameters necessary for calculating occValue
+
+ private double fileOcc;
+ private double[] occParams;
+ private double occSiteMultiplicity;
+ /**
+ * for Crenels (simple occupational modulation or Legendre displacement
modulation,
+ * the value determined here is absolute (0 or 1), not an adjustment;
+ * set in calculate() by one of the modulations
+ *
+ */
+ boolean occAbsolute;
+
+ /**
+ * modCalc is used for calculations independent of
+ * what the current setting is
+ *
+ */
+ private ModulationSet modCalc;
+
+ /**
+ * the modulated magnetic spin
+ */
+ public V3 mxyz;
+
+ /**
+ * current value of anisotropic parameter modulation
+ *
+ */
+ public Map<String, Float> htUij;
+
+ /**
+ * the current value of the occupancy modulation
+ */
+ public float vOcc = Float.NaN;
+
+ /**
+ * final occupancy value -- absolute; in range [0,1]
+ */
+ private float occValue = Float.NaN;
+
+ // values set in setModTQ
+
private P3 qtOffset = new P3();
private boolean isQ;
- private Matrix rI;
+ /**
+ * indicates state of modulated or unmodulated
+ */
+ private boolean enabled;
- private ModulationSet modTemp;
- private String strop;
- private boolean isSubsystem;
+ @Override
+ public boolean isEnabled() {
+ return enabled;
+ }
- private Matrix tFactorInv;
- private Matrix rsvs;
- private float spinOp;
+ /**
+ * an adjustable scaling factor, as for vibrations
+ *
+ */
+ private float scale = 1;
@Override
public float getScale() {
return scale;
}
- @Override
- public boolean isEnabled() {
- return enabled;
- }
+ // generator parameters
+ private M3 gammaE;
+ private Matrix gammaIinv;
+ private Matrix sigma;
+ private Matrix tau;
+ private Matrix rI;
+ private Matrix tFactorInv; // for subsystems
+
public ModulationSet() {
}
@@ -91,10 +201,12 @@
* @param gammaE
* @param factors
* including sigma and tFactor
+ * @param symmetry
* @param iop
- * @param symmetry
+ * @param nOps
* @param v
* TODO
+ * @param isCommensurate TODO
* @return this
*
*
@@ -102,8 +214,9 @@
public ModulationSet setMod(String id, P3 r00, P3 r0, int d,
Lst<Modulation> mods, M3 gammaE,
- Matrix[] factors, int iop,
- SymmetryInterface symmetry, Vibration v) {
+ Matrix[] factors,
+ SymmetryInterface symmetry, int nOps, int iop,
+ Vibration v, boolean isCommensurate) {
// The superspace operation matrix is (3+d+1)x(3+d+1) rotation/translation
matrix
// that can be blocked as follows:
@@ -221,14 +334,16 @@
//// need to bring in, sigma and tFactor, and two we need to compute,
//// GammaIinv and tau.
- this.id = id + "_" + symmetry.getSpaceGroupName();
+ this.id = id;// + "_" + symmetry.getSpaceGroupName();
+ this.symmetry = symmetry;
strop = symmetry.getSpaceGroupXyz(iop, false);
+ this.iop = iop;
+ this.nOps = nOps;
+
this.r0 = r0;
modDim = d;
rI = new Matrix(null, d, 1);
this.mods = mods;
- this.iop = iop;
- this.symmetry = symmetry;
this.gammaE = gammaE; // gammaE_nu, R, the real 3x3 rotation matrix, as M3
sigma = factors[0];
if (factors[1] != null) {
@@ -243,6 +358,7 @@
vib = v;
vib.modScale = 1;
mxyz = new V3(); // modulations of spin
+ axesLengths = symmetry.getUnitCellParams(); // required for calculating
mxyz
}
Matrix vR00 = Matrix.newT(r00, true);
Matrix vR0 = Matrix.newT(r0, true);
@@ -263,11 +379,6 @@
return this;
}
- @Override
- public SymmetryInterface getSubSystemUnitCell() {
- return (isSubsystem ? symmetry : null);
- }
-
/**
* Calculate r_I internal d-space coordinate of an atom.
