Revision: 20858
http://sourceforge.net/p/jmol/code/20858
Author: hansonr
Date: 2015-11-03 13:43:26 +0000 (Tue, 03 Nov 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.5.0_2015.11.03"
new feature: x = pointgroup([array of points],center)
-- center is optional, defaulting to average of the points
-- returns a map:
print pointgroup(pts,{1 0 0})
{
"C2" :
[
{-1.0 -2.647229E-6 0.0}
]
"C4" :
[
{-1.0 -2.647229E-6 0.0}
]
"Cs" :
[
{5.9132327E-7 0.70710725 0.70710635}
{2.1809963E-7 1.0 7.2699876E-8}
{-1.960397E-7 -0.7071069 0.70710665}
{7.269983E-8 1.4539965E-7 -1.0}
]
"center" : {1.0 0.0 0.0}
"detail" : "# 14 atoms;"
"distanceTolerance" : 0.2
"linearTolerance" : 8.0
"nAtoms" : 14
"nC2" : 1
"nC4" : 1
"nCi" : 0
"nCn" : 2
"nCs" : 4
"nSn" : 0
"nTotal" : 8
"name" : "C4v"
"principalAxis" : {-1.0 -2.647229E-6 0.0}
}
bug fix: FOR without {} but with ";" after sole statement
followed immediately by second FOR improperly loops
for (var i from [1,5])
print i;
for (var i from [1,5])
print i
bug fix: OXT missing from BACKBONE selection
bug fix: (JSmol) CIF parser fails to read CIF files containing only a single
(non-loop) _struct_ref_seq_dif.align_id
new feature: polyhedra ID xxx SCALE x.x
-- ID named polyhedra only
-- x.x is the scaling factor, initially 1
-- x.x > 0 does normal scaling
-- x.x < 0 does "explode" from {0 0 0} (for higher-order Brillouin zones, for
instance)
bug fix: slabbing should reset area and volume of isosurface
bug fix: meshSlicer may fail to add edge to sliced pmesh
FEATURE CHANGE: (Application only for now) PDB default for =xxxx
-- changed to
"pdb",
"http://ftp.wwpdb.org/pub/pdb/data/structures/divided/pdb/%c2%c3/pdb%file.ent.gz";
-- will be complemented with file.ent for non-binary transfer, but that is
not implemented yet at RCSB
-- mmCIF counterpart not implemented yet.
-- not HTML5 because for that we need the option to remove .gz
new feature: set testflag3 TRUE gives random triangle effect to polyhedra
new feature: POLYHEDRON ID "xxx" OFFSET {3 3 3}
-- allows cartesian offset of named polyhedra
bug fix: bug fix: empty format crashes Jmol -- print "testing".format("")
bug fix: polyhedron volume will be incorrect if there is a
face triangle that has no edges visible (requires a six or more sided
face)
bug fix: nested if...{...if... } else {...} gives compiler syntax error:
if (i=1) {
print "i=1"
if (j=1)
print "j != 1"
} else { // } closes if (j=1) instead of if (i=1) {
print "i != 1"
}
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/api/SymmetryInterface.java
trunk/Jmol/src/org/jmol/modelset/ModelSet.java
trunk/Jmol/src/org/jmol/script/T.java
trunk/Jmol/src/org/jmol/scriptext/MathExt.java
trunk/Jmol/src/org/jmol/shapespecial/Polyhedron.java
trunk/Jmol/src/org/jmol/symmetry/PointGroup.java
trunk/Jmol/src/org/jmol/symmetry/Symmetry.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
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 2015-11-03 12:36:49 UTC
(rev 20857)
+++ trunk/Jmol/src/org/jmol/api/SymmetryInterface.java 2015-11-03 13:43:26 UTC
(rev 20858)
@@ -156,10 +156,10 @@
public SymmetryInterface setPointGroup(
SymmetryInterface pointGroupPrevious,
- T3[] atomset, BS bsAtoms,
+ T3 center, T3[] atomset,
+ BS bsAtoms,
boolean haveVibration,
- float distanceTolerance,
- float linearTolerance, boolean
localEnvOnly);
+ float distanceTolerance, float
linearTolerance, boolean localEnvOnly);
public void setSpaceGroup(boolean doNormalize);
Modified: trunk/Jmol/src/org/jmol/modelset/ModelSet.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2015-11-03 12:36:49 UTC
(rev 20857)
