Revision: 20850
http://sourceforge.net/p/jmol/code/20850
Author: hansonr
Date: 2015-10-30 11:52:33 +0000 (Fri, 30 Oct 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.5.0_2015.10.30"
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: 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/modelset/BondCollection.java
trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java
trunk/Jmol/src/org/jmol/renderspecial/PolyhedraRenderer.java
trunk/Jmol/src/org/jmol/script/SV.java
trunk/Jmol/src/org/jmol/script/ScriptCompiler.java
trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
trunk/Jmol/src/org/jmol/scriptext/MathExt.java
trunk/Jmol/src/org/jmol/shapespecial/Polyhedra.java
trunk/Jmol/src/org/jmol/shapespecial/Polyhedron.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/Viewer.java
Modified: trunk/Jmol/src/org/jmol/modelset/BondCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/BondCollection.java 2015-10-28
03:41:32 UTC (rev 20849)
+++ trunk/Jmol/src/org/jmol/modelset/BondCollection.java 2015-10-30
11:52:33 UTC (rev 20850)
@@ -493,17 +493,17 @@
}
}
// now test non-O atoms
- for (int i = bsTest.nextSetBit(0); i >= 0; i = bsTest.nextSetBit(i + 1)) {
- bond = bo[i];
- if (!assignAromaticDouble(bond))
+ for (int i = bsTest.nextSetBit(0); i >= 0; i = bsTest.nextSetBit(i + 1))
+ if (!assignAromaticDouble(bond = bo[i]))
assignAromaticSingle(bond);
- }
// all done: do the actual assignments and clear arrays.
+ BS bsModels = new BS();
for (int i = i0; i >= 0; i = (isAll ? i - 1 : bsBonds.nextSetBit(i + 1))) {
bond = bo[i];
if (bsAromaticDouble.get(i)) {
if (!bond.is(Edge.BOND_AROMATIC_DOUBLE)) {
bsAromatic.set(i);
+ bsModels.set(bond.atom1.mi);
bond.setOrder(Edge.BOND_AROMATIC_DOUBLE);
}
} else if (bsAromaticSingle.get(i) || bond.isAromatic()) {
@@ -513,7 +513,11 @@
}
}
}
-
+ Model[] models = ((ModelSet) this).am;
+ for (int i = bsModels.nextSetBit(0); i >= 0; i = bsModels.nextSetBit(i +
1))
+ if (models[i].isBioModel)
+ models[i].isPdbWithMultipleBonds = true;
+
assignAromaticNandO(bsBonds);
bsAromaticSingle = null;
Modified: trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java 2015-10-28 03:41:32 UTC
(rev 20849)
+++ trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java 2015-10-30 11:52:33 UTC
(rev 20850)
@@ -121,10 +121,10 @@
Atom[] at = ms.at;
Model[] am = ms.am;
for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
- if (iLast != i - 1)
- monomerIndexCurrent = -1;
+ if (at[i].group.isAdded(i))
+ continue;
monomerIndexCurrent = at[i].group.setProteinStructureType(type,
- monomerIndexCurrent);
+ iLast == i - 1 ? -1 : monomerIndexCurrent);
int modelIndex = at[i].mi;
ms.proteinStructureTainted = am[modelIndex].structureTainted = true;
iLast = i = at[i].group.lastAtomIndex;
@@ -136,10 +136,14 @@
i = am[modelIndex].firstAtomIndex + am[modelIndex].act;
continue;
}
- iLast = at[i].group.getStrucNo();
- if (iLast < 1000 && iLast > lastStrucNo[modelIndex])
- lastStrucNo[modelIndex] = iLast;
- i = at[i].group.lastAtomIndex + 1;
+ Group g = at[i].group;