*
@@ -367,6 +478,8 @@
if (isQ)
qtOffset = null;
calculate(qtOffset, isQ);
+ if (!Float.isNaN(vOcc))
+ occValue = getOccupancy();
}
if (isOn) {
addTo(a, 1);
@@ -420,22 +533,24 @@
@Override
public Object getModulation(char type, T3 tuv) {
- getModTemp();
+ getModCalc();
switch (type) {
case 'D':
// return r0 if t456 is null, otherwise calculate dx,dy,dz for a given
t4,5,6
- return P3.newP(tuv == null ? r0 : modTemp.calculate(tuv, false));
+ return P3.newP(tuv == null ? r0 : modCalc.calculate(tuv, false));
case 'M':
- // return r0 if t456 is null, otherwise calculate dx,dy,dz for a given
t4,5,6
- return P3.newP(tuv == null ? v0 : modTemp.calculate(tuv, false).mxyz);
+ // return v0 if t456 is null, otherwise calculate vx,vy,vz for a given
t4,5,6
+ return P3.newP(tuv == null ? v0 : modCalc.calculate(tuv, false).mxyz);
case 'T':
- modTemp.calculate(tuv, false);
- double[][] ta = modTemp.rI.getArray();
+ // do a calculation and return the t-value for the first three
dimensions of modulation
+ modCalc.calculate(tuv, false);
+ double[][] ta = modCalc.rI.getArray();
return P3.new3((float) ta[0][0], (modDim > 1 ? (float) ta[1][0] : 0),
(modDim > 2 ? (float) ta[2][0] : 0));
case 'O':
- // return vOcc current or calculated
- return Float.valueOf((tuv == null ? vOcc : modTemp.calculate(tuv,
false).vOcc) * 100);
+ // return the currently modulated or calculated occupation on [0,100]
+ return Float.valueOf(Math.abs(tuv == null ? getOccupancy100(false)
+ : modCalc.calculate(tuv, false).getOccupancy100(false)));
}
return null;
}
@@ -443,35 +558,45 @@
P3 ptTemp = new P3();
private V3 v0;
+ /**
+ * get updated value for offset vector and for occupancy
+ */
@Override
- public void setTempPoint(T3 a, T3 t456, float vibScale, float scale) {
- if (!enabled)
- return;
- getModTemp();
- addTo(a, Float.NaN);
- modTemp.calculate(t456, false).addTo(a, scale);
+ public T3 setCalcPoint(T3 pt, T3 t456, float vibScale, float scale) {
+ if (enabled) {
+ addTo(pt, Float.NaN);
+ getModCalc().calculate(t456, false).addTo(pt, scale);
+ //System.out.println("MS setTempPoint " + id + " v=" + vOcc);
+ // note: this does not include setting occValue
+ }
+ return pt;
}
- private void getModTemp() {
- if (modTemp == null) {
- modTemp = new ModulationSet();
- modTemp.id = id;
- modTemp.tau = tau;
- modTemp.spinOp = spinOp;
- modTemp.mods = mods;
- modTemp.gammaE = gammaE;
- modTemp.modDim = modDim;
- modTemp.gammaIinv = gammaIinv;
- modTemp.sigma = sigma;
- modTemp.r0 = r0;
- modTemp.v0 = v0;
- modTemp.vib = vib;
- modTemp.symmetry = symmetry;
- modTemp.rI = rI;
- if (mxyz != null) {
- modTemp.mxyz = new V3();
- }
+ private ModulationSet getModCalc() {
+ if (modCalc == null) {
+ modCalc = new ModulationSet();
+ modCalc.id = id;
+ modCalc.tau = tau;
+ modCalc.spinOp = spinOp;
+ modCalc.mods = mods;
+ modCalc.gammaE = gammaE;
+ modCalc.modDim = modDim;
+ modCalc.gammaIinv = gammaIinv;
+ modCalc.sigma = sigma;
+ modCalc.r0 = r0;
+ modCalc.v0 = v0;
+ modCalc.vib = vib;
+ modCalc.symmetry = symmetry;
+ modCalc.rI = rI;
+ modCalc.fileOcc = fileOcc;
+ modCalc.occParams = occParams;
+ modCalc.occSiteMultiplicity = occSiteMultiplicity;
+ modCalc.nOps = nOps;
+ modCalc.enabled = true;
+ if (mxyz != null)
+ modCalc.mxyz = new V3();
}
+ return modCalc;
}
@Override
@@ -548,11 +673,60 @@
&& (mxyz.x != 0 || mxyz.y != 0 || mxyz.z != 0);
}
- private float[] axesLengths;
+ /**
+ *
+ * get the occupancy, first from the reader, then from renderer
+ *
+ * @param pt
+ * @param foccupancy
+ * @param siteMult or 0 is this is not relevant
