Revision: 20812
http://sourceforge.net/p/jmol/code/20812
Author: hansonr
Date: 2015-10-08 03:49:03 +0000 (Thu, 08 Oct 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.3.16_2015.10.06"
new feature: print within(distance, point, array_of_points)
-- point array distance iterator
-- returns subarray of points (in differing order, probably) of
array_of_points
that are within distance of point.
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/bspt/CubeIterator.java
trunk/Jmol/src/org/jmol/scriptext/MathExt.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/bspt/CubeIterator.java
===================================================================
--- trunk/Jmol/src/org/jmol/bspt/CubeIterator.java 2015-10-06 14:27:29 UTC
(rev 20811)
+++ trunk/Jmol/src/org/jmol/bspt/CubeIterator.java 2015-10-08 03:49:03 UTC
(rev 20812)
@@ -169,7 +169,7 @@
}
/**
- * checks one Point3f for distance
+ * checks one Point3f for box-based distance
* @param t
* @return boolean
*/
Modified: trunk/Jmol/src/org/jmol/scriptext/MathExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/MathExt.java 2015-10-06 14:27:29 UTC
(rev 20811)
+++ trunk/Jmol/src/org/jmol/scriptext/MathExt.java 2015-10-08 03:49:03 UTC
(rev 20812)
@@ -37,6 +37,8 @@
import org.jmol.api.JmolPatternMatcher;
import org.jmol.atomdata.RadiusData;
import org.jmol.atomdata.RadiusData.EnumType;
+import org.jmol.bspt.Bspt;
+import org.jmol.bspt.CubeIterator;
import org.jmol.c.VDW;
import org.jmol.i18n.GT;
import org.jmol.java.BS;
@@ -2844,8 +2846,8 @@
throws ScriptException {
if (args.length < 1 || args.length > 5)
return false;
- int i = args.length;
- if (i == 1 && args[0].tok == T.bitset)
+ int len = args.length;
+ if (len == 1 && args[0].tok == T.bitset)
return mp.addX(args[0]);
float distance = 0;
Object withinSpec = args[0].value;
@@ -2866,13 +2868,13 @@
RadiusData rd = null;
switch (tok) {
case T.varray:
- if (i == 1) {
+ if (len == 1) {
withinSpec = args[0].asString(); // units ids8
tok = T.nada;
}
break;
case T.branch:
- return (i == 3 && args[1].value instanceof BS
+ return (len == 3 && args[1].value instanceof BS
&& args[2].value instanceof BS && mp.addXBs(vwr.getBranchBitSet(
((BS) args[2].value).nextSetBit(0),
((BS) args[1].value).nextSetBit(0), true)));
@@ -2883,7 +2885,7 @@
// within("smiles", "...", {bitset})
BS bsSelected = null;
boolean isOK = true;
- switch (i) {
+ switch (len) {
case 2:
break;
case 3:
@@ -2901,25 +2903,24 @@
tok == T.search ? JC.SMILES_TYPE_SMARTS : JC.SMILES_TYPE_SMILES,
mp.asBitSet, false));
}
-
-
+
if (withinSpec instanceof String) {
if (tok == T.nada) {
tok = T.spec_seqcode;
- if (i > 2)
+ if (len > 2)
return false;
- i = 2;
+ len = 2;
}
} else if (isDistance) {
if (!isVdw)
distance = SV.fValue(args[0]);
- if (i < 2)
+ if (len < 2)
return false;
switch (tok = args[1].tok) {
case T.on:
case T.off:
isWithinModelSet = args[1].asBoolean();
- i = 0;
+ len = 0;
if (args.length > 2 && SV.sValue(args[2]).equalsIgnoreCase("unitcell"))
tok = T.unitcell;
break;
@@ -2930,8 +2931,8 @@
if (s.equalsIgnoreCase("group")) {
isWithinGroup = true;
tok = T.group;
- } else
- if (s.equalsIgnoreCase("vanderwaals") || s.equalsIgnoreCase("vdw")) {
+ } else if (s.equalsIgnoreCase("vanderwaals")
