Revision: 20267
http://sourceforge.net/p/jmol/code/20267
Author: hansonr
Date: 2015-02-04 12:52:20 +0000 (Wed, 04 Feb 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.2.12_2015.02.04"
bug fix: show mouse fails in JavaScript
-- we cannot test using PT.isAI() in org.jmol.viewer.binding.Binding
-- because of a Java2Script compiler creates standard array [...]
-- from new int[] {....} whereas it should create Clazz.newArray() and fill it
bug fix: label %r should print "1" for non-PDB file atoms
bug fix; lcaoCartoon broken in 14.3.10_2014.11.27/14.2.12_2015.01.22
bug fix: isosurface id surf1 solvent; select within(2.0, $surf1) broken
bug fix: 01.22 version may not correctly clear rasmol hydrogen bonds in
trajectories
bug fix: write "t.pdb" now correctly sequences groups and atoms
bug fix: select thisModel does not select all atoms in visible frame set
bug fix: select %w %x %y %z not implemented
Modified Paths:
--------------
branches/v14_2/Jmol/src/javajs/util/PT.java
branches/v14_2/Jmol/src/org/jmol/api/JmolPropertyManager.java
branches/v14_2/Jmol/src/org/jmol/jvxl/readers/Parameters.java
branches/v14_2/Jmol/src/org/jmol/jvxl/readers/SurfaceGenerator.java
branches/v14_2/Jmol/src/org/jmol/modelset/AtomCollection.java
branches/v14_2/Jmol/src/org/jmol/modelset/LabelToken.java
branches/v14_2/Jmol/src/org/jmol/modelsetbio/BioModel.java
branches/v14_2/Jmol/src/org/jmol/script/ScriptTokenParser.java
branches/v14_2/Jmol/src/org/jmol/scriptext/CmdExt.java
branches/v14_2/Jmol/src/org/jmol/scriptext/MathExt.java
branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties
branches/v14_2/Jmol/src/org/jmol/viewer/PropertyManager.java
branches/v14_2/Jmol/src/org/jmol/viewer/Viewer.java
branches/v14_2/Jmol/src/org/jmol/viewer/binding/Binding.java
Modified: branches/v14_2/Jmol/src/javajs/util/PT.java
===================================================================
--- branches/v14_2/Jmol/src/javajs/util/PT.java 2015-02-04 12:47:46 UTC (rev
20266)
+++ branches/v14_2/Jmol/src/javajs/util/PT.java 2015-02-04 12:52:20 UTC (rev
20267)
@@ -1438,6 +1438,13 @@
return sb.toString().replace('\1', '%');
}
+ /**
+ * left-justify s2 in s1 and append to s
+ *
+ * @param s
+ * @param s1
+ * @param s2
+ */
public static void leftJustify(SB s, String s1, String s2) {
s.append(s2);
int n = s1.length() - s2.length();
@@ -1445,6 +1452,13 @@
s.append(s1.substring(0, n));
}
+ /**
+ * right-justify s2 in s1 and append to s
+ *
+ * @param s
+ * @param s1
+ * @param s2
+ */
public static void rightJustify(SB s, String s1, String s2) {
int n = s1.length() - s2.length();
if (n > 0)
Modified: branches/v14_2/Jmol/src/org/jmol/api/JmolPropertyManager.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/api/JmolPropertyManager.java
2015-02-04 12:47:46 UTC (rev 20266)
+++ branches/v14_2/Jmol/src/org/jmol/api/JmolPropertyManager.java
2015-02-04 12:52:20 UTC (rev 20267)
@@ -35,7 +35,7 @@
String getModelExtract(BS atomBitSet, boolean doTransform, boolean
isModelKit,
String type);
- String getPdbAtomData(BS bs, OC sb);
+ String getPdbAtomData(BS bs, OC sb, boolean asPQR);
String getPdbData(int modelIndex, String type, BS bsA, Object[] parameters,
OC oc, boolean addStructure);
