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Fix CE-Symm bug with short repeats #1101

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Merged
sbliven merged 5 commits into from
Sep 4, 2024
Merged

Fix CE-Symm bug with short repeats #1101

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403241f
Fix some typos
sbliven Aug 30, 2024
e9e0f00
Add test for rcsb/symmetry#118
sbliven Aug 30, 2024
57a487d
Fix CE-Symm bug relating to short subunits.
sbliven Aug 30, 2024
bfbe710
Fix test result.
sbliven Aug 30, 2024
5b35c70
Add additional error checks to QuatSymmetry functions
sbliven Aug 30, 2024
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Fix some typos 
Most are in docstrings. One misspelled public method has been deprecated.
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@sbliven
sbliven committed Aug 30, 2024
commit 403241f1c45b9ceef58450cd1e6d42ad41ef9a80
2 changes: 1 addition & 1 deletion biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MenuCreator.java
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Expand Up @@ -76,7 +76,7 @@ public class MenuCreator {
* Menus included:
* <ul><li>File: open, save, export, import, exit.
* <li>Align: new pairwise alignment, new multiple alignment.
* <li>View: aligment panel, aligned pairs, text format,
* <li>View: alignment panel, aligned pairs, text format,
* FatCat format, distance matrices, dot plot.
* <li>Help
* </ul>
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11 changes: 10 additions & 1 deletion ...-gui/src/main/java/org/biojava/nbio/structure/align/gui/MultipleAlignmentJmolDisplay.java
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Expand Up @@ -92,6 +92,15 @@ else if (pos < ca.length) {
return lst;
}

/**
* @deprecated Replace with {@see showMultipleAlignmentPanel}
*/
@Deprecated
public static void showMultipleAligmentPanel(MultipleAlignment multAln,
AbstractAlignmentJmol jmol) throws StructureException {
showMultipleAlignmentPanel(multAln, jmol);
}

/**
* Creates a new Frame with the MultipleAlignment Sequence Panel.
* The panel can communicate with the Jmol 3D visualization by
Expand All @@ -102,7 +111,7 @@ else if (pos < ca.length) {

* @throws StructureException
*/
public static void showMultipleAligmentPanel(MultipleAlignment multAln,
public static void showMultipleAlignmentPanel(MultipleAlignment multAln,
AbstractAlignmentJmol jmol) throws StructureException {

MultipleAligPanel me = new MultipleAligPanel(multAln, jmol);
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2 changes: 1 addition & 1 deletion ...-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MySaveFileListener.java
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Expand Up @@ -47,7 +47,7 @@
* and from a Jmol view an XML format is saved.
*
* @author Aleix Lafita
* @version 2.0 - adapted for MultipleAligments
* @version 2.0 - adapted for MultipleAlignments
*
*/
public class MySaveFileListener implements ActionListener {
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2 changes: 1 addition & 1 deletion ...re-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/MultipleAlignmentJmol.java
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Expand Up @@ -385,7 +385,7 @@ public void actionPerformed(ActionEvent ae) {
.showAlignmentImage(multAln, result);

} else if (cmd.equals(MenuCreator.ALIGNMENT_PANEL)) {
MultipleAlignmentJmolDisplay.showMultipleAligmentPanel(multAln,
MultipleAlignmentJmolDisplay.showMultipleAlignmentPanel(multAln,
this);

