Revision: 20272
http://sourceforge.net/p/jmol/code/20272
Author: hansonr
Date: 2015-02-08 03:22:38 +0000 (Sun, 08 Feb 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.2.12_2015.02.07"
bug fix: zoomTo{xxx} 0 does not center (broken in 13.1.16_dev_2013.05.23)
bug fix: appending a model to a model with data can fail
bug fix: hydrogen addition should not follow component file
Modified Paths:
--------------
branches/v14_2/Jmol/src/org/jmol/modelsetbio/Resolver.java
branches/v14_2/Jmol/src/org/jmol/script/ScriptEval.java
branches/v14_2/Jmol/src/org/jmol/viewer/DataManager.java
branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: branches/v14_2/Jmol/src/org/jmol/modelsetbio/Resolver.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/modelsetbio/Resolver.java 2015-02-08
03:21:49 UTC (rev 20271)
+++ branches/v14_2/Jmol/src/org/jmol/modelsetbio/Resolver.java 2015-02-08
03:22:38 UTC (rev 20272)
@@ -126,7 +126,7 @@
group3Count = s.length() / 6;
Group.standardGroupList = s.toString();
for (int i = 0, n = predefinedGroup3Names.length; i < n; ++i)
- addGroup3Name(predefinedGroup3Names[i]);
+ addGroup3Name(predefinedGroup3Names[i].trim());
}
return this;
}
@@ -919,7 +919,7 @@
target = "HB3@HB2";
break;
case 'D': // CD
- target = "HD2@HD3";
+ target = "HD3@HD2";
break;
case 'G': // CG
target = "HG3@HG2";
@@ -955,41 +955,42 @@
public final static String[] pdbBondInfo = {
// added O3' HO3' O5' HO5' for nucleic and added 1 H atom for res 1 for
13.1.17
// this could throw off states from previous versions
+ // CH2 and NH2 labeling revised 2015.02.07
"",
/*ALA*/ "N N CA HA C O CB HB?",
- /*ARG*/ "N N CA HA C O CB HB2@HB3 CG HG2@HG3 CD D NE HE CZ NH1 NH1
HH11@HH12 NH2 HH21@HH22",
+ /*ARG*/ "N N CA HA C O CB B CG G CD D NE HE CZ NH1 NH1 HH11@HH12 NH2
HH22@HH21",
/*ASN*/ "N N CA HA C O CB B CG OD1 ND2 HD21@HD22",
/*ASP*/ "N N CA HA C O CB B CG OD1",
/*CYS*/ "N N CA HA C O CB B SG HG",
- /*GLN*/ "N N CA HA C O CB B CG G CD OE1 NE2 HE21@HE22",
+ /*GLN*/ "N N CA HA C O CB B CG G CD OE1 NE2 HE22@HE21",
/*GLU*/ "N N CA HA C O CB B CG G CD OE1",
/*GLY*/ "N N CA HA2@HA3 C O",
/*HIS*/ "N N CA HA C O CB B CG CD2 ND1 CE1 ND1 HD1 CD2 HD2 CE1 HE1 NE2
HE2",
- /*ILE*/ "N N CA HA C O CB HB CG1 HG12@HG13 CG2 HG2? CD1 HD1?",
