Revision: 20547
http://sourceforge.net/p/jmol/code/20547
Author: hansonr
Date: 2015-06-04 16:54:12 +0000 (Thu, 04 Jun 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.3.14_2015.06.04"
new feature: load "...." FILL BOUNDBOX
new feature: load "...." FILL UNITCELL
new feature: load "...." FILL UNITCELL [o a b c]
new feature: load "...." FILL BOUNDBOX [o a b c]
-- in development
-- loads a crystal structure such that a given volume is packed
-- volume can be the current boundbox or the current unitcell or a specified
origin and a,b,c vectors
-- if BOUNDBOX, sets the current boundbox after loading to be current boundbox
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/aflow/AFLOWReader.java
trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
trunk/Jmol/src/org/jmol/adapter/smarter/XtalSymmetry.java
trunk/Jmol/src/org/jmol/modelset/ModelSet.java
trunk/Jmol/src/org/jmol/script/ScriptEval.java
trunk/Jmol/src/org/jmol/script/ScriptParam.java
trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
trunk/Jmol/src/org/jmol/scriptext/IsoExt.java
trunk/Jmol/src/org/jmol/thread/MoveToThread.java
trunk/Jmol/src/org/jmol/util/BoxInfo.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/TransformManager.java
Modified: trunk/Jmol/src/org/jmol/adapter/readers/aflow/AFLOWReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/aflow/AFLOWReader.java
2015-06-04 04:57:46 UTC (rev 20546)
+++ trunk/Jmol/src/org/jmol/adapter/readers/aflow/AFLOWReader.java
2015-06-04 16:54:12 UTC (rev 20547)
@@ -113,6 +113,7 @@
readPRE = checkFilterKey("PRE");
// readPOST = !checkFilterKey("NOPOST");
String s = getFilter("CA=");
+ forcePacked = !checkFilterKey("NOPACK");
if (s != null)
fracA = parseFloatStr(s.substring(1));
s = getFilter("LIST=");
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
2015-06-04 04:57:46 UTC (rev 20546)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
2015-06-04 16:54:12 UTC (rev 20547)
@@ -46,6 +46,7 @@
import javajs.util.OC;
import javajs.util.PT;
import javajs.util.Quat;
+import javajs.util.T3;
import javajs.util.V3;
import javajs.util.Lst;
import javajs.util.SB;
@@ -159,6 +160,7 @@
// protected/public state variables
public int[] latticeCells;
+ public T3[] fillRange;
public boolean doProcessLines;
public boolean iHaveUnitCell;
public boolean iHaveSymmetryOperators;
@@ -375,36 +377,40 @@
protected void finalizeReaderASCR() throws Exception {
isFinalized = true;
if (asc.atomSetCount > 0) {
- if (asc.atomSetCount == 1)
+ if (asc.atomSetCount == 1)
asc.setCurrentModelInfo("dbName", htParams.get("dbName"));
applySymmetryAndSetTrajectory();
asc.finalizeStructures();
if (doCentralize)
asc.centralize();
+ if (fillRange != null)
+ asc.setInfo("boundbox", fillRange);
Map<String, Object> info = asc.getAtomSetAuxiliaryInfo(0);
- if (domains != null && info != null) {
- asc.setGlobalBoolean(AtomSetCollection.GLOBAL_DOMAINS);
- String s = ((SV) domains).getMapKeys(2, true);
- int pt = s.indexOf("{ ", 2);
- if (pt >= 0)
- s = s.substring(pt + 2);
- pt = s.indexOf("_metadata");
- if (pt < 0)
- pt = s.indexOf("metadata");
- if (pt >= 0)
- s = s.substring(0, pt);
- s = PT.rep(PT.replaceAllCharacters(s, "{}", "").trim(), "\n", "\n ")
- + "\n\nUse SHOW DOMAINS for details.";
- appendLoadNote("\nDomains loaded:\n " + s);
- for (int i = asc.atomSetCount; --i >= 0;) {
- info = asc.getAtomSetAuxiliaryInfo(i);
- info.put("domains", domains);
+ if (info != null) {
+ if (domains != null) {
+ asc.setGlobalBoolean(AtomSetCollection.GLOBAL_DOMAINS);
+ String s = ((SV) domains).getMapKeys(2, true);
+ int pt = s.indexOf("{ ", 2);
+ if (pt >= 0)
+ s = s.substring(pt + 2);
+ pt = s.indexOf("_metadata");
+ if (pt < 0)
+ pt = s.indexOf("metadata");
+ if (pt >= 0)
+ s = s.substring(0, pt);
+ s = PT.rep(PT.replaceAllCharacters(s, "{}", "").trim(), "\n", "\n ")
+ + "\n\nUse SHOW DOMAINS for details.";
+ appendLoadNote("\nDomains loaded:\n " + s);
+ for (int i = asc.atomSetCount; --i >= 0;) {
+ info = asc.getAtomSetAuxiliaryInfo(i);
+ info.put("domains", domains);
+ }
}
- }
- if (validation != null && info != null) {
- for (int i = asc.atomSetCount; --i >= 0;) {
- info = asc.getAtomSetAuxiliaryInfo(i);
- info.put("validation", validation);
+ if (validation != null) {
+ for (int i = asc.atomSetCount; --i >= 0;) {
+ info = asc.getAtomSetAuxiliaryInfo(i);
+ info.put("validation", validation);
+ }
}
}
}
@@ -543,7 +549,7 @@
strSupercell = (String) o;
else
ptSupercell = (P3) o;
-
+ fillRange = (T3[]) htParams.get("fillRange");
// ptFile < 0 indicates just one file being read
// ptFile >= 0 indicates multiple files are being loaded
// if the file is not the first read in the LOAD command, then
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/XtalSymmetry.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/XtalSymmetry.java 2015-06-04
04:57:46 UTC (rev 20546)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/XtalSymmetry.java 2015-06-04
16:54:12 UTC (rev 20547)
@@ -223,7 +223,7 @@
if (readerSymmetry != null)
symmetry.setSpaceGroupFrom(readerSymmetry);
//parameters are counts of unit cells as [a b c]
- applySymmetryLattice(acr.ms, acr.strSupercell);
+ applySymmetryLattice();
if (readerSymmetry != null && filterSymop == null)
setAtomSetSpaceGroupName(readerSymmetry.getSpaceGroupName());
}
@@ -247,12 +247,11 @@
asc.setCurrentModelInfo("spaceGroup", spaceGroupName + "");
}
- private void applySymmetryLattice(MSInterface ms, String supercell)
+ private void applySymmetryLattice()
throws Exception {
-
if (!asc.coordinatesAreFractional || symmetry.getSpaceGroup() == null)
return;
-
+
int maxX = latticeCells[0];
int maxY = latticeCells[1];
int maxZ = Math.abs(latticeCells[2]);
@@ -260,16 +259,18 @@
BS bsAtoms = null;
rminx = rminy = rminz = Float.MAX_VALUE;
rmaxx = rmaxy = rmaxz = -Float.MAX_VALUE;
- T3[] oabc = null;
+ T3[] oabc = acr.fillRange;
P3 offset = null;
P3 pt0 = null;
nVib = 0;
T3 va = null, vb = null, vc = null;
baseSymmetry = symmetry;
- if (supercell != null && supercell.indexOf(",") >= 0) {
+ String supercell = acr.strSupercell;
+ if (oabc != null || supercell != null && supercell.indexOf(",") >= 0) {
// expand range to accommodate this alternative cell
// oabc will be cartesian
- oabc = symmetry.getV0abc(supercell);
+ if (oabc == null)
+ oabc = symmetry.getV0abc(supercell);
if (oabc != null) {
// set the bounds for atoms in the new unit cell
// in terms of the old unit cell
@@ -376,7 +377,7 @@
if (asc.bsAtoms == null)
asc.bsAtoms = BSUtil.setAll(asc.ac);
bsAtoms = asc.bsAtoms;
- applyAllSymmetry(ms, null);
+ applyAllSymmetry(acr.ms, null);
doPackUnitCell = doPack0;
@@ -394,7 +395,7 @@
symmetry = getSymmetry();
setUnitCell(new float[] { 0, 0, 0, 0, 0, 0, va.x, va.y, va.z,
vb.x, vb.y, vb.z, vc.x, vc.y, vc.z }, null, offset);
- setAtomSetSpaceGroupName(oabc == null ? "P1" : "cell=" + supercell);
+ setAtomSetSpaceGroupName(oabc == null || supercell == null ? "P1" :
"cell=" + supercell);
symmetry.setSpaceGroup(doNormalize);
symmetry.addSpaceGroupOperation("x,y,z", 0);
@@ -421,7 +422,7 @@
if (oabc == null) {
minXYZ = new P3i();
maxXYZ = P3i.new3(maxX, maxY, maxZ);
- applyAllSymmetry(ms, bsAtoms);
+ applyAllSymmetry(acr.ms, bsAtoms);
} else if (acr.forcePacked || doPackUnitCell) {
// trim atom set based on original unit cell
symmetry.setMinMaxLatticeParameters(minXYZ, maxXYZ);
@@ -439,6 +440,10 @@
// but we leave matSupercell, because we might need it for vibrations in
CASTEP
}
+ /**
+ * range minima and maxima -- cartesians?
