Revision: 20870
http://sourceforge.net/p/jmol/code/20870
Author: hansonr
Date: 2015-11-29 22:18:42 +0000 (Sun, 29 Nov 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.5.0_2015.11.29"
new feature: drawing of spheres in 2D window
-- as percent position or absolute, as for ECHO
-- diameter is % if position is %; otherwise is pixels
-- examples
draw d1 diameter 5 [90 90 %] color blue // 5% diameter
draw d2 diameter 15 [90 90] color blue // pixel diameter
draw dO diameter 2 [90 90 %] color @{ {_O}.color }
set echo eO [95 90 %]; echo "O"
-- can be used in the context of an element key:
function createElementKey() {
var y = 90
for (var e in {*}.element.pivot){
var c = {element=@e}.color
draw ID @{"d_"+ e} diameter 2 [90 @y %] color @c
set echo ID @{"e_" + e} [91 @{y-1} %]
echo @e
font echo 24 bold sansserif
color echo black
y -= 5
}
}
load $caffeine
createElementKey
new feature: additional predefined sets for periodic table:
"@nonmetal _H,_He,_C,_N,_O,_F,_Ne,_S,_P,_Cl,_Ar,_Se,_Br,_Kr,_I,_Xe,_At,_Rn",
"@noblegas _He,_Ne,_Ar,_Kr,_Xe,_Rn",
"@metal !nonmetal",
"@alkaliMetal _Li,_Na,_K,_Rb,_Cs,_Fr",
"@alkalineEarth _Be,_Mg,_Ca,_Sr,_Ba,_Ra",
"@semimetal _B,_Si,_Ge,_As,_Sb,_Te,_Po",
"@transitionMetal
elemno>=21&elemno<=30|elemno>=39&elemno<=48|elemno>=72&elemno<=80|elemno>=104&elemno<=112",
"@lanthanide elemno>=57&elemno<=71",
"@actinide elemno>=89&elemno<=103",
new feature: load =am/<mineralName> loads last (earliest?) entry in American
Mineralogist Crystal Database
-- for example, load =am/corundum
-- reads mineral page such as
http://rruff.geo.arizona.edu/AMS/minerals/Corundum
and extracts from that the last database ID.
-- adding /1, /2, ..., /0 will return only the first, second, ..., last
structure on that page
-- requires a preliminary search followed by the actual file load.
-- only the final ID-based file load is saved in the state.
-- a hack; uses an evaluation of the string:
'http://rruff.geo.arizona.edu/AMS/CIF_text_files/'+load('http://rruff.geo.arizona.edu/AMS/minerals/%FILE').split(\"viewJmol('\")[%n].split(\"'\")[1]+'_cif.txt'
-- for example, see http://rruff.geo.arizona.edu/AMS/viewJmol.php?id=19280
bug fix: files with names containing "[]" cannot be loaded.
bug fix: print {cell=555}.find("cellFormula") can fail because of 2% slop
involved in defining cell=555
Modified Paths:
--------------
branches/v14_4/Jmol/src/org/jmol/popup/JmolGenericPopup.java
branches/v14_4/Jmol/src/org/jmol/script/ScriptEval.java
branches/v14_4/Jmol/src/org/jmol/scriptext/MathExt.java
branches/v14_4/Jmol/src/org/jmol/shapespecial/Draw.java
branches/v14_4/Jmol/src/org/jmol/symmetry/Symmetry.java
branches/v14_4/Jmol/src/org/jmol/util/SimpleUnitCell.java
branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties
branches/v14_4/Jmol/src/org/jmol/viewer/OutputManager.java
branches/v14_4/Jmol/src/org/jmol/viewer/Viewer.java
branches/v14_4/Jmol/src/org/openscience/jmol/app/jmolpanel/JmolPanel.java
trunk/Jmol/src/org/jmol/popup/JmolGenericPopup.java
trunk/Jmol/src/org/jmol/renderspecial/DrawRenderer.java
trunk/Jmol/src/org/jmol/script/ScriptEval.java
trunk/Jmol/src/org/jmol/script/ScriptParam.java
trunk/Jmol/src/org/jmol/shapespecial/Draw.java
trunk/Jmol/src/org/jmol/symmetry/Symmetry.java
trunk/Jmol/src/org/jmol/symmetry/UnitCellIterator.java
trunk/Jmol/src/org/jmol/util/SimpleUnitCell.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/OutputManager.java
trunk/Jmol/src/org/jmol/viewer/Viewer.java
trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/JmolPanel.java
Modified: branches/v14_4/Jmol/src/org/jmol/popup/JmolGenericPopup.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/popup/JmolGenericPopup.java
2015-11-27 11:57:16 UTC (rev 20869)
+++ branches/v14_4/Jmol/src/org/jmol/popup/JmolGenericPopup.java
2015-11-29 22:18:42 UTC (rev 20870)
@@ -362,8 +362,7 @@
int i = modelSetFileName.lastIndexOf(".");
isZapped = (JC.ZAP_TITLE.equals(modelSetName));
if (isZapped || "string".equals(modelSetFileName)
- || "files".equals(modelSetFileName)
- || "string[]".equals(modelSetFileName))
+ || "String[]".equals(modelSetFileName))
modelSetFileName = "";
modelSetRoot = modelSetFileName.substring(0,
i < 0 ? modelSetFileName.length() : i);
Modified: branches/v14_4/Jmol/src/org/jmol/script/ScriptEval.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/script/ScriptEval.java 2015-11-27
11:57:16 UTC (rev 20869)
+++ branches/v14_4/Jmol/src/org/jmol/script/ScriptEval.java 2015-11-29
22:18:42 UTC (rev 20870)
@@ -4408,7 +4408,7 @@
if (isSmiles) {
filename = "$" + filename;
} else {
- if (filename.indexOf("[]") >= 0)
+ if (filename.equals("String[]"))
return;
if (filename.indexOf("[") == 0) {
filenames = Escape.unescapeStringArray(filename);
@@ -4440,7 +4440,7 @@
i++;
// for whatever reason, we don't allow a filename with [] in it.
