Revision: 20091
http://sourceforge.net/p/jmol/code/20091
Author: hansonr
Date: 2014-11-07 13:23:58 +0000 (Fri, 07 Nov 2014)
Log Message:
-----------
Jmol.___JmolVersion="14.3.8_2014.11.07"
code: code clean-up in GData, Graphics3D, and Export3D
code: modifications to GIF writer. Not really satisfying; still using HSL
code: PDB reader CONECT efficiency
bug fix: PDB reader limited to 20 connections per atom
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/pdb/PdbReader.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/adapter/readers/pdb/PdbReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pdb/PdbReader.java 2014-11-06
22:35:13 UTC (rev 20090)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pdb/PdbReader.java 2014-11-07
13:23:58 UTC (rev 20091)
@@ -1102,9 +1102,8 @@
}
private boolean haveDoubleBonds;
-
+
private void conect() {
- // adapted for improper non-crossreferenced files such as 1W7R
if (sbConect == null) {
sbConect = new SB();
sb = new SB();
@@ -1115,14 +1114,24 @@
sourceSerial = getSerial(6, 11);
if (sourceSerial < 0)
return;
- for (int i = 0; i < 9; i += (i == 5 ? 2 : 1)) {
- int offset = i * 5 + 11;
- int offsetEnd = offset + 5;
- if (offsetEnd > lineLength)
+ int order = 1;
+ // skip ancient salt bridges
+ int pt1 = Math.min(line.trim().length(), 52);
+ for (int pt = 11; pt < pt1; pt += 5) {
+ switch (pt) {
+ case 31:
+ order = JmolAdapter.ORDER_HBOND;
break;
- int targetSerial = getSerial(offset, offsetEnd);
- if (targetSerial < 0)
+ case 41:
+ // old salt bridge
continue;
+ }
+ int targetSerial = getSerial(pt, pt + 5);
+ if (targetSerial < 0) {
+ if (pt <= 31) // no hbonds -- get out of here
+ break;
+ continue;
+ }
boolean isDoubleBond = (sourceSerial == lastSourceSerial && targetSerial
== lastTargetSerial);
if (isDoubleBond)
haveDoubleBonds = true;
@@ -1147,8 +1156,7 @@
sb.append(st1);
}
sbConect.append(st);
- addConnection(new int[] { i1, targetSerial,
- i < 4 ? 1 : JmolAdapter.ORDER_HBOND });
+ addConnection(new int[] { i1, targetSerial, order });
}
sbConect.appendSB(sb);
}
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2014-11-06 22:35:13 UTC
(rev 20090)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2014-11-07 13:23:58 UTC
(rev 20091)
@@ -14,11 +14,13 @@
TODO: design and implement sidechain mutation -- MUTATE command ?
TODO: remove HTML5 dependency on synchronous file loading (check SCRIPT
command for problems)
+TODO: CAPTURE to PNG
-Jmol.___JmolVersion="14.3.8_2014.11.06"
+Jmol.___JmolVersion="14.3.8_2014.11.07"
code: code clean-up in GData, Graphics3D, and Export3D
code: modifications to GIF writer. Not really satisfying; still using HSL
+code: PDB reader CONECT efficiency
bug fix: PDB reader limited to 20 connections per atom
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