+ if (!g.isAdded(i)) {
+ iLast = g.getStrucNo();
+ if (iLast < 1000 && iLast > lastStrucNo[modelIndex])
+ lastStrucNo[modelIndex] = iLast;
+ i = g.lastAtomIndex;
+ }
+ i++;
}
for (int i = 0; i < ms.ac;) {
int modelIndex = at[i].mi;
@@ -147,9 +151,13 @@
i = am[modelIndex].firstAtomIndex + am[modelIndex].act;
continue;
}
- if (at[i].group.getStrucNo() > 1000)
- at[i].group.setStrucNo(++lastStrucNo[modelIndex]);
- i = at[i].group.lastAtomIndex + 1;
+ Group g = at[i].group;
+ if (!g.isAdded(i)) {
+ i = g.lastAtomIndex;
+ if (g.getStrucNo() > 1000)
+ g.setStrucNo(++lastStrucNo[modelIndex]);
+ }
+ i++;
}
}
Modified: trunk/Jmol/src/org/jmol/renderspecial/PolyhedraRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/renderspecial/PolyhedraRenderer.java
2015-10-28 03:41:32 UTC (rev 20849)
+++ trunk/Jmol/src/org/jmol/renderspecial/PolyhedraRenderer.java
2015-10-30 11:52:33 UTC (rev 20850)
@@ -72,8 +72,8 @@
if (p.id == null) {
iAtom = p.centralAtom.i;
colix = (colixes == null || iAtom >= colixes.length ? C.INHERIT_ALL
- : colixes[iAtom]);
- colix = C.getColixInherited(colix, p.centralAtom.colixAtom);
+ : colixes[iAtom]);
+ colix = C.getColixInherited(colix, p.centralAtom.colixAtom);
} else {
colix = p.colix;
}
@@ -121,12 +121,15 @@
for (int i = planes.length; --i >= 0;) {
int[] pl = planes[i];
try {
- g3d.fillTriangleTwoSided(normixes[i], sc[pl[0]], sc[pl[1]],
sc[pl[2]]);
+ if (!showNumbers
+ || g3d.setC((short) (Math.round(Math.random() * 10) + 5)))
+ g3d.fillTriangleTwoSided(normixes[i], sc[pl[0]], sc[pl[1]],
+ sc[pl[2]]);
} catch (Exception e) {
System.out.println("PolyhedraRendererError");
}
-// if (pl[3] >= 0)
- // g3d.fillTriangleTwoSided(normixes[i], sc[pl[2]], sc[pl[3]],
sc[pl[0]]);
+ // if (pl[3] >= 0)
+ // g3d.fillTriangleTwoSided(normixes[i], sc[pl[2]], sc[pl[3]],
sc[pl[0]]);
}
// edges are not drawn translucently ever
if (bsSelected != null && bsSelected.get(iAtom))
@@ -136,13 +139,13 @@
if (g3d.setC(C.getColixTranslucent3(colix, false, 0)))
for (int i = planes.length; --i >= 0;) {
int[] pl = planes[i];
- // if (pl[3] < 0) {
- drawEdges(normixes[i], sc[pl[0]], sc[pl[1]], sc[pl[2]], -pl[3]);
-// break;
-// } else {
-// drawFace(normixes[i], sc[pl[0]], sc[pl[1]], sc[pl[2]], 3);
-// drawFace(normixes[i], sc[pl[0]], sc[pl[2]], sc[pl[3]], 6);
-// }
+ // if (pl[3] < 0) {
+ drawEdges(normixes[i], sc[pl[0]], sc[pl[1]], sc[pl[2]], -pl[3]);
+ // break;
+ // } else {
+ // drawFace(normixes[i], sc[pl[0]], sc[pl[1]], sc[pl[2]], 3);
+ // drawFace(normixes[i], sc[pl[0]], sc[pl[2]], sc[pl[3]], 6);
+ // }
}
return needTranslucent;
Modified: trunk/Jmol/src/org/jmol/script/SV.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/SV.java 2015-10-28 03:41:32 UTC (rev
20849)
+++ trunk/Jmol/src/org/jmol/script/SV.java 2015-10-30 11:52:33 UTC (rev
20850)
@@ -1224,13 +1224,14 @@
.indexOf(";" + format.toLowerCase() + ";"));
}
- /**
- * Accepts arguments from the format() function First argument is a
- * format string.
+ /**
+ * Accepts arguments from the format() function First argument is a format
+ * string.