- if (filename.indexOf("[]") >= 0)
+ if (filename.equals("String[]"))
return;
// MANIFEST "..."
if ((tok = tokAt(i)) == T.manifest) {
@@ -4581,7 +4581,7 @@
} else if (!isData) {
if (localName != null)
localName = vwr.fm.getFilePath(localName, false, false);
- if (!filename.equals("string") && !filename.equals("string[]"))
+ if (!filename.equals("string") && !filename.equals("String[]"))
loadScript.append("/*file*/").append(
(localName != null ? PT.esc(localName) : "$FILENAME$"));
}
Modified: branches/v14_4/Jmol/src/org/jmol/scriptext/MathExt.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/scriptext/MathExt.java 2015-11-27
11:57:16 UTC (rev 20869)
+++ branches/v14_4/Jmol/src/org/jmol/scriptext/MathExt.java 2015-11-29
22:18:42 UTC (rev 20870)
@@ -2766,15 +2766,14 @@
case T.split:
if (x.tok == T.bitset) {
BS bsSelected = SV.bsSelectVar(x);
- sArg = "\n";
int modelCount = vwr.ms.mc;
- s = "";
+ Lst<SV> lst = new Lst<SV>();
for (int i = 0; i < modelCount; i++) {
- s += (i == 0 ? "" : "\n");
BS bs = vwr.getModelUndeletedAtomsBitSet(i);
bs.and(bsSelected);
- s += Escape.eBS(bs);
+ lst.addLast(SV.getVariable(bs));
}
+ return mp.addXList(lst);
}
return mp.addXAS(PT.split(s, sArg));
case T.join:
Modified: branches/v14_4/Jmol/src/org/jmol/shapespecial/Draw.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/shapespecial/Draw.java 2015-11-27
11:57:16 UTC (rev 20869)
+++ branches/v14_4/Jmol/src/org/jmol/shapespecial/Draw.java 2015-11-29
22:18:42 UTC (rev 20870)
@@ -358,13 +358,6 @@
return;
}
- if ("coords" == propertyName) {
- Lst<SV> pts = (Lst<SV>) value;
- for (int i = 0, n = pts.size(); i < n; i++)
- vData.addLast(new Object[] { Integer.valueOf(PT_COORD),
SV.ptValue(pts.get(i)) });
- return;
- }
-
if ("offset" == propertyName) {
offset = V3.newV((P3) value);
if (thisMesh != null)
@@ -383,9 +376,13 @@
return;
}
+ if ("coords" == propertyName) {
+ addPoints(PT_COORD, value, false);
+ return;
+ }
+
if ("modelBasedPoints" == propertyName) {
- vData.addLast(new Object[] { Integer.valueOf(PT_MODEL_BASED_POINTS),
- value });
+ addPoints(PT_MODEL_BASED_POINTS, value, true);
return;
}
@@ -419,6 +416,26 @@
setPropertySuper(propertyName, value, bs);
}
+ private void addPoints(int type, Object value, boolean allowNull) {
+ @SuppressWarnings("unchecked")
+ Lst<SV> pts = (Lst<SV>) value;
+ Integer key = Integer.valueOf(type);
+ for (int i = 0, n = pts.size(); i < n; i++) {
+ SV v = pts.get(i);
+ P3 pt;
+ switch (v.tok) {
+ case T.bitset:
+ if (!allowNull && ((BS) v.value).isEmpty())
+ continue;
+ pt = vwr.ms.getAtomSetCenter((BS) v.value);
+ break;
+ default:
+ pt = SV.ptValue(v);
+ }
+ vData.addLast(new Object[] { key, pt });
+ }
+ }
+
private void deleteModels(int modelIndex) {
//int firstAtomDeleted = ((int[])((Object[])value)[2])[1];
//int nAtomsDeleted = ((int[])((Object[])value)[2])[2];
Modified: branches/v14_4/Jmol/src/org/jmol/symmetry/Symmetry.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/symmetry/Symmetry.java 2015-11-27
11:57:16 UTC (rev 20869)
+++ branches/v14_4/Jmol/src/org/jmol/symmetry/Symmetry.java 2015-11-29
22:18:42 UTC (rev 20870)
@@ -378,7 +378,6 @@
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
Modified: branches/v14_4/Jmol/src/org/jmol/util/SimpleUnitCell.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/util/SimpleUnitCell.java 2015-11-27
11:57:16 UTC (rev 20869)
+++ branches/v14_4/Jmol/src/org/jmol/util/SimpleUnitCell.java 2015-11-29
22:18:42 UTC (rev 20870)
@@ -373,18 +373,22 @@
cell.z = (nnn % f) + offset;
}
