Examples with Point3f javax.vecmath.Point3f used on opensource projects

Example 6 with Point3f

use of javax.vecmath.Point3f in project BuildCraft by BuildCraft.

the class PipeWireRenderer method getQuads.

private static MutableQuad[] getQuads(EnumWirePart part) {
    MutableQuad[] quads = new MutableQuad[6];
    Tuple3f center = new // 
    Point3f(// 
    0.5f + (part.x.getOffset() * 4.51f / 16f), // 
    0.5f + (part.y.getOffset() * 4.51f / 16f), // 
    0.5f + (part.z.getOffset() * 4.51f / 16f));
    Tuple3f radius = new Point3f(1 / 32f, 1 / 32f, 1 / 32f);
    UvFaceData uvs = new UvFaceData();
    int off = func(part.x) * 4 + func(part.y) * 2 + func(part.z);
    uvs.minU = off / 16f;
    uvs.maxU = (off + 1) / 16f;
    uvs.minV = 0;
    uvs.maxV = 1 / 16f;
    for (EnumFacing face : EnumFacing.VALUES) {
        quads[face.ordinal()] = ModelUtil.createFace(face, center, radius, uvs);
    }
    return quads;
}

Example 7 with Point3f

use of javax.vecmath.Point3f in project ffx by mjschnie.

the class GraphicsCanvas method postSwap.

/**
 * {@inheritDoc}
 *
 * Image capture from the 3D Canvas is done in postSwap.
 */
@Override
public void postSwap() {
    if (!imageCapture || mainPanel.getHierarchy().getActive() == null) {
        return;
    }
    GraphicsContext3D ctx = getGraphicsContext3D();
    Rectangle rect = getBounds();
    BufferedImage img = new BufferedImage(rect.width, rect.height, BufferedImage.TYPE_INT_RGB);
    ImageComponent2D comp = new ImageComponent2D(ImageComponent.FORMAT_RGB, img);
    Raster ras = new Raster(new Point3f(-1.0f, -1.0f, -1.0f), Raster.RASTER_COLOR, 0, 0, rect.width, rect.height, comp, null);
    ctx.readRaster(ras);
    img = ras.getImage().getImage();
    try {
        if (!ImageIO.write(img, imageFormat.toString(), imageName)) {
            logger.warning(String.format(" No image writer was found for %s.\n Please try a different image format.\n", imageFormat.toString()));
            imageName.delete();
        } else {
            logger.info(String.format(" %s was captured.", imageName));
        }
    } catch (IOException e) {
        logger.warning(e.getMessage());
    }
    imageCapture = false;
}

Example 8 with Point3f

use of javax.vecmath.Point3f in project mmtf-spark by sbl-sdsc.

the class StructureToBioassembly method call.

