Revision: 18433
http://sourceforge.net/p/jmol/code/18433
Author: hansonr
Date: 2013-07-05 16:59:05 +0000 (Fri, 05 Jul 2013)
Log Message:
-----------
unitcell center {atomset}
unitcell center {x y z} // assumed fractional
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/api/SymmetryInterface.java
trunk/Jmol/src/org/jmol/io2/BinaryDocument.java
trunk/Jmol/src/org/jmol/jvxl/readers/Parameters.java
trunk/Jmol/src/org/jmol/jvxl/readers/XsfReader.java
trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java
trunk/Jmol/src/org/jmol/script/ScriptCompilationTokenParser.java
trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java
trunk/Jmol/src/org/jmol/script/T.java
trunk/Jmol/src/org/jmol/symmetry/Symmetry.java
trunk/Jmol/src/org/jmol/util/Measure.java
trunk/Jmol/src/org/jmol/util/Parser.java
trunk/Jmol/src/org/jmol/viewer/ColorManager.java
trunk/Jmol/src/org/jmol/viewer/DataManager.java
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: trunk/Jmol/src/org/jmol/api/SymmetryInterface.java
===================================================================
--- trunk/Jmol/src/org/jmol/api/SymmetryInterface.java 2013-07-05 14:18:59 UTC
(rev 18432)
+++ trunk/Jmol/src/org/jmol/api/SymmetryInterface.java 2013-07-05 16:59:05 UTC
(rev 18433)
@@ -165,7 +165,9 @@
public Object getSymmetryInfo(ModelSet modelSet, int iModel, int iAtom,
SymmetryInterface uc, String xyz, int op,
P3 pt, P3 pt2, String id, int type);
- public void setCentroid(ModelSet modelSet, int iAtom0, int iAtom1,
+ public BS notInCentroid(ModelSet modelSet, BS bsAtoms,
int[] minmax);
+ public boolean checkUnitCell(SymmetryInterface uc, P3 cell, P3 ptTemp,
boolean isAbsolute);
+
}
Modified: trunk/Jmol/src/org/jmol/io2/BinaryDocument.java
===================================================================
--- trunk/Jmol/src/org/jmol/io2/BinaryDocument.java 2013-07-05 14:18:59 UTC
(rev 18432)
+++ trunk/Jmol/src/org/jmol/io2/BinaryDocument.java 2013-07-05 16:59:05 UTC
(rev 18433)
@@ -394,7 +394,7 @@
fracIEEE = new float[270];
for (int i = 0; i < 270; i++)
fracIEEE[i] = (float) Math.pow(2, i - 141);
- // System.out.println(fracIEEE[0] + " " + Float.MIN_VALUE);
+ // System.out.println(fracIEEE[0] + " " + Parser.FLOAT_MIN_SAFE);
// System.out.println(fracIEEE[269] + " " + Float.MAX_VALUE);
}
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/Parameters.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/Parameters.java 2013-07-05
14:18:59 UTC (rev 18432)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/Parameters.java 2013-07-05
16:59:05 UTC (rev 18433)
@@ -129,6 +129,7 @@
import org.jmol.util.Matrix3f;
import org.jmol.util.P3;
import org.jmol.util.P4;
+import org.jmol.util.Parser;
import org.jmol.util.V3;
import org.jmol.viewer.JC;
@@ -421,7 +422,7 @@
dataType = (isGeodesic ? SURFACE_GEODESIC : SURFACE_SPHERE);
distance = radius;
setEccentricity(P4.new4(0, 0, 1, 1));
- cutoff = Float.MIN_VALUE;
+ cutoff = Parser.FLOAT_MIN_SAFE;
isCutoffAbsolute = false;
isSilent = !logMessages;
script = getScriptParams() + " SPHERE " + radius + ";";
@@ -431,7 +432,7 @@
dataType = SURFACE_ELLIPSOID2;
distance = 1f;
setEccentricity(v);
- cutoff = Float.MIN_VALUE;
+ cutoff = Parser.FLOAT_MIN_SAFE;
isCutoffAbsolute = false;
isSilent = !logMessages;
//script = " center " + Escape.escape(center)
@@ -445,7 +446,7 @@
//for (int i = 0; i < 6; i++)System.out.print(bList[i] + "
");System.out.println( " in Parameters setEllipsoid" + center);
dataType = SURFACE_ELLIPSOID3;
distance = 0.3f * (Float.isNaN(scale) ? 1f : scale);
- cutoff = Float.MIN_VALUE;
+ cutoff = Parser.FLOAT_MIN_SAFE;
isCutoffAbsolute = false;
isSilent = !logMessages;
if (center.x == Float.MAX_VALUE)
@@ -574,7 +575,7 @@
void setFunctionXY(JmolList<Object> value) {
dataType = SURFACE_FUNCTIONXY;
functionInfo = value;
- cutoff = Float.MIN_VALUE;
+ cutoff = Parser.FLOAT_MIN_SAFE;
isEccentric = isAnisotropic = false;
}
@@ -582,7 +583,7 @@
dataType = SURFACE_FUNCTIONXYZ;
functionInfo = value;
if (cutoff == Float.MAX_VALUE)
- cutoff = Float.MIN_VALUE;
+ cutoff = Parser.FLOAT_MIN_SAFE;
isEccentric = isAnisotropic = false;
}
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/XsfReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/XsfReader.java 2013-07-05 14:18:59 UTC
