org.biojava.nbio.structure.domain.pdp.Cut Maven / Gradle / Ivy

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The protein structure modules of BioJava.
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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/
 *
 */
package org.biojava.nbio.structure.domain.pdp;

import org.biojava.nbio.structure.Atom;

import java.util.List;

public class Cut {

	static boolean verbose = CutDomain.verbose;

	public int cut( Atom[] ca, Domain dom, CutValues val, int[][] dist, PDPDistanceMatrix pdpMatrix) {

		int nclose = pdpMatrix.getNclose();

		int[] iclose = pdpMatrix.getIclose();
		int[] jclose = pdpMatrix.getJclose();

		int[] contacts = new int[PDPParameters.MAXLEN];
		double[] max_contacts = new double [PDPParameters.MAXLEN];
		double[] contact_density = new double[PDPParameters.MAXLEN];
		double average_density,x,y;

		int endsf,endst;
		int k,l,nc;
		int size1,size2;
		int size1t,size2t;
		int size11,size22,size0;
		int contactsd;
		int iseg,jseg,kseg;
		int from,to,from1,to1,from2,to2,lseg;


		int site_min = -1;


		// AP add sort here..
		//qsort(dom.segment,dom.nseg,sizeof(struct Segment),segcmp);
		// what is going on with the segments??

		List segments = dom.getSegments();

		java.util.Collections.sort(segments, new SegmentComparator());

		if ( verbose)
			System.out.println("  ---  Cut.cut " + dom + " ");
		average_density = 0.0;
		size0=0;
		for(iseg=0;iseg4) contactsd+=(dist[i][j]);
					}
				}
			}
			from = dom.getSegmentAtPos(iseg).getFrom();
			to = dom.getSegmentAtPos(iseg).getTo();
			for(k=from;k4) contacts[k]+=(dist[i][j]);
					}
				}
				/*
	if(k==392) printf("[from,k]x]iseg,nseg[ = %d\n",contacts[k]);
				 */
				for(int i=from;i<=k;i++) {
					for (int j=k+1;j<=to;j++)
						if(Math.abs(i-j)>4) contacts[k]+=(dist[i][j]);
				}
				/*
	if(k==392) printf("[from,k]x]k,to[ = %d\n",contacts[k]);
				 */
				for(int i=k+1;i<=to;i++) {
					for(kseg=0;kseg4) contacts[k]+=(dist[j][i]);
					}
				}
				/*
	if(k==392) printf("]k,to]x]0,iseg[ = %d\n",contacts[k]);
				 */
				size1=Math.min(size11,size22);
				size2=Math.max(size11,size22);
				x=Math.min(PDPParameters.MAXSIZE,size1);
				y=Math.min(PDPParameters.MAXSIZE,size2);
				if(x>150&&y>1.5*x) y=1.5*x;
				else if(y>2*x) y=2*x;
				/*
				 */
				x=Math.min(Math.pow(x,1.3/3)+PDPParameters.RG,Math.pow(x,1.1/3)+Math.pow(PDPParameters.TD,1.3/3)+PDPParameters.RG);
				y=Math.min(Math.pow(y,1.3/3)+PDPParameters.RG,Math.pow(y,1.1/3)+Math.pow(PDPParameters.TD,1.3/3)+PDPParameters.RG);
				/* max_ contacts depend on the size of domains */
				/* stella wanted comments at this point */
				/*
			max_contacts[k] = min(MAXCONT,x*y);
				 */
				max_contacts[k] = 10*x*y;
				if(size1>150) max_contacts[k] = 9*x*y;
				contact_density[k]=contacts[k]/max_contacts[k];
				/*
			if(contact_density[k]>2.5) contact_density[k]=2.5;
				 */
				/*
	if(first_cut)
		if(k==277 && !first_cut)
		printf("k=%d s1=%d s2=%d x=%f y=%f mc=%d c=%d cd=%f\n",k,size1,size2,x,y,max_contacts[k],contacts[k],contact_density[k]);
				 */
				//if(verbose) System.out.println(String.format("%d	%d	%d	%f	%f	%f	%d	%f",k,size1,size2,x,y,max_contacts[k],contacts[k],contact_density[k]));
				/*
				 */
				if(from==0) endsf = PDPParameters.ENDSEND;
				else endsf = PDPParameters.ENDS;
				if(to==ca.length-1) endst = PDPParameters.ENDSEND;
				else endst = PDPParameters.ENDS;
				if((contact_density[k])from+endsf&&kfrom+endsf&&kfrom+endsf&&iclose[l]from+endsf&&jclose[l]2*x) y=2*x;
			/*
			 */
			x=Math.min(Math.pow(x,1.3/3)+PDPParameters.RG,Math.pow(x,1.1/3)+Math.pow(PDPParameters.TD,1.3/3)+PDPParameters.RG);
			y=Math.min(Math.pow(y,1.3/3)+PDPParameters.RG,Math.pow(y,1.1/3)+Math.pow(PDPParameters.TD,1.3/3)+PDPParameters.RG);
			/*
		max_contacts[nc] = min(MAXCONT,x*y);
			 */
			max_contacts[nc] = x*y*10;
			if(size1>150) max_contacts[k] = 9*x*y;
			contact_density[nc]=contacts[nc]/max_contacts[nc];
			/*
	if(first_cut)
			 */
			//if ( verbose)
			//	System.out.println("double cut" + l + " " + ca[iclose[l]].getGroup().getType() + " " + iclose[l] + " " + jclose[l] + " " + contacts[nc]+
			//			" " + max_contacts[nc] + " " + x+ " " + y + " " + size11 + " " + size22 + " " + contact_density[nc] + " " + contact_density[nc]/val.AD );
			//if(verbose) System.out.println(String.format(" double cut: %d	%s %d %d c=%d mc=%d x=%f y=%f s1=%d s2=%d cd=%f cd/ad=%f\n",l,ca[iclose[l]].getGroup().getType(),iclose[l],jclose[l],contacts[nc],max_contacts[nc],x,y,size11,size22,contact_density[nc],contact_density[nc]/val.AD));
			if((contact_density[nc]/val.AD+PDPParameters.DBL)= PDPParameters.MAXSIZE)
				nc = PDPParameters.MAXSIZE-1;
		}
		val.first_cut=false;
		if(verbose)
			System.out.println(String.format("  --- E ... at the end of cut: s_min %f CUTOFF %f site_min %d *site2 %d",val.s_min,PDPParameters.CUT_OFF_VALUE,site_min,val.site2));
		if(val.s_min> PDPParameters.CUT_OFF_VALUE) return -1;

		return(site_min);
	}
}