@Override
public Iterator<Tuple2<String, StructureDataInterface>> call(Tuple2<String, StructureDataInterface> t) throws Exception {
    StructureDataInterface structure = t._2;
    // Map<Integer, Integer> atomMap = new HashMap<>();
    List<Tuple2<String, StructureDataInterface>> resList = new ArrayList<>();
    // for each of them, create one structure.
    for (int i = 0; i < structure.getNumBioassemblies(); i++) {
        // initiate the bioassembly structure.
        AdapterToStructureData bioAssembly = new AdapterToStructureData();
        // set the structureID.
        String structureId = structure.getStructureId() + "-BioAssembly" + structure.getBioassemblyName(i);
        int totAtoms = 0, totBonds = 0, totGroups = 0, totChains = 0, totModels = 0;
        int numTrans = structure.getNumTransInBioassembly(i);
        totModels = structure.getNumModels();
        int[][] bioChainList = new int[numTrans][];
        double[][] transMatrix = new double[numTrans][];
        // calculate the total data we will use to initialize the structure.
        for (int ii = 0; ii < numTrans; ii++) {
            bioChainList[ii] = structure.getChainIndexListForTransform(i, ii);
            transMatrix[ii] = structure.getMatrixForTransform(i, ii);
            for (int j = 0; j < totModels; j++) {
                totChains += bioChainList[ii].length;
                // System.out.println(bioChainList[ii].length);
                for (int k = 0, groupCounter = 0; k < structure.getChainsPerModel()[j]; k++) {
                    boolean adding = false;
                    for (int currChain : bioChainList[ii]) {
                        if (currChain == k)
                            adding = true;
                    }
                    if (adding) {
                        // System.out.println("adding groups");
                        totGroups += structure.getGroupsPerChain()[k];
                    }
                    for (int h = 0; h < structure.getGroupsPerChain()[k]; h++, groupCounter++) {
                        if (adding) {
                            int groupIndex = structure.getGroupTypeIndices()[groupCounter];
                            totAtoms += structure.getNumAtomsInGroup(groupIndex);
                            totBonds += structure.getGroupBondOrders(groupIndex).length;
                        }
                    }
                }
            }
        }
        // init
        // System.out.println("Initializing the structure with\n"
        // + " totModel = " + totModels + ", totChains = " + totChains + ", totGroups = " + totGroups + ", totAtoms = "
        // + totAtoms + ", totBonds = " + totBonds + ", name : " + structureId);
        bioAssembly.initStructure(totBonds, totAtoms, totGroups, totChains, totModels, structureId);
        DecoderUtils.addXtalographicInfo(structure, bioAssembly);
        DecoderUtils.addHeaderInfo(structure, bioAssembly);
        /*
			 * Now we have bioChainList and transMatrix.
			 * bioChainList[i] is the ith trans' list of chains it has.  
			 * transMatrix[i] is the matrix that is going to be applied on those chains.
			 */
        // initialize the indices.
        int modelIndex = 0;
        int chainIndex = 0;
        int groupIndex = 0;
        int atomIndex = 0;
        int chainCounter = 0;
        // loop through models
        for (int ii = 0; ii < structure.getNumModels(); ii++) {
            // precalculate indices
            int numChainsPerModel = structure.getChainsPerModel()[modelIndex] * numTrans;
            bioAssembly.setModelInfo(modelIndex, numChainsPerModel);
            int[] chainToEntityIndex = getChainToEntityIndex(structure);
            // loop through chains
            for (int j = 0; j < structure.getChainsPerModel()[modelIndex]; j++) {
                // loop through each trans
                int currGroupIndex = groupIndex;
                int currAtomIndex = atomIndex;
                for (int k = 0; k < numTrans; k++) {
                    // get the currChainList that needs to be added
                    int[] currChainList = bioChainList[k];
                    double[] currMatrix = transMatrix[k];
                    boolean addThisChain = false;
                    for (int currChain : currChainList) {
                        if (currChain == j)
                            addThisChain = true;
                    }
                    groupIndex = currGroupIndex;
                    atomIndex = currAtomIndex;
                    float[] xCoords = structure.getxCoords();
                    float[] yCoords = structure.getyCoords();
                    float[] zCoords = structure.getzCoords();
                    float[] floatMatrix = Floats.toArray(Doubles.asList(currMatrix));
                    Matrix4f m = new Matrix4f(floatMatrix);
                    if (addThisChain) {
                        int entityToChainIndex = chainToEntityIndex[chainIndex];
                        // System.out.println("adding chain : " + chainIndex);
                        // TODO
                        // not sure
                        bioAssembly.setEntityInfo(new int[] { chainCounter }, structure.getEntitySequence(entityToChainIndex), structure.getEntityDescription(entityToChainIndex), structure.getEntityType(entityToChainIndex));
                        bioAssembly.setChainInfo(structure.getChainIds()[chainIndex], structure.getChainNames()[chainIndex], structure.getGroupsPerChain()[chainIndex]);
                        chainCounter++;
                    }
                    // loop through the groups in the chain
                    for (int jj = 0; jj < structure.getGroupsPerChain()[chainIndex]; jj++) {
                        int currgroup = structure.getGroupTypeIndices()[groupIndex];
                        if (addThisChain) {
                            bioAssembly.setGroupInfo(structure.getGroupName(currgroup), structure.getGroupIds()[groupIndex], structure.getInsCodes()[groupIndex], structure.getGroupChemCompType(currgroup), structure.getNumAtomsInGroup(currgroup), structure.getGroupBondOrders(currgroup).length, structure.getGroupSingleLetterCode(currgroup), structure.getGroupSequenceIndices()[groupIndex], structure.getSecStructList()[groupIndex]);
                        }
                        for (int kk = 0; kk < structure.getNumAtomsInGroup(currgroup); kk++) {
                            // System.out.println("currgroup : " + currgroup + " curratom : " + kk);
                            if (addThisChain) {
                                Point3f p1 = new Point3f(xCoords[atomIndex], yCoords[atomIndex], zCoords[atomIndex]);
                                m.transform(p1);
                                // System.out.println(kk + " " + currgroup);
                                bioAssembly.setAtomInfo(structure.getGroupAtomNames(currgroup)[kk], structure.getAtomIds()[atomIndex], structure.getAltLocIds()[atomIndex], p1.x, p1.y, p1.z, structure.getOccupancies()[atomIndex], structure.getbFactors()[atomIndex], structure.getGroupElementNames(currgroup)[kk], structure.getGroupAtomCharges(currgroup)[kk]);
                            }
                            // inc the atomIndex
                            atomIndex++;
                        }
                        if (addThisChain) {
                            for (int l = 0; l < structure.getGroupBondOrders(currgroup).length; l++) {
                                // System.out.println(structure.getGroupBondOrders(currgroup).length + " " + l);
                                int bondIndOne = structure.getGroupBondIndices(currgroup)[l * 2];
                                int bondIndTwo = structure.getGroupBondIndices(currgroup)[l * 2 + 1];
                                int bondOrder = structure.getGroupBondOrders(currgroup)[l];
                                bioAssembly.setGroupBond(bondIndOne, bondIndTwo, bondOrder);
                            }
                        }
                        // inc the groupIndex
                        groupIndex++;
                    }
                    if (addThisChain) {
                    // Add inter-group bond info
                    // for(int l = 0;  l < structure.getInterGroupBondOrders().length; l++){
                    // int bondIndOne = structure.getInterGroupBondIndices()[l*2];
                    // int bondIndTwo = structure.getInterGroupBondIndices()[l*2+1];
                    // int bondOrder = structure.getInterGroupBondOrders()[l];
                    // Integer indexOne = atomMap.get(bondIndOne);
                    // if (indexOne != null) {
                    // Integer indexTwo = atomMap.get(bondIndTwo);
                    // if (indexTwo != null) {
                    // bioAssembly.setInterGroupBond(indexOne, indexTwo, bondOrder);
                    // }
                    // }
                    }
                }
                // inc the chainIndex
                chainIndex++;
            }
            // inc the modelIndex
            modelIndex++;
        }
        bioAssembly.finalizeStructure();
        resList.add(new Tuple2<String, StructureDataInterface>(structureId, bioAssembly));
    }
    return resList.iterator();
}