+ *
+ */
private float rminx, rminy, rminz, rmaxx, rmaxy, rmaxz;
private void setSymmetryMinMax(P3 c) {
@@ -456,11 +461,6 @@
rmaxz = c.z;
}
- private boolean isInSymmetryRange(P3 c) {
- return (c.x >= rminx && c.y >= rminy && c.z >= rminz && c.x <= rmaxx
- && c.y <= rmaxy && c.z <= rmaxz);
- }
-
private final P3 ptOffset = new P3();
private P3 unitCellOffset;
@@ -806,13 +806,13 @@
}
if (acr.fixJavaFloat)
PT.fixPtFloats(ptAtom, PT.FRACTIONAL_PRECISION);
- P3 cartesian = P3.newP(ptAtom);
- symmetry.toCartesian(cartesian, false);
+ P3 c = P3.newP(ptAtom); // cartesian position
+ symmetry.toCartesian(c, false);
if (doPackUnitCell) {
// note that COmmensurate structures may need
// modulation at this point.
- symmetry.toUnitCell(cartesian, ptOffset);
- ptAtom.setT(cartesian);
+ symmetry.toUnitCell(c, ptOffset);
+ ptAtom.setT(c);
symmetry.toFractional(ptAtom, false);
if (acr.fixJavaFloat)
PT.fixPtFloats(ptAtom, PT.FRACTIONAL_PRECISION);
@@ -821,7 +821,7 @@
continue;
}
if (checkSymmetryMinMax)
- setSymmetryMinMax(cartesian);
+ setSymmetryMinMax(c);
Atom special = null;
if (checkDistances) {
@@ -829,7 +829,8 @@
* same cartesian position.
*/
float minDist2 = Float.MAX_VALUE;
- if (checkSymmetryRange && !isInSymmetryRange(cartesian))
+ if (checkSymmetryRange && (c.x < rminx || c.y < rminy || c.z < rminz
+ || c.x > rmaxx || c.y > rmaxy || c.z > rmaxz))
continue;
int j0 = (checkAll ? asc.ac : pt0);
String name = a.atomName;
@@ -838,7 +839,7 @@
P3 pc = cartesians[j];
if (pc == null)
continue;
- float d2 = cartesian.distanceSquared(pc);
+ float d2 = c.distanceSquared(pc);
if (checkSpecial && d2 < 0.0001) {
special = asc.atoms[firstSymmetryAtom + j];
if ((special.atomName == null || special.atomName.equals(name))
@@ -878,7 +879,7 @@
atom1.bsSymmetry = BSUtil.newAndSetBit(iCellOpPt + iSym);
atom1.bsSymmetry.set(iSym);
if (addCartesian)
- cartesians[pt++] = cartesian;
+ cartesians[pt++] = c;
Lst<Object> tensors = a.tensors;
if (tensors != null) {
atom1.tensors = null;
@@ -960,8 +961,10 @@
}
public T3 getOverallSpan() {
- return V3.newVsub(maxXYZ0, minXYZ0);
+ return (maxXYZ0 == null ? V3.new3(maxXYZ.x - minXYZ.x, maxXYZ.y - minXYZ.y,
+ maxXYZ.z - minXYZ.z) : V3.newVsub(maxXYZ0, minXYZ0));
}
+
private int dtype = 3;
private V3[] unitCellTranslations;
private int latticeOp;
Modified: trunk/Jmol/src/org/jmol/modelset/ModelSet.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2015-06-04 04:57:46 UTC
(rev 20546)
+++ trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2015-06-04 16:54:12 UTC
(rev 20547)
@@ -489,6 +489,9 @@
}
private SymmetryInterface pointGroup;
+
+ private BoxInfo defaultBBox;
+
private Object calculatePointGroupForFirstModel(BS bsAtoms,
boolean doAll,
boolean asDraw,
@@ -1028,9 +1031,7 @@
}
public P3 getBoundBoxCenter(int modelIndex) {
- if (isJmolDataFrameForModel(modelIndex))
- return new P3();
- return boxInfo.getBoundBoxCenter();
+ return (isJmolDataFrameForModel(modelIndex) ? new P3() :
boxInfo.getBoundBoxCenter());
}
public V3 getBoundBoxCornerVector() {
@@ -1041,7 +1042,7 @@
return boxInfo.getBoundBoxVertices();
}
- public void setBoundBox(P3 pt1, P3 pt2, boolean byCorner, float scale) {
+ public void setBoundBox(T3 pt1, T3 pt2, boolean byCorner, float scale) {
isBbcageDefault = false;
bboxModels = null;
bboxAtoms = null;
@@ -1090,11 +1091,13 @@
return true;
}
- public float calcRotationRadius(int modelIndex, P3 center) {
+ public float calcRotationRadius(int modelIndex, P3 center, boolean
useBoundBox) {
if (isJmolDataFrameForModel(modelIndex)) {
float r = am[modelIndex].defaultRotationRadius;
return (r == 0 ? 10 : r);
}
+ if (useBoundBox && getDefaultBoundBox() != null)
+ return defaultBBox.getMaxDim() / 2 * 1.2f;
float maxRadius = 0;
for (int i = ac; --i >= 0;) {
if (isJmolDataFrameForAtom(at[i])) {
@@ -1117,16 +1120,35 @@
bs = null;
if (bs == null && isBbcageDefault || ac == 0)
return;
- bboxModels = getModelBS(bboxAtoms = BSUtil.copy(bs), false);
- if (calcAtomsMinMax(bs, boxInfo) == ac)
- isBbcageDefault = true;
- if (bs == null) { // from modelLoader or reset
- if (unitCells != null)
- calcUnitCellMinMax();
+ if (getDefaultBoundBox() == null) {
+ bboxModels = getModelBS(bboxAtoms = BSUtil.copy(bs), false);
+ if (calcAtomsMinMax(bs, boxInfo) == ac)
+ isBbcageDefault = true;
+ if (bs == null) { // from modelLoader or reset
+ if (unitCells != null)
+ calcUnitCellMinMax();
+ }
+ } else {
+ P3[] vertices = defaultBBox.getBoundBoxVertices();
+ boxInfo.reset();
+ for (int j = 0; j < 8; j++)
+ boxInfo.addBoundBoxPoint(vertices[j]);
}
boxInfo.setBbcage(scale);
}
+ private BoxInfo getDefaultBoundBox() {
+ T3[] bbox = (T3[]) getInfoM("boundbox");
+ if (bbox == null)
+ defaultBBox = null;
+ else {
+ if (defaultBBox == null)
+ defaultBBox = new BoxInfo();
+ defaultBBox.setBoundBoxFromCriticalPoints(bbox);
+ }
+ return defaultBBox;
+ }
+
public BoxInfo getBoxInfo(BS bs, float scale) {
if (bs == null)
return boxInfo;
Modified: trunk/Jmol/src/org/jmol/script/ScriptEval.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEval.java 2015-06-04 04:57:46 UTC
(rev 20546)
+++ trunk/Jmol/src/org/jmol/script/ScriptEval.java 2015-06-04 16:54:12 UTC
(rev 20547)
@@ -23,16 +23,30 @@
*/
package org.jmol.script;
+import java.util.Arrays;
+import java.util.Hashtable;