- /*LEU*/ "N N CA HA C O CB HB2@HB3 CG HG CD1 HD1? CD2 HD2?",
+ /*ILE*/ "N N CA HA C O CB HB CG1 HG13@HG12 CG2 HG2? CD1 HD1?",
+ /*LEU*/ "N N CA HA C O CB B CG HG CD1 HD1? CD2 HD2?",
/*LYS*/ "N N CA HA C O CB B CG G CD HD2@HD3 CE HE3@HE2 NZ HZ?",
- /*MET*/ "N N CA HA C O CB HB2@HB3 CG HG2@HG3 CE HE?",
+ /*MET*/ "N N CA HA C O CB B CG G CE HE?",
/*PHE*/ "N N CA HA C O CB B CG CD1 CD1 HD1 CD2 CE2 CD2 HD2 CE1 CZ CE1 HE1
CE2 HE2 CZ HZ",
- /*PRO*/ "N H CA HA C O CB B CG G CD HD2@HD3",
+ /*PRO*/ "N H CA HA C O CB B CG G CD D",
/*SER*/ "N N CA HA C O CB B OG HG",
/*THR*/ "N N CA HA C O CB HB OG1 HG1 CG2 HG2?",
/*TRP*/ "N N CA HA C O CB B CG CD1 CD1 HD1 CD2 CE2 NE1 HE1 CE3 CZ3 CE3 HE3
CZ2 CH2 CZ2 HZ2 CZ3 HZ3 CH2 HH2",
/*TYR*/ "N N CA HA C O CB B CG CD1 CD1 HD1 CD2 CE2 CD2 HD2 CE1 CZ CE1 HE1
CE2 HE2 OH HH",
/*VAL*/ "N N CA HA C O CB HB CG1 HG1? CG2 HG2?",
- /*ASX*/ "CA HA C O CB HB2@HB1 C H",
- /*GLX*/ "CA HA C O CB HB1 CB HB2 CG HG1 CG HG2",
+ /*ASX*/ "N N CA HA C O CB B",
+ /*GLX*/ "N N CA HA C O CB B CG G",
/*UNK*/ "",
- /*G*/ "P OP1 C5' 5 C4' H4' C3' H3' C2' H2' O2' HO2' C1' H1' C8 N7 C8 H8 C5
C4 C6 O6 N1 H1 C2 N3 N2 H21@H22 O3' HO3' O5' HO5'",
+ /*G*/ "P OP1 C5' 5 C4' H4' C3' H3' C2' H2' O2' HO2' C1' H1' C8 N7 C8 H8 C5
C4 C6 O6 N1 H1 C2 N3 N2 H22@H21 O3' HO3' O5' HO5'",
/*C*/ "P OP1 C5' 5 C4' H4' C3' H3' C2' H2' O2' HO2' C1' H1' C2 O2 N3 C4 N4
H41@H42 C5 C6 C5 H5 C6 H6 O3' HO3' O5' HO5'",
/*A*/ "P OP1 C5' 5 C4' H4' C3' H3' C2' H2' O2' HO2' C1' H1' C8 N7 C8 H8 C5
C4 C6 N1 N6 H61@H62 C2 N3 C2 H2 O3' HO3' O5' HO5'",
/*T*/ "P OP1 C5' 5 C4' H4' C3' H3' C2' 2 C1' H1' C2 O2 N3 H3 C4 O4 C5 C6
C7 H7? C6 H6 O3' HO3' O5' HO5'",
/*U*/ "P OP1 C5' 5 C4' H4' C3' H3' C2' H2' O2' HO2' C1' H1' C2 O2 N3 H3 C4
O4 C5 C6 C5 H5 C6 H6 O3' HO3' O5' HO5'",
/*I*/ "P OP1 C5' 5 C4' H4' C3' H3' C2' H2' O2' HO2' C1' H1' C8 N7 C8 H8 C5
C4 C6 O6 N1 H1 C2 N3 C2 H2 O3' HO3' O5' HO5'",
- /*DG*/ "P OP1 C5' 5 C4' H4' C3' H3' C2' 2 C1' H1' C8 N7 C8 H8 C5 C4 C6 O6
N1 H1 C2 N3 N2 H21@H22 O3' HO3' O5' HO5'",
+ /*DG*/ "P OP1 C5' 5 C4' H4' C3' H3' C2' 2 C1' H1' C8 N7 C8 H8 C5 C4 C6 O6
N1 H1 C2 N3 N2 H22@H21 O3' HO3' O5' HO5'",
/*DC*/ "P OP1 C5' 5 C4' H4' C3' H3' C2' 2 C1' H1' C2 O2 N3 C4 N4 H41@H42
C5 C6 C5 H5 C6 H6 O3' HO3' O5' HO5'",
/*DA*/ "P OP1 C5' 5 C4' H4' C3' H3' C2' 2 C1' H1' C8 N7 C8 H8 C5 C4 C6 N1
