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sblivensbliven
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Add information for construction of full list of symmetry axes.
For debugging, temporarily switched all axes to be default. Add CyclicForm methods to SymmetryAxes, which give a more compact representation of the aligned repeats
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4 files changed

+281
-49
lines changed

4 files changed

+281
-49
lines changed

‎biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryDisplay.java‎

Lines changed: 24 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -30,22 +30,22 @@
3030
import javax.swing.JMenu;
3131
import javax.swing.JMenuBar;
3232
import javax.swing.JMenuItem;
33-
import javax.vecmath.Matrix4d;
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3534
import org.biojava.nbio.structure.Atom;
3635
import org.biojava.nbio.structure.Group;
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import org.biojava.nbio.structure.StructureException;
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import org.biojava.nbio.structure.StructureTools;
38+
import org.biojava.nbio.structure.align.gui.MultipleAlignmentJmolDisplay;
3939
import org.biojava.nbio.structure.align.gui.StructureAlignmentDisplay;
4040
import org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol;
41-
import org.biojava.nbio.structure.align.gui.MultipleAlignmentJmolDisplay;
4241
import org.biojava.nbio.structure.align.gui.jmol.MultipleAlignmentJmol;
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import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
4443
import org.biojava.nbio.structure.align.util.RotationAxis;
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import org.biojava.nbio.structure.symmetry.core.AxisAligner;
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import org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults;
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import org.biojava.nbio.structure.symmetry.internal.CeSymmResult;
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import org.biojava.nbio.structure.symmetry.internal.SymmetryAxes;
48+
import org.biojava.nbio.structure.symmetry.internal.SymmetryAxes.Axis;
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import org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator;
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import org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup;
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import org.biojava.nbio.structure.symmetry.utils.SymmetryTools;
@@ -208,16 +208,35 @@ private static void addSymmetryMenu(MultipleAlignmentJmol jmol,
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*/
209209
public static String printSymmetryAxes(CeSymmResult symm)
210210
throws StructureException {
211+
return printSymmetryAxes(symm,true);
212+
}
213+
/**
214+
* Generates a String that displays the symmetry axes of a structure.
215+
*
216+
* @param symm
217+
* CeSymmResult
218+
* @param allAxes Indicates whether all axes should be displayed or just
219+
* the elemenatary ones
220+
* @return
221+
* @throws StructureException
222+
*/
223+
public static String printSymmetryAxes(CeSymmResult symm,boolean allAxes)
224+
throws StructureException {
211225

212226
int id = 0;
213227
String script = "";
214228
SymmetryAxes axes = symm.getAxes();
215229
List<Atom[]> repeats = SymmetryTools.toRepeatsAlignment(symm)
216230
.getAtomArrays();
217231

218-
List<Matrix4d> symmAxes = axes.getElementaryAxes();
219-
for (int a = 0; a < symmAxes.size(); a++) {
220-
RotationAxis rot = new RotationAxis(symmAxes.get(a));
232+
List<Axis> symmAxes;
233+
if(allAxes) {
234+
symmAxes = axes.getSymmetryAxes();
235+
} else {
236+
symmAxes= axes.getElementaryAxesObjects();
237+
}
238+
for (Axis a : symmAxes) {
239+
RotationAxis rot = a.getRotationAxis();
221240
Set<Integer> repIndex = new TreeSet<Integer>(axes
222241
.getRepeatRelation(a).get(0));
223242
repIndex.addAll(axes.getRepeatRelation(a).get(1));

‎biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/RotationAxis.java‎

Lines changed: 43 additions & 20 deletions
Original file line numberDiff line numberDiff line change
@@ -25,6 +25,7 @@
2525
import org.biojava.nbio.structure.Calc;
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import org.biojava.nbio.structure.StructureException;
2727
import org.biojava.nbio.structure.align.model.AFPChain;
28+
import org.biojava.nbio.structure.contact.Pair;
2829
import org.biojava.nbio.structure.jama.Matrix;
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import javax.vecmath.AxisAngle4d;
@@ -112,6 +113,10 @@ public Atom getScrewTranslation() {
112113
public Vector3d getVector3dScrewTranslation() {
113114
return new Vector3d(screwTranslation.getX(),screwTranslation.getY(),screwTranslation.getZ());
114115
}
116+
117+
public double getTranslation() {
118+
return Calc.amount(screwTranslation);
119+
}
115120