+ public final static float SLOP = 0.02f;
+ private final static float SLOP1 = 1 - SLOP;
+
/**
* calculate weighting of 1 (interior), 0.5 (face), 0.25 (edge), or 0.125
(vertex)
* @param pt
+ * @param tolerance fractional allowance to consider this on an edge
* @return weighting
*/
public static float getCellWeight(P3 pt) {
float f = 1;
- if (pt.x == 0)
+ if (pt.x <= SLOP || pt.x >= SLOP1)
f /= 2;
- if (pt.y == 0)
+ if (pt.y <= SLOP || pt.y >= SLOP1)
f /= 2;
- if (pt.z == 0)
+ if (pt.z <= SLOP || pt.z >= SLOP1)
f /= 2;
return f;
}
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2015-11-27
11:57:16 UTC (rev 20869)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2015-11-29
22:18:42 UTC (rev 20870)
@@ -8,8 +8,17 @@
# see also http://chemapps.stolaf.edu/jmol/zip for daily updates
-Jmol.___JmolVersion="14.4.0_2015.11.26"
+Jmol.___JmolVersion="14.4.0_2015.11.29"
+bug fix: files with names containing "[]" cannot be loaded.
+bug fix: print {cell=555}.find("cellFormula") can fail because of 2% slop
involved in defining cell=555
+
+JmolVersion="14.4.0_2015.11.27"
+
+bug fix: {atomset}.split() [split atomset by model] returns array of strings,
not array of atoms
+
+JmolVersion="14.4.0_2015.11.26"
+
bug fix: getproperty SHAPEINFO fails if CGO is present
bug fix: CGO from state deletes DRAW objects
bug fix: CGO not properly isolated to current model; "fixed" not implemented
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/OutputManager.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/OutputManager.java 2015-11-27
11:57:16 UTC (rev 20869)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/OutputManager.java 2015-11-29
22:18:42 UTC (rev 20870)
@@ -565,7 +565,7 @@
fileName = fullPath[0];
String pathName = (type.equals("FILE") ? vwr.fm.getFullPathName(false) :
null);
boolean getCurrentFile = (pathName != null && (pathName.equals("string")
- || pathName.indexOf("[]") >= 0 || pathName.equals("JSNode")));
+ || pathName.equals("String[]") || pathName.equals("JSNode")));
boolean asBytes = (pathName != null && !getCurrentFile);
if (asBytes) {
pathName = vwr.getModelSetPathName();
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/Viewer.java 2015-11-27 11:57:16 UTC
(rev 20869)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/Viewer.java 2015-11-29 22:18:42 UTC
(rev 20870)
@@ -1851,7 +1851,7 @@
Map<String, Object> htParams, SB loadScript) {
if (fileName == null)
return null;
- if (fileName.indexOf("[]") >= 0) {
+ if (fileName.equals("String[]")) {
// no reloading of string[] or file[] data -- just too complicated
return null;
}
@@ -2287,7 +2287,7 @@
String filename = fm.getFullPathName(false);
if (filename.equals("string") || filename.equals(JC.MODELKIT_ZAP_TITLE))
return ms.getInlineData(am.cmi);
- if (filename.indexOf("[]") >= 0)
+ if (filename.equals("String[]"))
return filename;
if (filename == "JSNode")
return "<DOM NODE>";
Modified:
branches/v14_4/Jmol/src/org/openscience/jmol/app/jmolpanel/JmolPanel.java
===================================================================
--- branches/v14_4/Jmol/src/org/openscience/jmol/app/jmolpanel/JmolPanel.java
2015-11-27 11:57:16 UTC (rev 20869)
+++ branches/v14_4/Jmol/src/org/openscience/jmol/app/jmolpanel/JmolPanel.java
2015-11-29 22:18:42 UTC (rev 20870)
@@ -1576,7 +1576,7 @@
static final String chemFileProperty = "chemFile";
void notifyFileOpen(String fullPathName, String title) {
- if (fullPathName == null || !fullPathName.equals("file[]")) {
+ if (fullPathName == null || !fullPathName.equals("String[]")) {
