Revision: 20483
http://sourceforge.net/p/jmol/code/20483
Author: hansonr
Date: 2015-05-07 11:51:43 +0000 (Thu, 07 May 2015)
Log Message:
-----------
JmolVersion="14.3.13_2015.05.07"
bug fix: isolated bio groups such as AMP, which are not part of biopolymers,
can result in crashes
when colored or queried about their parameters
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/modelsetbio/AlphaMonomer.java
trunk/Jmol/src/org/jmol/modelsetbio/AminoMonomer.java
trunk/Jmol/src/org/jmol/modelsetbio/Monomer.java
trunk/Jmol/src/org/jmol/modelsetbio/NucleicMonomer.java
trunk/Jmol/src/org/jmol/modelsetbio/PhosphorusMonomer.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/modelsetbio/AlphaMonomer.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/AlphaMonomer.java 2015-05-07
03:08:03 UTC (rev 20482)
+++ trunk/Jmol/src/org/jmol/modelsetbio/AlphaMonomer.java 2015-05-07
11:51:43 UTC (rev 20483)
@@ -226,6 +226,8 @@
}
protected Quat getQuaternionAlpha(char qType) {
+ if (monomerIndex < 0)
+ return null;
/*
* also NucleicMonomer, AminoMonomer
*
Modified: trunk/Jmol/src/org/jmol/modelsetbio/AminoMonomer.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/AminoMonomer.java 2015-05-07
03:08:03 UTC (rev 20482)
+++ trunk/Jmol/src/org/jmol/modelsetbio/AminoMonomer.java 2015-05-07
11:51:43 UTC (rev 20483)
@@ -208,7 +208,7 @@
public boolean getNHPoint(P3 aminoHydrogenPoint, V3 vNH,
boolean jmolHPoint, boolean dsspIgnoreHydrogens) {
- if (monomerIndex == 0 || groupID == JC.GROUPID_PROLINE)
+ if (monomerIndex <= 0 || groupID == JC.GROUPID_PROLINE)
return false;
Atom nitrogenPoint = getNitrogenAtom();
P3 nhPoint = getNitrogenHydrogenPoint();
@@ -252,6 +252,8 @@
@Override
P3 getQuaternionFrameCenter(char qType) {
+ if (monomerIndex < 0)
+ return null;
switch (qType) {
default:
case 'a':
@@ -278,6 +280,8 @@
@Override
public Quat getQuaternion(char qType) {
+ if (monomerIndex < 0)
+ return null;
/*
* also NucleicMonomer
*
Modified: trunk/Jmol/src/org/jmol/modelsetbio/Monomer.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/Monomer.java 2015-05-07 03:08:03 UTC
(rev 20482)
+++ trunk/Jmol/src/org/jmol/modelsetbio/Monomer.java 2015-05-07 11:51:43 UTC
(rev 20483)
@@ -44,6 +44,13 @@
import java.util.Map;
+/**
+ * A class to maintain information about biomolecule groups that are
(potentially)
+ * part of biopolymers -- peptides, nucleic acid strands, or complex
carbohydrates.
+ * Note that it is possible that a monomer is created but is not part of a
BioPolymer.
+ *
+ *
+ */
public abstract class Monomer extends Group {
@@ -58,6 +65,8 @@
protected byte[] offsets;
+ int monomerIndex = -1;
+
protected static boolean have(byte[] offsets, byte n) {
return (offsets[n] & 0xFF) != 0xFF;
}
@@ -76,26 +85,24 @@
leadAtomIndex = firstAtomIndex + offset;
}
- int monomerIndex;
-
void setBioPolymer(BioPolymer polymer, int index) {
- this.bioPolymer = polymer;
+ bioPolymer = polymer;
monomerIndex = index;
}
@Override
public int getSelectedMonomerCount() {
- return bioPolymer.getSelectedMonomerCount();
+ return (bioPolymer == null ? 0 : bioPolymer.getSelectedMonomerCount());
}
@Override
public int getSelectedMonomerIndex() {
- return (monomerIndex >= 0 && bioPolymer.isMonomerSelected(monomerIndex) ?