Modified: branches/v14_2/Jmol/src/org/jmol/jvxl/readers/Parameters.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/jvxl/readers/Parameters.java
2015-02-04 12:47:46 UTC (rev 20266)
+++ branches/v14_2/Jmol/src/org/jmol/jvxl/readers/Parameters.java
2015-02-04 12:52:20 UTC (rev 20267)
@@ -467,7 +467,7 @@
cutoff = PT.FLOAT_MIN_SAFE;
isCutoffAbsolute = false;
isSilent = !logMessages;
- if (center.x == Float.MAX_VALUE)
+ if (Float.isNaN(center.x))
center.set(0, 0, 0);
if (resolution == Float.MAX_VALUE)
resolution = 6;
Modified: branches/v14_2/Jmol/src/org/jmol/jvxl/readers/SurfaceGenerator.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/jvxl/readers/SurfaceGenerator.java
2015-02-04 12:47:46 UTC (rev 20266)
+++ branches/v14_2/Jmol/src/org/jmol/jvxl/readers/SurfaceGenerator.java
2015-02-04 12:52:20 UTC (rev 20267)
@@ -790,7 +790,7 @@
if ("lcaoCartoonCenter" == propertyName) {
if (++params.state != Parameters.STATE_DATA_READ)
return true;
- if (params.center.x == Float.MAX_VALUE)
+ if (Float.isNaN(params.center.x))
params.center.setT((V3) value);
return false;
}
Modified: branches/v14_2/Jmol/src/org/jmol/modelset/AtomCollection.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/modelset/AtomCollection.java
2015-02-04 12:47:46 UTC (rev 20266)
+++ branches/v14_2/Jmol/src/org/jmol/modelset/AtomCollection.java
2015-02-04 12:52:20 UTC (rev 20267)
@@ -2539,7 +2539,7 @@
return bsResult;
}
- public BS getAtomsNearPts(float distance, P3[] points,
+ public BS getAtomsNearPts(float distance, T3[] points,
BS bsInclude) {
BS bsResult = new BS();
if (points.length == 0 || bsInclude != null && bsInclude.cardinality() ==
0)
Modified: branches/v14_2/Jmol/src/org/jmol/modelset/LabelToken.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/modelset/LabelToken.java 2015-02-04
12:47:46 UTC (rev 20266)
+++ branches/v14_2/Jmol/src/org/jmol/modelset/LabelToken.java 2015-02-04
12:52:20 UTC (rev 20267)
@@ -568,6 +568,8 @@
break;
case 'r':
strT = atom.getSeqcodeString();
+ if (strT == null)
+ strT = "1";
break;
case T.strucid:
strT = atom.getStructureId();
Modified: branches/v14_2/Jmol/src/org/jmol/modelsetbio/BioModel.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/modelsetbio/BioModel.java 2015-02-04
12:47:46 UTC (rev 20266)
+++ branches/v14_2/Jmol/src/org/jmol/modelsetbio/BioModel.java 2015-02-04
12:52:20 UTC (rev 20267)
@@ -465,19 +465,37 @@
public void calcRasmolHydrogenBonds(ModelSet ms, BS bsA, BS bsB, Lst<Bond>
vHBonds,
boolean nucleicOnly, int nMax,
boolean dsspIgnoreHydrogens, BS
bsHBonds) {
- boolean isSame = (bsB == null || bsA.equals(bsB));
Model[] am = ms.am;
+ if (vHBonds == null) {
+ // autobond -- clear all hydrogen bonds
+ BS bsAtoms = bsA;
+ if (bsB != null && !bsA.equals(bsB))
+ (bsAtoms = BSUtil.copy(bsA)).or(bsB);
+ BS bsDelete = new BS();
+ BS bsOK = new BS();
+ Model[] models = ms.am;
+ Bond[] bonds = ms.bo;
+ for (int i = ms.bondCount; --i >= 0;) {
+ Bond bond = bonds[i];
+ if ((bond.order & Edge.BOND_H_CALC_MASK) == 0)
+ continue;
+ // trajectory atom .mi will be pointing to their trajectory;
+ // here we check to see if their base model is this model
+ if (bsAtoms.get(bond.atom1.i))
+ bsDelete.set(i);