+import java.util.Map;
+
import javajs.awt.Font;
+import javajs.util.A4;
+import javajs.util.AU;
+import javajs.util.BArray;
+import javajs.util.Base64;
import javajs.util.Lst;
+import javajs.util.M3;
+import javajs.util.M4;
+import javajs.util.Measure;
+import javajs.util.OC;
+import javajs.util.P3;
+import javajs.util.P4;
+import javajs.util.PT;
+import javajs.util.Quat;
import javajs.util.SB;
+import javajs.util.T3;
+import javajs.util.V3;
-import java.util.Arrays;
-import java.util.Hashtable;
-
-import java.util.Map;
-
import org.jmol.api.Interface;
+import org.jmol.api.JmolParallelProcessor;
import org.jmol.api.JmolScriptFunction;
import org.jmol.api.SymmetryInterface;
import org.jmol.atomdata.RadiusData;
@@ -46,37 +60,19 @@
import org.jmol.modelset.Atom;
import org.jmol.modelset.BondSet;
import org.jmol.modelset.Group;
+import org.jmol.modelset.TickInfo;
import org.jmol.shape.MeshCollection;
import org.jmol.shape.Shape;
import org.jmol.thread.JmolThread;
import org.jmol.util.BSUtil;
import org.jmol.util.ColorEncoder;
+import org.jmol.util.Edge;
+import org.jmol.util.Elements;
import org.jmol.util.Escape;
-import org.jmol.util.Elements;
-import org.jmol.util.Edge;
import org.jmol.util.Logger;
+import org.jmol.util.Parser;
import org.jmol.util.SimpleUnitCell;
import org.jmol.util.Txt;
-
-import javajs.util.PT;
-import org.jmol.util.Parser;
-
-import javajs.util.A4;
-import javajs.util.AU;
-import javajs.util.BArray;
-import javajs.util.Base64;
-import javajs.util.Measure;
-import javajs.util.OC;
-import javajs.util.M3;
-import javajs.util.M4;
-import javajs.util.P3;
-import javajs.util.P4;
-import javajs.util.Quat;
-import javajs.util.T3;
-
-import javajs.util.V3;
-import org.jmol.modelset.TickInfo;
-import org.jmol.api.JmolParallelProcessor;
import org.jmol.viewer.ActionManager;
import org.jmol.viewer.FileManager;
import org.jmol.viewer.JC;
@@ -4442,7 +4438,7 @@
tok = tokAt(i = ++iToken);
break;
}
- i = getLoadSymmetryParams(i, sOptions, htParams);
+ i = getCmdExt().getLoadSymmetryParams(i, sOptions, htParams);
// .... APPEND DATA "appendedData" .... end "appendedData"
// option here to designate other than "appendedData"
@@ -4740,6 +4736,9 @@
// SUPERCELL {i j k}
case T.supercell:
// RANGE x.x or RANGE -x.x
+ case T.fill: // new in Jmol 14.3.14
+ // FILL BOUNDBOX
+ // FILL UNITCELL
case T.range:
// SPACEGROUP "nameOrNumber"
// or SPACEGROUP "IGNOREOPERATORS"
@@ -4793,193 +4792,6 @@
}
}
- private int getLoadSymmetryParams(int i, SB sOptions,
- Map<String, Object> htParams) throws
ScriptException {
- // {i j k}
-
- P3 lattice = null;
- int tok = tokAt(i);
- if (tok == T.leftbrace || tok == T.point3f) {
- lattice = getPoint3f(i, false);
- i = iToken + 1;
- tok = tokAt(i);
- }
-
- // default lattice {555 555 -1} (packed)
- // for PACKED, CENTROID, SUPERCELL, RANGE, SPACEGROUP, UNITCELL
-
- switch (tok) {
- case T.packed:
- case T.centroid:
- case T.supercell:
- case T.range:
- case T.spacegroup:
- case T.unitcell:
- if (lattice == null)
- lattice = P3.new3(555, 555, -1);
- iToken = i - 1;
- }
- P3 offset = null;
- if (lattice != null) {
- htParams.put("lattice", lattice);
- i = iToken + 1;
- sOptions.append( " {" + (int) lattice.x + " " + (int) lattice.y + " "
- + (int) lattice.z + "}");
-
- // {i j k} PACKED, CENTROID -- either or both; either order
-
- i = checkPacked(i, htParams, sOptions);
- if (tokAt(i) == T.centroid) {
- htParams.put("centroid", Boolean.TRUE);
- sOptions.append(" CENTROID");
- i = checkPacked(++i, htParams, sOptions);
- }
-
- // {i j k} ... SUPERCELL {i' j' k'}
-
- if (tokAt(i) == T.supercell) {
- Object supercell;
- sOptions.append(" SUPERCELL ");
- if (isPoint3f(++i)) {
- P3 pt = getPoint3f(i, false);
- if (pt.x != (int) pt.x || pt.y != (int) pt.y || pt.z != (int) pt.z
- || pt.x < 1 || pt.y < 1 || pt.z < 1) {
- iToken = i;
- invArg();
- }
- supercell = pt;
- i = iToken;
- } else {
- supercell = stringParameter(i);
- }
- sOptions.append(Escape.e(supercell));
- htParams.put("supercell", supercell);
- i = checkPacked(++i, htParams, sOptions);
- }
-
- // {i j k} ... RANGE x.y (from full unit cell set)
- // {i j k} ... RANGE -x.y (from non-symmetry set)
-
- float distance = 0;
- if (tokAt(i) == T.range) {
- /*
- * # Jmol 11.3.9 introduces the capability of visualizing the close
- * contacts around a crystalline protein (or any other cyrstal
- * structure) that are to atoms that are in proteins in adjacent unit
- * cells or adjacent to the protein itself. The option RANGE x, where x
- * is a distance in angstroms, placed right after the braces containing
- * the set of unit cells to load does this. The distance, if a positive
- * number, is the maximum distance away from the closest atom in the {1
- * 1 1} set. If the distance x is a negative number, then -x is the
- * maximum distance from the {not symmetry} set. The difference is that
- * in the first case the primary unit cell (555) is first filled as
- * usual, using symmetry operators, and close contacts to this set are
- * found. In the second case, only the file-based atoms (
Jones-Faithful
- * operator x,y,z) are initially included, then close contacts to that
- * set are found. Depending upon the application, one or the other of
- * these options may be desirable.