116121
/**
117122
* Get the component of translation perpendicular to the axis of rotation.
@@ -385,27 +390,17 @@ public String getJmolScript(Atom[] atoms){
385390
}
386391

387392
/**
388-
* Returns a Jmol script which will display the axis of rotation. This
389-
* consists of a cyan arrow along the axis, plus an arc showing the angle
390-
* of rotation.
393+
* Find a segment of the axis that covers the specified set of atoms.
391394
* <p>
392-
* As the rotation angle gets smaller, the axis of rotation becomes poorly
393-
* defined and would need to get farther and farther away from the protein.
394-
* This is not particularly useful, so we arbitrarily draw it parallel to
395-
* the translation and omit the arc.
396-
* @param atoms Some atoms from the protein, used for determining the bounds
397-
* of the axis.
398-
* @param axisID in case of representing more than one axis in the same jmol
399-
* panel, indicate the ID number.
400-
*
401-
* @return The Jmol script, suitable for calls to
402-
* {@link org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol#evalString() jmol.evalString()}
395+
* Projects the input atoms onto the rotation axis and returns the bounding
396+
* points.
397+
* <p>
398+
* In the case of a pure translational axis, the axis location is undefined
399+
* so the center of mass will be used instead.
400+
* @param atoms
401+
* @return two points defining the axis segment
403402
*/
404-
public String getJmolScript(Atom[] atoms, int axisID){
405-
final double width=.5;// width of JMol object
406-
final String axisColor = "yellow"; //axis color
407-
final String screwColor = "orange"; //screw translation color
408-
403+
public Pair<Atom> getAxisEnds(Atom[] atoms) {
409404
// Project each Atom onto the rotation axis to determine limits
410405
double min, max;
411406
min = max = Calc.scalarProduct(rotationAxis,atoms[0]);
@@ -417,7 +412,7 @@ public String getJmolScript(Atom[] atoms, int axisID){
417412
double uLen = Calc.scalarProduct(rotationAxis,rotationAxis);// Should be 1, but double check
418413
min/=uLen;
419414
max/=uLen;
420-
415+
421416
// Project the origin onto the axis. If the axis is undefined, use the center of mass
422417
Atom axialPt;
423418
if(rotationPos == null) {
@@ -439,6 +434,34 @@ public String getJmolScript(Atom[] atoms, int axisID){
439434
Atom axisMax = (Atom) axialPt.clone();
440435
Calc.scaleAdd(max, rotationAxis, axisMax);
441436

437+
return new Pair<>(axisMin, axisMax);
438+
}
439+
/**
440+
* Returns a Jmol script which will display the axis of rotation. This
441+
* consists of a cyan arrow along the axis, plus an arc showing the angle
442+
* of rotation.
443+
* <p>
444+
* As the rotation angle gets smaller, the axis of rotation becomes poorly
445+
* defined and would need to get farther and farther away from the protein.
446+
* This is not particularly useful, so we arbitrarily draw it parallel to
447+
* the translation and omit the arc.
448+
* @param atoms Some atoms from the protein, used for determining the bounds
449+
* of the axis.
450+
* @param axisID in case of representing more than one axis in the same jmol
451+
* panel, indicate the ID number.
452+
*
453+
* @return The Jmol script, suitable for calls to
454+
* {@link org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol#evalString() jmol.evalString()}
455+
*/
456+
public String getJmolScript(Atom[] atoms, int axisID){
457+
final double width=.5;// width of JMol object
458+
final String axisColor = "yellow"; //axis color
459+
final String screwColor = "orange"; //screw translation color
460+
461+
Pair<Atom> endPoints = getAxisEnds(atoms);
462+
Atom axisMin = endPoints.getFirst();
463+
Atom axisMax = endPoints.getSecond();
464+
442465
StringWriter result = new StringWriter();
443466

444467
// set arrow heads to a reasonable length

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