Revision: 20948
http://sourceforge.net/p/jmol/code/20948
Author: hansonr
Date: 2016-02-06 06:22:04 +0000 (Sat, 06 Feb 2016)
Log Message:
-----------
Jmol.___JmolVersion="14.4.2_2016.02.06"
bug fix: small MRC map files mistaken for DELPHI files, which start with the
4-byte integer 20.
bug fix: MRC/CCP4 surface/map files still sometimes inside out.
Modified Paths:
--------------
branches/v14_4/Jmol/src/org/jmol/jvxl/data/JvxlData.java
branches/v14_4/Jmol/src/org/jmol/jvxl/readers/JvxlXmlReader.java
branches/v14_4/Jmol/src/org/jmol/jvxl/readers/MapFileReader.java
branches/v14_4/Jmol/src/org/jmol/jvxl/readers/MrcBinaryReader.java
branches/v14_4/Jmol/src/org/jmol/jvxl/readers/Parameters.java
branches/v14_4/Jmol/src/org/jmol/jvxl/readers/SurfaceGenerator.java
branches/v14_4/Jmol/src/org/jmol/jvxl/readers/SurfaceReader.java
branches/v14_4/Jmol/src/org/jmol/scriptext/IsoExt.java
branches/v14_4/Jmol/src/org/jmol/shapesurface/Isosurface.java
branches/v14_4/Jmol/src/org/jmol/viewer/FileManager.java
branches/v14_4/Jmol/src/org/jmol/viewer/JC.java
branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties
branches/v14_4/Jmol/src/org/jmol/viewer/Viewer.java
Modified: branches/v14_4/Jmol/src/org/jmol/jvxl/data/JvxlData.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/jvxl/data/JvxlData.java 2016-02-05
05:56:22 UTC (rev 20947)
+++ branches/v14_4/Jmol/src/org/jmol/jvxl/data/JvxlData.java 2016-02-06
06:22:04 UTC (rev 20948)
@@ -111,7 +111,6 @@
public int colorFractionBase = JvxlCoder.defaultColorFractionBase;
public int colorFractionRange = JvxlCoder.defaultColorFractionRange;
- public boolean dataXYReversed;
public boolean insideOut;
public boolean isXLowToHigh;
public boolean isContoured;
Modified: branches/v14_4/Jmol/src/org/jmol/jvxl/readers/JvxlXmlReader.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/jvxl/readers/JvxlXmlReader.java
2016-02-05 05:56:22 UTC (rev 20947)
+++ branches/v14_4/Jmol/src/org/jmol/jvxl/readers/JvxlXmlReader.java
2016-02-06 06:22:04 UTC (rev 20948)
@@ -403,10 +403,9 @@
jvxlData.mappedDataMin = params.mappedDataMin;
jvxlData.mappedDataMax = params.mappedDataMax;
jvxlData.isColorReversed = params.isColorReversed;
- jvxlData.insideOut = insideOut;
if (params.insideOut)
- jvxlData.insideOut = !jvxlData.insideOut;
- params.insideOut = jvxlData.insideOut;
+ insideOut = !insideOut;
+ params.insideOut = jvxlData.insideOut = insideOut;
}
@Override
Modified: branches/v14_4/Jmol/src/org/jmol/jvxl/readers/MapFileReader.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/jvxl/readers/MapFileReader.java
2016-02-05 05:56:22 UTC (rev 20947)
+++ branches/v14_4/Jmol/src/org/jmol/jvxl/readers/MapFileReader.java
2016-02-06 06:22:04 UTC (rev 20948)
@@ -84,7 +84,7 @@
protected void getVectorsAndOrigin() {
- Logger.info("grid parameters: nx,ny,nz: " + nx + "," + ny + "," + nz);
+ Logger.info("grid parameters: nx,ny,nz: " + nx + "," + ny + "," + nz);
Logger.info("grid parameters: nxStart,nyStart,nzStart: " + nxyzStart[0]
+ "," + nxyzStart[1] + "," + nxyzStart[2]);
