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The protein structure modules of BioJava.
There is a newer version: 7.1.3
/*
 *                    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.domain.pdp;

import org.biojava.nbio.structure.*;


public class GetDistanceMatrix {


	/** A set of Calpha atoms that are representing the protein
	 *
	 * @param protein
	 */
	public  PDPDistanceMatrix getDistanceMatrix(Atom[] protein) throws StructureException{
		int[][] dist = new int[protein.length+3][protein.length+3];
		int i,j;
		double d,dt1,dt2,dt3,dt4;
		int nclose=0;
		int[] iclose = new int[protein.length*protein.length];
		int[] jclose= new int[protein.length*protein.length];

		if(protein.length >= PDPParameters.MAXLEN) {
			System.err.println(String.format("%d protein.len > MAXLEN %d\n",protein.length,PDPParameters.MAXLEN));
			return null;
		}
		for(i=0;i35) {
							iclose[nclose]=i;
							jclose[nclose]=j;
							nclose++;
						}
						if(d=2&&j-i>5) {
					if(dist[i-1][j-1]>=2&&dist[i+1][j+1]>=2||dist[i-1][j+1]>=2&&dist[i+1][j-1]>=2) {
						dist[i][j]+=4;
						dist[j][i]+=4;
						/*
					printf("1: %d %d %d\n",i,j,dist[i][j]);
						 */
					}
					/* alpha-helices */
					else if(i>2&&j=1&&dist[i+3][j+3]>=1||dist[i-3][j+3]>=1&&dist[i+3][j-3]>=1) {
							dist[i][j]+=4;
							dist[j][i]+=4;
							/*
						printf("3: %d %d %d\n",i,j,dist[i][j]);
							 */
						}
						else if(i>3&&j=1||dist[i-3][j-4]>=1||dist[i-4][j-3]>=1||dist[i-4][j-4]>=1)&&
									(dist[i+4][j+4]>=1||dist[i+4][j+3]>=1||dist[i+3][j+3]>=1||dist[i+3][j+4]>=1)
									||(dist[i-4][j+4]>=1||dist[i-4][j+3]>=1||dist[i-3][j+4]>=1||dist[i-3][j+3]>=1)&&
									(dist[i+4][j-4]>=1||dist[i+4][j-3]>=1||dist[i+3][j-4]>=1||dist[i+3][j-3]>=1)) {
								dist[i][j]+=4;
								dist[j][i]+=4;
								/*
							printf("4: %d %d %d\n",i,j,dist[i][j]);
								 */
							}
						}
					}
				}
			}
		}

		PDPDistanceMatrix matrix = new PDPDistanceMatrix();

		matrix.setNclose(nclose);
		matrix.setIclose(iclose);
		matrix.setJclose(jclose);
		matrix.setDist(dist);
		return matrix;

	}



	private Atom getCBeta(Group g1) {
		Atom cb = null;


		cb = g1.getAtom("CB");
		if ( cb == null)
			{
			if ( g1 instanceof AminoAcid) {
				AminoAcid aa = (AminoAcid) g1;

				try {
					cb = Calc.createVirtualCBAtom(aa);
				} catch (StructureException e1) {
					// TODO Auto-generated catch block
					e1.printStackTrace();
				}
			}
		}
		return cb;
	}









}