int pt = (fullPathName == null ? -1 : fullPathName.lastIndexOf("|"));
if (pt > 0)
fullPathName = fullPathName.substring(0, pt);
Modified: trunk/Jmol/src/org/jmol/popup/JmolGenericPopup.java
===================================================================
--- trunk/Jmol/src/org/jmol/popup/JmolGenericPopup.java 2015-11-27 11:57:16 UTC
(rev 20869)
+++ trunk/Jmol/src/org/jmol/popup/JmolGenericPopup.java 2015-11-29 22:18:42 UTC
(rev 20870)
@@ -362,8 +362,7 @@
int i = modelSetFileName.lastIndexOf(".");
isZapped = (JC.ZAP_TITLE.equals(modelSetName));
if (isZapped || "string".equals(modelSetFileName)
- || "files".equals(modelSetFileName)
- || "string[]".equals(modelSetFileName))
+ || "String[]".equals(modelSetFileName))
modelSetFileName = "";
modelSetRoot = modelSetFileName.substring(0,
i < 0 ? modelSetFileName.length() : i);
Modified: trunk/Jmol/src/org/jmol/renderspecial/DrawRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/renderspecial/DrawRenderer.java 2015-11-27
11:57:16 UTC (rev 20869)
+++ trunk/Jmol/src/org/jmol/renderspecial/DrawRenderer.java 2015-11-29
22:18:42 UTC (rev 20870)
@@ -133,20 +133,24 @@
if (diameter == 0)
diameter = 1;
}
- if ((dmesh.isVector) && dmesh.haveXyPoints) {
- int ptXY = 0;
- // [x y] or [x,y] refers to an xy point on the screen
- // just a Point3f with z = Float.MAX_VALUE
- // [x y %] or [x,y %] refers to an xy point on the screen
- // as a percent
- // just a Point3f with z = -Float.MAX_VALUE
- for (int i = 0; i < 2; i++)
- if (vertices[i].z == Float.MAX_VALUE
- || vertices[i].z == -Float.MAX_VALUE)
- ptXY += i + 1;
- if (--ptXY < 2) {
- renderXyArrow(ptXY);
- return;
+ if (dmesh.haveXyPoints) {
+ if (dmesh.isVector) {
+ int ptXY = 0;
+ // [x y] or [x,y] refers to an xy point on the screen
+ // just a Point3f with z = Float.MAX_VALUE
+ // [x y %] or [x,y %] refers to an xy point on the screen
+ // as a percent
+ // just a Point3f with z = -Float.MAX_VALUE
+ for (int i = 0; i < 2; i++)
+ if (vertices[i].z == Float.MAX_VALUE
+ || vertices[i].z == -Float.MAX_VALUE)
+ ptXY += i + 1;
+ if (--ptXY < 2) {
+ renderXyArrow(ptXY);
+ return;
+ }
+ } else if (drawType == Draw.EnumDrawType.POINT){
+ renderXyPoint();
}
}
int tension = 5;
@@ -353,7 +357,26 @@
}
}
+ private void renderXyPoint() {
+ // new in Jmol 14.5
+ pt0.setT(vertices[0]);
+ if (diameter == 0)
+ diameter = (int) width;
+ if (pt0.z == -Float.MAX_VALUE) {
+ pt0.x *= vwr.tm.width / 100f;
+ pt0.y *= vwr.tm.height / 100f;
+ diameter = (int) (diameter * vwr.getScreenDim() / 100f);
+ }
+ if (g3d.isAntialiased())
+ diameter *= 2;
+ pt0.y = vwr.tm.height - pt0.y;
+ pt0.z = vwr.tm.cameraDistance;
+ pt1i.set((int) pt0.x, (int) pt0.y, (int) pt0.z);
+ g3d.fillSphereI(diameter, pt1i);
+ }
+
private void renderXyArrow(int ptXY) {
+ // only 0 or 1 here; so ptXYZ is 1 or 0
int ptXYZ = 1 - ptXY;
P3[] arrowPt = new P3[2];
arrowPt[ptXYZ] = pt1;
Modified: trunk/Jmol/src/org/jmol/script/ScriptEval.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEval.java 2015-11-27 11:57:16 UTC
(rev 20869)
+++ trunk/Jmol/src/org/jmol/script/ScriptEval.java 2015-11-29 22:18:42 UTC
(rev 20870)
@@ -4407,7 +4407,7 @@
if (isSmiles) {
filename = "$" + filename;
} else {
- if (filename.indexOf("[]") >= 0)
+ if (filename.equals("String[]"))
return;
if (filename.indexOf("[") == 0) {
filenames = Escape.unescapeStringArray(filename);
@@ -4439,7 +4439,7 @@
i++;
// for whatever reason, we don't allow a filename with [] in it.
- if (filename.indexOf("[]") >= 0)
+ if (filename.equals("String[]"))
return;
// MANIFEST "..."