+ else
+ bsOK.set(models[bond.atom1.mi].trajectoryBaseIndex);
+ }
+ for (int i = ms.mc; --i >= 0;)
+ if (models[i].isBioModel)
+ ((BioModel) models[i]).hasRasmolHBonds = bsOK.get(i);
+ if (bsDelete.nextSetBit(0) >= 0)
+ ms.deleteBonds(bsDelete, false);
+ }
for (int i = ms.mc; --i >= 0;)
- if (am[i].isBioModel && am[i].trajectoryBaseIndex == i) {
- BioModel m = (BioModel) am[i];
- if (vHBonds == null) {
- clearRasmolHydrogenBonds(ms, m, bsA);
- if (!isSame)
- clearRasmolHydrogenBonds(ms, m, bsB);
- }
- m.getRasmolHydrogenBonds(bsA, bsB, vHBonds, nucleicOnly, nMax,
+ if (am[i].isBioModel && !ms.isTrajectorySubFrame(i))
+ ((BioModel) am[i]).getRasmolHydrogenBonds(bsA, bsB, vHBonds,
nucleicOnly, nMax,
dsspIgnoreHydrogens, bsHBonds);
- }
}
private void getRasmolHydrogenBonds(BS bsA, BS bsB,
Modified: branches/v14_2/Jmol/src/org/jmol/script/ScriptTokenParser.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/script/ScriptTokenParser.java
2015-02-04 12:47:46 UTC (rev 20266)
+++ branches/v14_2/Jmol/src/org/jmol/script/ScriptTokenParser.java
2015-02-04 12:52:20 UTC (rev 20267)
@@ -1287,6 +1287,10 @@
case T.string:
case T.integer:
case T.identifier:
+ case T.x:
+ case T.y:
+ case T.z:
+ case T.w:
break;
default:
return error(ERROR_invalidModelSpecification);
Modified: branches/v14_2/Jmol/src/org/jmol/scriptext/CmdExt.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/scriptext/CmdExt.java 2015-02-04
12:47:46 UTC (rev 20266)
+++ branches/v14_2/Jmol/src/org/jmol/scriptext/CmdExt.java 2015-02-04
12:52:20 UTC (rev 20267)
@@ -3301,12 +3301,6 @@
data = vwr.getPdbAtomData(null, null);
} else {
doDefer = true;
- /*
- * OutputStream os = vwr.getOutputStream(fileName, fullPath); msg =
- * vwr.getPdbData(null, new BufferedOutputStream(os)); if (msg !=
- * null) msg = "OK " + msg + " " + fullPath[0]; try { os.close(); }
- * catch (IOException e) { // TODO }
- */
}
} else if (data == "FILE") {
if (isShow)
Modified: branches/v14_2/Jmol/src/org/jmol/scriptext/MathExt.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/scriptext/MathExt.java 2015-02-04
12:47:46 UTC (rev 20266)
+++ branches/v14_2/Jmol/src/org/jmol/scriptext/MathExt.java 2015-02-04
12:52:20 UTC (rev 20267)
@@ -2558,7 +2558,7 @@
private BS getAtomsNearSurface(float distance, String surfaceId) {
Object[] data = new Object[] { surfaceId, null, null };
if (e.getShapePropertyData(JC.SHAPE_ISOSURFACE, "getVertices", data))
- return vwr.ms.getAtomsNearPts(distance, (P3[]) data[1], (BS) data[2]);
+ return vwr.ms.getAtomsNearPts(distance, (T3[]) data[1], (BS) data[2]);
data[1] = Integer.valueOf(0);
data[2] = Integer.valueOf(-1);
if (e.getShapePropertyData(JC.SHAPE_DRAW, "getCenter", data))
Modified: branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties 2015-02-04
12:47:46 UTC (rev 20266)
+++ branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties 2015-02-04
12:52:20 UTC (rev 20267)
@@ -5,6 +5,20 @@
# THIS IS THE RELEASE BRANCH
# BUG FIXES ONLY, PLEASE
+Jmol.___JmolVersion="14.2.12_2015.02.04"
+
+bug fix: show mouse fails in JavaScript
+ -- we cannot test using PT.isAI() in org.jmol.viewer.binding.Binding
+ -- because of a Java2Script compiler creates standard array [...]