N6 H61@H62 C2 N3 C2 H2 O3' HO3' O5' HO5'",
- /*DT*/ "P OP1 C5' H5'@H5'' C4' H4' C3' H3' C2' H2'@H2'' C1' H1' C2 O2 N3
H3 C4 O4 C5 C6 C7 H7? C6 H6 O3' HO3' O5' HO5'",
- /*DU*/ "P OP1 C5' 5 C4' H4' C3' H3' C2' H2'@H2'' C1' H1' C2 O2 N3 H3 C4 O4
C5 C6 C5 H5 C6 H6 O3' HO3' O5' HO5'",
+ /*DT*/ "P OP1 C5' 5 C4' H4' C3' H3' C2' 2 C1' H1' C2 O2 N3 H3 C4 O4 C5 C6
C7 H7? C6 H6 O3' HO3' O5' HO5'",
+ /*DU*/ "P OP1 C5' 5 C4' H4' C3' H3' C2' 2 C1' H1' C2 O2 N3 H3 C4 O4 C5 C6
C5 H5 C6 H6 O3' HO3' O5' HO5'",
/*DI*/ "P OP1 C5' 5 C4' H4' C3' H3' C2' 2 C1' H1' C8 N7 C8 H8 C5 C4 C6 O6
N1 H1 C2 N3 C2 H2 O3' HO3' O5' HO5'",
};
private final static int[] pdbHydrogenCount = {
@@ -1053,6 +1054,7 @@
Short boxedGroupID = Group.htGroup.get(group3);
return (boxedGroupID == null ? -1 : boxedGroupID.shortValue());
}
+
/**
* @param group3 a potential group3 name
* @return whether this is a carbohydrate from the list
@@ -1061,7 +1063,9 @@
return (group3 != null
&& allCarbohydrates.indexOf("[" + group3.toUpperCase() + "]") >= 0);
}
+
private static int group3Count;
+
final static char[] predefinedGroup1Names = {
/* rmh
*
@@ -1214,6 +1218,35 @@
};
+
+ @Override
+ public short getGroupID(String g3) {
+ return getGroupIdFor(g3);
+ }
+
+ static short getGroupIdFor(String group3) {
+ group3 = group3.trim();
+ short groupID = knownGroupID(group3);
+ return (groupID == -1 ?
+ addGroup3Name(group3) :
+ groupID);
+ }
+
+ /**
+ * These can overrun 3 characters; that is not significant.
+ *
+ * @param group3
+ * @return a short group ID
+ */
+ private synchronized static short addGroup3Name(String group3) {
+ if (group3NameCount == Group.group3Names.length)
+ Group.group3Names = AU.doubleLengthS(Group.group3Names);
+ short groupID = group3NameCount++;
+ Group.group3Names[groupID] = group3;
+ Group.htGroup.put(group3, Short.valueOf(groupID));
+ return groupID;
+ }
+
private static int getStandardPdbHydrogenCount(String group3) {
int pt = knownGroupID(group3);
return (pt < 0 || pt >= pdbHydrogenCount.length ? -1 :
pdbHydrogenCount[pt]);
@@ -1708,31 +1741,6 @@
return null;
}
- @Override
- public short getGroupID(String g3) {
- return getGroupIdFor(g3);
- }
-
- /**
- * These can overrun 3 characters; that is not significant.