Modified: branches/v14_4/Jmol/src/org/jmol/jvxl/readers/MrcBinaryReader.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/jvxl/readers/MrcBinaryReader.java
2016-02-05 05:56:22 UTC (rev 20947)
+++ branches/v14_4/Jmol/src/org/jmol/jvxl/readers/MrcBinaryReader.java
2016-02-06 06:22:04 UTC (rev 20948)
@@ -121,13 +121,14 @@
if (nx < 0 || nx > 1<<8) {
setStream(null, false);
nx = binarydoc.swapBytesI(nx);
- if (params.thePlane == null)
- params.insideOut = !params.insideOut;
+ //removed for PDBE CCP4 files
+ //if (params.thePlane == null)
+ //params.insideOut = !params.insideOut;
if (nx < 0 || nx > 1000) {
Logger.info("nx=" + nx + " not displayable as MRC file");
throw new Exception("MRC file type not readable");
}
- Logger.info("reading nonstandard little-endian MRC file");
+ Logger.info("reading little-endian MRC file");
}
ny = binarydoc.readInt();
nz = binarydoc.readInt();
@@ -182,10 +183,13 @@
mapr = binarydoc.readInt();
maps = binarydoc.readInt();
- Logger.info("MRC header: mapc mapr maps: " + mapc + " " + mapr + " " +
maps);
+ String s = "" + mapc + mapr + maps;
+ Logger.info("MRC header: mapc mapr maps: " + s);
- if (mapc != 1 && params.thePlane == null)
+ if (params.thePlane == null && "21321".indexOf(s) >= 1) {
+ Logger.info("MRC header: data are xy-reversed");
params.dataXYReversed = true;
+ }
dmin = binarydoc.readFloat();
dmax = binarydoc.readFloat();
@@ -223,7 +227,7 @@
labels[0] = "Jmol MrcBinaryReader";
for (int i = 0; i < 10; i++) {
- String s = binarydoc.readString(80).trim();
+ s = binarydoc.readString(80).trim();
if (i < nlabel) {
labels[i] = s;
Logger.info(labels[i]);
@@ -232,7 +236,7 @@
for (int i = 0; i < nsymbt; i += 80) {
long position = binarydoc.getPosition();
- String s = binarydoc.readString(80).trim();
+ s = binarydoc.readString(80).trim();
if (s.indexOf('\0') != s.lastIndexOf('\0')) {
// must not really be symmetry info!
Logger.error("File indicates " + nsymbt + " symmetry lines, but " + i
+ " found!");
Modified: branches/v14_4/Jmol/src/org/jmol/jvxl/readers/Parameters.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/jvxl/readers/Parameters.java
2016-02-05 05:56:22 UTC (rev 20947)
+++ branches/v14_4/Jmol/src/org/jmol/jvxl/readers/Parameters.java
2016-02-06 06:22:04 UTC (rev 20948)
@@ -882,4 +882,13 @@
slabInfo.addLast(slabObject);
}
+ public boolean isInsideOut() {
+ return insideOut != dataXYReversed;
+ }
+
+ public boolean isFullyLit() {
+ return (thePlane != null || fullyLit);
+ }
+
+
}
Modified: branches/v14_4/Jmol/src/org/jmol/jvxl/readers/SurfaceGenerator.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/jvxl/readers/SurfaceGenerator.java
2016-02-05 05:56:22 UTC (rev 20947)
+++ branches/v14_4/Jmol/src/org/jmol/jvxl/readers/SurfaceGenerator.java
2016-02-06 06:22:04 UTC (rev 20948)
@@ -185,14 +185,6 @@
jvxlData.version = version;
}
- public boolean isInsideOut() {
- return params.insideOut != params.dataXYReversed;
- }
-
- public boolean isFullyLit() {
- return (params.thePlane != null || params.fullyLit);
- }
-
//////////////////////////////////////////////////////////////
/**
Modified: branches/v14_4/Jmol/src/org/jmol/jvxl/readers/SurfaceReader.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/jvxl/readers/SurfaceReader.java