+++ trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2015-11-03 13:43:26 UTC
(rev 20858)
@@ -542,9 +542,9 @@
}
if (type != null && type.indexOf(":") >= 0)
type = type.substring(0, type.indexOf(":"));
- pointGroup = symmetry.setPointGroup(pointGroup, pts, bs, haveVibration,
- vwr.getFloat(T.pointgroupdistancetolerance),
- vwr.getFloat(T.pointgrouplineartolerance), localEnvOnly);
+ pointGroup = symmetry.setPointGroup(pointGroup, null, pts, bs,
+ haveVibration,
+ vwr.getFloat(T.pointgroupdistancetolerance),
vwr.getFloat(T.pointgrouplineartolerance), localEnvOnly);
if (!isPolyhedron)
this.pointGroup = pointGroup;
if (!doAll && !asInfo)
Modified: trunk/Jmol/src/org/jmol/script/T.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/T.java 2015-11-03 12:36:49 UTC (rev
20857)
+++ trunk/Jmol/src/org/jmol/script/T.java 2015-11-03 13:43:26 UTC (rev
20858)
@@ -702,6 +702,7 @@
public final static int within = 31 | 0 << 9 | mathfunc;
public final static int write = 32 | 0 << 9 | mathfunc |
scriptCommand;
public final static int _ = 33 | 0 << 9 | mathfunc |
mathproperty; // same as getProperty
+ public final static int pointgroup = 34 | 0 << 9 | mathfunc;
// xxx(a)
@@ -1267,7 +1268,6 @@
public final static int playrev = misc | 274;
public final static int planarparam = misc | 275;
public final static int pocket = misc | 276;
- public final static int pointgroup = misc | 278;
public final static int pointsperangstrom = misc | 280;
public final static int polygon = misc | 282;
public final static int prev = misc | 284;
Modified: trunk/Jmol/src/org/jmol/scriptext/MathExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/MathExt.java 2015-11-03 12:36:49 UTC
(rev 20857)
+++ trunk/Jmol/src/org/jmol/scriptext/MathExt.java 2015-11-03 13:43:26 UTC
(rev 20858)
@@ -190,6 +190,8 @@
return evaluateString(mp, op.intValue, args);
case T.point:
return evaluatePoint(mp, args);
+ case T.pointgroup:
+ return evaluatePointGroup(mp, args);
case T.prompt:
return evaluatePrompt(mp, args);
case T.random:
@@ -221,6 +223,31 @@
return false;
}
+ @SuppressWarnings("unchecked")
+ private boolean evaluatePointGroup(ScriptMathProcessor mp, SV[] args) {
+ // pointGroup(points)
+ // pointGroup(points, center)
+ P3 center = null;
+ T3[] pts;
+ switch (args.length) {
+ case 2:
+ center = SV.ptValue(args[1]);
+ //$FALL-THROUGH$
+ case 1:
+ Lst<SV> points = args[0].getList();
+ pts = new T3[points.size()];
+ for (int i = pts.length; --i >= 0;)
+ pts[i] = SV.ptValue(points.get(i));
+ break;
+ default:
+ return false;
+ }
+ SymmetryInterface pointGroup = vwr.ms.getSymTemp(true).setPointGroup(null,
center, pts,
+ null, false,
+ vwr.getFloat(T.pointgroupdistancetolerance),
vwr.getFloat(T.pointgrouplineartolerance), true);
+ return mp.addXMap((Map<String, ?>) pointGroup.getPointGroupInfo(-1, false,
true, null, 0, 1));
+ }
+
private boolean evaluateUnitCell(ScriptMathProcessor mp, SV[] args) {
// optional last parameter: scale
// unitcell()
Modified: trunk/Jmol/src/org/jmol/shapespecial/Polyhedron.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapespecial/Polyhedron.java 2015-11-03
12:36:49 UTC (rev 20857)
+++ trunk/Jmol/src/org/jmol/shapespecial/Polyhedron.java 2015-11-03
13:43:26 UTC (rev 20858)
@@ -283,15 +283,15 @@
// first time through includes all atoms as atoms
for (int i = pts.length; --i >= 0;)
pts[i] = vertices[i];
- pointGroup = vwr.ms.getSymTemp(true).setPointGroup(null, pts, null,
- false, vwr.getFloat(T.pointgroupdistancetolerance),
- vwr.getFloat(T.pointgrouplineartolerance), true);
+ pointGroup = vwr.ms.getSymTemp(true).setPointGroup(null, null, pts,
