Revision: 20271
http://sourceforge.net/p/jmol/code/20271
Author: hansonr
Date: 2015-02-08 03:21:49 +0000 (Sun, 08 Feb 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.3.12_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: 02.04 select conformation=1 broken
bug fix: 02.04 select within(chain,...) broken
bug fix: hydrogen addition should not follow component file
ILE7 HG12 != ILE7 HG13
ILE7 HG13 != ILE7 HG12
ARG10 HB2 != ARG10 HB3
ARG10 HB3 != ARG10 HB2
ARG10 HG2 != ARG10 HG3
ARG10 HG3 != ARG10 HG2
ARG10 HD2 != ARG10 HD3
ARG10 HD3 != ARG10 HD2
LEU18 HB3 != LEU18 HB2
LEU18 HB2 != LEU18 HB3
PRO19 HD2 != PRO19 HD3
PRO19 HD3 != PRO19 HD2
ILE25 HG12 != ILE25 HG13
ILE25 HG13 != ILE25 HG12
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/modelsetbio/Resolver.java
trunk/Jmol/src/org/jmol/script/ScriptEval.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/openscience/jmol/app/nbo/NBOService.java
Modified: trunk/Jmol/src/org/jmol/modelsetbio/Resolver.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/Resolver.java 2015-02-07 23:56:03 UTC
(rev 20270)
+++ trunk/Jmol/src/org/jmol/modelsetbio/Resolver.java 2015-02-08 03:21:49 UTC
(rev 20271)
@@ -128,7 +128,7 @@
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;
}
@@ -925,13 +925,13 @@
target = "HB3@HB2";
break;
case 'D': // CD
- target = "HD2@HD3";
+ target = "HD3@HD2";
break;
case 'G': // CG
target = "HG3@HG2";
break;
case '2': // C2'
- target = "H2''@H2'";
+ target = "H2'@H2''";
break;
case '5': // C5'
target = "H5''@H5'";
@@ -961,43 +961,43 @@
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
- // 2005.02.05 fixing methylene atom names
+ // 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 HB3@HB2 CG HG3@HG2 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 HG13@HG12 CG2 HG2? CD1 HD1?",
- /*LEU*/ "N N CA HA C O CB HB3@HB2 CG HG CD1 HD1? CD2 HD2?",
+ /*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 HD3@HD2",
+ /*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 = {
@@ -1023,7 +1023,7 @@
/*TYR*/ 10,
/*VAL*/ 10,
/*ASX*/ 3,
- /*GSX*/ 5,
+ /*GLX*/ 5,
/*UNK*/ 0,
/*G*/ 13,
/*C*/ 13,
@@ -1250,6 +1250,32 @@
return s.toString().substring(1);
}
+ @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;
+ 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]);
@@ -1744,31 +1770,6 @@
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;
- 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: trunk/Jmol/src/org/jmol/script/ScriptEval.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEval.java 2015-02-07 23:56:03 UTC
(rev 20270)
+++ trunk/Jmol/src/org/jmol/script/ScriptEval.java 2015-02-08 03:21:49 UTC
(rev 20271)
@@ -8168,10 +8168,10 @@
}
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: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-02-07 23:56:03 UTC
(rev 20270)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-02-08 03:21:49 UTC
(rev 20271)
@@ -15,12 +15,13 @@
TODO: remove HTML5 dependency on synchronous file loading (check SCRIPT
command for problems)
TODO: add 2D graphics panel for Ramachandran and NBO-style 2D graphics -- send
to browser as data uri?
-Jmol.___JmolVersion="14.3.12_2015.02.06"
+Jmol.___JmolVersion="14.3.12_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: 02.04 select conformation=1 broken
bug fix: 02.04 select within(chain,...) broken
-
+
bug fix: hydrogen addition should not follow component file
ILE7 HG12 != ILE7 HG13
ILE7 HG13 != ILE7 HG12
Modified: trunk/Jmol/src/org/openscience/jmol/app/nbo/NBOService.java
===================================================================
--- trunk/Jmol/src/org/openscience/jmol/app/nbo/NBOService.java 2015-02-07
23:56:03 UTC (rev 20270)
+++ trunk/Jmol/src/org/openscience/jmol/app/nbo/NBOService.java 2015-02-08
03:21:49 UTC (rev 20271)
@@ -36,7 +36,6 @@
import java.util.Map;
import java.util.Scanner;
-import javajs.util.Lst;
import javajs.util.PT;
import javajs.util.SB;
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