2016-02-05 05:56:22 UTC (rev 20947)
+++ branches/v14_4/Jmol/src/org/jmol/jvxl/readers/SurfaceReader.java
2016-02-06 06:22:04 UTC (rev 20948)
@@ -370,8 +370,7 @@
nPointsY = voxelCounts[1];
nPointsZ = voxelCounts[2];
jvxlData.isSlabbable = ((params.dataType & Parameters.IS_SLABBABLE) != 0);
- jvxlData.insideOut = params.insideOut;
- jvxlData.dataXYReversed = params.dataXYReversed;
+ jvxlData.insideOut = params.isInsideOut();
jvxlData.isBicolorMap = params.isBicolorMap;
jvxlData.nPointsX = nPointsX;
jvxlData.nPointsY = nPointsY;
Modified: branches/v14_4/Jmol/src/org/jmol/scriptext/IsoExt.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/scriptext/IsoExt.java 2016-02-05
05:56:22 UTC (rev 20947)
+++ branches/v14_4/Jmol/src/org/jmol/scriptext/IsoExt.java 2016-02-06
06:22:04 UTC (rev 20948)
@@ -2422,7 +2422,14 @@
* Or =xxxx, an EDM from Uppsala Electron Density Server
* If the model auxiliary info has "jmolSufaceInfo", we use that.
*/
- if (filename.startsWith("=") && filename.length() > 1) {
+ boolean checkWithin = false;
+ if (filename.startsWith("*") && filename.length() > 1) {
+ // new PDB ccp4 option
+ filename = (String) vwr.setLoadFormat(filename, '_', false);
+ // filename = info[0];
+ checkWithin = true;
+ } else if (filename.startsWith("=") && filename.length() > 1) {
+ checkWithin = true;
String[] info = (String[]) vwr.setLoadFormat(filename, '_', false);
filename = info[0];
String strCutoff = (!firstPass || !Float.isNaN(cutoff) ? null
@@ -2456,8 +2463,10 @@
sbCommand.append(" cutoff ").appendF(cutoff);
}
}
+ }
+ if (checkWithin) {
if (ptWithin == 0) {
- onlyOneModel = "=xxxx";
+ onlyOneModel = filename;
if (modelIndex < 0)
modelIndex = vwr.am.cmi;
bs = vwr.getModelUndeletedAtomsBitSet(modelIndex);
@@ -2469,7 +2478,6 @@
if (firstPass)
defaultMesh = true;
}
-
if (firstPass && vwr.getP("_fileType").equals("Pdb")
&& Float.isNaN(sigma) && Float.isNaN(cutoff)) {
// negative sigma just indicates that
Modified: branches/v14_4/Jmol/src/org/jmol/shapesurface/Isosurface.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/shapesurface/Isosurface.java
2016-02-05 05:56:22 UTC (rev 20947)
+++ branches/v14_4/Jmol/src/org/jmol/shapesurface/Isosurface.java
2016-02-06 06:22:04 UTC (rev 20948)
@@ -1480,7 +1480,7 @@
public boolean notifySurfaceGenerationCompleted() {
setMeshI();
setBsVdw();
- thisMesh.insideOut = sg.isInsideOut();
+ thisMesh.insideOut = sg.params.isInsideOut();
thisMesh.isModelConnected = sg.params.isModelConnected;
thisMesh.vertexSource = sg.params.vertexSource;
thisMesh.spanningVectors = sg.getSpanningVectors();
@@ -1488,7 +1488,7 @@
thisMesh.calculatedVolume = null;
// from JVXL file:
if (!thisMesh.isMerged) {
- thisMesh.initialize(sg.isFullyLit() ? T.fullylit
+ thisMesh.initialize(sg.params.isFullyLit() ? T.fullylit
: T.frontlit, null, sg.params.thePlane);
if (jvxlData.fixedLattice != null) {
thisMesh.lattice = jvxlData.fixedLattice;
@@ -1511,7 +1511,7 @@
@Override
public void notifySurfaceMappingCompleted() {
if (!thisMesh.isMerged)
- thisMesh.initialize(sg.isFullyLit() ? T.fullylit : T.frontlit, null,