+ -- from new int[] {....} whereas it should create Clazz.newArray() and fill
it
+bug fix: label %r should print "1" for non-PDB file atoms
+bug fix; lcaoCartoon broken in 14.3.10_2014.11.27/14.2.12_2015.01.22
+bug fix: isosurface id surf1 solvent; select within(2.0, $surf1) broken
+bug fix: 01.22 version may not correctly clear rasmol hydrogen bonds in
trajectories
+bug fix: write "t.pdb" now correctly sequences groups and atoms
+bug fix: select thisModel does not select all atoms in visible frame set
+bug fix: select %w %x %y %z not implemented
+
Jmol.___JmolVersion="14.2.12_2015.01.27"
bug fix: CGO LINE_LOOP not closing
Modified: branches/v14_2/Jmol/src/org/jmol/viewer/PropertyManager.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/viewer/PropertyManager.java
2015-02-04 12:47:46 UTC (rev 20266)
+++ branches/v14_2/Jmol/src/org/jmol/viewer/PropertyManager.java
2015-02-04 12:52:20 UTC (rev 20267)
@@ -41,6 +41,7 @@
import java.util.Arrays;
import java.util.Calendar;
+import java.util.Comparator;
import java.util.Date;
import java.util.Enumeration;
import java.util.Hashtable;
@@ -82,7 +83,7 @@
@J2SIgnoreImport({ javajs.util.XmlUtil.class })
-public class PropertyManager implements JmolPropertyManager {
+public class PropertyManager implements JmolPropertyManager,
Comparator<String> {
public PropertyManager() {
// required for reflection
@@ -1643,7 +1644,7 @@
* @return PDB file data string
*/
@Override
- public String getPdbAtomData(BS bs, OC out) {
+ public String getPdbAtomData(BS bs, OC out, boolean asPQR) {
if (vwr.ms.ac == 0 || bs.nextSetBit(0) < 0)
return "";
if (out == null)
@@ -1653,6 +1654,7 @@
int iModel = atoms[bs.nextSetBit(0)].mi;
int iModelLast = -1;
boolean isPQR = "PQR".equals(out.getType());
+ boolean isBiomodel = false;
String occTemp = "%6.2Q%6.2b ";
if (isPQR) {
occTemp = "%8.4P%7.4V ";
@@ -1671,21 +1673,25 @@
int lastAtomIndex = bs.length() - 1;
boolean showModels = (iModel != atoms[lastAtomIndex].mi);
SB sbCONECT = (showModels ? null : new SB());
+ SB sbATOMS = new SB();
boolean isMultipleBondPDB = models[iModel].isPdbWithMultipleBonds;
LabelToken[] tokens;
P3 ptTemp = new P3();
+ boolean doConnect = false;
for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
Atom a = atoms[i];
+ isBiomodel = models[a.mi].isBioModel;
+ doConnect = (isBiomodel && !showModels);
if (showModels && a.mi != iModelLast) {
if (iModelLast != -1)
out.append("ENDMDL\n");
iModelLast = a.mi;
out.append("MODEL " + (iModelLast + 1) + "\n");
+ sbATOMS = new SB();
}
String sa = a.getAtomName();
boolean leftJustify = (a.getElementSymbol().length() == 2
|| sa.length() >= 4 || PT.isDigit(sa.charAt(0)));
- boolean isBiomodel = models[a.mi].isBioModel;
boolean isHetero = a.isHetero();
if (!isBiomodel)
tokens = (leftJustify ? LabelToken.compile(vwr,
@@ -1709,38 +1715,55 @@