- */
- i++;
- distance = floatParameter(i++);
- sOptions.append( " range " + distance);
- }
- htParams.put("symmetryRange", Float.valueOf(distance));
-
- // {i j k} ... SPACEGROUP "nameOrNumber"
- // {i j k} ... SPACEGROUP "IGNOREOPERATORS"
- // {i j k} ... SPACEGROUP ""
-
- String spacegroup = null;
- SymmetryInterface sg;
- int iGroup = Integer.MIN_VALUE;
- if (tokAt(i) == T.spacegroup) {
- ++i;
- spacegroup = PT.rep(paramAsStr(i++), "''", "\"");
- sOptions.append( " spacegroup " + PT.esc(spacegroup));
- if (spacegroup.equalsIgnoreCase("ignoreOperators")) {
- iGroup = -999;
- } else {
- if (spacegroup.length() == 0) {
- sg = vwr.getCurrentUnitCell();
- if (sg != null)
- spacegroup = sg.getSpaceGroupName();
- } else {
- if (spacegroup.indexOf(",") >= 0) // Jones Faithful
- if ((lattice.x < 9 && lattice.y < 9 && lattice.z == 0))
- spacegroup += "#doNormalize=0";
- }
- htParams.put("spaceGroupName", spacegroup);
- iGroup = -2;
- }
- }
-
- // {i j k} ... UNITCELL [a b c alpha beta gamma]
- // {i j k} ... UNITCELL [ax ay az bx by bz cx cy cz]
- // {i j k} ... UNITCELL "" // same as current
-
- float[] fparams = null;
- if (tokAt(i) == T.unitcell) {
- ++i;
- if (optParameterAsString(i).length() == 0) {
- // unitcell "" -- use current unit cell
- sg = vwr.getCurrentUnitCell();
- if (sg != null) {
- fparams = sg.getUnitCellAsArray(true);
- offset = sg.getCartesianOffset();
- }
- } else {
- fparams = floatParameterSet(i, 6, 9);
- }
- if (fparams == null || fparams.length != 6 && fparams.length != 9)
- invArg();
- sOptions.append( " unitcell {");
- for (int j = 0; j < fparams.length; j++)
- sOptions.append( (j == 0 ? "" : " ") + fparams[j]);
- sOptions.append( "}");
- htParams.put("unitcell", fparams);
- if (iGroup == Integer.MIN_VALUE)
- iGroup = -1;
- i = iToken + 1;
- }
- if (iGroup != Integer.MIN_VALUE)
- htParams.put("spaceGroupIndex", Integer.valueOf(iGroup));
- }
-
- // OFFSET {x y z} (fractional or not) (Jmol 12.1.17)
-
- if (offset != null)
- coordinatesAreFractional = false;
- else if (tokAt(i) == T.offset)
- offset = getPoint3f(++i, true);
- if (offset != null) {
- if (coordinatesAreFractional) {
- offset.setT(fractionalPoint);
- htParams.put("unitCellOffsetFractional",
- (coordinatesAreFractional ? Boolean.TRUE : Boolean.FALSE));
- sOptions.append( " offset {" + offset.x + " " + offset.y + " " +
offset.z
- + "/1}");
- } else {
- sOptions.append( " offset " + Escape.eP(offset));
- }
- htParams.put("unitCellOffset", offset);
- i = iToken + 1;
- }
- return i;
- }
-
- private int checkPacked(int i, Map<String, Object> htParams, SB sOptions)
throws ScriptException {
- if (tokAt(i) == T.packed) {
- htParams.put("packed", Boolean.TRUE);
- sOptions.append(" PACKED");
- if (isFloatParameter(++i)) {
- float f = floatParameter(i++);
- htParams.put("packingError", Float.valueOf(f));
- sOptions.append(" " + f);
- }
- }
- return i;
- }
-
private void finalizeLoad(boolean isAppend, boolean appendNew,
boolean isConcat, boolean doOrient,
int nFiles, int ac0, int modelCount0) throws
ScriptException {
@@ -7912,142 +7724,7 @@
vwr.undoMoveAction(tokAt(0), n);
}
- private void cmdUnitcell(int i) throws ScriptException {
- int icell = Integer.MAX_VALUE;
- int mad = Integer.MAX_VALUE;
- T3 pt = null;
- TickInfo tickInfo = tickParamAsStr(i, true, false, false);
- i = iToken;
- String id = null;
- T3[] oabc = null;
- Object newUC = null;
- String ucname = null;
- boolean isOffset = false;
- boolean isReset = false;
- int tok = tokAt(++i);
- switch (tok) {
- case T.restore:
- case T.reset:
- isReset = true;
- pt = P4.new4(0, 0, 0, -1); // reset offset and range
- iToken++;
- break;
- case T.string:
- case T.identifier:
- String s = paramAsStr(i).toLowerCase();
- ucname = s;
- if (s.indexOf(",") < 0 && !chk) {
- // parent, standard, conventional
- setCurrentCagePts(null, null);
- if (PT.isOneOf(s, ";parent;standard;primitive;")) {
- newUC = vwr.ms.getInfo(vwr.am.cmi, "unitcell_conventional");
- if (newUC != null)
- setCurrentCagePts(vwr.getV0abc(newUC), "" + newUC);
- }
- s = (String) vwr.ms.getInfo(vwr.am.cmi, "unitcell_" + s);
- showString(s);
- }
- newUC = s;
- break;
- case T.isosurface:
- case T.dollarsign:
- id = objectNameParameter(++i);
- break;
- case T.boundbox:
- P3 o = P3.newP(vwr.getBoundBoxCenter());
- pt = vwr.getBoundBoxCornerVector();
- o.sub(pt);
- oabc = new P3[] {o, P3.new3(pt.x * 2, 0, 0), P3.new3(0, pt.y * 2, 0),
P3.new3(0, 0, pt.z * 2) };
- pt = null;
- iToken = i;
- break;
- case T.matrix3f:
- case T.matrix4f:
- newUC = getToken(i).value;
- break;
- case T.center:
- switch (tokAt(++i)) {
- case T.bitset:
- case T.expressionBegin:
- pt = P3.newP(vwr.ms.getAtomSetCenter(atomExpressionAt(i)));
- vwr.toFractional(pt, true);
- i = iToken;
- break;
- default:
- if (isCenterParameter(i)) {
- pt = centerParameter(i);
- i = iToken;
- break;
- }
- invArg();
- }
- pt.x -= 0.5f;
- pt.y -= 0.5f;
- pt.z -= 0.5f;
- break;
- case T.bitset:
- case T.expressionBegin:
- int iAtom = atomExpressionAt(i).nextSetBit(0);
- if (!chk)
- vwr.am.cai = iAtom;
- if (iAtom < 0)
- return;
- i = iToken;
- break;