+ *
+ * @return occupancy on [0,1]
+ */
+ public float setOccupancy(double[] pt, double foccupancy,
+ double siteMult) {
+ occParams = pt;
+ fileOcc = foccupancy;
+ occSiteMultiplicity = siteMult;
+ return getOccupancy();
+ }
+
+ @Override
+ public int getOccupancy100(boolean isTemp) {
+ if (isCommensurate || Float.isNaN(vOcc))
+ return Integer.MIN_VALUE;
+ if (!isTemp && !enabled)
+ return (int) (-fileOcc * 100);
+ if (isTemp && modCalc != null) {
+ modCalc.getOccupancy();
+ return modCalc.getOccupancy100(false);
+ }
+ return (int) (occValue * 100);
+ }
- float[] getAxesLengths() {
- return (axesLengths == null ? (axesLengths = symmetry.getUnitCellParams())
- : axesLengths);
+ private float getOccupancy() {
+ double occ;
+ if (occAbsolute) {
+ // Crenel
+ occ = vOcc;
+ } else if (occParams == null) {
+ // cif Fourier
+ // _atom_site_occupancy + SUM
+ occ = fileOcc + vOcc;
+ } else if (occSiteMultiplicity > 0) {
+ // cif with m40 Fourier
+ // occ_site * (occ_0 + SUM)
+ double o_site = fileOcc * occSiteMultiplicity / nOps / occParams[1];
+ occ = o_site * (occParams[1] + vOcc);
+ } else {
+ // m40 Fourier
+ // occ_site * (occ_0 + SUM)
+ occ = occParams[0] * (occParams[1] + vOcc);
+ }
+ // 49/50 is an important range for cutoffs -- we never return a value in
this range
+ occ = (occ > 0.49 && occ < 0.50 ? 0.489 : Math.min(1, Math.max(0, occ)));
+ return occValue = (float) occ;
}
+
}
Modified: trunk/Jmol/src/org/jmol/util/Vibration.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Vibration.java 2015-05-02 17:47:14 UTC (rev
20475)
+++ trunk/Jmol/src/org/jmol/util/Vibration.java 2015-05-03 18:46:39 UTC (rev
20476)
@@ -35,8 +35,9 @@
* @param t456
* @param scale
* @param modulationScale
+ * @return pt
*/
- public void setTempPoint(T3 pt, T3 t456, float scale, float modulationScale)
{
+ public T3 setCalcPoint(T3 pt, T3 t456, float scale, float modulationScale) {
switch (modDim) {
// case TYPE_DISPLACEMENT:
// break;
@@ -46,6 +47,7 @@
pt.scaleAdd2((float) (Math.cos(t456.x * twoPI) * scale), this, pt);
break;
}
+ return pt;
}
public void getInfo(Map<String, Object> info) {
@@ -78,4 +80,12 @@
return x != 0 || y != 0 || z != 0;
}
+ /**
+ * @param isTemp used only in ModulationSet
+ * @return Integer.MIN_VALUE if not applicable, occupancy if enabled,
-occupancy if not enabled
+ */
+ public int getOccupancy100(boolean isTemp) {
+ return Integer.MIN_VALUE;
+ }
+
}
Modified: trunk/Jmol/src/org/jmol/viewer/GlobalSettings.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/GlobalSettings.java 2015-05-02 17:47:14 UTC
(rev 20475)
+++ trunk/Jmol/src/org/jmol/viewer/GlobalSettings.java 2015-05-03 18:46:39 UTC
(rev 20476)
@@ -454,10 +454,12 @@
int smallMoleculeMaxAtoms = 40000;
boolean smartAromatic = true;
boolean zeroBasedXyzRasmol = false;
- public boolean legacyAutoBonding = false;
+ boolean legacyAutoBonding = false;
public boolean legacyHAddition = false;
- public boolean legacyJavaFloat = false;
+ public boolean legacyJavaFloat = false; // float/double issue with
crystallographic symmetry before Jmol 14.2.5
+ boolean modulateOccupancy = true;
+
//centering and perspective
boolean allowRotateSelected = false;
Modified: trunk/Jmol/src/org/jmol/viewer/JC.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/JC.java 2015-05-02 17:47:14 UTC (rev
20475)
+++ trunk/Jmol/src/org/jmol/viewer/JC.java 2015-05-03 18:46:39 UTC (rev
20476)
@@ -696,18 +696,6 @@
public final static int SHAPE_HOVER = 35;
public final static int SHAPE_FRANK = 36;