(rev 18432)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/XsfReader.java 2013-07-05 16:59:05 UTC
(rev 18433)
@@ -32,6 +32,8 @@
class XsfReader extends VolumeFileReader {
+ // from XCrysDen; see http://www.xcrysden.org/doc/XSF.html
+
XsfReader(){}
@Override
Modified: trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2013-07-05
14:18:59 UTC (rev 18432)
+++ trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2013-07-05
16:59:05 UTC (rev 18433)
@@ -301,12 +301,12 @@
// the maximum BondingRadius seen in this set of atoms
// used in autobonding
- protected float maxBondingRadius = Float.MIN_VALUE;
- private float maxVanderwaalsRadius = Float.MIN_VALUE;
+ protected float maxBondingRadius = Parser.FLOAT_MIN_SAFE;
+ private float maxVanderwaalsRadius = Parser.FLOAT_MIN_SAFE;
public float getMaxVanderwaalsRadius() {
//Dots
- if (maxVanderwaalsRadius == Float.MIN_VALUE)
+ if (maxVanderwaalsRadius == Parser.FLOAT_MIN_SAFE)
findMaxRadii();
return maxVanderwaalsRadius;
}
Modified: trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelCollection.java 2013-07-05
14:18:59 UTC (rev 18432)
+++ trunk/Jmol/src/org/jmol/modelset/ModelCollection.java 2013-07-05
16:59:05 UTC (rev 18433)
@@ -1654,19 +1654,25 @@
* deletes molecules based on: CENTROID -- molecular centroid is not in unit
* cell CENTROID PACKED -- all molecule atoms are not in unit cell
*
- * @param iAtom0
- * @param iAtom1
+ * @param bs
* @param minmax
* fractional [xmin, ymin, zmin, xmax, ymax, zmax, 1=packed]
*/
- public void setCentroid(int iAtom0, int iAtom1, int[] minmax) {
+ public void setCentroid(BS bs, int[] minmax) {
+ BS bsDelete = getNotInCentroid(bs, minmax);
+ if (bsDelete != null && bsDelete.nextSetBit(0) >= 0)
+ viewer.deleteAtoms(bsDelete, false);
+ }
+
+ private BS getNotInCentroid(BS bs, int[] minmax) {
+ int iAtom0 = bs.nextSetBit(0);
+ if (iAtom0 < 0)
+ return null;
SymmetryInterface uc = getUnitCell(atoms[iAtom0].modelIndex);
- if (uc == null)
- return;
- uc.setCentroid((ModelSet) this, iAtom0, iAtom1, minmax);
+ return (uc == null ? null : uc.notInCentroid((ModelSet) this, bs, minmax));
}
- public JmolMolecule[] getMolecules() {
+ public JmolMolecule[] getMolecules() {
if (moleculeCount > 0)
return molecules;
if (molecules == null)
@@ -1898,13 +1904,27 @@
// select cell=555 (an absolute quantity)
bs = new BS();
info = (int[]) specInfo;
- ptTemp1.set(info[0] / 1000f, info[1] / 1000f,
- info[2] / 1000f);
+ ptTemp1.set(info[0] / 1000f, info[1] / 1000f, info[2] / 1000f);
boolean isAbsolute = !viewer.getBoolean(T.fractionalrelative);
for (int i = atomCount; --i >= 0;)
if (isInLatticeCell(i, ptTemp1, ptTemp2, isAbsolute))
bs.set(i);
return bs;
+ case T.centroid:
+ // select centroid=555 -- like cell=555 but for whole molecules
+ // if it is one full molecule, then return the EMPTY bitset
+ bs = BSUtil.newBitSet2(0, atomCount);
+ info = (int[]) specInfo;
+ int[] minmax = new int[] { info[0] / 1000 - 1, info[1] / 1000 - 1,
info[2] / 1000 - 1, info[0] / 1000, info[1] / 1000, info[2] / 1000, 0 };
+ for (int i = modelCount; --i >= 0;) {
+ SymmetryInterface uc = getUnitCell(i);
+ if (uc == null) {
+ BSUtil.andNot(bs, models[i].bsAtoms);
+ continue;
+ }
+ bs.andNot(uc.notInCentroid((ModelSet) this, models[i].bsAtoms,
minmax));
+ }
+ return bs;
case T.molecule:
return getMoleculeBitSet((BS) specInfo);
case T.sequence:
@@ -1953,8 +1973,8 @@
}
return bs;
case T.symmetry:
- return BSUtil.copy(bsSymmetry == null ? bsSymmetry = BSUtil.newBitSet(
- atomCount) : bsSymmetry);
+ return BSUtil.copy(bsSymmetry == null ? bsSymmetry = BSUtil
+ .newBitSet(atomCount) : bsSymmetry);
case T.unitcell:
// select UNITCELL (a relative quantity)
bs = new BS();
@@ -1963,33 +1983,23 @@
return bs;
ptTemp1.set(1, 1, 1);
for (int i = atomCount; --i >= 0;)
- if (isInLatticeCell(i, ptTemp1, ptTemp2, false))
+ if (isInLatticeCell(i, ptTemp1, ptTemp2, false))
bs.set(i);
return bs;
}
}
- private boolean isInLatticeCell(int i, P3 cell, P3 pt,
+ private boolean isInLatticeCell(int i, P3 cell, P3 ptTemp,
boolean isAbsolute) {
// this is the one method that allows for an absolute fractional cell
business
// but it is always called with isAbsolute FALSE.
