org.biojava.nbio.structure.align.helper.AlignUtils Maven / Gradle / Ivy

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/*
 *                  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/
 *
 * Created on May 27, 2006
 *
 */
package org.biojava.nbio.structure.align.helper;

import org.biojava.nbio.structure.Atom;
import org.biojava.nbio.structure.AtomImpl;
import org.biojava.nbio.structure.Calc;
import org.biojava.nbio.structure.jama.Matrix;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

/**
 * Low level helper methods for CE and FATCAT algorithms.
 *
 * @author Andreas Prlic
 */
public class AlignUtils {

	private static final Logger logger = LoggerFactory.getLogger(AlignUtils.class);

	/**
	 * Get a subset of Atoms based by their positions
	 *
	 * @param caall
	 * @param idx an array where each element is a position of all the Atoms to return
	 * @return at Atom[] array
	 */
	public static Atom[] getFragmentFromIdxList(Atom[] caall, int[] idx){
		Atom[] subset = new Atom[idx.length];

		for (int p = 0 ; p < idx.length;p++){

			int pos1 =  idx[p];
			subset[p] =  (Atom) caall[pos1].clone();
		}
		return subset;
	}

	/**
	 * Get a continue subset of Atoms based by the starting position and the length
	 *
	 * @param caall
	 * @param pos the start position
	 * @param fragmentLength the length of the subset to extract.
	 * @return an Atom[] array
	 */
	public static Atom[] getFragment(Atom[] caall, int pos, int fragmentLength){

		if ( pos+fragmentLength > caall.length)
			return null;

		Atom[] tmp = new Atom[fragmentLength];

		for (int i=0;i< fragmentLength;i++){
			tmp[i] = (Atom)caall[i+pos].clone();
		}
		return tmp;

	}


	/**
	 * Get a continue subset of Atoms based by the starting position and the length
	 * does not clone the original atoms.
	 *
	 * @param caall
	 * @param pos the start position
	 * @param fragmentLength the length of the subset to extract.
	 * @return an Atom[] array
	 */
	public static Atom[] getFragmentNoClone(Atom[] caall, int pos, int fragmentLength){

		if ( pos+fragmentLength > caall.length)
			return null;

		Atom[] tmp = new Atom[fragmentLength];

		for (int i=0;i< fragmentLength;i++){
			tmp[i] = caall[i+pos];
		}
		return tmp;

	}

	/**
	 * Get the centroid for the set of atoms starting from position pos, length fragmentLenght
	 *
	 * @param ca
	 * @param pos
	 * @param fragmentLength
	 * @return an Atom
	 */
	public static Atom getCenter(Atom[] ca, int pos, int fragmentLength){
		Atom center = new AtomImpl();

		if ( pos+fragmentLength > ca.length) {
			logger.info("pos ("+pos+"), fragL ("+fragmentLength +") > ca.length"+ca.length);
			return center;
		}

		Atom[] tmp = getFragmentNoClone(ca,pos,fragmentLength);

		return Calc.getCentroid(tmp);
	}


	/**
	 * Get distances along diagonal k from coordinate array coords.
	 *
	 * @param atoms set of atoms to be used
	 * @param k number of diagonal to be used
	 */
	public static double[] getDiagonalAtK (Atom[] atoms,int k) {

		int l = atoms.length;

		double[] dk = new double[(l-k)];

		for ( int i = 0 ; i< (l-k); i++){

			double dist = Calc.getDistance(atoms[i],atoms[i+k]);
			dk[i] = dist;

		}

		return dk;
	}

	/**
	 * Given distance matrix diagonals dk1, dk2, get the rmsd of a fpair.
	 * i,j is the fpair start in mol1 and mol2, l is the length of the fragment
	 *
	 * @param dk1 distances of structure 1
	 * @param dk2 distance of structure 2
	 * @param i position in structure 1
	 * @param j position in structure 2
	 * @param l length of the fragments
	 * @param k diagonal used
	 * @return a double
	 */
	public static double rms_dk_diag(double[] dk1, double[] dk2, int i, int j, int l, int k) {
		//        dk = 0
		//        for x in range(l-k):
		//            dk += (dk1[x+i]-dk2[x+j])*(dk1[x+i]-dk2[x+j])
		//        dk /= (l-k)
		//        return math.sqrt(dk)

		double dk = 0.0;
		for (int x = 0 ; x < (l-k) ; x++)
			dk += (dk1[x+i]-dk2[x+j])*(dk1[x+i]-dk2[x+j]);

		dk /= ( l-k);
		return Math.sqrt(dk);

	}

	/**
	 * Matrix of all distances between two sets of Atoms. Does not
	 * superimpose or modify the Atoms.
	 *
	 * @param ca1
	 * @param ca2
	 * @return a Matrix
	 */
	public static Matrix getDistanceMatrix(Atom[] ca1, Atom[] ca2){

		int r = ca1.length;
		int c = ca2.length;

		Matrix out = new Matrix(r,c);

		for (int i=0; i