Examples with DistanceBox org.biojava.nbio.structure.symmetry.geometry.DistanceBox used on opensource projects

Example 1 with DistanceBox

use of org.biojava.nbio.structure.symmetry.geometry.DistanceBox in project mmtf-spark by sbl-sdsc.

the class StructureToProteinDimers method getAllAtomsDistanceBoxes.

private static List<DistanceBox<Integer>> getAllAtomsDistanceBoxes(List<StructureDataInterface> chains, double cutoffDistance) {
    List<DistanceBox<Integer>> distanceBoxes = new ArrayList<DistanceBox<Integer>>();
    for (int i = 0; i < chains.size(); i++) {
        StructureDataInterface tmp = chains.get(i);
        DistanceBox<Integer> newBox = new DistanceBox<Integer>(cutoffDistance);
        // System.out.println(tmp.getNumAtoms());
        for (int j = 0; j < tmp.getNumAtoms(); j++) {
            double xCoord = tmp.getxCoords()[j];
            double yCoord = tmp.getyCoords()[j];
            double zCoord = tmp.getzCoords()[j];
            Point3d newPoint = new Point3d(xCoord, yCoord, zCoord);
            // System.out.println(newPoint);
            newBox.addPoint(newPoint, j);
        }
        distanceBoxes.add(newBox);
    }
    return distanceBoxes;
}

Example 2 with DistanceBox

use of org.biojava.nbio.structure.symmetry.geometry.DistanceBox in project mmtf-spark by sbl-sdsc.

the class StructureToProteinDimers method call.

@Override
public Iterator<Tuple2<String, StructureDataInterface>> call(Tuple2<String, StructureDataInterface> t) throws Exception {
    StructureDataInterface structure = t._2;
    List<Tuple2<String, StructureDataInterface>> resList = new ArrayList<>();
    // split the structure into a list of structure of chains
    List<StructureDataInterface> chains = splitToChains(structure);
    List<Vector3d> chainVectors = getChainVectors(chains);
    // for each chain, create a distance box
    List<DistanceBox<Integer>> boxes;
    if (useAllAtoms == true)
        boxes = getAllAtomsDistanceBoxes(chains, cutoffDistance);
    else
        boxes = getCBetaAtomsDistanceBoxes(chains, cutoffDistance);
    List<Vector3d> exclusiveList = new ArrayList<Vector3d>();
    // loop through chains
    for (int i = 0; i < chains.size(); i++) {
        for (int j = 0; j < i; j++) {
            // for each pair of chains, check if they are in contact or not
            if (checkPair(boxes.get(i), boxes.get(j), chains.get(i), chains.get(j), cutoffDistance, contacts)) {
                if (exclusive) {
                    // String es1 = chains.get(i).getEntitySequence(getChainToEntityIndex(chains.get(i))[0]);
                    // String es2 = chains.get(j).getEntitySequence(getChainToEntityIndex(chains.get(j))[0]);
                    Vector3d newVec = calcDiff(chainVectors.get(i), chainVectors.get(j));
                    // System.out.println(newVec);
                    if (!checkList(newVec, exclusiveList)) {
                        resList.add(combineChains(chains.get(i), chains.get(j)));
                        exclusiveList.add(newVec);
                    }
                } else
                    resList.add(combineChains(chains.get(i), chains.get(j)));
            }
        }
    }
    // System.out.println(exclusiveList);
    return resList.iterator();
}

Example 3 with DistanceBox

use of org.biojava.nbio.structure.symmetry.geometry.DistanceBox in project mmtf-spark by sbl-sdsc.

the class StructureToAtomInteractions method getDistanceBox.

private DistanceBox<Integer> getDistanceBox(ColumnarStructure arrays) {
    DistanceBox<Integer> box = new DistanceBox<>(filter.getDistanceCutoff());
    float[] x = arrays.getxCoords();
    float[] y = arrays.getyCoords();
    float[] z = arrays.getzCoords();
    String[] elements = arrays.getElements();
    String[] groupNames = arrays.getGroupNames();
    for (int i = 0; i < arrays.getNumAtoms(); i++) {
        if (filter.isTargetGroup(groupNames[i]) && filter.isTargetElement(elements[i])) {
            box.addPoint(new Point3d(x[i], y[i], z[i]), i);
        }
    }
    return box;
}

Example 4 with DistanceBox

use of org.biojava.nbio.structure.symmetry.geometry.DistanceBox in project mmtf-spark by sbl-sdsc.

the class StructureToProteinDimers method getCBetaAtomsDistanceBoxes.

private static List<DistanceBox<Integer>> getCBetaAtomsDistanceBoxes(List<StructureDataInterface> chains, double cutoffDistance) {
    List<DistanceBox<Integer>> distanceBoxes = new ArrayList<DistanceBox<Integer>>();
    for (int i = 0; i < chains.size(); i++) {
        StructureDataInterface tmp = chains.get(i);
        DistanceBox<Integer> newBox = new DistanceBox<Integer>(cutoffDistance);
        int groupIndex = 0;
        int atomIndex = 0;
        for (int k = 0; k < tmp.getGroupsPerChain()[0]; k++) {
            int groupType = tmp.getGroupTypeIndices()[groupIndex];
            for (int m = 0; m < tmp.getNumAtomsInGroup(groupType); m++) {
                String atomName = tmp.getGroupAtomNames(groupType)[m];
                if (atomName.equals("CB")) {
                    double xCoord = tmp.getxCoords()[atomIndex];
                    double yCoord = tmp.getyCoords()[atomIndex];
                    double zCoord = tmp.getzCoords()[atomIndex];
                    Point3d newPoint = new Point3d(xCoord, yCoord, zCoord);
                    newBox.addPoint(newPoint, atomIndex);
                }
                atomIndex++;
            }
            groupIndex++;
        }
        distanceBoxes.add(newBox);
    }
    return distanceBoxes;
}