// so then it is determining values for select UNITCELL and the like.
+
int iModel = atoms[i].modelIndex;
SymmetryInterface uc = getUnitCell(iModel);
- if (uc == null)
- return false;
- pt.setT(atoms[i]);
- uc.toFractional(pt, isAbsolute);
- float slop = 0.02f;
- // {1 1 1} here is the original cell
- if (pt.x < cell.x - 1f - slop || pt.x > cell.x + slop)
- return false;
- if (pt.y < cell.y - 1f - slop || pt.y > cell.y + slop)
- return false;
- if (pt.z < cell.z - 1f - slop || pt.z > cell.z + slop)
- return false;
- return true;
+ ptTemp.setT(atoms[i]);
+ return (uc != null && uc.checkUnitCell(uc, cell, ptTemp, isAbsolute));
}
/**
@@ -2274,7 +2284,7 @@
if (mad == 0)
mad = 1;
// null values for bitsets means "all"
- if (maxBondingRadius == Float.MIN_VALUE)
+ if (maxBondingRadius == Parser.FLOAT_MIN_SAFE)
findMaxRadii();
float bondTolerance = viewer.getFloat(T.bondtolerance);
float minBondDistance = viewer.getFloat(T.minbonddistance);
@@ -2365,7 +2375,7 @@
if (mad == 0)
mad = 1;
// null values for bitsets means "all"
- if (maxBondingRadius == Float.MIN_VALUE)
+ if (maxBondingRadius == Parser.FLOAT_MIN_SAFE)
findMaxRadii();
float bondTolerance = viewer.getFloat(T.bondtolerance);
float minBondDistance = viewer.getFloat(T.minbonddistance);
Modified: trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java 2013-07-05 14:18:59 UTC
(rev 18432)
+++ trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java 2013-07-05 16:59:05 UTC
(rev 18433)
@@ -36,6 +36,7 @@
import org.jmol.util.BS;
import org.jmol.util.Logger;
import org.jmol.util.P3;
+import org.jmol.util.Parser;
import org.jmol.util.Quaternion;
import org.jmol.util.SB;
import org.jmol.util.TextFormat;
@@ -267,7 +268,7 @@
leadMidpoints = new P3[monomerCount + 1];
leadPoints = new P3[monomerCount + 1];
wingVectors = new V3[monomerCount + 1];
- sheetSmoothing = Float.MIN_VALUE;
+ sheetSmoothing = Parser.FLOAT_MIN_SAFE;
}
if (reversed == null)
reversed = BS.newN(monomerCount);
Modified: trunk/Jmol/src/org/jmol/script/ScriptCompilationTokenParser.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptCompilationTokenParser.java
2013-07-05 14:18:59 UTC (rev 18432)
+++ trunk/Jmol/src/org/jmol/script/ScriptCompilationTokenParser.java
2013-07-05 16:59:05 UTC (rev 18433)
@@ -441,7 +441,8 @@
// create a file_model integer as part of the token
return addTokenToPostfixInt(T.spec_model2, fixModelSpec(getToken()),
theValue);
case T.cell:
- return clauseCell();
+ case T.centroid:
+ return clauseCell(tok);
case T.connected:
return clauseConnected();
case T.search:
@@ -932,7 +933,7 @@
return true;
}
- private boolean clauseCell() {
+ private boolean clauseCell(int tok) {
P3 cell = new P3();
tokenNext(); // CELL
if (!tokenNextTok(T.opEQ)) // =
@@ -946,7 +947,7 @@
cell.x = nnn / 100 - 4;
cell.y = (nnn % 100) / 10 - 4;
cell.z = (nnn % 10) - 4;
- return addTokenToPostfix(T.cell, cell);
+ return addTokenToPostfix(tok, cell);
}
if (!isToken(T.leftbrace) || !getNumericalToken())
return error(ERROR_coordinateExpected); // i
@@ -961,7 +962,7 @@
if (!getNumericalToken() || !tokenNextTok(T.rightbrace))
return error(ERROR_coordinateExpected); // k
cell.z = floatValue();
- return addTokenToPostfix(T.cell, cell);
+ return addTokenToPostfix(tok, cell);
}
private boolean clauseDefine(boolean haveToken, boolean forceString) {
Modified: trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2013-07-05 14:18:59 UTC
(rev 18432)
+++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2013-07-05 16:59:05 UTC
(rev 18433)
@@ -3868,9 +3868,10 @@
if (chainID != -1)
pc += 2;
break;
+ case T.centroid:
case T.cell:
P3 pt = (P3) value;
- rpn.addXBs(getAtomBits(T.cell, new int[] { (int) Math.floor(pt.x *
1000),
+ rpn.addXBs(getAtomBits(instruction.tok, new int[] { (int)
Math.floor(pt.x * 1000),
(int) Math.floor(pt.y * 1000), (int) Math.floor(pt.z * 1000) }));
break;
case T.thismodel:
@@ -8208,7 +8209,7 @@
prefix = "atom";
}
// don't allow isosurface partial translucency (yet)
- //translucentLevel = Float.MIN_VALUE;
+ //translucentLevel = Parser.FLOAT_MIN_SAFE;
getToken(index = iToken + 1);
break;
}
@@ -8217,7 +8218,7 @@
return;
boolean isTranslucent = (theTok == T.translucent);