+ null, false,
+ vwr.getFloat(T.pointgroupdistancetolerance),
vwr.getFloat(T.pointgrouplineartolerance), true);
// second time through includes all atoms as points only
for (int i = pts.length; --i >= 0;)
pts[i] = P3.newP(vertices[i]);
- pointGroupFamily = vwr.ms.getSymTemp(true).setPointGroup(null, pts, null,
- false, vwr.getFloat(T.pointgroupdistancetolerance),
- vwr.getFloat(T.pointgrouplineartolerance), true);
+ pointGroupFamily = vwr.ms.getSymTemp(true).setPointGroup(null, null, pts,
+ null, false,
+ vwr.getFloat(T.pointgroupdistancetolerance),
vwr.getFloat(T.pointgrouplineartolerance), true);
}
return (center == null ? centralAtom : center) + " " +
pointGroup.getPointGroupName() + " "
+ "("+pointGroupFamily.getPointGroupName()+")";
Modified: trunk/Jmol/src/org/jmol/symmetry/PointGroup.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/PointGroup.java 2015-11-03 12:36:49 UTC
(rev 20857)
+++ trunk/Jmol/src/org/jmol/symmetry/PointGroup.java 2015-11-03 13:43:26 UTC
(rev 20858)
@@ -125,6 +125,7 @@
private final static int c8 = firstProper + 8;
private final static int maxAxis = axesMaxN.length;
+ private boolean isAtoms;
String drawInfo;
Map<String, Object> info;
String textInfo;
@@ -143,6 +144,7 @@
private Operation principalAxis;
private Operation principalPlane;
+
String getName() {
return name;
}
@@ -151,7 +153,7 @@
private int centerAtomIndex = -1;
private boolean haveInversionCenter;
- final private P3 center = new P3();
+ private T3 center;
private T3[] points;
private int[] elements;
@@ -166,6 +168,7 @@
/**
*
* @param pgLast
+ * @param center TODO
* @param atomset
* @param bsAtoms
* @param haveVibration
@@ -175,15 +178,17 @@
* @return a PointGroup
*/
- static PointGroup getPointGroup(PointGroup pgLast, T3[] atomset,
- BS bsAtoms, boolean haveVibration,
- float distanceTolerance,
- float linearTolerance, boolean
localEnvOnly) {
+ static PointGroup getPointGroup(PointGroup pgLast, T3 center,
+ T3[] atomset, BS bsAtoms,
+ boolean haveVibration,
+ float distanceTolerance, float
linearTolerance, boolean localEnvOnly) {
PointGroup pg = new PointGroup();
pg.distanceTolerance = distanceTolerance;
pg.linearTolerance = linearTolerance;
+ pg.isAtoms = (bsAtoms != null);
pg.bsAtoms = (bsAtoms == null ? BSUtil.newBitSet2(0, atomset.length) :
bsAtoms);
pg.haveVibration = haveVibration;
+ pg.center = center;
pg.localEnvOnly = localEnvOnly;
return (pg.set(pgLast, atomset) ? pg : pgLast);
}
@@ -388,13 +393,16 @@
private boolean getPointsAndElements(T3[] atomset) {
int ac = BSUtil.cardinalityOf(bsAtoms);
- if (ac > ATOM_COUNT_MAX)
+ if (isAtoms && ac > ATOM_COUNT_MAX)
return false;
points = new P3[ac];
elements = new int[ac];
if (ac == 0)
return true;
nAtoms = 0;
+ boolean needCenter = (center == null);
+ if (needCenter)
+ center = new P3();
// we optionally include bonding information
for (int i = bsAtoms.nextSetBit(0); i >= 0; i = bsAtoms.nextSetBit(i + 1),
nAtoms++) {
T3 p = points[nAtoms] = atomset[i];
@@ -403,9 +411,11 @@
((Node) p).getCovalentBondCount()));
elements[nAtoms] = ((Node) p).getElementNumber() * bondIndex;
}
- center.add(points[nAtoms]);
+ if (needCenter)
+ center.add(points[nAtoms]);
}
- center.scale(1f / nAtoms);
+ if (needCenter)
+ center.scale(1f / nAtoms);
for (int i = nAtoms; --i >= 0;) {
float r = center.distance(points[i]);
if (r < distanceTolerance)
@@ -423,7 +433,7 @@
}
}
- private boolean checkOperation(Quat q, P3 center, int iOrder) {
+ private boolean checkOperation(Quat q, T3 center, int iOrder) {
P3 pt = new P3();
int nFound = 0;
boolean isInversion = (iOrder < firstProper);