- case T.offset:
- isOffset = true;
- //$FALL-THROUGH$
- case T.range:
- pt = (P3) getPointOrPlane(++i, false, true, false, true, 3, 3);
- pt = P4.new4(pt.x, pt.y, pt.z, (isOffset ? 1 : 0));
- i = iToken;
- break;
- case T.decimal:
- case T.integer:
- float f = floatParameter(i);
- if (f < 111) {
- // diameter
- i--;
- break;
- }
- icell = intParameter(i);
- break;
- default:
- if (isArrayParameter(i)) {
- // Origin vA vB vC
- // these are VECTORS, though
- oabc = getPointArray(i, 4, false);
- i = iToken;
- } else if (slen > i + 1) {
- pt = (P3) getPointOrPlane(i, false, true, false, true, 3, 3);
- i = iToken;
- } else {
- // backup for diameter
- i--;
- }
- }
- mad = getSetAxesTypeMad(++i);
- checkLast(iToken);
- if (chk || mad == Integer.MAX_VALUE)
- return;
- if (mad == Integer.MAX_VALUE)
- vwr.am.cai = -1;
- if (newUC != null)
- oabc = vwr.getV0abc(newUC);
- if (icell != Integer.MAX_VALUE)
- vwr.ms.setUnitCellOffset(vwr.getCurrentUnitCell(), null, icell);
- else if (id != null)
- vwr.setCurrentCage(id);
- else if (isReset || oabc != null)
- setCurrentCagePts(oabc, ucname);
- setObjectMad(JC.SHAPE_UCCAGE, "unitCell", mad);
- if (pt != null)
- vwr.ms.setUnitCellOffset(vwr.getCurrentUnitCell(), pt, 0);
- if (tickInfo != null)
- setShapeProperty(JC.SHAPE_UCCAGE, "tickInfo", tickInfo);
- }
-
- private void setCurrentCagePts(T3[] originABC, String name) {
+ public void setCurrentCagePts(T3[] originABC, String name) {
SymmetryInterface sym = Interface.getSymmetry(vwr, "eval");
if (sym == null && vwr.async)
throw new NullPointerException();
@@ -8059,6 +7736,9 @@
}
}
+ private void cmdUnitcell(int i) throws ScriptException {
+ getCmdExt().dispatch(T.unitcell, i == 2, null);
+ }
private void cmdVector() throws ScriptException {
EnumType type = EnumType.SCREEN;
@@ -8870,7 +8550,7 @@
return data;
}
- private int getSetAxesTypeMad(int index) throws ScriptException {
+ public int getSetAxesTypeMad(int index) throws ScriptException {
if (index == slen)
return 1;
switch (getToken(checkLast(index)).tok) {
Modified: trunk/Jmol/src/org/jmol/script/ScriptParam.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptParam.java 2015-06-04 04:57:46 UTC
(rev 20546)
+++ trunk/Jmol/src/org/jmol/script/ScriptParam.java 2015-06-04 16:54:12 UTC
(rev 20547)
@@ -52,8 +52,8 @@
// passed back as globals
- protected P3 fractionalPoint;
- protected boolean coordinatesAreFractional;
+ public P3 fractionalPoint;
+ public boolean coordinatesAreFractional;
public boolean isBondSet;
public Object expressionResult;
@@ -385,7 +385,7 @@
return Measure.getPlaneThroughPoints(pt1, pt2, pt3, new V3(), new V3(),
new P4());
}
- protected Object getPointOrPlane(int index, boolean integerOnly,
+ public Object getPointOrPlane(int index, boolean integerOnly,
boolean allowFractional, boolean doConvert,
boolean implicitFractional, int minDim,
int maxDim) throws ScriptException {
@@ -585,7 +585,7 @@
/**
* may return null values in some cases
* @param i
- * @param nPoints
+ * @param nPoints -1 for unspecified number of points
* @param allowNull if allowing null values (as in setting atom properties
such as vxyz or xyz)
* @return array of P3, with possible null values
* @throws ScriptException
Modified: trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2015-06-04 04:57:46 UTC
(rev 20546)
+++ trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2015-06-04 16:54:12 UTC
(rev 20547)
@@ -31,6 +31,7 @@
import org.jmol.api.Interface;
import org.jmol.api.JmolDataManager;
import org.jmol.api.MinimizerInterface;
+import org.jmol.api.SymmetryInterface;
import org.jmol.atomdata.RadiusData;
import org.jmol.c.STER;
import org.jmol.c.VDW;
@@ -56,6 +57,7 @@
import org.jmol.script.ScriptParam;
import org.jmol.script.T;
import org.jmol.util.BSUtil;
+import org.jmol.util.BoxInfo;
import org.jmol.util.C;
import org.jmol.util.Elements;
import org.jmol.util.Escape;
@@ -76,8 +78,10 @@
import javajs.util.M4;
import javajs.util.Measure;
import javajs.util.P3;
+import javajs.util.P4;
import javajs.util.PT;
import javajs.util.Quat;
+import javajs.util.T3;
import javajs.util.V3;
import org.jmol.viewer.FileManager;
@@ -164,6 +168,9 @@
case T.stereo:
stereo();
break;
+ case T.unitcell:
+ unitcell(b ? 2 : 1);
+ break;
case T.write:
return write(b ? st : null);
case JC.SHAPE_MEASURES:
@@ -192,6 +199,8 @@
*/
public boolean evalParallel(ScriptContext context,
ShapeManager shapeManager) {
+ chk = e.chk;
+ slen = e.slen;
ScriptEval se = new ScriptEval().setViewer(vwr);
se.historyDisabled = true;
se.compiler = new ScriptCompiler(vwr);
@@ -274,6 +283,227 @@
return nmax == 1 && !isExplicitlyAll ? sout[0] : (Object) sout;
}
+
+ public int getLoadSymmetryParams(int i, SB sOptions,
+ Map<String, Object> htParams) throws
ScriptException {
+ // {i j k}
+ ScriptEval eval = e;
+ chk = eval.chk;
+ slen = eval.slen;
+ P3 lattice = null;
+ int tok = tokAt(i);
+ if (tok == T.leftbrace || tok == T.point3f) {
+ lattice = getPoint3f(i, false);
+ i = eval.iToken + 1;
+ tok = tokAt(i);
+ }
+
+ // default lattice {555 555 -1} (packed)
+ // for PACKED, CENTROID, SUPERCELL, RANGE, SPACEGROUP, UNITCELL