if (isTranslucent || theTok == T.opaque) {
- if (translucentLevel == Float.MIN_VALUE)
+ if (translucentLevel == Parser.FLOAT_MIN_SAFE)
error(ERROR_invalidArgument);
translucency = parameterAsString(index++);
if (isTranslucent && isFloatParameter(index))
@@ -8881,8 +8882,7 @@
// if it is just LOAD "xxxx.xxx"
// so as to avoid the ZAP in case these
// do not contain a full state script
- if (modelName.endsWith(".spt")
- || modelName.endsWith(".png")
+ if (modelName.endsWith(".spt") || modelName.endsWith(".png")
|| modelName.endsWith(".pngj")) {
script(0, modelName);
return;
@@ -8936,9 +8936,9 @@
i++;
loadScript.append(" " + modelName);
tokType = (tok == T.identifier
- && Parser.isOneOf(modelName.toLowerCase(),
- JC.LOAD_ATOM_DATA_TYPES) ? T
- .getTokFromName(modelName) : T.nada);
+ && Parser.isOneOf(modelName.toLowerCase(),
JC.LOAD_ATOM_DATA_TYPES) ? T
+ .getTokFromName(modelName)
+ : T.nada);
if (tokType != T.nada) {
// loading just some data here
// xyz vxyz vibration temperature occupancy partialcharge
@@ -9024,7 +9024,7 @@
String filename = null;
String appendedData = null;
String appendedKey = null;
-
+
if (slen == i + 1) {
// end-of-command options:
@@ -9050,15 +9050,14 @@
if (loadScript.indexOf(" files") < 0)
error(ERROR_invalidArgument);
for (int j = 0; j < filenames.length; j++)
- loadScript.append(" /*file*/")
- .append(Escape.eS(filenames[j]));
+ loadScript.append(" /*file*/").append(Escape.eS(filenames[j]));
}
}
}
} else if (getToken(i + 1).tok == T.manifest
// model/vibration index or list of model indices
- || theTok == T.integer || theTok == T.varray
- || theTok == T.leftsquare || theTok == T.spacebeforesquare
+ || theTok == T.integer || theTok == T.varray || theTok == T.leftsquare
+ || theTok == T.spacebeforesquare
// {i j k} (lattice)
|| theTok == T.leftbrace || theTok == T.point3f
// PACKED/CENTROID, either order
@@ -9324,7 +9323,6 @@
// .... APPEND DATA "appendedData" .... end "appendedData"
// option here to designate other than "appendedData"
// .... APPEND "appendedData" @x ....
-
if (tokAt(i) == T.append) {
// for CIF reader -- experimental
@@ -9357,7 +9355,7 @@
P3 pt = null;
BS bs = null;
- JmolList<String> fNames = new JmolList<String>();
+ JmolList<String> fNames = new JmolList<String>();
while (i < slen) {
switch (tokAt(i)) {
case T.filter:
@@ -9367,7 +9365,7 @@
case T.coord:
htParams.remove("isTrajectory");
if (firstLastSteps == null) {
- firstLastSteps = new JmolList<Object>();
+ firstLastSteps = new JmolList<Object>();
pt = P3.new3(0, -1, 1);
}
if (isPoint3f(++i)) {
@@ -9384,7 +9382,8 @@
}
fNames.addLast(filename = parameterAsString(i++));
if (pt != null) {
- firstLastSteps.addLast(new int[] { (int) pt.x, (int) pt.y, (int)
pt.z });
+ firstLastSteps
+ .addLast(new int[] { (int) pt.x, (int) pt.y, (int) pt.z });
loadScript.append(" COORD " + Escape.eP(pt));
} else if (bs != null) {
firstLastSteps.addLast(bs);
@@ -9410,8 +9409,9 @@
// get default filter if necessary
if (appendedData != null) {
- sOptions += " APPEND data \"" + appendedKey + "\"\n" + appendedData
- + (appendedData.endsWith("\n") ? "" : "\n") + "end \"" + appendedKey +
"\"";
+ sOptions += " APPEND data \"" + appendedKey + "\"\n" + appendedData
+ + (appendedData.endsWith("\n") ? "" : "\n") + "end \"" + appendedKey
+ + "\"";
}
if (filter == null)
filter = viewer.getDefaultLoadFilter();
@@ -9434,9 +9434,9 @@
isVariable = true;
String s = getStringParameter(filename.substring(1), false);
htParams.put("fileData", s);
- loadScript = new SB().append("{\n var ")
- .append(filename.substring(1)).append(" = ")
- .append(Escape.eS(s)).append(";\n ").appendSB(loadScript);
+ loadScript = new SB().append("{\n var ").append(
+ filename.substring(1)).append(" = ").append(Escape.eS(s)).append(
+ ";\n ").appendSB(loadScript);
}
}
@@ -9499,8 +9499,7 @@
}
if (errMsg != null && !isCmdLine_c_or_C_Option) {
if (errMsg.indexOf(JC.NOTE_SCRIPT_FILE) == 0) {
- filename = errMsg.substring(JC.NOTE_SCRIPT_FILE.length())
- .trim();
+ filename = errMsg.substring(JC.NOTE_SCRIPT_FILE.length()).trim();
script(0, filename);
return;
}
@@ -9517,9 +9516,10 @@
+ (filenames == null ? htParams.get("fullPathName") : modelName));