+ thisMesh.initialize(sg.params.isFullyLit() ? T.fullylit : T.frontlit,
null,
sg.params.thePlane);
setBsVdw();
thisMesh.isColorSolid = false;
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/FileManager.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/FileManager.java 2016-02-05
05:56:22 UTC (rev 20947)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/FileManager.java 2016-02-06
06:22:04 UTC (rev 20948)
@@ -1107,7 +1107,7 @@
///// FILE TYPING /////
- private final static String DELPHI_BINARY_MAGIC_NUMBER = "\24\0\0\0";
+ private final static String DELPHI_BINARY_MAGIC_NUMBER = "\24\0\0\0"; //0x14
0 0 0 == "20-byte character string follows"
public final static String PMESH_BINARY_MAGIC_NUMBER = "PM\1\0";
public static final String JPEG_CONTINUE_STRING = " #Jmol...\0";
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/JC.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/JC.java 2016-02-05 05:56:22 UTC
(rev 20947)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/JC.java 2016-02-06 06:22:04 UTC
(rev 20948)
@@ -70,7 +70,9 @@
"aflow",
"http://aflowlib.mems.duke.edu/users/jmolers/binary_new/%FILE.aflow_binary";,
// _#CHANGEABLE_ flag indicates that the loaded file should be saved in
any state in full
// ' at start indicates a Jmol script evaluation
- "ams", "'http://rruff.geo.arizona.edu/AMS/viewJmol.php?'+(0+'%file'==0?
'mineral':('%file'.length==7? 'amcsd':'id'))+'=%file&action=showcif#_DOCACHE_'"
+ "ams", "'http://rruff.geo.arizona.edu/AMS/viewJmol.php?'+(0+'%file'==0?
'mineral':('%file'.length==7? 'amcsd':'id'))+'=%file&action=showcif#_DOCACHE_'",
+ "pdbemap", "http://wwwdev.ebi.ac.uk/pdbe/coordinates/files/%file.ccp4";,
+ "pdbemapdiff",
"http://wwwdev.ebi.ac.uk/pdbe/coordinates/files/%file_diff.ccp4";
};
public static String[] macros = {
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2016-02-05
05:56:22 UTC (rev 20947)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2016-02-06
06:22:04 UTC (rev 20948)
@@ -7,7 +7,12 @@
# see also http://chemapps.stolaf.edu/jmol/zip for daily updates
-Jmol.___JmolVersion="14.4.2_2016.02.05"
+Jmol.___JmolVersion="14.4.2_2016.02.06"
+
+bug fix: small MRC map files mistaken for DELPHI files, which start with the
4-byte integer 20.
+bug fix: MRC/CCP4 surface/map files still sometimes inside out.
+
+JmolVersion="14.4.2_2016.02.05"
released
bug fix: LOAD $benzene; SHOW smiles should give c1ccccc1 not c1=cc=cc=c1
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/Viewer.java 2016-02-05 05:56:22 UTC
(rev 20947)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/Viewer.java 2016-02-06 06:22:04 UTC
(rev 20948)
@@ -4055,6 +4055,13 @@
return (withPrefix ? "MOL3D::" : "")
+ PT.formatStringS(format, "FILE", id);
case '_': // isosurface "=...", but we code that type as '_'
+ if (name.startsWith("*")) {
+ boolean isDiff = id.startsWith("*");
+ if (isDiff)
+ id = id.substring(1);
+ return g.resolveDataBase((isDiff ? "pdbemapdiff" : "pdbemap"), id,
+ null);
+ }
return g.fixSurfaceFileNameVariables(id);
}
return id;
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