} else if (cmd.equals(MenuCreator.FATCAT_TEXT)) {
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11 changes: 6 additions & 5 deletions ...org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorPointGroup.java
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Expand Up @@ -684,7 +684,8 @@ private String drawSymmetryAxes() {
return s.toString();
}

private Vector3d getAligmentVector(Point3d point, Vector3d axis) {

private Vector3d getAlignmentVector(Point3d point, Vector3d axis) {
// for system with a single Cn axis
if (rotationGroup.getPointGroup().startsWith("C") || rotationGroup.getPointGroup().startsWith("D")) {
// if axis is orthogonal to principal axis, use principal axis as reference axis
Expand Down Expand Up @@ -760,14 +761,14 @@ private String getSymmetryAxis(int i, int j, String pointGroup, int n, Vector3d
if (drawPolygon) {
double polygonRadius = getMeanExtension() * 0.06;
if (n == 2) {
referenceAxis = getAligmentVector(p1, axis);
referenceAxis = getAlignmentVector(p1, axis);
s.append(getC2PolygonJmol(i, p1, referenceAxis, axis, color, polygonRadius, name));
referenceAxis = getAligmentVector(p2, axis);
referenceAxis = getAlignmentVector(p2, axis);
s.append(getC2PolygonJmol(j, p2, referenceAxis, axis, color, polygonRadius, name));
} else if (n > 2) {
referenceAxis = getAligmentVector(p1, axis);
referenceAxis = getAlignmentVector(p1, axis);
s.append(getPolygonJmol(i, p1, referenceAxis, axis, n, color, polygonRadius, name));
referenceAxis = getAligmentVector(p2, axis);
referenceAxis = getAlignmentVector(p2, axis);
s.append(getPolygonJmol(j, p2, referenceAxis, axis, n, color, polygonRadius, name));
}
}
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8 changes: 4 additions & 4 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/Block.java
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Expand Up @@ -124,8 +124,8 @@ public interface Block extends ScoresCache {

/**
* Calculates and returns the first position of the specified structure in
* the alignment that is not null. This will return the aligment index, not
* the reisude aligned in that position.
* the alignment that is not null. This will return the alignment index, not
* the residue aligned in that position.
*
* @param str
* structure index
Expand All @@ -148,8 +148,8 @@ public interface Block extends ScoresCache {

/**
* Calculates and returns the last position of the specified structure in
* the alignment that is not null. This will return the aligment index, not
* the reisude aligned in that position.
* the alignment that is not null. This will return the alignment index, not
* the residue aligned in that position.
*
* @param str
* structure index
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2 changes: 1 addition & 1 deletion ...cture/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcOptimizer.java
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Expand Up @@ -210,7 +210,7 @@ private void initialize() throws StructureException {
}
}

// Set the superposition and score for the seed aligment
// Set the superposition and score for the seed alignment
checkGaps();
msa.clear();
imposer.superimpose(msa);
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2 changes: 1 addition & 1 deletion .../src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentTools.java
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Expand Up @@ -721,7 +721,7 @@ public static List<Atom[]> transformAtoms(MultipleAlignment alignment) {

/**
* Calculate a List of alignment indicies that correspond to the core of a
* Block, which means that all structures have a residue in that positon.
* Block, which means that all structures have a residue in that position.
*
* @param block
* alignment Block
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4 changes: 2 additions & 2 deletions ...tructure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetrySubunits.java
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Expand Up @@ -213,7 +213,7 @@ private void run() {
calcOriginalCenters();
calcCentroid();
calcCenters();
calcMomentsOfIntertia();
calcMomentsOfInertia();
}

private void calcOriginalCenters() {
Expand Down Expand Up @@ -272,7 +272,7 @@ public Point3d getUpperBound() {
return upper;
}

private void calcMomentsOfIntertia() {
private void calcMomentsOfInertia() {
for (Point3d[] trace : caCoords) {
for (Point3d p : trace) {
momentsOfInertia.addPoint(p, 1.0f);
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2 changes: 1 addition & 1 deletion ...a-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmOptimizer.java
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Expand Up @@ -101,7 +101,7 @@ public class SymmOptimizer {
private List<Double> mcScoreHistory;

/**
* Constructor with a seed MultipleAligment storing a refined symmetry
* Constructor with a seed MultipleAlignment storing a refined symmetry
* alignment of the repeats. To perform the optimization use the call or
* optimize methods after instantiation.
*
Expand Down