Map<String, Object> info = viewer.getModelSetAuxiliaryInfo();
if (info != null && info.containsKey("centroidMinMax")
- && viewer.getAtomCount() > 0)
- viewer.setCentroid(isAppend ? atomCount0 : 0, viewer.getAtomCount() - 1,
- (int[]) info.get("centroidMinMax"));
+ && viewer.getAtomCount() > 0) {
+ BS bs = BSUtil.newBitSet2(isAppend ? atomCount0 : 0,
viewer.getAtomCount());
+ viewer.setCentroid(bs, (int[]) info.get("centroidMinMax"));
+ }
String script = viewer.getDefaultLoadScript();
String msg = "";
if (script.length() > 0)
@@ -10388,7 +10388,7 @@
}
BS bsAtoms = null;
- float degreesPerSecond = Float.MIN_VALUE;
+ float degreesPerSecond = Parser.FLOAT_MIN_SAFE;
int nPoints = 0;
float endDegrees = Float.MAX_VALUE;
boolean isMolecular = false;
@@ -10456,7 +10456,7 @@
// rotate spin ... [degreesPerSecond]
// rotate spin ... [endDegrees] [degreesPerSecond]
// rotate spin BRANCH <DihedralList> [seconds]
- if (degreesPerSecond == Float.MIN_VALUE) {
+ if (degreesPerSecond == Parser.FLOAT_MIN_SAFE) {
degreesPerSecond = floatParameter(i);
continue;
} else if (endDegrees == Float.MAX_VALUE) {
@@ -10470,7 +10470,7 @@
if (endDegrees == Float.MAX_VALUE) {
endDegrees = floatParameter(i);
continue;
- } else if (degreesPerSecond == Float.MIN_VALUE) {
+ } else if (degreesPerSecond == Parser.FLOAT_MIN_SAFE) {
degreesPerSecond = floatParameter(i);
isSpin = true;
continue;
@@ -10630,7 +10630,7 @@
if (bsAtoms == null)
bsAtoms = bsCompare;
}
- float rate = (degreesPerSecond == Float.MIN_VALUE ? 10
+ float rate = (degreesPerSecond == Parser.FLOAT_MIN_SAFE ? 10
: endDegrees == Float.MAX_VALUE ? degreesPerSecond
: (degreesPerSecond < 0) == (endDegrees > 0) ?
// -n means number of seconds, not degreesPerSecond
@@ -10712,7 +10712,7 @@
&& (endDegrees == 0 || degreesPerSecond == 0)) {
// need a token rotation
endDegrees = 0.01f;
- rate = (degreesPerSecond == Float.MIN_VALUE ? 0.01f
+ rate = (degreesPerSecond == Parser.FLOAT_MIN_SAFE ? 0.01f
: degreesPerSecond < 0 ?
// -n means number of seconds, not degreesPerSecond
-endDegrees / degreesPerSecond
@@ -11679,7 +11679,7 @@
break;
case T.set:
sm.loadShape(JC.SHAPE_ELLIPSOIDS);
- setShapeProperty(JC.SHAPE_ELLIPSOIDS, "select", parameterAsString(2));
+ setShapeProperty(JC.SHAPE_ELLIPSOIDS, "select", stringParameter(2));
i = iToken;
checkMore = true;
isSet = true;
@@ -14430,11 +14430,32 @@
index++;
id = objectNameParameter(++index);
break;
+ case T.center:
+ ++index;
+ switch (tokAt(++index)) {
+ case T.bitset:
+ case T.expressionBegin:
+ pt = P3.newP(viewer.getAtomSetCenter(atomExpressionAt(index)));
+ viewer.toFractional(pt, true);
+ index = iToken;
+ break;
+ default:
+ if (isCenterParameter(index)) {
+ pt = centerParameter(index);
+ index = iToken;
+ break;
+ }
+ error(ERROR_invalidArgument);
+ }
+ pt.x -= 0.5f;
+ pt.y -= 0.5f;
+ pt.z -= 0.5f;
+ break;
default:
if (isArrayParameter(index + 1)) {
points = getPointArray(++index, 4);
index = iToken;
- }else if (slen == index + 2) {
+ } else if (slen == index + 2) {
if (getToken(index + 1).tok == T.integer
&& intParameter(index + 1) >= 111)
icell = intParameter(++index);
Modified: trunk/Jmol/src/org/jmol/script/T.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/T.java 2013-07-05 14:18:59 UTC (rev
18432)
+++ trunk/Jmol/src/org/jmol/script/T.java 2013-07-05 16:59:05 UTC (rev
18433)
@@ -580,6 +580,7 @@
public final static int atomindex = intproperty | 3;
public final static int bondcount = intproperty | 4;
public final static int cell = intproperty | 5;
+ public final static int centroid = intproperty | 6;
public final static int configuration = intproperty | 6 | scriptCommand;
//color: see xxx(a, b, c, d)
public final static int elemisono = intproperty | 7;
@@ -1098,7 +1099,6 @@
final static int cancel = misc | 50;
public final static int cap = misc | 51 | expression;
final static int cavity = misc | 52;
- final static int centroid = misc | 53;
final static int check = misc | 54;
final static int chemical = misc | 55;
final static int circle = misc | 56;
Modified: trunk/Jmol/src/org/jmol/symmetry/Symmetry.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/Symmetry.java 2013-07-05 14:18:59 UTC
