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The protein structure modules of BioJava.
/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
package org.biojava.nbio.structure.xtal;
import org.biojava.nbio.structure.Calc;
import org.biojava.nbio.structure.Chain;
import org.biojava.nbio.structure.Structure;
import org.biojava.nbio.structure.StructureTools;
import org.biojava.nbio.structure.contact.BoundingBox;
import java.util.List;
import javax.vecmath.Matrix4d;
import javax.vecmath.Vector3d;
/**
* A class to contain the BoundingBoxes of all polymeric molecules in a full unit cell.
*
* @author Jose Duarte
*
*/
public class UnitCellBoundingBox {
/**
* An array with dimensions numOperatorsSg x numPolyChainsAu to contain all
* bounding boxes of all chains of all AUs in unit cell
* e.g. chainBbs[0] would be the bounding boxes for all chains in the original AU
*/
private BoundingBox[][] chainBbs;
/**
* An array with dimensions numOperatorsSg to contain all bounding boxes of
* all AUs in unit cell
*/
private BoundingBox[] auBbs;
private int numOperatorsSg; // i.e. multiplicity of space group
private int numPolyChainsAu;
public UnitCellBoundingBox(int numOperatorsSg, int numPolyChainsAu) {
this.numOperatorsSg = numOperatorsSg;
this.numPolyChainsAu = numPolyChainsAu;
this.chainBbs = new BoundingBox[numOperatorsSg][numPolyChainsAu];
this.auBbs = new BoundingBox[numOperatorsSg];
}
public void setBbs(Structure structure, Matrix4d[] ops, boolean includeHetAtoms) {
setBb(structure, includeHetAtoms, 0);
for (int i=1;i polyChains = s.getPolyChains();
int j = 0;
for (Chain polyChain : polyChains) {
chainBbs[i][j] = new BoundingBox(StructureTools.getAllNonHCoordsArray(polyChain, includeHetAtoms));
j++;
}
auBbs[i] = new BoundingBox(chainBbs[i]);
}
/**
* Get the chain BoundingBox for the given cell index (cellIdx=0 would be original AU)
* and chain index
* @param cellIdx
* @param chainIdx
* @return
*/
public BoundingBox getChainBoundingBox(int cellIdx, int chainIdx) {
return chainBbs[cellIdx][chainIdx];
}
/**
* Get the AU BoundingBox for the given cell index (cellIdx=0 would be original AU)
* The AU BoundingBox is the BoundingBox that bounds all chains belonging to the AU
* @param cellIdx
* @return
*/
public BoundingBox getAuBoundingBox(int cellIdx) {
return auBbs[cellIdx];
}
/**
* Returns a new BoundingBoxes object containing the same bounds as this
* BoundingBoxes object translated by the given translation
* @param translation
* @return
*/
public UnitCellBoundingBox getTranslatedBbs(Vector3d translation) {
UnitCellBoundingBox translatedBbs = new UnitCellBoundingBox(numOperatorsSg, numPolyChainsAu);
for (int i=0; i