+
+ switch (tok) {
+ case T.fill:
+ case T.packed:
+ case T.centroid:
+ case T.supercell:
+ case T.range:
+ case T.spacegroup:
+ case T.unitcell:
+ if (lattice == null)
+ lattice = P3.new3(555, 555, -1);
+ // re-read this token
+ eval.iToken = i - 1;
+ }
+
+ P3 offset = null;
+ if (lattice != null) {
+ htParams.put("lattice", lattice);
+ i = eval.iToken + 1;
+ sOptions.append( " {" + (int) lattice.x + " " + (int) lattice.y + " "
+ + (int) lattice.z + "}");
+
+ // {i j k} PACKED, CENTROID -- either or both; either order
+
+ i = checkPacked(i, htParams, sOptions);
+ if (tokAt(i) == T.centroid) {
+ htParams.put("centroid", Boolean.TRUE);
+ sOptions.append(" CENTROID");
+ i = checkPacked(++i, htParams, sOptions);
+ }
+
+ // {i j k} ... SUPERCELL {i' j' k'}
+
+ if (tokAt(i) == T.supercell) {
+ Object supercell;
+ sOptions.append(" SUPERCELL ");
+ if (eval.isPoint3f(++i)) {
+ P3 pt = getPoint3f(i, false);
+ if (pt.x != (int) pt.x || pt.y != (int) pt.y || pt.z != (int) pt.z
+ || pt.x < 1 || pt.y < 1 || pt.z < 1) {
+ eval.iToken = i;
+ invArg();
+ }
+ supercell = pt;
+ i = eval.iToken;
+ } else {
+ supercell = stringParameter(i);
+ }
+ sOptions.append(Escape.e(supercell));
+ htParams.put("supercell", supercell);
+ i = checkPacked(++i, htParams, sOptions);
+ }
+
+ // {i j k} ... RANGE x.y (from full unit cell set)
+ // {i j k} ... RANGE -x.y (from non-symmetry set)
+
+ float distance = 0;
+ if (tokAt(i) == T.range) {
+ /*
+ * # Jmol 11.3.9 introduces the capability of visualizing the close
+ * contacts around a crystalline protein (or any other crystal
+ * structure) that are to atoms that are in proteins in adjacent unit
+ * cells or adjacent to the protein itself. The option RANGE x, where x
+ * is a distance in angstroms, placed right after the braces containing
+ * the set of unit cells to load does this. The distance, if a positive
+ * number, is the maximum distance away from the closest atom in the {1
+ * 1 1} set. If the distance x is a negative number, then -x is the
+ * maximum distance from the {not symmetry} set. The difference is that
+ * in the first case the primary unit cell (555) is first filled as
+ * usual, using symmetry operators, and close contacts to this set are
+ * found. In the second case, only the file-based atoms ( Jones-Faithful
+ * operator x,y,z) are initially included, then close contacts to that
+ * set are found. Depending upon the application, one or the other of
+ * these options may be desirable.
+ */
+ i++;
+ distance = floatParameter(i++);
+ sOptions.append( " range " + distance);
+ }
+ htParams.put("symmetryRange", Float.valueOf(distance));
+
+ // {i j k} ... SPACEGROUP "nameOrNumber"
+ // {i j k} ... SPACEGROUP "IGNOREOPERATORS"
+ // {i j k} ... SPACEGROUP ""
+
+ String spacegroup = null;
+ SymmetryInterface sg;
+ int iGroup = Integer.MIN_VALUE;
+ if (tokAt(i) == T.spacegroup) {
+ ++i;
+ spacegroup = PT.rep(paramAsStr(i++), "''", "\"");
+ sOptions.append( " spacegroup " + PT.esc(spacegroup));
+ if (spacegroup.equalsIgnoreCase("ignoreOperators")) {
+ iGroup = -999;
+ } else {
+ if (spacegroup.length() == 0) {
+ sg = vwr.getCurrentUnitCell();
+ if (sg != null)
+ spacegroup = sg.getSpaceGroupName();
+ } else {
+ if (spacegroup.indexOf(",") >= 0) // Jones Faithful
+ if ((lattice.x < 9 && lattice.y < 9 && lattice.z == 0))
+ spacegroup += "#doNormalize=0";
+ }
+ htParams.put("spaceGroupName", spacegroup);
+ iGroup = -2;
+ }
+ }
+
+ // {i j k} ... UNITCELL [a b c alpha beta gamma]
+ // {i j k} ... UNITCELL [ax ay az bx by bz cx cy cz]
+ // {i j k} ... UNITCELL "" // same as current
+
+ float[] fparams = null;
+ if (tokAt(i) == T.unitcell) {
+ ++i;
+ if (eval.optParameterAsString(i).length() == 0) {
+ // unitcell "" -- use current unit cell
+ sg = vwr.getCurrentUnitCell();
+ if (sg != null) {
+ fparams = sg.getUnitCellAsArray(true);
+ offset = sg.getCartesianOffset();
+ }
+ } else {
+ fparams = eval.floatParameterSet(i, 6, 9);
+ }
+ if (fparams == null || fparams.length != 6 && fparams.length != 9)
+ invArg();
+ sOptions.append( " unitcell {");
+ for (int j = 0; j < fparams.length; j++)
+ sOptions.append( (j == 0 ? "" : " ") + fparams[j]);
+ sOptions.append( "}");
+ htParams.put("unitcell", fparams);
+ if (iGroup == Integer.MIN_VALUE)
+ iGroup = -1;
+ i = eval.iToken + 1;
+ }
+ if (iGroup != Integer.MIN_VALUE)
+ htParams.put("spaceGroupIndex", Integer.valueOf(iGroup));
+ }
+
+ // OFFSET {x y z} (fractional or not) (Jmol 12.1.17)
+
+ if (offset != null)
+ eval.coordinatesAreFractional = false;
+ else if (tokAt(i) == T.offset)
+ offset = getPoint3f(++i, true);
+ if (offset != null) {
+ if (eval.coordinatesAreFractional) {
+ offset.setT(eval.fractionalPoint);
+ htParams.put("unitCellOffsetFractional",
+ (eval.coordinatesAreFractional ? Boolean.TRUE : Boolean.FALSE));
+ sOptions.append( " offset {" + offset.x + " " + offset.y + " " +
offset.z
+ + "/1}");
+ } else {
+ sOptions.append( " offset " + Escape.eP(offset));
+ }
+ htParams.put("unitCellOffset", offset);
+ i = eval.iToken + 1;
+ }
+ return i;
+ }
+
+ /**
+ * Process FILL and PACKED and all their variants.