(rev 18432)
+++ trunk/Jmol/src/org/jmol/symmetry/Symmetry.java 2013-07-05 16:59:05 UTC
(rev 18433)
@@ -567,21 +567,20 @@
}
}
- public void setCentroid(ModelSet modelSet, int iAtom0, int iAtom1,
+ public BS notInCentroid(ModelSet modelSet, BS bsAtoms,
int[] minmax) {
try {
BS bsDelete = new BS();
+ int iAtom0 = bsAtoms.nextSetBit(0);
JmolMolecule[] molecules = modelSet.getMolecules();
int moleculeCount = molecules.length;
Atom[] atoms = modelSet.atoms;
-
boolean isOneMolecule = (molecules[moleculeCount - 1].firstAtomIndex ==
modelSet
- .models[atoms[iAtom1].modelIndex].firstAtomIndex);
+ .models[atoms[iAtom0].modelIndex].firstAtomIndex);
P3 center = new P3();
boolean centroidPacked = (minmax[6] == 1);
nextMol: for (int i = moleculeCount; --i >= 0
- && molecules[i].firstAtomIndex >= iAtom0
- && molecules[i].firstAtomIndex < iAtom1;) {
+ && bsAtoms.get(molecules[i].firstAtomIndex);) {
BS bs = molecules[i].atomList;
center.set(0, 0, 0);
int n = 0;
@@ -602,10 +601,9 @@
if (centroidPacked || n > 0 && isNotCentroid(center, n, minmax, false))
bsDelete.or(bs);
}
- if (bsDelete.nextSetBit(0) >= 0)
- modelSet.viewer.deleteAtoms(bsDelete, false);
+ return bsDelete;
} catch (Exception e) {
- // ignore
+ return null;
}
}
@@ -619,10 +617,20 @@
return (center.x + 0.000005f <= minmax[0] || center.x - 0.000005f >
minmax[3]
|| center.y + 0.000005f <= minmax[1] || center.y - 0.000005f >
minmax[4]
|| center.z + 0.000005f <= minmax[2] || center.z - 0.000005f >
minmax[5]);
- return (center.x + 0.000005f <= minmax[0] || center.x + 0.00001f >
minmax[3]
- || center.y + 0.000005f <= minmax[1] || center.y + 0.00001f > minmax[4]
- || center.z + 0.000005f <= minmax[2] || center.z + 0.00001f > minmax[5]);
+
+ return (center.x + 0.000005f <= minmax[0] || center.x + 0.00005f >
minmax[3]
+ || center.y + 0.000005f <= minmax[1] || center.y + 0.00005f > minmax[4]
+ || center.z + 0.000005f <= minmax[2] || center.z + 0.00005f > minmax[5]);
}
+ public boolean checkUnitCell(SymmetryInterface uc, P3 cell, P3 ptTemp,
+ boolean isAbsolute) {
+ uc.toFractional(ptTemp, isAbsolute);
+ float slop = 0.02f;
+ // {1 1 1} here is the original cell
+ return (ptTemp.x >= cell.x - 1f - slop && ptTemp.x <= cell.x + slop
+ && ptTemp.y >= cell.y - 1f - slop && ptTemp.y <= cell.y + slop
+ && ptTemp.z >= cell.z - 1f - slop && ptTemp.z <= cell.z + slop);
+ }
}
Modified: trunk/Jmol/src/org/jmol/util/Measure.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Measure.java 2013-07-05 14:18:59 UTC (rev
18432)
+++ trunk/Jmol/src/org/jmol/util/Measure.java 2013-07-05 16:59:05 UTC (rev
18433)
@@ -134,7 +134,7 @@
V3 vda = new V3();
V3 vcb = V3.newV(n);
if (v_dot_n == 0)
- v_dot_n = Float.MIN_VALUE; // allow for perpendicular axis to vab
+ v_dot_n = Parser.FLOAT_MIN_SAFE; // allow for perpendicular axis to vab
vcb.scale(v_dot_n);
vda.sub2(vcb, vab);
vda.scale(0.5f);
@@ -150,7 +150,7 @@
if (tokType == T.point) {
return pt_a_prime;
}
- if (v_dot_n != Float.MIN_VALUE)
+ if (v_dot_n != Parser.FLOAT_MIN_SAFE)
n.scale(v_dot_n);
// must calculate directed angle:
P3 pt_b_prime = P3.newP(pt_a_prime);
@@ -174,7 +174,7 @@
return "measure " + Escape.eP(a) + Escape.eP(pt_a_prime) +
Escape.eP(pt_b_prime) + Escape.eP(b);
// for now... array:
float residuesPerTurn = Math.abs(theta == 0 ? 0 : 360f / theta);
- float pitch = Math.abs(v_dot_n == Float.MIN_VALUE ? 0 : n.length() *
(theta == 0 ? 1 : 360f / theta));
+ float pitch = Math.abs(v_dot_n == Parser.FLOAT_MIN_SAFE ? 0 : n.length() *
(theta == 0 ? 1 : 360f / theta));
switch (tokType) {
case T.array:
return new Object[] {pt_a_prime, n, r, P3.new3(theta, pitch,
residuesPerTurn)};
Modified: trunk/Jmol/src/org/jmol/util/Parser.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Parser.java 2013-07-05 14:18:59 UTC (rev
18432)
+++ trunk/Jmol/src/org/jmol/util/Parser.java 2013-07-05 16:59:05 UTC (rev
18433)
@@ -29,6 +29,9 @@
public class Parser {
+ public final static float FLOAT_MIN_SAFE = 2E-45f;
+ // Float.MIN_ VALUE is not reliable with JavaScript because of the
float/double difference there
+
/// general static string-parsing class ///
// next[0] tracks the pointer within the string so these can all be static.