if ((tok = tokAt(i)) == T.manifest) {
@@ -4580,7 +4580,7 @@
} else if (!isData) {
if (localName != null)
localName = vwr.fm.getFilePath(localName, false, false);
- if (!filename.equals("string") && !filename.equals("string[]"))
+ if (!filename.equals("string") && !filename.equals("String[]"))
loadScript.append("/*file*/").append(
(localName != null ? PT.esc(localName) : "$FILENAME$"));
}
Modified: trunk/Jmol/src/org/jmol/script/ScriptParam.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptParam.java 2015-11-27 11:57:16 UTC
(rev 20869)
+++ trunk/Jmol/src/org/jmol/script/ScriptParam.java 2015-11-29 22:18:42 UTC
(rev 20870)
@@ -553,6 +553,40 @@
return pt;
}
+ public P4 xyzpParameter(int index) throws ScriptException {
+ // [x y z] or [x,y,z] refers to an xy point on the screen
+ // return a P4 with w = Float.MAX_VALUE
+ // [x y z%] or [x,y,z %] refers to an xyz point on the screen
+ // as a percent
+ // return a P4 with w = -Float.MAX_VALUE
+
+ int tok = tokAt(index);
+ if (tok == T.spacebeforesquare)
+ tok = tokAt(++index);
+ if (tok != T.leftsquare || !isFloatParameter(++index))
+ return null;
+ P4 pt = new P4();
+ pt.x = floatParameter(index);
+ if (tokAt(++index) == T.comma)
+ index++;
+ if (!isFloatParameter(index))
+ return null;
+ pt.y = floatParameter(index);
+ if (tokAt(++index) == T.comma)
+ index++;
+ if (!isFloatParameter(index))
+ return null;
+ pt.z = floatParameter(index);
+ boolean isPercent = (tokAt(++index) == T.percent);
+ if (isPercent)
+ ++index;
+ if (tokAt(index) != T.rightsquare)
+ return null;
+ iToken = index;
+ pt.w = (isPercent ? -1 : 1) * Float.MAX_VALUE;
+ return pt;
+ }
+
public String optParameterAsString(int i) throws ScriptException {
if (i >= slen)
return "";
Modified: trunk/Jmol/src/org/jmol/shapespecial/Draw.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapespecial/Draw.java 2015-11-27 11:57:16 UTC
(rev 20869)
+++ trunk/Jmol/src/org/jmol/shapespecial/Draw.java 2015-11-29 22:18:42 UTC
(rev 20870)
@@ -880,7 +880,8 @@
if (nVertices == 3 && isPlane)
isPlane = false;
length = Float.MAX_VALUE;
- thisMesh.diameter = 0;
+ if (isVector)
+ thisMesh.diameter = 0;
} else if (nVertices == 2 && isVector) {
ptList[1].add(ptList[0]);
}
Modified: trunk/Jmol/src/org/jmol/symmetry/Symmetry.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/Symmetry.java 2015-11-27 11:57:16 UTC
(rev 20869)
+++ trunk/Jmol/src/org/jmol/symmetry/Symmetry.java 2015-11-29 22:18:42 UTC
(rev 20870)
@@ -378,11 +378,10 @@
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);
+ return (ptTemp.x >= cell.x - 1f - SimpleUnitCell.SLOP && ptTemp.x <=
cell.x + SimpleUnitCell.SLOP
+ && ptTemp.y >= cell.y - 1f - SimpleUnitCell.SLOP && ptTemp.y <= cell.y
+ SimpleUnitCell.SLOP
+ && ptTemp.z >= cell.z - 1f - SimpleUnitCell.SLOP && ptTemp.z <= cell.z
+ SimpleUnitCell.SLOP);
}
@Override
Modified: trunk/Jmol/src/org/jmol/symmetry/UnitCellIterator.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/UnitCellIterator.java 2015-11-27
11:57:16 UTC (rev 20869)
+++ trunk/Jmol/src/org/jmol/symmetry/UnitCellIterator.java 2015-11-29
22:18:42 UTC (rev 20870)
@@ -44,10 +44,13 @@
* @param atom
* @param atoms
* @param bsAtoms
- * @param distance <= 0 indicates that distance will be set later, probably
from a point
+ * @param distance
+ * <= 0 indicates that distance will be set later, probably from a
+ * point
* @return
*/
- public UnitCellIterator set(SymmetryInterface unitCell, Atom atom, Atom[]
atoms, BS bsAtoms, float distance) {
+ public UnitCellIterator set(SymmetryInterface unitCell, Atom atom,
+ Atom[] atoms, BS bsAtoms, float distance) {
this.unitCell = unitCell;
this.atoms = atoms;
addAtoms(bsAtoms);
@@ -95,13 +98,15 @@
if (max.z < p.z)
max.z = p.z;
}
- minXYZ = P3i.new3((int)Math.floor(min.x), (int)Math.floor(min.y),
(int)Math.floor(min.z));
- maxXYZ = P3i.new3((int)Math.ceil(max.x), (int)Math.ceil(max.y),
(int)Math.ceil(max.z));
+ minXYZ = P3i.new3((int) Math.floor(min.x), (int) Math.floor(min.y),
+ (int) Math.floor(min.z));
+ maxXYZ = P3i.new3((int) Math.ceil(max.x), (int) Math.ceil(max.y),
+ (int) Math.ceil(max.z));
if (Logger.debugging)
Logger.info("UnitCellIterator minxyz/maxxyz " + minXYZ + " " + maxXYZ);
t = P3i.new3(minXYZ.x - 1, minXYZ.y, minXYZ.z);