public final static int SHAPE_MAX = SHAPE_FRANK + 1;
-
- // ATOM_IN_FRAME simply associates an atom with the current model
- // but doesn't necessarily mean it is visible
- // ATOM_VIS_SET and ATOM_VISIBLE are checked once only for each atom per
rendering
-
- public final static int ATOM_INFRAME = 1;
- public final static int ATOM_VISSET = 2;
- public final static int ATOM_VISIBLE = 4;
- public final static int ATOM_NOTHIDDEN = 8;
- public final static int ATOM_NOFLAGS = ~63; // all of the above, plus
balls and sticks
- public final static int ATOM_INFRAME_NOTHIDDEN = ATOM_INFRAME |
ATOM_NOTHIDDEN;
- public final static int ATOM_SHAPE_VIS_MASK = ~ATOM_INFRAME_NOTHIDDEN;
public final static int getShapeVisibilityFlag(int shapeID) {
return 16 << Math.min(shapeID, SHAPE_LAST_ATOM_VIS_FLAG);
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-05-02 17:47:14 UTC
(rev 20475)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-05-03 18:46:39 UTC
(rev 20476)
@@ -14,8 +14,14 @@
TODO: remove HTML5 dependency on synchronous file loading (check SCRIPT
command for problems)
-Jmol.___JmolVersion="14.3.13_2015.05.02"
+Jmol.___JmolVersion="14.3.13_2015.05.03"
+new feature: for msCIF (modulated structure files), setting modulation or
using vibration ON
+ now also indicates occupancy changes
+
+
+JmolVersion="14.3.13_2015.05.02"
+
bug fix: color atoms property vxyz crashes Jmol if no vibrations
bug fix: with msCIF, select subsystem=1 does not select anything
bug fix: vibrations in trajectories not animating (14.3.6_2014.08.14)
Modified: trunk/Jmol/src/org/jmol/viewer/ShapeManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/ShapeManager.java 2015-05-02 17:47:14 UTC
(rev 20475)
+++ trunk/Jmol/src/org/jmol/viewer/ShapeManager.java 2015-05-03 18:46:39 UTC
(rev 20476)
@@ -355,8 +355,8 @@
}
/**
- * Sets shape visibility flags, including ATOM_VIS_INFRAME
- * and ATOM_VIS_NOTHIDDEN.
+ * Sets shape visibility flags, including ATOM_VIS_INFRAME and
+ * ATOM_VIS_NOTHIDDEN.
*
*/
void setModelVisibility() {
@@ -372,7 +372,7 @@
// so isTranslucent = isTranslucent || f() would NOT work.
BS bs = vwr.getVisibleFramesBitSet();
-
+
// i=2 skips balls and sticks
// as these are handled differently.
@@ -381,32 +381,36 @@
for (int i = JC.SHAPE_MIN_HAS_SETVIS; i < JC.SHAPE_MAX_HAS_SETVIS; i++)
if (shapes[i] != null)
shapes[i].setModelVisibilityFlags(bs);
-
+
// now check ATOM_IN_FRAME, and ATOM_NOTHIDDEN, VIS_BALLS_FLAG
-
-// todo: deleted atoms not showing up in state
+
+ // todo: deleted atoms not showing up in state
boolean showHydrogens = vwr.getBoolean(T.showhydrogens);
BS bsDeleted = vwr.slm.bsDeleted;
Atom[] atoms = ms.at;
- for (int i = ms.ac; --i >= 0;) {
- Atom atom = atoms[i];
- atom.shapeVisibilityFlags &= JC.ATOM_NOFLAGS;
- if (bsDeleted != null && bsDeleted.get(i) || !showHydrogens
- && atom.getElementNumber() == 1)
- continue;
- if (bs.get(atom.mi)) {
- int f = JC.ATOM_INFRAME;
- if (!ms.isAtomHidden(i)) {
- f |= JC.ATOM_NOTHIDDEN;
- if (atom.madAtom != 0)
- f |= JC.VIS_BALLS_FLAG;
- atom.setShapeVisibility(f, true);
+ ms.clearVisibleSets();
+ if (atoms.length > 0) {
+ for (int i = ms.ac; --i >= 0;) {
+ Atom atom = atoms[i];
+ atom.shapeVisibilityFlags &= Atom.ATOM_NOFLAGS;
+ if (bsDeleted != null && bsDeleted.get(i))
+ continue;
+ if (bs.get(atom.mi)) {
+ int f = Atom.ATOM_INFRAME;
+ if (!ms.isAtomHidden(i)
+ && (showHydrogens || atom.getElementNumber() != 1)) {
+ f |= Atom.ATOM_NOTHIDDEN;
+ if (atom.madAtom != 0)
+ f |= JC.VIS_BALLS_FLAG;
+ atom.setShapeVisibility(f, true);
+ }
}
}
}