Example 9 with Point3f

use of javax.vecmath.Point3f in project mmtf-spark by sbl-sdsc.

the class ColumnarStructureX method getcAlphaCoordinatesF.

public Point3f[] getcAlphaCoordinatesF() {
    List<Integer> indices = getCalphaAtomIndices();
    float[] x = getxCoords();
    float[] y = getyCoords();
    float[] z = getzCoords();
    Point3f[] calpha = new Point3f[indices.size()];
    for (int i = 0; i < calpha.length; i++) {
        int index = indices.get(i);
        calpha[i] = new Point3f(x[index], y[index], z[index]);
    }
    return calpha;
}

Example 10 with Point3f

use of javax.vecmath.Point3f in project Solar by Martacus.

the class PageRitualComponent method draw.

@Override
public void draw(int mouseX, int mouseY, FontRenderer fontRenderer) {
    int yTranslate = (160 - this.width) / 2;
    GlStateManager.translate(yTranslate, 30, 0);
    Matrix4f mat = getMatrix(GL11.GL_MODELVIEW_MATRIX);
    Point3f point = new Point3f();
    mat.transform(point);
    this.hovered = mouseX >= point.x && mouseY >= point.y && mouseX < point.x + this.width && mouseY < point.y + this.height;
    Minecraft mc = Minecraft.getMinecraft();
    GlStateManager.enableBlend();
    GlStateManager.enableAlpha();
    GlStateManager.disableLighting();
    mc.fontRenderer.drawString(this.text, 0, 0, Color.BLACK.getRGB());
    if (this.hovered) {
        this.drawHorizontalLine(0, this.width, 9, Color.BLACK.getRGB());
    }
    GlStateManager.enableLighting();
    GlStateManager.disableAlpha();
    GlStateManager.disableBlend();
}