+ *
+ * @param i
+ * @param htParams
+ * @param sOptions
+ * @return new token position
+ * @throws ScriptException
+ */
+ private int checkPacked(int i, Map<String, Object> htParams, SB sOptions)
+ throws ScriptException {
+ switch (tokAt(i)) {
+ case T.fill:
+ int tok = tokAt(++i);
+ e.iToken = i;
+ SymmetryInterface unitCell = null;
+ boolean isArray = e.isArrayParameter(i + 1);
+ T3[] pts = (isArray ? e.getPointArray(++i, 4, false) : null);
+ if (!isArray && tok == T.unitcell) {
+ unitCell = vwr.getCurrentUnitCell();
+ if (unitCell != null)
+ pts = BoxInfo.getUnitCellPoints(unitCell.getUnitCellVertices(),
+ unitCell.getCartesianOffset());
+ }
+ if (pts == null)
+ pts = BoxInfo.getUnitCellPoints(vwr.ms.getBBoxVertices(), null);
+ return ++e.iToken;
+ case T.packed:
+ htParams.put("packed", Boolean.TRUE);
+ sOptions.append(" PACKED");
+ if (isFloatParameter(++i)) {
+ float f = floatParameter(i++);
+ htParams.put("packingError", Float.valueOf(f));
+ sOptions.append(" " + f);
+ }
+ break;
+ }
+ return i;
+ }
+
+
///////////////// Jmol script commands ////////////
private void cache() throws ScriptException {
@@ -4275,8 +4505,144 @@
return true;
}
+ private void unitcell(int i) throws ScriptException {
+ ScriptEval eval = e;
+ int icell = Integer.MAX_VALUE;
+ int mad = Integer.MAX_VALUE;
+ T3 pt = null;
+ TickInfo tickInfo = eval.tickParamAsStr(i, true, false, false);
+ i = eval.iToken;
+ String id = null;
+ T3[] oabc = null;
+ Object newUC = null;
+ String ucname = null;
+ boolean isOffset = false;
+ boolean isReset = false;
+ int tok = tokAt(++i);
+ switch (tok) {
+ case T.restore:
+ case T.reset:
+ isReset = true;
+ pt = P4.new4(0, 0, 0, -1); // reset offset and range
+ eval.iToken++;
+ break;
+ case T.string:
+ case T.identifier:
+ String s = paramAsStr(i).toLowerCase();
+ ucname = s;
+ if (s.indexOf(",") < 0 && !chk) {
+ // parent, standard, conventional
+ eval.setCurrentCagePts(null, null);
+ if (PT.isOneOf(s, ";parent;standard;primitive;")) {
+ newUC = vwr.ms.getInfo(vwr.am.cmi, "unitcell_conventional");
+ if (newUC != null)
+ eval.setCurrentCagePts(vwr.getV0abc(newUC), "" + newUC);
+ }
+ s = (String) vwr.ms.getInfo(vwr.am.cmi, "unitcell_" + s);
+ showString(s);
+ }
+ newUC = s;
+ break;
+ case T.isosurface:
+ case T.dollarsign:
+ id = eval.objectNameParameter(++i);
+ break;
+ case T.boundbox:
+ P3 o = P3.newP(vwr.getBoundBoxCenter());
+ pt = vwr.getBoundBoxCornerVector();
+ o.sub(pt);
+ oabc = new P3[] {o, P3.new3(pt.x * 2, 0, 0), P3.new3(0, pt.y * 2, 0),
P3.new3(0, 0, pt.z * 2) };
+ pt = null;
+ eval.iToken = i;
+ break;
+ case T.matrix3f:
+ case T.matrix4f:
+ newUC = getToken(i).value;
+ break;
+ case T.center:
+ switch (tokAt(++i)) {
+ case T.bitset:
+ case T.expressionBegin:
+ pt = P3.newP(vwr.ms.getAtomSetCenter(atomExpressionAt(i)));
+ vwr.toFractional(pt, true);
+ i = eval.iToken;
+ break;
+ default:
+ if (eval.isCenterParameter(i)) {
+ pt = centerParameter(i);
+ i = eval.iToken;
+ break;
+ }
+ invArg();
+ }
+ pt.x -= 0.5f;
+ pt.y -= 0.5f;
+ pt.z -= 0.5f;
+ break;
+ case T.bitset:
+ case T.expressionBegin:
+ int iAtom = atomExpressionAt(i).nextSetBit(0);
+ if (!chk)
+ vwr.am.cai = iAtom;
+ if (iAtom < 0)
+ return;
+ i = eval.iToken;
+ break;
+ case T.offset:
+ isOffset = true;
+ //$FALL-THROUGH$
+ case T.range:
+ pt = (P3) eval.getPointOrPlane(++i, false, true, false, true, 3, 3);
+ pt = P4.new4(pt.x, pt.y, pt.z, (isOffset ? 1 : 0));
+ i = eval.iToken;
+ break;
+ case T.decimal:
+ case T.integer:
+ float f = floatParameter(i);
+ if (f < 111) {
+ // diameter
+ i--;
+ break;
+ }
+ icell = intParameter(i);
+ break;
+ default:
+ if (eval.isArrayParameter(i)) {
+ // Origin vA vB vC
+ // these are VECTORS, though
+ oabc = eval.getPointArray(i, 4, false);
+ i = eval.iToken;
+ } else if (slen > i + 1) {
+ pt = (P3) eval.getPointOrPlane(i, false, true, false, true, 3, 3);
+ i = eval.iToken;
+ } else {
+ // backup for diameter
+ i--;
+ }
+ }
+ mad = eval.getSetAxesTypeMad(++i);
+ eval.checkLast(eval.iToken);
+ if (chk || mad == Integer.MAX_VALUE)
+ return;
+ if (mad == Integer.MAX_VALUE)
+ vwr.am.cai = -1;
+ if (newUC != null)
+ oabc = vwr.getV0abc(newUC);
+ if (icell != Integer.MAX_VALUE)
+ vwr.ms.setUnitCellOffset(vwr.getCurrentUnitCell(), null, icell);
+ else if (id != null)
+ vwr.setCurrentCage(id);
+ else if (isReset || oabc != null)
+ eval.setCurrentCagePts(oabc, ucname);
+ eval.setObjectMad(JC.SHAPE_UCCAGE, "unitCell", mad);
+ if (pt != null)
+ vwr.ms.setUnitCellOffset(vwr.getCurrentUnitCell(), pt, 0);
+ if (tickInfo != null)
+ setShapeProperty(JC.SHAPE_UCCAGE, "tickInfo", tickInfo);
+ }
+
///////// private methods used by commands ///////////
@@ -4523,5 +4889,4 @@
return data;
}
-
}
Modified: trunk/Jmol/src/org/jmol/scriptext/IsoExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/IsoExt.java 2015-06-04 04:57:46 UTC
(rev 20546)
+++ trunk/Jmol/src/org/jmol/scriptext/IsoExt.java 2015-06-04 16:54:12 UTC
(rev 20547)
@@ -3380,7 +3380,7 @@
break;
case T.boundbox:
eval.iToken = i + 1;
- data = BoxInfo.getCriticalPoints(vwr.ms.getBBoxVertices(), null);
+ data = BoxInfo.getUnitCellPoints(vwr.ms.getBBoxVertices(), null);
break;
//case Token.slicebox:
// data =
BoxInfo.getCriticalPoints(((JmolViewer)(vwr)).slicer.getSliceVert(), null);
@@ -3394,7 +3394,7 @@
if (tok == T.unitcell)
invArg();
} else {
- pts = BoxInfo.getCriticalPoints(unitCell.getUnitCellVertices(),
+ pts = BoxInfo.getUnitCellPoints(unitCell.getUnitCellVertices(),
unitCell.getCartesianOffset());
int iType = (int) unitCell
.getUnitCellInfoType(SimpleUnitCell.INFO_DIMENSIONS);
Modified: trunk/Jmol/src/org/jmol/thread/MoveToThread.java
===================================================================
--- trunk/Jmol/src/org/jmol/thread/MoveToThread.java 2015-06-04 04:57:46 UTC
(rev 20546)
+++ trunk/Jmol/src/org/jmol/thread/MoveToThread.java 2015-06-04 16:54:12 UTC
(rev 20547)
@@ -207,7 +207,7 @@
yTrans = newSlider(transformManager.getTranslationYPercent(), f[3]);
rotationRadius = newSlider(transformManager.modelRadius,
(center == null || Float.isNaN(f[4]) ? transformManager.modelRadius
- : f[4] <= 0 ? vwr.ms.calcRotationRadius(vwr.am.cmi, center) :
f[4]));
+ : f[4] <= 0 ? vwr.ms.calcRotationRadius(vwr.am.cmi, center, false)
: f[4]));
pixelScale = newSlider(transformManager.scaleDefaultPixelsPerAngstrom,
f[5]);
if (f[6] != 0) {
navCenter = (P3) options[2];
Modified: trunk/Jmol/src/org/jmol/util/BoxInfo.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/BoxInfo.java 2015-06-04 04:57:46 UTC (rev
20546)
+++ trunk/Jmol/src/org/jmol/util/BoxInfo.java 2015-06-04 16:54:12 UTC (rev
20547)
@@ -36,6 +36,11 @@
import javajs.util.V3;
import javajs.util.T3;
+/**
+ * The BoxInfo class holds critical information about boundboxes.