*
* @param args
- * @param pt 0: to JSON, 5: to base64, 12: to bytearray, 22: to array
- * @param array2D
+ * @param pt
+ * 0: to JSON, 5: to base64, 12: to bytearray, 22: to array
+ * @param array2D
* @return formatted string
*/
public static Object format(SV[] args, int pt, boolean array2D) {
@@ -1271,7 +1272,7 @@
break;
default:
String s = args[1].asString();
- if (s.startsWith(";base64,")){
+ if (s.startsWith(";base64,")) {
if (pt == 5)
return s;
bytes = Base64.decodeBase64(s);
@@ -1279,19 +1280,20 @@
bytes = s.getBytes();
}
}
- return (pt == 22 ? getVariable(bytes) : pt == 12 ? new BArray(bytes) :
";base64,"
- + javajs.util.Base64.getBase64(bytes).toString());
+ return (pt == 22 ? getVariable(bytes) : pt == 12 ? new BArray(bytes)
+ : ";base64," + javajs.util.Base64.getBase64(bytes).toString());
}
}
// use values to replace codes in format string
+ String[] format = PT.split(PT.rep(sValue(args[0]), "%%", "\1"), "%");
+ if (format.length == 0)
+ return "";
SB sb = new SB();
- String[] format = PT.split(PT.rep(sValue(args[0]), "%%", "\1"), "%");
sb.append(format[0]);
for (int i = 1; i < format.length; i++) {
Object ret = sprintf(PT.formatCheck("%" + format[i]),
- (args[1].tok == hash ? args[1]
- : args[1].tok == varray ? args[1].getList().get(i - 1)
- : i < args.length ? args[i] : null));
+ (args[1].tok == hash ? args[1] : args[1].tok == varray ? args[1]
+ .getList().get(i - 1) : i < args.length ? args[i] : null));
if (AU.isAS(ret)) {
String[] list = (String[]) ret;
for (int j = 0; j < list.length; j++)
Modified: trunk/Jmol/src/org/jmol/script/ScriptCompiler.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptCompiler.java 2015-10-28 03:41:32 UTC
(rev 20849)
+++ trunk/Jmol/src/org/jmol/script/ScriptCompiler.java 2015-10-30 11:52:33 UTC
(rev 20850)
@@ -143,7 +143,7 @@
private String ident, identLC;
private Lst<T> vPush = new Lst<T>();
private int pushCount;
- private ScriptFlowContext lastFlowContext;
+ private ScriptFlowContext forceFlowContext;
synchronized ScriptContext compile(String filename, String script,
boolean isPredefining, boolean isSilent,
@@ -333,7 +333,7 @@
isEndOfCommand = false;
needRightParen = false;
lastFlowCommand = null;
- lastFlowContext = null;
+ forceFlowContext = null;
theTok = T.nada;
short iLine = 1;
@@ -731,7 +731,7 @@
if (lastFlowCommand.tok != T.process && (tokAt(0) == T.leftbrace))
ltoken.remove(0);
lastFlowCommand = null;
- lastFlowContext = flowContext;
+ forceFlowContext = flowContext;
// lastFlowImplicitEnd = flowContext.nextFlowImplicitEnd;
}
}
@@ -823,7 +823,7 @@
} else if (n > 0 && !haveENDIF || isOneLine) {
forceFlowEnd(flowContext.token);
if (!isOneLine) {
- lastFlowContext.forceEndIf = true;
+ forceFlowContext.forceEndIf = true;
}
}
isEndOfCommand = true;
@@ -1542,12 +1542,12 @@
// specifically for else { but not elseIf ( ) {
isEndOfCommand = true;
ScriptFlowContext f = (flowContext != null && flowContext.addLine == 0
- || lastFlowContext == null ? flowContext : lastFlowContext);
+ || forceFlowContext == null ? flowContext : forceFlowContext);
if (f != null) {
f.addLine = 0;
f.forceEndIf = false;
lastToken = T.tokenLeftBrace;
- lastFlowContext = f;
+ forceFlowContext = f;
}
return CONTINUE;
}
@@ -1684,10 +1684,10 @@
// unexpectedly allows if (x) { print x else print y}
fixFlowAddLine(flowContext);
if (lltoken.get(iCommand - 1)[0].tok == T.end
- && lastFlowContext != null && lastFlowContext.forceEndIf
- && lastFlowContext.addLine > 0
- && isFlowIfContextOK(lastFlowContext)) {
- flowContext = lastFlowContext;
