Revision: 18255
http://sourceforge.net/p/jmol/code/18255
Author: hansonr
Date: 2013-05-27 00:29:50 +0000 (Mon, 27 May 2013)
Log Message:
-----------
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/pymol/JmolObject.java
trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/adapter/readers/pymol/JmolObject.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pymol/JmolObject.java
2013-05-26 22:54:47 UTC (rev 18254)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pymol/JmolObject.java
2013-05-27 00:29:50 UTC (rev 18255)
@@ -320,6 +320,7 @@
void setSize(float size) {
this.size = (int) (size * 1000);
+ System.out.println("JmolObject " + id + " size=" + size);
}
}
\ No newline at end of file
Modified: trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
2013-05-26 22:54:47 UTC (rev 18254)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
2013-05-27 00:29:50 UTC (rev 18255)
@@ -1576,7 +1576,6 @@
for (Map.Entry<Float, BS> e : htSpacefill.entrySet()) {
float r = e.getKey().floatValue();
BS bs = e.getValue();
- System.out.println(r + " sf " + Escape.eBS(bs));
addJmolObject(JC.SHAPE_BALLS, bs, null).rd = new RadiusData(null, r,
RadiusData.EnumType.ABSOLUTE, EnumVdw.AUTO);
}
@@ -1715,21 +1714,27 @@
*/
private void createTraceObject(BS bs) {
JmolObject jo;
+ checkNucleicObject(bs, true);
+ if (bs.isEmpty())
+ return;
+ jo = addJmolObject(JC.SHAPE_TRACE, bs, null);
+ jo.translucency = cartoonTranslucency;
+ jo.setSize(floatSetting(PyMOL.cartoon_tube_radius) * 2);
+ }
+
+ private void checkNucleicObject(BS bs, boolean isTrace) {
+ JmolObject jo;
BS bsNuc = BSUtil.copy(bsNucleic);
bsNuc.and(bs);
- if (cartoonLadderMode && !bsNuc.isEmpty()) {
- haveNucleicLadder = true;
+ if (!bsNuc.isEmpty()) {
+ if (isTrace && cartoonLadderMode)
+ haveNucleicLadder = true;
// we will just use cartoons for ladder mode
jo = addJmolObject(JC.SHAPE_CARTOON, bsNuc, null);
jo.translucency = cartoonTranslucency;
jo.setSize(floatSetting(PyMOL.cartoon_tube_radius) * 2);
bs.andNot(bsNuc);
- if (bs.isEmpty())
- return;
}
- jo = addJmolObject(JC.SHAPE_TRACE, bs, null);
- jo.translucency = cartoonTranslucency;
- jo.setSize(floatSetting(PyMOL.cartoon_tube_radius) * 2);
}
/**
@@ -1755,14 +1760,14 @@
* @param bs
*/
private void createRibbonObject(BS bs) {
- // 2ace: 0, 1 ==> backbone
- // fig8: 0, 1 ==> backbone
- // casp: 0, 1 ==> backbone
- // NLG3_AchE: 0, 1 ==> backbone
+ // 2ace: 0, 1 ==> backbone // r rpc w 0.0 1.3 3.0 too small
+ // fig8: 0, 1 ==> backbone // r rpc w 0.0 1.0 3.0 OK
+ // casp: 0, 1 ==> backbone // r rpc w 0.0 1.3 3.0 too small
+ // NLG3_AchE: 0, 1 ==> backbone //r rpc w 0.0 1.3 4.0 too small
// NLG3_HuAChE: 0, 10 ==> trace
// tach: 0, 10 ==> trace
// tah-lev: 0, 10 ==> trace
- // 496: -1, 1 ==> backbone
+ // 496: -1, 1 ==> backbone // r rpc 0.0 1.3 3.0 too small
// kinases: -1, 1 ==> backbone
// 443_D1: -1, 1 ==> backbone
// 476Rainbow_New: 10, 8 ==> trace
@@ -1772,9 +1777,10 @@
boolean isTrace = (sampling > 1);
float r = floatSetting(PyMOL.ribbon_radius) * 2;
float rpc = floatSetting(PyMOL.ray_pixel_scale);
+ System.out.println("r rpc w " + r + " " + rpc + " " +
floatSetting(PyMOL.ribbon_width));
if (r == 0)
r = floatSetting(PyMOL.ribbon_width)
- * (isTrace ? 0.1f : (rpc < 1 ? 1 : rpc) * 0.05f);
+ * (isTrace ? 1 : (rpc <= 1 ? 0.5f : rpc)) * 0.1f;
addJmolObject((isTrace ? JC.SHAPE_TRACE : JC.SHAPE_BACKBONE), bs, null)
.setSize(r);
}
@@ -1786,6 +1792,11 @@
bs.and(reps[PyMOL.REP_CARTOON]);
if (bs.isEmpty())
return;
+ if (key.equals(" ")) {
+ checkNucleicObject(bs, false);
+ if (bs.isEmpty())
+ return;
+ }
JmolObject jo = addJmolObject(JC.SHAPE_CARTOON, bs, null);
jo.translucency = cartoonTranslucency;
jo.setSize(floatSetting(sizeID) * 2);
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-05-26 22:54:47 UTC
(rev 18254)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-05-27 00:29:50 UTC
(rev 18255)
@@ -9,7 +9,7 @@
# The quotes above look odd for a parameter file, but they are
# important for the JavaScript version of Jmol.
-___JmolVersion="13.1.16_dev_2013.05.26"
+___JmolVersion="13.1.16_dev_2013.05.26a"
PyMOL: first phase of reader development complete (working with Jaime Prilusky)
-- 104 test models http://ispcsrv3.weizmann.ac.il/a2jmolb/browse
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