nextCell();
- }
+ }
@Override
public void addAtoms(BS bsAtoms) {
@@ -109,7 +114,7 @@
if (done)
return;
unitList = new Lst<P3[]>();
- String cat = "";
+ String cat = "";
M4[] ops = unitCell.getSymmetryOperations();
int nOps = ops.length;
for (int i = bsAtoms.nextSetBit(0); i >= 0; i = bsAtoms.nextSetBit(i + 1))
{
@@ -123,7 +128,7 @@
unitCell.unitize(pt);
unitCell.toCartesian(pt, false);
} else {
- unitCell.toUnitCell(pt, null);
+ unitCell.toUnitCell(pt, null);
}
String key = "_" + (int) (pt.x * 100) + "_" + (int) (pt.y * 100) + "_"
+ (int) (pt.z * 100) + "_";
@@ -151,9 +156,9 @@
}
return false;
}
-
+
private boolean nextCell() {
- if (done)
+ if (done)
return false;
if (++t.x >= maxXYZ.x) {
t.x = minXYZ.x;
@@ -176,7 +181,7 @@
public int next() {
return (done || ipt < 0 ? -1 : getAtom().i);
}
-
+
private Atom getAtom() {
return ((Atom) unitList.get(listPt)[0]);
}
@@ -190,7 +195,7 @@
public P3 getPosition() {
Atom a = getAtom();
if (Logger.debugging)
- Logger.info("draw ID p_" + nFound + " " + p + " //" + a + " " + t);
+ Logger.info("draw ID p_" + nFound + " " + p + " //" + a + " " + t);
if (this.p.distanceSquared(a) < 0.0001f)
return a;
Point3fi p = new Point3fi();
Modified: trunk/Jmol/src/org/jmol/util/SimpleUnitCell.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/SimpleUnitCell.java 2015-11-27 11:57:16 UTC
(rev 20869)
+++ trunk/Jmol/src/org/jmol/util/SimpleUnitCell.java 2015-11-29 22:18:42 UTC
(rev 20870)
@@ -373,18 +373,22 @@
cell.z = (nnn % f) + offset;
}
+ public final static float SLOP = 0.02f;
+ private final static float SLOP1 = 1 - SLOP;
+
/**
* calculate weighting of 1 (interior), 0.5 (face), 0.25 (edge), or 0.125
(vertex)
* @param pt
+ * @param tolerance fractional allowance to consider this on an edge
* @return weighting
*/
public static float getCellWeight(P3 pt) {
float f = 1;
- if (pt.x == 0)
+ if (pt.x <= SLOP || pt.x >= SLOP1)
f /= 2;
- if (pt.y == 0)
+ if (pt.y <= SLOP || pt.y >= SLOP1)
f /= 2;
- if (pt.z == 0)
+ if (pt.z <= SLOP || pt.z >= SLOP1)
f /= 2;
return f;
}
Modified: trunk/Jmol/src/org/jmol/viewer/GlobalSettings.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/GlobalSettings.java 2015-11-27 11:57:16 UTC
(rev 20869)
+++ trunk/Jmol/src/org/jmol/viewer/GlobalSettings.java 2015-11-29 22:18:42 UTC
(rev 20870)
@@ -889,32 +889,42 @@
return structureList;
}
- String resolveDataBase(String database, String id, String format) {
- if (format == null) {
- if ((format = databases.get(database.toLowerCase())) == null)
- return null;
- if (id.indexOf("/") < 0) {
- if (database.equals("pubchem"))
- id = "name/" + id;
- else if (database.equals("nci"))
- id += "/file?format=sdf&get3d=True";
- }
- } else if (id.indexOf(".") >= 0 && format.indexOf("%FILE.") >= 0) {
- // replace RCSB format extension when a file extension is made
explicit
- format = format.substring(0, format.indexOf("%FILE"));
+ String resolveDataBase(String database, String id, String format) {
+ if (format == null) {
+ if ((format = databases.get(database.toLowerCase())) == null)
+ return null;
+ int pt = id.indexOf("/");
+ if (pt < 0) {
+ if (database.equals("pubchem"))
+ id = "name/" + id;
+ else if (database.equals("nci"))
+ id += "/file?format=sdf&get3d=True";
}
- try {
- while (format.indexOf("%c") >= 0)
- for (int i = 1; i < 10; i++) {
- format = PT.rep(format, "%c" + i, id.substring(i - 1, i));
- }
- } catch (Exception e) {
- // too bad.
+ if (format.startsWith("'")) {
+ // needs evaluation
+ int n = (pt > 0 ? PT.parseInt(id.substring(pt + 1)) : 0);
+ if (n > 0)
+ n++;
+ if (pt > 0)
+ id = id.substring(0, pt);
+ format = PT.rep(format, "%n", "" + n);
}
- return (format.indexOf("%FILE") >= 0 ? PT.formatStringS(format, "FILE",
id)
- : format.indexOf("%file") >= 0 ? PT.formatStringS(format, "file",
- id.toLowerCase()) : format + id);
+ } else if (id.indexOf(".") >= 0 && format.indexOf("%FILE.") >= 0) {
+ // replace RCSB format extension when a file extension is made explicit
+ format = format.substring(0, format.indexOf("%FILE"));
}
+ try {
+ while (format.indexOf("%c") >= 0)
+ for (int i = 1; i < 10; i++) {
+ format = PT.rep(format, "%c" + i, id.substring(i - 1, i));
+ }
+ } catch (Exception e) {
+ // too bad.