+ && forceFlowContext != null && forceFlowContext.forceEndIf
+ && forceFlowContext.addLine > 0
+ && isFlowIfContextOK(forceFlowContext)) {
+ flowContext = forceFlowContext;
flowContext.forceEndIf = true;
lltoken.remove(--iCommand);
} else if (flowContext != null && flowContext.addLine > 0) {
@@ -1745,6 +1745,8 @@
}
if (theTok == T.rightbrace) {
// if }, just push onto vBrace, but NOT onto ltoken
+ // no longer necessary to force end
+ forceFlowContext = null;
addBrace(tokenCommand);
tokCommand = T.nada;
return CONTINUE;
@@ -2152,7 +2154,7 @@
}
private int forceFlowEnd(T token) {
T t0 = tokenCommand;
- lastFlowContext = flowContext;
+ forceFlowContext = flowContext;
token = flowStart(token);
if (!checkFlowEnd(token.tok, (String) token.value, ichBrace, false))
return ERROR;
Modified: trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2015-10-28 03:41:32 UTC
(rev 20849)
+++ trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2015-10-30 11:52:33 UTC
(rev 20850)
@@ -3165,7 +3165,7 @@
return "";
}
- private boolean polyhedra() throws ScriptException {
+ private void polyhedra() throws ScriptException {
ScriptEval eval = e;
// polyhedra
// polyhedra on/off/delete
@@ -3198,6 +3198,7 @@
setShapeProperty(JC.SHAPE_POLYHEDRA, "init", Boolean.TRUE);
float translucentLevel = Float.MAX_VALUE;
int[] colorArgb = new int[] { Integer.MIN_VALUE };
+ P3 offset = null;
String id = null;
for (int i = 1; i < slen; ++i) {
String propertyName = null;
@@ -3259,7 +3260,11 @@
needsGenerating = true;
break;
case T.offset:
- eval.theTok = T.facecenteroffset;
+ if (!isFloatParameter(i + 1)) {
+ offset = getPoint3f(++i, true);
+ i = eval.iToken;
+ continue;
+ }
//$FALL-THROUGH$
case T.facecenteroffset:
setShapeProperty(JC.SHAPE_POLYHEDRA, "collapsed", Boolean.TRUE);
@@ -3361,14 +3366,13 @@
case T.id:
case T.times:
case T.identifier:
+ case T.string:
if (!eval.isColorParam(i)) {
if (i != 1)
invPO();
- setShapeProperty(
- JC.SHAPE_POLYHEDRA,
- "thisID",
- id = (eval.theTok == T.id ? stringParameter(++i) : eval
- .optParameterAsString(i)));
+ id = (eval.theTok == T.id ? stringParameter(++i) : eval
+ .optParameterAsString(i));
+ setShapeProperty(JC.SHAPE_POLYHEDRA, "thisID", id);
setShapeProperty(JC.SHAPE_POLYHEDRA, "model",
Integer.valueOf(vwr.am.cmi));
if (!eval.isCenterParameter(i + 1))
@@ -3391,15 +3395,17 @@
if (propertyName != null)
setShapeProperty(JC.SHAPE_POLYHEDRA, propertyName, propertyValue);
if (onOffDelete)
- return false;
+ return;
}
if (needsGenerating) {
if (!typeSeen && haveBonds)
setShapeProperty(JC.SHAPE_POLYHEDRA, "bonds", null);
setShapeProperty(JC.SHAPE_POLYHEDRA, "generate", null);
- } else if (!edgeParameterSeen) {// && lighting == T.nada)
+ } else if (!edgeParameterSeen && offset == null) {// && lighting == T.nada)
error(ScriptError.ERROR_insufficientArguments);
}
+ if (offset != null)
+ setShapeProperty(JC.SHAPE_POLYHEDRA, "offset", offset);
if (colorArgb[0] != Integer.MIN_VALUE)
setShapeProperty(JC.SHAPE_POLYHEDRA, "colorThis",
Integer.valueOf(colorArgb[0]));
@@ -3409,7 +3415,6 @@
// if (lighting != T.nada)
// setShapeProperty(JC.SHAPE_POLYHEDRA, "token",
Integer.valueOf(lighting));
setShapeProperty(JC.SHAPE_POLYHEDRA, "init", Boolean.FALSE);
- return true;
}
/**
Modified: trunk/Jmol/src/org/jmol/scriptext/MathExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/MathExt.java 2015-10-28 03:41:32 UTC
(rev 20849)
+++ trunk/Jmol/src/org/jmol/scriptext/MathExt.java 2015-10-30 11:52:33 UTC
(rev 20850)
@@ -3197,8 +3197,11 @@
Point3fi p;
Point3fi[] pt3 = new Point3fi[sv.size()];