"ATOM %5.-5i %-3.3a%1A%3.-3n %1c%4.-4R%1E %8.3x%8.3y%8.3z"
+ occTemp, '\0', null));
String XX = a.getElementSymbolIso(false).toUpperCase();
- out.append(LabelToken.formatLabelAtomArray(vwr, a, tokens, '\0', null,
ptTemp))
+ if (isBiomodel && doConnect)
+ PT.leftJustify(sbATOMS, " ", "" + a.getPolymerIndexInModel());
+ sbATOMS
+ .append(
+ LabelToken.formatLabelAtomArray(vwr, a, tokens, '\0', null,
+ ptTemp))
.append(XX.length() == 1 ? " " + XX : XX.substring(0, 2))
.append(" \n");
- if (!showModels && (!isBiomodel || isHetero || isMultipleBondPDB)) {
- Bond[] bonds = a.bonds;
- if (bonds != null)
- for (int j = 0; j < bonds.length; j++) {
- int iThis = a.getAtomNumber();
- Atom a2 = bonds[j].getOtherAtom(a);
- if (!bs.get(a2.i))
- continue;
- int n = bonds[j].getCovalentOrder();
- if (n == 1 && isMultipleBondPDB && !isHetero)
- continue;
- int iOther = a2.getAtomNumber();
- switch (n) {
- case 2:
- case 3:
- if (iOther < iThis)
- continue; // only one entry in this case -- pseudo-PDB style
- //$FALL-THROUGH$
- case 1:
- sbCONECT.append("CONECT").append(
- PT.formatStringI("%5i", "i", iThis));
- for (int k = 0; k < n; k++)
- sbCONECT.append(PT.formatStringI("%5i", "i", iOther));
- sbCONECT.appendC('\n');
- break;
+ }
+ Map<Integer, Integer> map = (doConnect ? new Hashtable<Integer, Integer>()
: null);
+ String sAtoms = fixPDBFormat(sbATOMS.toString(), map);
+ if (doConnect) {
+ for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
+ Atom a = atoms[i];
+ boolean isHetero = a.isHetero();
+ boolean isCysS = !isHetero && (a.getElementNumber() == 16);
+ if (isHetero || isMultipleBondPDB || isCysS) {
+ Bond[] bonds = a.bonds;
+ if (bonds != null)
+ for (int j = 0; j < bonds.length; j++) {
+ int iThis = a.getAtomNumber();
+ Atom a2 = bonds[j].getOtherAtom(a);
+ if (!bs.get(a2.i))
+ continue;
+ int n = bonds[j].getCovalentOrder();
+ if (n == 1 && (isMultipleBondPDB && !isHetero && !isCysS
+ || isCysS && a2.getElementNumber() != 16))
+ continue;
+ int iOther = a2.getAtomNumber();
+ switch (n) {
+ case 2:
+ case 3:
+ if (iOther < iThis)
+ continue; // only one entry in this case -- pseudo-PDB style
+ //$FALL-THROUGH$
+ case 1:
+ sbCONECT.append("CONECT").append(
+ PT.formatStringI("%5i", "i",
map.get(Integer.valueOf(iThis)).intValue()));
+ String s = PT.formatStringI("%5i", "i",
map.get(Integer.valueOf(iOther)).intValue());
+ for (int k = 0; k < n; k++)
+ sbCONECT.append(s);
+ sbCONECT.appendC('\n');
+ break;
+ }
}
- }
+ }
}
}
+ out.append(sAtoms);
if (showModels)
out.append("ENDMDL\n");
else
@@ -1748,13 +1771,40 @@
return out.toString();
}
- /* **********************
- *
- * Jmol Data Frame methods
- *
- *****************************/
+ /**
+ * must re-order by resno and then renumber atoms
+ * @param s
+ * @param map
+ * @return fixed string
+ */
+ private String fixPDBFormat(String s, Map<Integer, Integer> map) {