Modified: trunk/Jmol/src/org/jmol/viewer/ColorManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/ColorManager.java 2013-07-05 14:18:59 UTC
(rev 18432)
+++ trunk/Jmol/src/org/jmol/viewer/ColorManager.java 2013-07-05 16:59:05 UTC
(rev 18433)
@@ -31,6 +31,7 @@
import org.jmol.util.Elements;
import org.jmol.util.GData;
import org.jmol.util.Logger;
+import org.jmol.util.Parser;
import org.jmol.constant.EnumPalette;
import org.jmol.constant.StaticConstants;
import org.jmol.modelset.Atom;
@@ -311,7 +312,7 @@
colorData = data;
propertyColorEncoder.currentPalette =
propertyColorEncoder.createColorScheme(
colorScheme, true, false);
- propertyColorEncoder.hi = Float.MIN_VALUE;
+ propertyColorEncoder.hi = Parser.FLOAT_MIN_SAFE;
propertyColorEncoder.lo = Float.MAX_VALUE;
if (data == null)
return;
Modified: trunk/Jmol/src/org/jmol/viewer/DataManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/DataManager.java 2013-07-05 14:18:59 UTC
(rev 18432)
+++ trunk/Jmol/src/org/jmol/viewer/DataManager.java 2013-07-05 16:59:05 UTC
(rev 18433)
@@ -58,6 +58,15 @@
dataValues.clear();
}
+ private final static int DATA_TYPE_STRING = 0;
+ private final static int DATA_TYPE_AF = 1;
+ private final static int DATA_ARRAY_FF = 2;
+ private final static int DATA_ARRAY_FFF = 3;
+ //private final static int DATA_LABEL = 0;
+ private final static int DATA_VALUE = 1;
+ private final static int DATA_SELECTION_MAP = 2;
+ private final static int DATA_TYPE = 3;
+
void setData(String type, Object[] data, int arrayCount, int actualAtomCount,
int matchField, int matchFieldColumnCount, int field,
int fieldColumnCount) {
@@ -80,7 +89,7 @@
}
type = type.toLowerCase();
if (type.equals("element_vdw")) {
- String stringData = ((String) data[1]).trim();
+ String stringData = ((String) data[DATA_VALUE]).trim();
if (stringData.length() == 0) {
userVdwMars = null;
userVdws = null;
@@ -90,12 +99,12 @@
if (bsUserVdws == null)
setUserVdw(defaultVdw);
Parser.parseFloatArrayFromMatchAndField(stringData, bsUserVdws, 1, 0,
- (int[]) data[2], 2, 0, userVdws, 1);
+ (int[]) data[DATA_SELECTION_MAP], 2, 0, userVdws, 1);
for (int i = userVdws.length; --i >= 0;)
userVdwMars[i] = (int) Math.floor(userVdws[i] * 1000);
return;
}
- if (data[2] != null && arrayCount > 0) {
+ if (data[DATA_SELECTION_MAP] != null && arrayCount > 0) {
boolean createNew = (matchField != 0 || field != Integer.MIN_VALUE
&& field != Integer.MAX_VALUE);
Object[] oldData = dataValues.get(type);
@@ -106,9 +115,9 @@
// check to see if the data COULD be interpreted as a string of float
values
// and if so, do that. This pre-fetches the tokens in that case.
