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Curve/Protein/RibbonDiagram: Clean up and documentation improved
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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|
@@ -51,10 +51,19 @@ import kotlin.math.min | |
| * by Richardson et al.) | ||
| * | ||
| * @author Justin Buerger <[email protected]> | ||
| * @param [protein] The polypeptide you wish to visualize, stored in the class Protein | ||
| * | ||
| * @param [showSecondaryStructures] Whether or not to show secondary structures as well | ||
| * | ||
| * @param [verticesPerSection] How many vertices should be rendered per section. The default is 20, and can also | ||
| * be overridden by the system property `scenery.Proteins.VerticesPerSection`. | ||
| */ | ||
|
|
||
| class RibbonDiagram( | ||
| val protein: Protein, | ||
| private val showSecondaryStructures: Boolean = false, | ||
| val verticesPerSection: Int = System.getProperty("scenery.Proteins.VerticesPerSection", "20").toInt() | ||
| ): Mesh("ribbon") { | ||
|
|
||
| /* | ||
| *[structure] the structure of the protein stored in the class Structure of BioJava | ||
|
|
@@ -75,12 +84,11 @@ class RibbonDiagram(val protein: Protein, private val showSecondaryStructures: B | |
| */ | ||
| private val structure = protein.structure | ||
| private val chains = structure.chains | ||
| private val groups = chains.flatMap { it.atomGroups } | ||
| private val widthAlpha = 2.0f | ||
| private val widthBeta = 2.2f | ||
| private val widthCoil = 1.0f | ||
| private val chainList = ArrayList<List<Group>>(groups.size) | ||
| private val secStruc = dssp() | ||
| //calculate the centroid of the protein | ||
| private val centroid = Axis.getCentroid(groups.flatMap { it.atoms }.filter{it.name == "CA"}.map{it.getVector()}) | ||
|
|
@@ -129,31 +137,6 @@ class RibbonDiagram(val protein: Protein, private val showSecondaryStructures: B | |
| { splinePointCentered.subList(0, splinePointCentered.lastIndex) } | ||
| else{splinePointCentered} | ||
|
|
||
| /* | ||
| In the following lines of code(144-211), we build a curve for each secondary structure. How does this work, step | ||
| by step? First, we iterate through the guide points. A guide point represents a residue, therefore, it can be | ||
|
|
@@ -181,7 +164,7 @@ class RibbonDiagram(val protein: Protein, private val showSecondaryStructures: B | |
| val coils = Mesh("coil") | ||
|
|
||
| //exclude dummy points for spline calculation | ||
| val ssSections = getSecondaryStructureLengths(guidePointList.drop(1).dropLast(1), splinePoints, verticesPerSection) | ||
| //configure offset for helix computation below | ||
| var guidePointOffset = 1 | ||
| //iterate through all secondary structure sections | ||
|
|
@@ -199,15 +182,15 @@ class RibbonDiagram(val protein: Protein, private val showSecondaryStructures: B | |
| } | ||
| val axis = Axis(caList) | ||
| val axisLine = PositionDirection(axis.position, axis.direction) | ||
| val helixCurve = Helix(axisLine, DummySpline(subSpline, verticesPerSection)) { listOf(Shape.makeRectangle()) } | ||
| if (showSecondaryStructures) { | ||
| alphas.addChild(helixCurve) | ||
| } else { | ||
| subParent.addChild(helixCurve) | ||
| } | ||
| } | ||
| else { | ||
| val ssSubList = ArrayList<Shape>(verticesPerSection * length) | ||
|
|
||
| val iterationLength = subSpline.size | ||
|
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||
|
|
@@ -216,7 +199,7 @@ class RibbonDiagram(val protein: Protein, private val showSecondaryStructures: B | |
| if (type.isBetaStrand) { | ||
| val seventyPercent = (iterationLength * 0.70).toInt() | ||
| for (j in 0 until seventyPercent) { | ||
| ssSubList.add(Shape.makeReversedRectangle()) | ||
| } | ||
| val thirtyPercent = iterationLength - seventyPercent | ||
| for (j in thirtyPercent downTo 1) { | ||
|
|
@@ -232,18 +215,18 @@ class RibbonDiagram(val protein: Protein, private val showSecondaryStructures: B | |
| ) | ||
| } | ||
| val betaCurve = DefaultCurve( | ||
| DummySpline(subSpline, verticesPerSection), { ssSubList }) | ||
| if (showSecondaryStructures) { | ||
| betas.addChild(betaCurve) | ||
| } else { | ||
| subParent.addChild(betaCurve) | ||
| } | ||
| } else { | ||
| for (j in 0 until iterationLength) { | ||
| ssSubList.add(Shape.makeOctagon()) | ||
| } | ||
| val coilCurve = | ||
| DefaultCurve(DummySpline(subSpline, verticesPerSection), { ssSubList }) | ||
| if (showSecondaryStructures) { | ||
| coils.addChild(coilCurve) | ||
| } else { | ||
|
|
@@ -303,24 +286,27 @@ class RibbonDiagram(val protein: Protein, private val showSecondaryStructures: B | |
| * (a spline which list of controlPoints is equal to its guidePoints) | ||
| */ | ||
| private fun ribbonSpline(guidePoints: ArrayList<GuidePoint>): Spline { | ||
| val finalSpline = ArrayList<Vector3f>(guidePoints.size * verticesPerSection) | ||
| val skeleton = splineSkeleton(guidePoints) | ||
| val spline1 = UniformBSpline(skeleton.splineSkeleton1, verticesPerSection).splinePoints() | ||
| val spline2 = UniformBSpline(skeleton.splineSkeleton2, verticesPerSection).splinePoints() | ||
| spline1.forEachIndexed { i, _ -> | ||
| val splinePoint = Vector3f() | ||
| spline1[i].add(spline2[i], splinePoint) | ||
| splinePoint.mul(0.5f) | ||
| finalSpline.add(splinePoint) | ||
| } | ||
| return DummySpline(finalSpline, verticesPerSection) | ||
| } | ||
|
|
||
| companion object { | ||
|
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||
| /** | ||
| * Calculates the GuidePoints from the list of amino acids. | ||
| */ | ||
| @JvmStatic | ||
| fun calculateGuidePoints(aminoList: List<Group>, ssList: List<SecStrucElement>): ArrayList<GuidePoint> { | ||
| //To include all points in the visualization, dummy points need to be made. | ||
| //First, a list without these dummy points is calculated. | ||
|
|
@@ -510,6 +496,7 @@ class RibbonDiagram(val protein: Protein, private val showSecondaryStructures: B | |
| * Extension function to make a Vector out of an atom position. We do not | ||
| * need any information about an atom besides its name and its position. | ||
| */ | ||
| @JvmStatic | ||
| fun Atom.getVector(): Vector3f { | ||
| return Vector3f(this.x.toFloat(), this.y.toFloat(), this.z.toFloat()) | ||
| } | ||
|
|
||
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