+ }
+ return (format.indexOf("%FILE") >= 0 ? PT.formatStringS(format, "FILE", id)
+ : format.indexOf("%file") >= 0 ? PT.formatStringS(format, "file",
+ id.toLowerCase()) : format + id);
+ }
static boolean doReportProperty(String name) {
return (name.charAt(0) != '_' && unreportedProperties.indexOf(";" + name
Modified: trunk/Jmol/src/org/jmol/viewer/JC.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/JC.java 2015-11-27 11:57:16 UTC (rev
20869)
+++ trunk/Jmol/src/org/jmol/viewer/JC.java 2015-11-29 22:18:42 UTC (rev
20870)
@@ -67,7 +67,8 @@
"pubchem",
"http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/%FILE/SDF?record_type=3d";,
"map",
"http://www.ebi.ac.uk/pdbe/api/%TYPE/%FILE?pretty=false&metadata=true";,
"rna3d", "http://rna.bgsu.edu/rna3dhub/%TYPE/download/%FILE";,
- "aflow",
"http://aflowlib.mems.duke.edu/users/jmolers/binary_new/%FILE.aflow_binary";
+ "aflow",
"http://aflowlib.mems.duke.edu/users/jmolers/binary_new/%FILE.aflow_binary";,
+ "am",
"'http://rruff.geo.arizona.edu/AMS/CIF_text_files/'+load('http://rruff.geo.arizona.edu/AMS/minerals/%FILE').split(\"viewJmol('\")[%n].split(\"'\")[1]+'_cif.txt'"
};
public static String[] macros = {
@@ -561,6 +562,7 @@
"@ssSegments within(dssr,'ssSegments')",
"@stacks within(dssr,'stacks')",
"@stems within(dssr,'stems')",
+
};
// these are only updated once per file load or file append
@@ -627,8 +629,19 @@
"@spine protein&_a>=1&_a<4|nucleic&(_a>=6&_a<11|_a=13)",
"@sidechain (protein,nucleic) & !backbone",
"@base nucleic & !backbone",
- "@dynamic_flatring search('[a]')"
+ "@dynamic_flatring search('[a]')",
+ //periodic table
+ "@nonmetal
_H,_He,_C,_N,_O,_F,_Ne,_S,_P,_Cl,_Ar,_Se,_Br,_Kr,_I,_Xe,_At,_Rn",
+ "@noblegas _He,_Ne,_Ar,_Kr,_Xe,_Rn",
+ "@metal !nonmetal",
+ "@alkaliMetal _Li,_Na,_K,_Rb,_Cs,_Fr",
+ "@alkalineEarth _Be,_Mg,_Ca,_Sr,_Ba,_Ra",
+ "@semimetal _B,_Si,_Ge,_As,_Sb,_Te,_Po",
+ "@transitionMetal
elemno>=21&elemno<=30|elemno>=39&elemno<=48|elemno>=72&elemno<=80|elemno>=104&elemno<=112",
+ "@lanthanide elemno>=57&elemno<=71",
+ "@actinide elemno>=89&elemno<=103",
+
// "@hetero", handled specially
};
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-11-27 11:57:16 UTC
(rev 20869)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-11-29 22:18:42 UTC
(rev 20870)
@@ -62,8 +62,59 @@
TODO: consider if models with no atoms will cause issues in relation to
model.firstAtomIndex
-Jmol.___JmolVersion="14.5.0_2015.11.27"
+Jmol.___JmolVersion="14.5.0_2015.11.29"
+new feature: drawing of spheres in 2D window
+ -- as percent position or absolute, as for ECHO
+ -- diameter is % if position is %; otherwise is pixels
+ -- examples
+ draw d1 diameter 5 [90 90 %] color blue // 5% diameter
+ draw d2 diameter 15 [90 90] color blue // pixel diameter
+ draw dO diameter 2 [90 90 %] color @{ {_O}.color }
+ set echo eO [95 90 %]; echo "O"
+ -- can be used in the context of an element key:
+ function createElementKey() {
+ var y = 90
+ for (var e in {*}.element.pivot){
+ var c = {element=@e}.color
+ draw ID @{"d_"+ e} diameter 2 [90 @y %] color @c
+ set echo ID @{"e_" + e} [91 @{y-1} %]
+ echo @e
+ font echo 24 bold sansserif
+ color echo black
+ y -= 5
+ }
+ }
+ load $caffeine
+ createElementKey
+
+new feature: additional predefined sets for periodic table:
+ "@nonmetal
_H,_He,_C,_N,_O,_F,_Ne,_S,_P,_Cl,_Ar,_Se,_Br,_Kr,_I,_Xe,_At,_Rn",
+ "@noblegas _He,_Ne,_Ar,_Kr,_Xe,_Rn",
+ "@metal !nonmetal",
+ "@alkaliMetal _Li,_Na,_K,_Rb,_Cs,_Fr",
+ "@alkalineEarth _Be,_Mg,_Ca,_Sr,_Ba,_Ra",
+ "@semimetal _B,_Si,_Ge,_As,_Sb,_Te,_Po",
+ "@transitionMetal
elemno>=21&elemno<=30|elemno>=39&elemno<=48|elemno>=72&elemno<=80|elemno>=104&elemno<=112",
+ "@lanthanide elemno>=57&elemno<=71",
+ "@actinide elemno>=89&elemno<=103",
+
+new feature: load =am/<mineralName> loads last (earliest?) entry in American
Mineralogist Crystal Database
+ -- for example, load =am/corundum
+ -- reads mineral page such as
http://rruff.geo.arizona.edu/AMS/minerals/Corundum
+ and extracts from that the last database ID.