+ String[] lines = PT.split(s, "\n");
+ Arrays.sort(lines, this);
+ SB sb = new SB();
+ for (int i = 0; i < lines.length; i++) {
+ s = lines[i];
+ int p = PT.parseInt(lines[i].substring(6, 12));
+ if (map != null)
+ map.put(Integer.valueOf(p), Integer.valueOf(i + 1));
+ String si = " " + (i + 1);
+ sb.append(s.substring(0, 6))
+ .append(si.substring(si.length() - 5))
+ .append(s.substring(11)).append("\n");
+ }
+ return sb.toString();
+ }
@Override
+ public int compare(String s1, String s2) {
+ int atA = PT.parseInt(s1.substring(10, 16));
+ int atB = PT.parseInt(s2.substring(10, 16));
+ int resA = PT.parseInt(s1.substring(26, 30));
+ int resB = PT.parseInt(s2.substring(26, 30));
+ return (resA < resB ? -1 : resA > resB ? 1 : atA < atB ? -1
+ : atA > atB ? 1 : 0);
+ }
+
+ @Override
@SuppressWarnings("static-access")
public String getPdbData(int modelIndex, String type, BS bsSelected,
Object[] parameters, OC out, boolean addStructure) {
Modified: branches/v14_2/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/viewer/Viewer.java 2015-02-04 12:47:46 UTC
(rev 20266)
+++ branches/v14_2/Jmol/src/org/jmol/viewer/Viewer.java 2015-02-04 12:52:20 UTC
(rev 20267)
@@ -7192,7 +7192,7 @@
}
public String getPdbAtomData(BS bs, OC sb) {
- return getPropertyManager().getPdbAtomData(bs == null ? bsA() : bs, sb);
+ return getPropertyManager().getPdbAtomData(bs == null ? bsA() : bs, sb,
false);
}
public boolean isJmolDataFrame() {
Modified: branches/v14_2/Jmol/src/org/jmol/viewer/binding/Binding.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/viewer/binding/Binding.java
2015-02-04 12:47:46 UTC (rev 20266)
+++ branches/v14_2/Jmol/src/org/jmol/viewer/binding/Binding.java
2015-02-04 12:52:20 UTC (rev 20267)
@@ -307,7 +307,16 @@
Lst<String>[] names = new Lst[actionInfo.length];
Lst<String[]> user = new Lst<String[]>();
for (Object obj : bindings.values()) {
- if (PT.isAI(obj)) {
+ if (PT.isAS(obj)) {
+ String action = ((String[]) obj)[0];
+ String script = ((String[]) obj)[1];
+ if (qlow == null || qlow.indexOf("user") >= 0 || action.indexOf(qlow)
>= 0 || script.indexOf(qlow) >= 0)
+ user.addLast((String[]) obj);
+ } else {
+
+ // we cannot test using PT.isAI() here because of a Java2Script
compiler error
+ // in relation to new int[] {.....} BH 2015.02.03
+
int[] info = (int[]) obj;
int i = info[1];
if (names[i] == null)
@@ -316,11 +325,6 @@
if (qlow == null
|| (actionNames[i] + ";" + actionInfo[i] + ";" +
name).toLowerCase().indexOf(qlow) >= 0)
names[i].addLast(name);
- } else if (PT.isAS(obj)) {
- String action = ((String[]) obj)[0];
- String script = ((String[]) obj)[1];
- if (qlow == null || qlow.indexOf("user") >= 0 || action.indexOf(qlow)
>= 0 || script.indexOf(qlow) >= 0)
- user.addLast((String[]) obj);
}
}
for (int i = 0; i < actionInfo.length; i++) {
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