Revision: 20782
http://sourceforge.net/p/jmol/code/20782
Author: hansonr
Date: 2015-09-21 02:16:07 +0000 (Mon, 21 Sep 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.3.16_2015.09.21"
bug fix: minor fixes for DSSR
bug fix: print within(0, "XXX", ...) ignores the "XXX" entirely. Should throw
an error (Ron Mignery)
bug fix: print within(0, "vdw", ...) ignores "vdw"; should accept that as
"vanderwaal"
bug fix: print within(-1.0, "vanderwaal", ...) ignores "vanderwaal" and does a
fractional-coordinate calculation
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/dssx/DSSR1.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/dssx/DSSR1.java
===================================================================
--- trunk/Jmol/src/org/jmol/dssx/DSSR1.java 2015-09-21 01:43:27 UTC (rev
20781)
+++ trunk/Jmol/src/org/jmol/dssx/DSSR1.java 2015-09-21 02:16:07 UTC (rev
20782)
@@ -89,7 +89,7 @@
"..junctions.nts_long" +
"..kissingloops.hairpins.nts_long" +
"..multiplets.nts_long" +
- "..nonstacks.nts_long" +
+ "..nonstack.nts_long" +
"..nts.nt_id" +
"..pairs.nt*" +
"..sssegments.nts_long" +
@@ -151,57 +151,27 @@
/**
* kissingLoops and coaxStacks use index arrays instead of duplication;
- * hbonds need nt_ids residue unitIDs as well
*
* @param map
* @return msg
*/
- @SuppressWarnings("unchecked")
@Override
public String fixDSSRJSONMap(Map<String, Object> map) {
String s = "";
+
try {
- Lst<Object>lst = (Lst<Object>) map.get("kissingLoops");
- if (lst != null) {
- Lst<Object> hpins = (Lst<Object>) map.get("hairpins");
- for (int i = lst.size(); --i >= 0;) {
- Map<String, Object> kmap = (Map<String, Object>) lst.get(i);
- Lst<Object> khlist = (Lst<Object>) kmap.get("hairpin_indices");
- int n = khlist.size();
- if (n > 0) {
- Lst<Object> khpins = new Lst<Object>();
- kmap.put("hairpins", khpins);
- for (int j = n; --j >= 0;)
- khpins.addLast(hpins.get(((Integer) khlist.get(j)).intValue() -
1));
- }
- }
- }
+
+ fixIndices(map, "kissingLoops", "hairpin");
+ fixIndices(map, "coaxStacks", "stem");
-
- lst = (Lst<Object>) map.get("coaxStacks");
- if (lst != null) {
- Lst<Object> stems = (Lst<Object>) map.get("stems");
- for (int i = lst.size(); --i >= 0;) {
- Map<String, Object> smap = (Map<String, Object>) lst.get(i);
- Lst<Object> slist = (Lst<Object>) smap.get("stem_indices");
- int n =slist.size();
- if (n > 0) {
- Lst<Object> spins = new Lst<Object>();
- smap.put("stems", spins);
- for (int j = n; --j >= 0;)
- spins.addLast(stems.get(((Integer) slist.get(j)).intValue() -
1));
- }
- }
- }
-
- lst = (Lst<Object>) map.get("hbonds");
- if (lst != null) {
- for (int i = lst.size(); --i >= 0;) {
- Map<String, Object> smap = (Map<String, Object>) lst.get(i);
- smap.put("nts_long", removeUnitAtom((String) smap.get("atom1_id"))
- + "," + removeUnitAtom((String) smap.get("atom2_id")));
- }
- }
+// lst = (Lst<Object>) map.get("hbonds");
+// if (lst != null) {
+// for (int i = lst.size(); --i >= 0;) {
+// Map<String, Object> smap = (Map<String, Object>) lst.get(i);
+// smap.put("res_long", removeUnitAtom((String) smap.get("atom1_id"))
+// + "," + removeUnitAtom((String) smap.get("atom2_id")));
+// }
+// }
if (map.containsKey("counts"))
s += "_M.dssr.counts = " + map.get("counts").toString() + "\n";
@@ -214,24 +184,52 @@
return s;
}
- private static String removeUnitAtom(String unitID) {
- int pt1 = 0;
- int pt2 = unitID.length();
- for (int i = 0, pt = -1; i < 7 && (pt = unitID.indexOf("|", pt + 1)) >=
0;i++) {
- switch (i) {
- case 4:
- pt1 = pt + 1;
- break;
- case 6:
- pt2 = pt;
- break;
+ /**
+ * create a key/value pair root+"s" for all indices of root+"_indices"
+ * @param map
+ * @param key
+ * @param root
+ */
+ @SuppressWarnings("unchecked")
+ private void fixIndices(Map<String, Object> map, String key,
+ String root) {
+ String indices = root + "_indices";
+ String original = root + "s";
+ Lst<Object>lst = (Lst<Object>) map.get(key);
+ if (lst != null) {
+ Lst<Object> hpins = (Lst<Object>) map.get(original);
+ for (int i = lst.size(); --i >= 0;) {
+ Map<String, Object> kmap = (Map<String, Object>) lst.get(i);
+ Lst<Object> khlist = (Lst<Object>) kmap.get(indices);
+ int n = khlist.size();
+ if (n > 0) {
+ Lst<Object> khpins = new Lst<Object>();
+ kmap.put(original, khpins);
+ for (int j = n; --j >= 0;)
+ khpins.addLast(hpins.get(((Integer) khlist.get(j)).intValue() -
1));
+ }
}
}
- unitID = unitID.substring(0, pt1) + "|" + unitID.substring(pt2);
- return unitID;
}
- @SuppressWarnings("unchecked")
+// private static String removeUnitAtom(String unitID) {
+// int pt1 = 0;
+// int pt2 = unitID.length();
+// for (int i = 0, pt = -1; i < 7 && (pt = unitID.indexOf("|", pt + 1)) >=
0;i++) {
+// switch (i) {
+// case 4:
+// pt1 = pt + 1;
+// break;
+// case 6:
+// pt2 = pt;
+// break;
+// }
+// }
+// unitID = unitID.substring(0, pt1) + "|" + unitID.substring(pt2);
+// return unitID;
+// }
+
+ @SuppressWarnings("unchecked")
@Override
public void getBasePairs(Viewer vwr, int modelIndex) {
ModelSet ms = vwr.ms;
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-09-21 01:43:27 UTC
(rev 20781)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-09-21 02:16:07 UTC
(rev 20782)
@@ -59,15 +59,16 @@
TODO: image off stops JSmol
-TODO: Switch to dssr1 prior to full release
+TODO: ketene messes up orbitals for O;
Jmol.___JmolVersion="14.3.16_2015.09.21"
+bug fix: minor fixes for DSSR
+
bug fix: print within(0, "XXX", ...) ignores the "XXX" entirely. Should throw
an error (Ron Mignery)
bug fix: print within(0, "vdw", ...) ignores "vdw"; should accept that as
"vanderwaal"
bug fix: print within(-1.0, "vanderwaal", ...) ignores "vanderwaal" and does a
fractional-coordinate calculation
-
JmolVersion="14.3.16_2015.09.20"
FEATURE CHANGE: 3DNA DSSR has switched over to JSON; some array names are
changed.
This was sent by the SourceForge.net collaborative development platform, the
world's largest Open Source development site.
------------------------------------------------------------------------------
_______________________________________________
Jmol-commits mailing list
Jmol-commits@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-commits