+ -- adding /1, /2, ..., /0 will return only the first, second, ..., last
structure on that page
+ -- requires a preliminary search followed by the actual file load.
+ -- only the final ID-based file load is saved in the state.
+ -- a hack; uses an evaluation of the string:
+
'http://rruff.geo.arizona.edu/AMS/CIF_text_files/'+load('http://rruff.geo.arizona.edu/AMS/minerals/%FILE').split(\"viewJmol('\")[%n].split(\"'\")[1]+'_cif.txt'
+ -- for example, see http://rruff.geo.arizona.edu/AMS/viewJmol.php?id=19280
+
+bug fix: files with names containing "[]" cannot be loaded.
+bug fix: print {cell=555}.find("cellFormula") can fail because of 2% slop
involved in defining cell=555
+
+JmolVersion="14.5.0_2015.11.27"
+
bug fix: {atomset}.split() [split atomset by model] returns array of strings,
not array of atoms
code: BSUtil.cardinalityOf cleanup.
Modified: trunk/Jmol/src/org/jmol/viewer/OutputManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/OutputManager.java 2015-11-27 11:57:16 UTC
(rev 20869)
+++ trunk/Jmol/src/org/jmol/viewer/OutputManager.java 2015-11-29 22:18:42 UTC
(rev 20870)
@@ -565,7 +565,7 @@
fileName = fullPath[0];
String pathName = (type.equals("FILE") ? vwr.fm.getFullPathName(false) :
null);
boolean getCurrentFile = (pathName != null && (pathName.equals("string")
- || pathName.indexOf("[]") >= 0 || pathName.equals("JSNode")));
+ || pathName.equals("String[]") || pathName.equals("JSNode")));
boolean asBytes = (pathName != null && !getCurrentFile);
if (asBytes) {
pathName = vwr.getModelSetPathName();
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2015-11-27 11:57:16 UTC (rev
20869)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2015-11-29 22:18:42 UTC (rev
20870)
@@ -139,8 +139,9 @@
*
* The JmolViewer runs on Java 1.5+ virtual machines. The 3d graphics rendering
* package is a software implementation of a z-buffer. It does not use Java3D
- * and does not use Graphics2D from Java 1.2.
+ * and does not use Graphics2D from Java 1.2. "
*
+ *
* public here is a test for applet-applet and JS-applet communication the idea
* being that applet.getProperty("jmolViewer") returns this Viewer object,
* allowing direct inter-process access to public methods.
@@ -1851,7 +1852,7 @@
Map<String, Object> htParams, SB loadScript) {
if (fileName == null)
return null;
- if (fileName.indexOf("[]") >= 0) {
+ if (fileName.equals("String[]")) {
// no reloading of string[] or file[] data -- just too complicated
return null;
}
@@ -1863,7 +1864,7 @@
boolean haveFileData = (htParams.containsKey("fileData"));
if (fileName.indexOf('$') == 0)
htParams.put("smilesString", fileName.substring(1));
- boolean isString = (fileName.equalsIgnoreCase("string") || fileName
+ boolean isString = (fileName.equals("string") || fileName
.equals(JC.MODELKIT_ZAP_TITLE));
String strModel = null;
if (haveFileData) {
@@ -2287,7 +2288,7 @@
String filename = fm.getFullPathName(false);
if (filename.equals("string") || filename.equals(JC.MODELKIT_ZAP_TITLE))
return ms.getInlineData(am.cmi);
- if (filename.indexOf("[]") >= 0)
+ if (filename.equals("String[]"))
return filename;
if (filename == "JSNode")
return "<DOM NODE>";
@@ -3906,7 +3907,9 @@
int pt = f.indexOf("/");
String database = f.substring(0, pt);
f = g.resolveDataBase(database, f.substring(pt + 1), null);
- return (f == null ? name : f);
+ if (f != null && f.startsWith("'"))
+ f = evaluateExpression(f).toString();
+ return (f == null || f.length() == 0 ? name : f);
} catch (Exception e) {
return name;
}
Modified: trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/JmolPanel.java
===================================================================
--- trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/JmolPanel.java
2015-11-27 11:57:16 UTC (rev 20869)
+++ trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/JmolPanel.java
2015-11-29 22:18:42 UTC (rev 20870)
@@ -1576,7 +1576,7 @@
static final String chemFileProperty = "chemFile";
void notifyFileOpen(String fullPathName, String title) {
- if (fullPathName == null || !fullPathName.equals("file[]")) {
+ if (fullPathName == null || !fullPathName.equals("String[]")) {
int pt = (fullPathName == null ? -1 : fullPathName.lastIndexOf("|"));
if (pt > 0)
fullPathName = fullPathName.substring(0, pt);
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