for (int i = pt3.length; --i >= 0;) {
+ P3 p3 = SV.ptValue(sv.get(i));
+ if (p3 == null)
+ return false;
p = new Point3fi();
- p.setT(SV.ptValue(sv.get(i)));
+ p.setT(p3);
p.i = i;
pt3[i] = p;
bspt.addTuple(p);
Modified: trunk/Jmol/src/org/jmol/shapespecial/Polyhedra.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapespecial/Polyhedra.java 2015-10-28 03:41:32 UTC
(rev 20849)
+++ trunk/Jmol/src/org/jmol/shapespecial/Polyhedra.java 2015-10-30 11:52:33 UTC
(rev 20850)
@@ -156,6 +156,12 @@
return;
}
+ if ("offset" == propertyName) {
+ if (thisID != null)
+ offsetPolyhedra((P3) value);
+ return;
+ }
+
if ("model" == propertyName) {
modelIndex = ((Integer) value).intValue();
return;
@@ -285,7 +291,7 @@
for (int i = bs1.nextSetBit(0); i >= 0; i = bs1.nextSetBit(i + 1)) {
p = polyhedrons[i];
if (p.id == null) {
- p.colixEdge = colixEdge;
+ p.colixEdge = colixEdge;
} else {
p.colixEdge = colixEdge;
p.colix = colix;
@@ -354,6 +360,12 @@
setPropAS(propertyName, value, bs);
}
+ private void offsetPolyhedra(P3 value) {
+ BS bs = findPolyBS(null);
+ for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1))
+ polyhedrons[i].setOffset(P3.newP(value));
+ }
+
@Override
public Object getProperty(String propertyName, int index) {
if (propertyName == "symmetry") {
Modified: trunk/Jmol/src/org/jmol/shapespecial/Polyhedron.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapespecial/Polyhedron.java 2015-10-28
03:41:32 UTC (rev 20849)
+++ trunk/Jmol/src/org/jmol/shapespecial/Polyhedron.java 2015-10-30
11:52:33 UTC (rev 20850)
@@ -64,6 +64,8 @@
public short colix = C.GOLD;
public int modelIndex = Integer.MIN_VALUE;
+
+ private P3 offset;
Polyhedron() {
@@ -105,6 +107,8 @@
modelIndex = info.get("modelIndex").intValue;
colix = C.getColixS(info.get("color").asString());
colixEdge = C.getColixS(info.get("colorEdge").asString());
+ if (info.containsKey("offset"))
+ offset = P3.newP(SV.ptValue(info.get("offset")));
}
Lst<SV> lst = info.get("vertices").getList();
SV vc = info.get("vertexCount");
@@ -214,6 +218,8 @@
info.put("modelIndex", Integer.valueOf(mi));
info.put("color", C.getHexCode(colix));
info.put("colorEdge", C.getHexCode(colixEdge == 0 ? colix : colixEdge));
+ if (offset != null)
+ info.put("offset", offset);
}
if (faces != null)
info.put("faces", faces);
@@ -302,10 +308,7 @@
if (bsFlat.cardinality() < triangles.length)
for (int i = triangles.length; --i >= 0;) {
int[] face = triangles[i];
- for (int j = face.length - 2; --j >= 0;)
- if (face[j + 2] >= 0)
- v += triangleVolume(face[j], face[j + 1], face[j + 2], vAB, vAC,
- vTemp);
+ v += triangleVolume(face[0], face[1], face[2], vAB, vAC, vTemp);
}
return Float.valueOf(v / 6);
}
@@ -316,7 +319,7 @@
vAC.setT(vertices[j]);
vTemp.cross(vAB, vAC);
vAC.setT(vertices[k]);
- return vAC.dot(vTemp);
+ return vAC.dot(vTemp);
}
String getState(Viewer vwr) {
@@ -350,4 +353,16 @@
return normixes;
}
+ void setOffset(P3 value) {
+ if (center == null)
+ return; // ID polyhedra only
+ P3 v = P3.newP(value);
+ if (offset != null)
+ value.sub(offset);
+ offset = v;
+ center.add(value);
+ for (int i = vertices.length; --i >= 0;)
+ vertices[i].add(value);
+ }
+
}
Modified: trunk/Jmol/src/org/jmol/viewer/GlobalSettings.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/GlobalSettings.java 2015-10-28 03:41:32 UTC
(rev 20849)
+++ trunk/Jmol/src/org/jmol/viewer/GlobalSettings.java 2015-10-30 11:52:33 UTC
(rev 20850)
@@ -75,8 +75,9 @@
getDataBaseList(JC.databases);
getDataBaseList(userDatabases);
}
- loadFormat = databases.get("pdb");
- loadLigandFormat = databases.get("ligand");