- *
- * @param group3
- * @return a short group ID
- */
- public synchronized static short addGroup3Name(String group3) {
- if (group3NameCount == Group.group3Names.length)
- Group.group3Names = AU.doubleLengthS(Group.group3Names);
- short groupID = group3NameCount++;
- Group.group3Names[groupID] = group3;
- Group.htGroup.put(group3, Short.valueOf(groupID));
- return groupID;
- }
-
- public static short getGroupIdFor(String group3) {
- short groupID = knownGroupID(group3);
- return (groupID == -1 ? addGroup3Name(group3) : groupID);
- }
-
}
Modified: branches/v14_2/Jmol/src/org/jmol/script/ScriptEval.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/script/ScriptEval.java 2015-02-08
03:21:49 UTC (rev 20271)
+++ branches/v14_2/Jmol/src/org/jmol/script/ScriptEval.java 2015-02-08
03:22:38 UTC (rev 20272)
@@ -8127,10 +8127,10 @@
}
if (chk)
return;
- //if (Float.isNaN(xTrans))
- //xTrans = 0;
- //if (Float.isNaN(yTrans))
- //yTrans = 0;
+ if (Float.isNaN(xTrans))
+ xTrans = 0;
+ if (Float.isNaN(yTrans))
+ yTrans = 0;
if (isSameAtom && Math.abs(zoom - newZoom) < 1)
floatSecondsTotal = 0;
vwr.moveTo(this, floatSecondsTotal, center, JC.center, Float.NaN, null,
Modified: branches/v14_2/Jmol/src/org/jmol/viewer/DataManager.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/viewer/DataManager.java 2015-02-08
03:21:49 UTC (rev 20271)
+++ branches/v14_2/Jmol/src/org/jmol/viewer/DataManager.java 2015-02-08
03:22:38 UTC (rev 20272)
@@ -158,13 +158,15 @@
// just get the selected token values
bs = (BS) data[DATA_SELECTION_MAP];
if (floatData != null) {
- if (floatData.length == bs.cardinality())
+ int n = floatData.length;
+ if (n == bs.cardinality()) {
for (int i = bs.nextSetBit(0), pt = 0; i >= 0; i = bs
.nextSetBit(i + 1), pt++)
f[i] = floatData[pt];
- else
- for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1))
+ } else {
+ for (int i = bs.nextSetBit(0); i >= 0 && i < n; i =
bs.nextSetBit(i + 1))
f[i] = floatData[i];
+ }
} else {
Parser.parseFloatArrayBsData(
strData == null ? PT.getTokens(stringData) : strData, bs, f);
Modified: branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties 2015-02-08
03:21:49 UTC (rev 20271)
+++ branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties 2015-02-08
03:22:38 UTC (rev 20272)
@@ -5,12 +5,19 @@
# THIS IS THE RELEASE BRANCH
# BUG FIXES ONLY, PLEASE
-Jmol.___JmolVersion="14.2.12_2015.02.04"
+Jmol.___JmolVersion="14.2.12_2015.02.07"
+bug fix: zoomTo{xxx} 0 does not center (broken in 13.1.16_dev_2013.05.23)
+bug fix: appending a model to a model with data can fail
+bug fix: hydrogen addition should not follow component file
+
+JmolVersion="14.2.12_2015.02.04"
+released
+
bug fix: show mouse fails in JavaScript
-- we cannot test using PT.isAI() in org.jmol.viewer.binding.Binding
- -- because of a Java2Script compiler creates standard array [...]
- -- from new int[] {....} whereas it should create Clazz.newArray() and fill
it
+ because the Java2Script compiler creates standard array [...]
+ from new int[] {....} whereas it should use Clazz.newIntArray(-1,....)
bug fix: label %r should print "1" for non-PDB file atoms
bug fix; lcaoCartoon broken in 14.3.10_2014.11.27/14.2.12_2015.01.22
bug fix: isosurface id surf1 solvent; select within(2.0, $surf1) broken
@@ -19,7 +26,7 @@
bug fix: select thisModel does not select all atoms in visible frame set
bug fix: select %w %x %y %z not implemented
-Jmol.___JmolVersion="14.2.12_2015.01.27"
+JmolVersion="14.2.12_2015.01.27"
bug fix: CGO LINE_LOOP not closing
bug fix: configuration 1 broken
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