+ setShapeVis();
+ }
- ms.clearVisibleSets();
-
+ private void setShapeVis() {
//set clickability -- this enables measures and such
for (int i = 0; i < JC.SHAPE_MAX; ++i) {
Shape shape = shapes[i];
@@ -432,17 +436,19 @@
vwr.setAtomCoordsRelative(pt, bsAtoms);
ptOffset.set(0, 0, 0);
}
- ms.getRenderable(bs);
- Object[] vibrationVectors = ms.vibrations;
+ ms.getAtomsInFrame(bs);
+ Vibration[] vibrationVectors = ms.vibrations;
boolean vibs = (vibrationVectors != null && tm.vibrationOn);
+ boolean checkOccupancy = (ms.bsModulated != null);
Atom[] atoms = ms.at;
+ boolean haveMods = false;
for (int i = bs.nextSetBit(0); i >= 0; i = bs.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,
- (Vibration) vibrationVectors[i]) : tm.transformPt(atom));
+ vibrationVectors[i]) : tm.transformPt(atom));
atom.sX = screen.x;
atom.sY = screen.y;
atom.sZ = screen.z;
@@ -450,7 +456,24 @@
if (d == Atom.MAD_GLOBAL)
d = (int) (vwr.getFloat(T.atoms) * 2000);
atom.sD = (short) vwr.tm.scaleToScreen(screen.z, d);
+ if (checkOccupancy) {
+ int occ = vibrationVectors[i].getOccupancy100(vibs);
+ if (occ != Integer.MIN_VALUE) {
+ //System.out.println(atom + " " + occ);
+ haveMods = true;
+ atom.setShapeVisibility(Atom.ATOM_VISSET, false);
+ if (occ >= 0 && occ < 50)
+ atom.setShapeVisibility(Atom.ATOM_NOTHIDDEN | JC.VIS_BALLS_FLAG,
+ false);
+ else
+ atom.setShapeVisibility(Atom.ATOM_NOTHIDDEN
+ | (atom.madAtom > 0 ? JC.VIS_BALLS_FLAG : 0), true);
+ ms.occupancies[atom.i] = Math.abs(occ);
+ }
+ }
}
+ if (haveMods)
+ setShapeVis();
GData gdata = vwr.gdata;
if (tm.slabEnabled) {
boolean slabByMolecule = vwr.getBoolean(T.slabbymolecule);
Modified: trunk/Jmol/src/org/jmol/viewer/TransformManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/TransformManager.java 2015-05-02
17:47:14 UTC (rev 20475)
+++ trunk/Jmol/src/org/jmol/viewer/TransformManager.java 2015-05-03
18:46:39 UTC (rev 20476)
@@ -1365,7 +1365,7 @@
protected final P3 point3fScreenTemp = new P3();
protected final P3i point3iScreenTemp = new P3i();
- private final Point3fi ptVibTemp = new Point3fi();
+ final Point3fi ptVibTemp = new Point3fi();
public boolean navigating = false;
public int mode = MODE_STANDARD;
@@ -1526,11 +1526,17 @@
ptVibTemp.setT(ptXYZ);
return applyPerspective(getVibrationPoint(v, ptVibTemp, Float.NaN), ptXYZ);
}
-
+
+ /**
+ * return
+ * @param v
+ * @param pt temporary value; also returned
+ * @param scale
+ * @return pt
+ */
public T3 getVibrationPoint(Vibration v, T3 pt, float scale) {
- v.setTempPoint(pt, vibrationT,
+ return v.setCalcPoint(pt, vibrationT,
(Float.isNaN(scale) ? vibrationScale : scale), vwr.g.modulationScale);
- return pt;
}
public void transformPt3f(T3 ptXYZ, P3 screen) {
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2015-05-02 17:47:14 UTC (rev
20475)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2015-05-03 18:46:39 UTC (rev
20476)
@@ -5052,9 +5052,6 @@
case T.legacyhaddition:
// aargh -- Some atoms missed before Jmol 13.1.17
return g.legacyHAddition;
- case T.legacyjavafloat:
- // float/double issue with crystallographic symmetry before Jmol 14.2.5
- return g.legacyJavaFloat;
case T.loggestures:
return g.logGestures;
case T.measureallmodels:
@@ -5878,6 +5875,10 @@
private void setBooleanPropertyTok(String key, int tok, boolean value) {
boolean doRepaint = true;
switch (tok) {
+ case T.modulateoccupancy:
+ // 12.0.RC6
+ g.modulateOccupancy = value;
+ break;
case T.legacyjavafloat:
// 14.3.5
g.legacyJavaFloat = value;
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