+ loadFormat = pdbLoadFormat = databases.get("pdb");
+ pdbLoadFormat0 = databases.get("pdb0");
+ pdbLoadLigandFormat = databases.get("ligand");
nmrUrlFormat = databases.get("nmr");
nmrPredictFormat = databases.get("nmrdb");
smilesUrlFormat = databases.get("nci") + "/file?format=sdf&get3d=True";
@@ -283,7 +284,7 @@
setB("legacyJavaFloat", legacyJavaFloat);
setF("loadAtomDataTolerance", loadAtomDataTolerance);
setO("loadFormat", loadFormat);
- setO("loadLigandFormat", loadLigandFormat);
+ setO("loadLigandFormat", pdbLoadLigandFormat);
setB("logCommands", logCommands);
setB("logGestures", logGestures);
setB("measureAllModels", measureAllModels);
@@ -440,7 +441,7 @@
boolean forceAutoBond = false;
boolean fractionalRelative = true;// true: {1/2 1/2 1/2} relative to
current (possibly offset) unit cell
char inlineNewlineChar = '|'; //pseudo static
- String loadFormat, loadLigandFormat, nmrUrlFormat, nmrPredictFormat,
smilesUrlFormat, nihResolverFormat, pubChemFormat;
+ String loadFormat, pdbLoadFormat, pdbLoadFormat0, pdbLoadLigandFormat,
nmrUrlFormat, nmrPredictFormat, smilesUrlFormat, nihResolverFormat,
pubChemFormat;
String edsUrlFormat =
"http://eds.bmc.uu.se/eds/dfs/%LC13/%LCFILE/%LCFILE.omap";;
String edsUrlFormatDiff =
"http://eds.bmc.uu.se/eds/dfs/%LC13/%LCFILE/%LCFILE_diff.omap";;
@@ -888,28 +889,33 @@
return structureList;
}
- String resolveDataBase(String database, String id) {
- String format = databases.get(database.toLowerCase());
- if (format == 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";
- }
- try {
- while (format.indexOf("%c") >= 0)
- for (int i = 1; i < 10; i++) {
- format = PT.rep(format, "%c" + i, id.substring(i - 1, i));
+ 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";
}
- } catch (Exception e) {
- // too bad.
+ } 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);
}
- return (format.indexOf("%FILE") < 0 ? format + id : PT.formatStringS(
- format, "FILE", id));
- }
-
+
static boolean doReportProperty(String name) {
return (name.charAt(0) != '_' && unreportedProperties.indexOf(";" + name
+ ";") < 0);
@@ -1018,7 +1024,7 @@
app(str, "set forceAutoBond " + forceAutoBond);
app(str, "#set defaultDirectory " + PT.esc(defaultDirectory));
app(str, "#set loadFormat " + PT.esc(loadFormat));
- app(str, "#set loadLigandFormat " + PT.esc(loadLigandFormat));
+ app(str, "#set loadLigandFormat " + PT.esc(pdbLoadLigandFormat));
app(str, "#set smilesUrlFormat " + PT.esc(smilesUrlFormat));
app(str, "#set nihResolverFormat " + PT.esc(nihResolverFormat));
app(str, "#set pubChemFormat " + PT.esc(pubChemFormat));
Modified: trunk/Jmol/src/org/jmol/viewer/JC.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/JC.java 2015-10-28 03:41:32 UTC (rev
20849)
+++ trunk/Jmol/src/org/jmol/viewer/JC.java 2015-10-30 11:52:33 UTC (rev
20850)
@@ -60,7 +60,8 @@
"cod",
"http://www.crystallography.net/cod/cif/%c1/%c2%c3/%c4%c5/%FILE.cif";,
"nmr", "http://www.nmrdb.org/new_predictor?POST?molfile=";,
"nmrdb", "http://www.nmrdb.org/service/predictor?POST?molfile=";,
- "pdb", "http://www.rcsb.org/pdb/files/%FILE.pdb.gz";,
+ "pdb",
"http://ftp.wwpdb.org/pub/pdb/data/structures/divided/pdb/%c2%c3/pdb%file.ent.gz";,
// new Jmol 14.5.0 10/28/2015
+ "pdb0", "http://www.rcsb.org/pdb/files/%FILE.pdb.gz";,
"pdbe", "http://www.ebi.ac.uk/pdbe/entry-files/download/%FILE.cif";,
"pdbe2", "http://www.ebi.ac.uk/pdbe/static/entry/%FILE_updated.cif";,
"pubchem",
"http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/%FILE/SDF?record_type=3d";,
