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package proteinstructure; |
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import java.util.TreeMap; |
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import javax.vecmath.Point3d; |
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import javax.vecmath.Point3i; |
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|
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public class Box { |
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Point3i floor; |
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|
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private TreeMap<Integer,Point3d> i_pointsInBox; |
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private TreeMap<Integer,Point3d> j_pointsInBox; |
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|
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public Box(Point3i floor){ |
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this.floor=floor; |
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i_pointsInBox = new TreeMap<Integer, Point3d>(); |
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j_pointsInBox = new TreeMap<Integer, Point3d>(); |
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} |
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|
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public void put_i_Point(int serial, Point3d point){ |
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i_pointsInBox.put(serial, point); |
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} |
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|
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public void put_j_Point(int serial, Point3d point){ |
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j_pointsInBox.put(serial, point); |
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} |
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public void getDistancesWithinBox(float[][] distMatrix, boolean crossed){ //we pass a reference to the distMatrix that we alter within this method |
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for (int i_serial:i_pointsInBox.keySet()) { |
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for (int j_serial:j_pointsInBox.keySet()) { |
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if (!crossed) { |
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if (j_serial>i_serial) { |
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// this only works if previously we have made sure that atom serials are sequential from 0 to MAXATOMSERIAL |
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distMatrix[i_serial][j_serial] = (float)i_pointsInBox.get(i_serial).distance(j_pointsInBox.get(j_serial)); |
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} |
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} else { |
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// We need to check this because it can happen when the 2 contact types (i/j) have overlapping atoms, e.g. ALL/BB |
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// It is not strictly necessary, because distance in case i=j would be 0 (atom to itself). It's just to make sure that |
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// there wouldn't be rounding problems in comparing to 0.0 in get_graph in Pdb |
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if (j_serial!=i_serial) { |
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distMatrix[i_serial][j_serial] = (float)i_pointsInBox.get(i_serial).distance(j_pointsInBox.get(j_serial)); |
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} |
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} |
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} |
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} |
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|
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} |
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|
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public void getDistancesToNeighborBox(Box nbBox ,float[][] distMatrix, boolean crossed){ |
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for (int i_serial:i_pointsInBox.keySet()){ |
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for (int j_serial:nbBox.j_pointsInBox.keySet()){ |
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if (!crossed) { |
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if (j_serial>i_serial) { |
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// this only works if previously we have made sure that atom serials are sequential from 0 to MAXATOMSERIAL |
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if (distMatrix[i_serial][j_serial]==0.0f){ // i.e. if we haven't passed through this cell yet |
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distMatrix[i_serial][j_serial] = (float)i_pointsInBox.get(i_serial).distance(nbBox.j_pointsInBox.get(j_serial)); |
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} |
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} |
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} else { |
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distMatrix[i_serial][j_serial] = (float)i_pointsInBox.get(i_serial).distance(nbBox.j_pointsInBox.get(j_serial)); |
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} |
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} |
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} |
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} |
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|
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// Beware, this returns only the size for i |
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public int size() { |
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return i_pointsInBox.size(); |
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} |
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|
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} |