+ || s.equalsIgnoreCase("vdw")) {
withinSpec = null;
isVdw = true;
tok = T.vanderwaals;
@@ -2945,11 +2946,10 @@
} else {
return false;
}
-
-
+
P3 pt = null;
P4 plane = null;
- switch (i) {
+ switch (len) {
case 1:
// within (sheet)
// within (helix)
@@ -2994,6 +2994,7 @@
case T.plane:
case T.hkl:
case T.coord:
+ case T.point3f:
break;
case T.sequence:
// within ("sequence", "CII", *.ca)
@@ -3008,28 +3009,56 @@
// within (distance, coord, [point or atom center] )
break;
}
- i = args.length - 1;
- if (args[i].value instanceof P4) {
- plane = (P4) args[i].value;
- } else if (args[i].value instanceof P3) {
- pt = (P3) args[i].value;
+ int last = args.length - 1;
+ switch (args[last].tok) {
+ case T.point4f:
+ plane = (P4) args[last].value;
+ break;
+ case T.point3f:
+ pt = (P3) args[last].value;
if (SV.sValue(args[1]).equalsIgnoreCase("hkl"))
plane = e.getHklPlane(pt);
+ break;
+ case T.varray:
+ if (last != 2)
+ return false;
+ pt = SV.ptValue(args[1]);
+ break;
}
- if (i > 0 && plane == null && pt == null && !(args[i].value instanceof BS))
+ if (last > 0 && plane == null && pt == null
+ && !(args[last].value instanceof BS))
return false;
- // if we have anythink, it must have a point or a plane or a bitset from
here on out
+ // if we have anything, it must have a point or a plane or a bitset from
here on out
if (plane != null)
return mp.addXBs(ms.getAtomsNearPlane(distance, plane));
- bs = (args[i].tok == T.bitset ? SV.bsSelectVar(args[i]) : null);
+ bs = (args[last].tok == T.bitset ? SV.bsSelectVar(args[last]) : null);
if (tok == T.unitcell) {
boolean asMap = isWithinModelSet;
return mp
.addXObj(vwr.ms.getUnitCellPointsWithin(distance, bs, pt, asMap));
}
- if (pt != null)
+ if (pt != null) {
+ if (args[last].tok == T.varray) {
+ // within(dist, pt, [pt1, pt2, pt3...])
+ Lst<SV> sv = args[2].getList();
+ Lst<T3> pts = new Lst<T3>();
+ Bspt bspt = new Bspt(3, 0);
+ for (int i = sv.size(); --i >= 0;) {
+ bspt.addTuple(SV.ptValue(sv.get(i)));
+ }
+ CubeIterator iter = bspt.allocateCubeIterator();
+ iter.initialize(pt, distance, false);
+ float d2 = distance * distance;
+ while (iter.hasMoreElements()) {
+ T3 pt2 = iter.nextElement();
+ if (pt2.distanceSquared(pt) <= d2)
+ pts.addLast(pt2);
+ }
+ return mp.addXList(pts);
+ }
return mp.addXBs(vwr.getAtomsNearPt(distance, pt));
+ }
if (tok == T.sequence)
return mp.addXBs(vwr.ms.getSequenceBits(withinStr, bs, new BS()));
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-10-06 14:27:29 UTC
(rev 20811)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-10-08 03:49:03 UTC
(rev 20812)
@@ -64,9 +64,14 @@
Jmol.___JmolVersion="14.3.16_2015.10.06"
+new feature: print within(distance, point, array_of_points)
+ -- point array distance iterator
+ -- returns subarray of points (in differing order, probably) of
array_of_points
+ that are within distance of point.
+
bug fix: MRC surface reader: new version of EMAN2 leaves out alpha,beta,gamma;
does not load properly
-bug fix: for (a in {*}) with no VAR fails
+bug fix: for (a in {*}) with no VAR fails if a has already been defined as an
integer
bug fix: better error reporting
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