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-10-28 03:41:32 UTC
(rev 20849)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-10-30 11:52:33 UTC
(rev 20850)
@@ -62,10 +62,40 @@
TODO: consider if models with no atoms will cause issues in relation to
model.firstAtomIndex
-TODO: working on ID for polyhedra without atom refs
+Jmol.___JmolVersion="14.5.0_2015.10.30"
-Jmol.___JmolVersion="14.5.0_2015.10.28"
+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: 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"
+ }
+
+JmolVersion="14.5.0_2015.10.29"
+
+bug fix: after CALCULATE HYDROGENS TRUE and then deleting hydrogens, hydrogens
are not added to aromatic rings in PDB models
+bug fix: reading saved state after adding hydrogen atoms results in infinite
loop
+
+JmolVersion="14.5.0_2015.10.28"
+
bug fix: XODYDATA file reader does not read bond info or formal charge //
changes in 14.4.0_2015.10.28
FEATURE CHANGE: default RCSB/PDB load format (=xxxx) changed to
http://ftp.wwpdb.org/pub/pdb/data/structures/divided/pdb/%c2%c3/pdb%file.ent.gz
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2015-10-28 03:41:32 UTC (rev
20849)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2015-10-30 11:52:33 UTC (rev
20850)
@@ -3905,7 +3905,7 @@
try {
int pt = f.indexOf("/");
String database = f.substring(0, pt);
- f = g.resolveDataBase(database, f.substring(pt + 1));
+ f = g.resolveDataBase(database, f.substring(pt + 1), null);
return (f == null ? name : f);
} catch (Exception e) {
return name;
@@ -3913,10 +3913,13 @@
}
//$FALL-THROUGH$
case '#': // ligand
- String s = (type == '=' ? g.loadFormat : g.loadLigandFormat);
- if (f.indexOf(".") > 0 && s.indexOf("%FILE.") >= 0)
- s = s.substring(0, s.indexOf("%FILE") + 5);
- return PT.formatStringS(s, "FILE", f);
+ 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);
case '*':
// European Bioinformatics Institute
int pt = name.lastIndexOf("/");
@@ -3924,23 +3927,23 @@
// *dom/.../.../.../xxxx
f = name.substring(pt + 1);
format = (pt > 4 ? name.substring(5) : "mappings");
- return PT.rep(g.resolveDataBase("map", f), "%TYPE", format);
+ return PT.rep(g.resolveDataBase("map", f, null), "%TYPE", format);
} else if (name.startsWith("*val/")) {
// *val/.../.../.../xxxx
f = name.substring(pt + 1);
format = (pt > 4 ? name.substring(5) : "validation/outliers/all");
- return PT.rep(g.resolveDataBase("map", f), "%TYPE", format);
+ return PT.rep(g.resolveDataBase("map", f, null), "%TYPE", format);
} else if (name.startsWith("*rna3d/")) {
// *rna3d/.../.../.../xxxx
f = name.substring(pt + 1);
format = (pt > 6 ? name.substring(6) : "loops");
- return PT.rep(g.resolveDataBase("rna3d", f), "%TYPE", format);
+ return PT.rep(g.resolveDataBase("rna3d", f, null), "%TYPE", format);
} else if (name.startsWith("*dssr/")) {
f = name.substring(pt + 1);
- return g.resolveDataBase("dssr", f);
+ return g.resolveDataBase("dssr", f, null);
} else if (name.startsWith("*dssr1/")) {
f = name.substring(pt + 1);
- return g.resolveDataBase("dssr1", f);
+ return g.resolveDataBase("dssr1", f, null);
}
// these are processed in SmarterJmolAdapter
String pdbe = "pdbe";
@@ -3948,7 +3951,7 @@
pdbe = "pdbe2";
f = f.substring(0, 4);
}
- return g.resolveDataBase(pdbe, f);
+ return g.resolveDataBase(pdbe, f, null);
case ':': // PubChem
format = g.pubChemFormat;
if (f.equals("")) {
@@ -5365,7 +5368,7 @@
return;
case T.loadligandformat:
// /12.1.51//
- g.loadLigandFormat = value;
+ g.pdbLoadLigandFormat = value;
break;
// 12.1.50
case T.defaultlabelpdb:
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