+ * These are simple tetragonal spaces lined up with x,y,z.
+ *
+ */
public class BoxInfo {
@@ -43,6 +48,11 @@
public final P3 bbCorner1 = new P3();
private final P3 bbCenter = new P3();
private final V3 bbVector = new V3();
+
+ /**
+ * The ordering of these vertices is given below. Do not mess with that.
+ *
+ */
private final Point3fi[] bbVertices = new Point3fi[8];
private boolean isScaleSet;
private float margin;
@@ -125,17 +135,7 @@
P3 vb = new P3();
P3 vc = new P3();
- P3[] vertices = new P3[8];
- for (int i = 0; i < 8; i++) {
- vertices[i] = P3.newP(points[0]);
- if ((i & 1) == 1)
- vertices[i].add(points[1]);
- if ((i & 2) == 2)
- vertices[i].add(points[2]);
- if ((i & 4) == 4)
- vertices[i].add(points[3]);
- }
-
+ P3[] vertices = getVerticesFromCriticalPoints(points);
for (int i = 0; i < 6; i++) {
va.setT(vertices[facePoints[i].x]);
vb.setT(vertices[facePoints[i].y]);
@@ -198,7 +198,28 @@
P3i.new3(0, 1, 1) //7 pt + z + 1
};
- public final static P3[] getCriticalPoints(P3[] bbVertices, T3 offset) {
+ public static P3[] getVerticesFromCriticalPoints(P3[] points) {
+ P3[] vertices = new P3[8];
+ for (int i = 0; i < 8; i++) {
+ vertices[i] = P3.newP(points[0]);
+ if ((i & 1) == 1)
+ vertices[i].add(points[1]);
+ if ((i & 2) == 2)
+ vertices[i].add(points[2]);
+ if ((i & 4) == 4)
+ vertices[i].add(points[3]);
+ }
+ return vertices;
+ }
+
+ /**
+ * Delivers [center a b c] for generation of unit cells from a boundbox
+ *
+ * @param bbVertices
+ * @param offset
+ * @return [center a b c]
+ */
+ public final static P3[] getUnitCellPoints(P3[] bbVertices, T3 offset) {
P3 center = P3.newP(bbVertices[0]);
P3 a = P3.newP(bbVertices[1]);
P3 b = P3.newP(bbVertices[2]);
@@ -231,6 +252,13 @@
return bbVector;
}
+ /**
+ * Return basic info on boundbox in the form of an array.
+ *
+ * @param isAll to include center and diagonal
+ * @return isAll: [(0.5 0.5 0.5), diagonal, (0 0 0), (1 1 1)], otherwise
just [(0 0 0), (1 1 1)]
+ *
+ */
public P3[] getBoundBoxPoints(boolean isAll) {
if (!isScaleSet)
setBbcage(1);
@@ -244,7 +272,15 @@
return bbVertices;
}
- public void setBoundBox(P3 pt1, P3 pt2, boolean byCorner, float scale) {
+ public void setBoundBoxFromCriticalPoints(T3[] points) {
+ P3 origin = P3.newP(points[0]);
+ P3 pt111 = new P3();
+ for (int i = 0; i < 4; i++)
+ pt111.add(points[i]);
+ setBoundBox(origin, pt111, true, 1);
+ }
+
+ public void setBoundBox(T3 pt1, T3 pt2, boolean byCorner, float scale) {
if (pt1 != null) {
if (scale == 0)
return;
@@ -342,4 +378,8 @@
&& pt.z >= bbCorner0.z && pt.z <= bbCorner1.z);
}
+ public float getMaxDim() {
+ return bbVector.length() * 2;
+ }
+
}
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-06-04 04:57:46 UTC
(rev 20546)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-06-04 16:54:12 UTC
(rev 20547)
@@ -14,8 +14,21 @@
TODO: remove HTML5 dependency on synchronous file loading (check SCRIPT
command for problems)
-Jmol.___JmolVersion="14.3.14_2015.06.03"
+Jmol.___JmolVersion="14.3.14_2015.06.04"
+new feature: load "...." FILL BOUNDBOX
+new feature: load "...." FILL UNITCELL
+new feature: load "...." FILL UNITCELL [o a b c]
+new feature: load "...." FILL BOUNDBOX [o a b c]
+
+ -- in development
+ -- loads a crystal structure such that a given volume is packed
+ -- volume can be the current boundbox or the current unitcell or a specified
origin and a,b,c vectors
+ -- if BOUNDBOX, sets the current boundbox after loading to be current boundbox
+
+
+JmolVersion="14.3.14_2015.06.03"
+
new feature: AFLOW binary alloy file reader centers unit cells in all frames
at the same point
new feature; AFLOW binary alloy file reader can filter "list=xx" to produce a
list of values start with xx.
Modified: trunk/Jmol/src/org/jmol/viewer/TransformManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/TransformManager.java 2015-06-04
04:57:46 UTC (rev 20546)
+++ trunk/Jmol/src/org/jmol/viewer/TransformManager.java 2015-06-04
16:54:12 UTC (rev 20547)
@@ -129,6 +129,7 @@
rotationCenterDefault.setT(vwr.getBoundBoxCenter());
setFixedRotationCenter(rotationCenterDefault);
rotationRadiusDefault = setRotationRadius(0, true);
+ System.out.println("TM rotraddef=" +rotationRadiusDefault);
windowCentered = true;
setRotationCenterAndRadiusXYZ(null, true);
resetRotation();
@@ -2284,7 +2285,7 @@
public float setRotationRadius(float angstroms, boolean doAll) {
angstroms = (modelRadius = (angstroms <= 0 ? vwr.ms.calcRotationRadius(
- vwr.am.cmi, fixedRotationCenter) : angstroms));
+ vwr.am.cmi, fixedRotationCenter, true) : angstroms));
if (doAll)
vwr.setRotationRadius(angstroms, false);
return angstroms;
@@ -2300,7 +2301,7 @@
}
setFixedRotationCenter(newCenterOfRotation);
if (andRadius && windowCentered)
- modelRadius = vwr.ms.calcRotationRadius(vwr.am.cmi, fixedRotationCenter);
+ modelRadius = vwr.ms.calcRotationRadius(vwr.am.cmi, fixedRotationCenter,
true);
}
void setNewRotationCenter(P3 center, boolean doScale) {
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