monomerIndex : -1);
+ return (bioPolymer == null || !bioPolymer.isMonomerSelected(monomerIndex)
? -1 : monomerIndex);
}
@Override
public int getBioPolymerLength() {
- return bioPolymer == null ? 0 : bioPolymer.monomerCount;
+ return (bioPolymer == null ? 0 : bioPolymer.monomerCount);
}
@Override
@@ -105,19 +112,21 @@
@Override
public int getAtomIndex(String name, int offset) {
- Group[] groups = bioPolymer.monomers;
- int ipt = monomerIndex + offset;
- if (ipt >= 0 && ipt < groups.length) {
- Group m = groups[ipt];
- if (offset == 1 && !m.isConnectedPrevious())
- return -1;
- if ("0".equals(name))
- return m.leadAtomIndex;
- Atom[] atoms = chain.model.ms.at;
- // this is OK -- only used for finding special atom by name
- for (int i = m.firstAtomIndex; i <= m.lastAtomIndex; i++)
- if (name == null || name.equalsIgnoreCase(atoms[i].getAtomName()))
- return i;
+ if (bioPolymer != null) {
+ Group[] groups = bioPolymer.monomers;
+ int ipt = monomerIndex + offset;
+ if (ipt >= 0 && ipt < groups.length) {
+ Group m = groups[ipt];
+ if (offset == 1 && !m.isConnectedPrevious())
+ return -1;
+ if ("0".equals(name))
+ return m.leadAtomIndex;
+ Atom[] atoms = chain.model.ms.at;
+ // this is OK -- only used for finding special atom by name
+ for (int i = m.firstAtomIndex; i <= m.lastAtomIndex; i++)
+ if (name == null || name.equalsIgnoreCase(atoms[i].getAtomName()))
+ return i;
+ }
}
return -1;
}
@@ -360,6 +369,8 @@
}
protected Object getHelixData2(int tokType, char qType, int mStep) {
+ if (monomerIndex < 0)
+ return null;
int iPrev = monomerIndex - mStep;
Monomer prev = (mStep < 1 || monomerIndex <= 0 ? null
: bioPolymer.monomers[iPrev]);
@@ -478,6 +489,8 @@
@Override
public float getGroupParameter(int tok) {
+ if (bioPolymer == null)
+ return 0;
if (!bioPolymer.haveParameters)
bioPolymer.calcParameters();
switch (tok) {
Modified: trunk/Jmol/src/org/jmol/modelsetbio/NucleicMonomer.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/NucleicMonomer.java 2015-05-07
03:08:03 UTC (rev 20482)
+++ trunk/Jmol/src/org/jmol/modelsetbio/NucleicMonomer.java 2015-05-07
11:51:43 UTC (rev 20483)
@@ -385,6 +385,8 @@
@Override
public Quat getQuaternion(char qType) {
+ if (bioPolymer == null)
+ return null;
// quaternionFrame 'c' from
// Sarver M, Zirbel CL, Stombaugh J, Mokdad A, Leontis NB.
// FR3D: finding local and composite recurrent structural motifs in RNA 3D
structures.
@@ -547,6 +549,7 @@
}
private Lst<BasePair> bps;
+
public void addBasePair(BasePair bp) {
if (bps == null)
bps = new Lst<BasePair>();
@@ -559,8 +562,12 @@
group1 = g;
}
+ /**
+ *
+ * @return list of base pairs associated with this monomer, possibly more
than one if noncanonical
+ */
public Lst<BasePair> getBasePairs() {
- if (!((NucleicPolymer) bioPolymer).isDssrSet)
+ if (bioPolymer != null && !((NucleicPolymer) bioPolymer).isDssrSet)
bioPolymer.model.ms.vwr.getAnnotationParser().setAllDSSRParametersForModel(bioPolymer.model.ms.vwr,
bioPolymer.model.modelIndex);
return bps;
}
Modified: trunk/Jmol/src/org/jmol/modelsetbio/PhosphorusMonomer.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/PhosphorusMonomer.java 2015-05-07
03:08:03 UTC (rev 20482)
+++ trunk/Jmol/src/org/jmol/modelsetbio/PhosphorusMonomer.java 2015-05-07
11:51:43 UTC (rev 20483)
@@ -131,7 +131,7 @@
//vA = ptP(i+1) - ptP
//vB = ptP(i-1) - ptP
int i = monomerIndex;
- if (i == 0 || i >= bioPolymer.monomerCount - 1)
+ if (i <= 0 || i >= bioPolymer.monomerCount - 1)
return null;
P3 ptP = bioPolymer.monomers[i].getAtomFromOffsetIndex(P);
P3 ptA, ptB;
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-05-07 03:08:03 UTC
(rev 20482)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-05-07 11:51:43 UTC
(rev 20483)
@@ -14,6 +14,12 @@
TODO: remove HTML5 dependency on synchronous file loading (check SCRIPT
command for problems)
+JmolVersion="14.3.13_2015.05.07"
+
+bug fix: isolated bio groups such as AMP, which are not part of biopolymers,
can result in crashes
+ when colored or queried about their parameters
+
+
Jmol.___JmolVersion="14.3.13_2015.05.06"
new feature: "drilling" in associative arrays for sub arrays with a given
property (Rolf Huehne)
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