- int depth = ((Integer)data[3]).intValue();
- String stringData = (depth == 0 ? (String) data[1] : null);
- float[] floatData = (depth == 1 ? (float[]) data[1] : null);
+ int depth = ((Integer)data[DATA_TYPE]).intValue();
+ String stringData = (depth == DATA_TYPE_STRING ? (String)
data[DATA_VALUE] : null);
+ float[] floatData = (depth == DATA_TYPE_AF ? (float[]) data[DATA_VALUE]
: null);
String[] strData = null;
if (field == Integer.MIN_VALUE
&& (strData = Parser.getTokens(stringData)).length > 1)
@@ -116,11 +125,11 @@
if (field == Integer.MIN_VALUE) {
// set the selected data elements to a single value
- bs = (BS) data[2];
+ bs = (BS) data[DATA_SELECTION_MAP];
Parser.setSelectedFloats(Parser.parseFloatStr(stringData), bs, f);
} else if (field == 0 || field == Integer.MAX_VALUE) {
// just get the selected token values
- bs = (BS) data[2];
+ bs = (BS) data[DATA_SELECTION_MAP];
if (floatData != null) {
if (floatData.length == bs.cardinality())
for (int i = bs.nextSetBit(0), pt = 0; i >= 0; i = bs
@@ -135,13 +144,13 @@
}
} else if (matchField <= 0) {
// get the specified field >= 1 for the selected atoms
- bs = (BS) data[2];
+ bs = (BS) data[DATA_SELECTION_MAP];
Parser.parseFloatArrayFromMatchAndField(stringData, bs, 0, 0, null,
field, fieldColumnCount, f, 1);
} else {
// get the selected field, with an integer match in a specified field
// in this case, bs is created and indicates which data points were set
- int[] iData = (int[]) data[2];
+ int[] iData = (int[]) data[DATA_SELECTION_MAP];
Parser.parseFloatArrayFromMatchAndField(stringData, null, matchField,
matchFieldColumnCount, iData, field, fieldColumnCount, f, 1);
bs = new BS();
@@ -149,11 +158,11 @@
if (iData[i] >= 0)
bs.set(iData[i]);
}
- if (oldData != null && oldData[2] instanceof BS && !createNew)
- bs.or((BS) (oldData[2]));
- data[3] = Integer.valueOf(1);
- data[2] = bs;
- data[1] = f;
+ if (oldData != null && oldData[DATA_SELECTION_MAP] instanceof BS &&
!createNew)
+ bs.or((BS) (oldData[DATA_SELECTION_MAP]));
+ data[DATA_TYPE] = Integer.valueOf(DATA_TYPE_AF);
+ data[DATA_SELECTION_MAP] = bs;
+ data[DATA_VALUE] = f;
if (type.indexOf("property_atom.") == 0) {
int tok = T.getSettableTokFromString(type = type.substring(14));
if (tok == T.nada) {
@@ -192,16 +201,16 @@
if (dataValues == null)
return null;
Object[] data = getData(label);
- if (data == null || ((Integer)data[3]).intValue() != 1)
+ if (data == null || ((Integer)data[DATA_TYPE]).intValue() != DATA_TYPE_AF)
return null;
- return (float[]) data[1];
+ return (float[]) data[DATA_VALUE];
}
float getDataFloat(String label, int atomIndex) {
if (dataValues != null) {
Object[] data = getData(label);
- if (data != null && ((Integer)data[3]).intValue() == 1) {
- float[] f = (float[]) data[1];
+ if (data != null && ((Integer)data[DATA_TYPE]).intValue() ==
DATA_TYPE_AF) {
+ float[] f = (float[]) data[DATA_VALUE];
if (atomIndex < f.length)
return f[atomIndex];
}
@@ -213,18 +222,18 @@
if (dataValues == null)
return null;
Object[] data = getData(label);
- if (data == null || ((Integer)data[3]).intValue() != 2)
+ if (data == null || ((Integer)data[DATA_TYPE]).intValue() != DATA_ARRAY_FF)
return null;
- return (float[][]) data[1];
+ return (float[][]) data[DATA_VALUE];
}
float[][][] getDataFloat3D(String label) {
if (dataValues == null)
return null;
Object[] data = getData(label);
- if (data == null || ((Integer)data[3]).intValue() != 3)
+ if (data == null || ((Integer)data[DATA_TYPE]).intValue() !=
DATA_ARRAY_FFF)
return null;
- return (float[][][]) data[1];
+ return (float[][][]) data[DATA_VALUE];
}
void deleteModelAtoms(int firstAtomIndex, int nAtoms, BS bsDeleted) {
@@ -237,10 +246,10 @@
Object[] obj = dataValues.get(name);
BSUtil.deleteBits((BS) obj[2], bsDeleted);
switch (((Integer)obj[3]).intValue()) {
- case 1:
+ case DATA_TYPE_AF:
obj[1] = ArrayUtil.deleteElements(obj[1], firstAtomIndex, nAtoms);
break;
- case 2:
+ case DATA_ARRAY_FF:
obj[1] = ArrayUtil.deleteElements(obj[1], firstAtomIndex, nAtoms);
break;
default:
@@ -326,4 +335,5 @@
.append(loadFilter == null || loadFilter.length() == 0 ? "" : "
filter" + Escape.eS(loadFilter))
.append("\";");
}
+
}
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2013-07-05 14:18:59 UTC (rev
18432)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2013-07-05 16:59:05 UTC (rev
18433)
@@ -9769,8 +9769,8 @@
modelSet.setModelAuxiliaryInfo(modelIndex, "modelID", id);
}
- public void setCentroid(int iAtom0, int iAtom1, int[] minmax) {
- modelSet.setCentroid(iAtom0, iAtom1, minmax);
+ public void setCentroid(BS bs, int[] minmax) {
+ modelSet.setCentroid(bs, minmax);
}
public String getPathForAllFiles() {
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