@@ -682,7 +692,7 @@
return n;
}
- private boolean checkAxisOrder(int iOrder, V3 v, P3 center) {
+ private boolean checkAxisOrder(int iOrder, V3 v, T3 center) {
switch (iOrder) {
case c8:
if (nAxes[c3] > 0)
Modified: trunk/Jmol/src/org/jmol/symmetry/Symmetry.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/Symmetry.java 2015-11-03 12:36:49 UTC
(rev 20857)
+++ trunk/Jmol/src/org/jmol/symmetry/Symmetry.java 2015-11-03 13:43:26 UTC
(rev 20858)
@@ -96,14 +96,14 @@
@Override
public SymmetryInterface setPointGroup(SymmetryInterface siLast,
- T3[] atomset, BS bsAtoms,
+ T3 center, T3[] atomset,
+ BS bsAtoms,
boolean haveVibration,
float distanceTolerance,
- float linearTolerance,
- boolean localEnvOnly) {
+ float linearTolerance, boolean
localEnvOnly) {
pointGroup = PointGroup.getPointGroup(siLast == null ? null
- : ((Symmetry) siLast).pointGroup, atomset, bsAtoms, haveVibration,
- distanceTolerance, linearTolerance, localEnvOnly);
+ : ((Symmetry) siLast).pointGroup, center, atomset, bsAtoms,
+ haveVibration, distanceTolerance, linearTolerance, localEnvOnly);
return this;
}
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-11-03 12:36:49 UTC
(rev 20857)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-11-03 13:43:26 UTC
(rev 20858)
@@ -64,6 +64,43 @@
Jmol.___JmolVersion="14.5.0_2015.11.03"
+new feature: x = pointgroup([array of points],center)
+ -- center is optional, defaulting to average of the points
+ -- returns a map:
+
+ print pointgroup(pts,{1 0 0})
+ {
+ "C2" :
+ [
+ {-1.0 -2.647229E-6 0.0}
+ ]
+ "C4" :
+ [
+ {-1.0 -2.647229E-6 0.0}
+ ]
+ "Cs" :
+ [
+ {5.9132327E-7 0.70710725 0.70710635}
+ {2.1809963E-7 1.0 7.2699876E-8}
+ {-1.960397E-7 -0.7071069 0.70710665}
+ {7.269983E-8 1.4539965E-7 -1.0}
+ ]
+ "center" : {1.0 0.0 0.0}
+ "detail" : "# 14 atoms;"
+ "distanceTolerance" : 0.2
+ "linearTolerance" : 8.0
+ "nAtoms" : 14
+ "nC2" : 1
+ "nC4" : 1
+ "nCi" : 0
+ "nCn" : 2
+ "nCs" : 4
+ "nSn" : 0
+ "nTotal" : 8
+ "name" : "C4v"
+ "principalAxis" : {-1.0 -2.647229E-6 0.0}
+ }
+
bug fix: FOR without {} but with ";" after sole statement
followed immediately by second FOR improperly loops
for (var i from [1,5])
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2015-11-03 12:36:49 UTC (rev
20857)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2015-11-03 13:43:26 UTC (rev
20858)
@@ -3893,7 +3893,7 @@
* @return String or String[]
*/
public Object setLoadFormat(String name, char type, boolean withPrefix) {
- String format;
+ String format = null;
String f = name.substring(1);
switch (type) {
case '=':
@@ -3910,16 +3910,19 @@
} catch (Exception e) {
return name;
}
+ } else {
+ format = (
+ // following is temporary, until issues are resolved for AJAX asych
+ isJS && g.loadFormat.equals(g.pdbLoadFormat) ? g.pdbLoadFormat0
+ : g.loadFormat);
}
//$FALL-THROUGH$
case '#': // ligand
- String s = (type != '=' ? g.pdbLoadLigandFormat
- // following is temporary, until issues are resolved for AJAX asych
- : isJS && g.loadFormat.equals(g.pdbLoadFormat) ? g.pdbLoadFormat0
- : g.loadFormat);
- if (f.indexOf(".") >= 0 && s.equals(g.pdbLoadFormat))
- s = g.pdbLoadFormat0; // older version for =1crn.cif or =1crn.pdb
- return g.resolveDataBase(null, f, s);
+ if (format == null)
+ format = g.pdbLoadLigandFormat;
+ if (f.indexOf(".") >= 0 && format.equals(g.pdbLoadFormat))
+ format = g.pdbLoadFormat0; // older version for =1crn.cif or
=1crn.pdb
+ return g.resolveDataBase(null, f, format);
case '*':
// European Bioinformatics Institute
int pt = name.lastIndexOf("/");
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