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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.domain.pdp;
import java.util.ArrayList;
import java.util.List;
public class ClusterDomains {
static private boolean verbose = CutDomain.verbose;
private static int ndom;
public static List cluster(List domains, PDPDistanceMatrix pdpDistMatrix){
ndom = domains.size();
int Si = -1;
int Sj = -1;
int Sis = -1;
int Sjs = -1;
int Sim = -1;
int Sjm = -1;
long total_max_contacts = 0;
double maximum_values = PDPParameters.CUT_OFF_VALUE1S;
double maximum_valuem = PDPParameters.CUT_OFF_VALUE1M;
double maximum_value = PDPParameters.CUT_OFF_VALUE1;
if (ndom < 2) return domains;
/*
for(i=0;i150&&maxDomSize>1.5*minDomSize) maxDomSize=1.5*minDomSize;
else if(maxDomSize>2*minDomSize) maxDomSize=2*minDomSize;
long size1= new Double(Math.min(PDPParameters.MAXSIZE,minDomSize)).longValue();
long size2= new Double(Math.min(PDPParameters.MAXSIZE,maxDomSize)).longValue();
minDomSize=Math.min(Math.pow(minDomSize,1.6/3)+PDPParameters.RG1,Math.pow(minDomSize,1.4/3)+Math.pow(PDPParameters.TD1,1.6/3)+PDPParameters.RG1);
maxDomSize=Math.min(Math.pow(maxDomSize,1.6/3)+PDPParameters.RG1,Math.pow(maxDomSize,1.4/3)+Math.pow(PDPParameters.TD1,1.6/3)+PDPParameters.RG1);
/*
total_max_contacts = 10.+
(long)( (10.*(size1)/(size1+10.)+(size1)*pow((double)(size1),(double)(2./3.))/(size1+10.))*(10.*(size2)/(size2+10.)+(size2)*pow((double)(size2),(double)(2./3.))/(size2+10.)));
total_max_contacts = (min(200,size1))*(min(200,size2))/4;
*/
/*
total_max_contacts = min(x*y,MAXCONT);
*/
total_max_contacts=new Double(minDomSize*maxDomSize*10).longValue();
if(size1>130) total_max_contacts=new Double(minDomSize*maxDomSize*9).longValue();
/*
avd=(domains.get(i).avd+domains.get(j).avd)/2;
S_value=(double)total_contacts/total_max_contacts/avd;
*/
double S_value= total_contacts/(double)total_max_contacts;
if(verbose) System.out.println(String.format(" size1=%d size2=%d minDomSize=%5.2f maxDomSize=%5.2f total_contacts = %d ", size1,size2,minDomSize,maxDomSize,total_contacts));
if(verbose) System.out.println(String.format(" total_contacts = %d total_max_contacts = %d", total_contacts, total_max_contacts));
if(verbose) System.out.println(String.format(" maximum_value = %f S_value = %f\n",maximum_value, S_value));
if (S_value > maximum_value) {
maximum_value = S_value;
Si = i;
Sj = j;
}
if (S_value > maximum_valuem&&size1<70) {
maximum_valuem = S_value;
Sim = i;
Sjm = j;
}
if (S_value > maximum_values&&size1<52) {
maximum_values = S_value;
Sis = i;
Sjs = j;
}
total_contacts = 0;
total_max_contacts = 0;
}
}
if ( verbose) {
System.out.println("Check for combining: " + maximum_value + " 1 :" + PDPParameters.CUT_OFF_VALUE1);
System.out.println(" " + maximum_valuem + " 1M:" + PDPParameters.CUT_OFF_VALUE1M );
System.out.println(" " + maximum_values + " 1S:" + PDPParameters.CUT_OFF_VALUE1S);
}
if (maximum_value > PDPParameters.CUT_OFF_VALUE1) {
/*
avd=(domains.get(Si).avd+domains.get(Sj).avd)/2;
*/
if(verbose) System.out.println(" Criteria 1 matched");
if(verbose) System.out.println(String.format(" maximum_value = %f", maximum_value));
if(verbose) System.out.println(String.format(" Si = %d Sj = %d ", Si, Sj));
domains = combine(domains,Si, Sj, maximum_value);
maximum_value = PDPParameters.CUT_OFF_VALUE1-.1;
maximum_values = PDPParameters.CUT_OFF_VALUE1S-.1;
maximum_valuem = PDPParameters.CUT_OFF_VALUE1M-.1;
/*
domains.get(Si).avd=domcont(domains.get(Si));
domains.get(Sj).avd=domcont(domains.get(Sj));
*/
if(verbose) System.out.println(String.format(" Listing the domains after combining..."));
if(verbose) listdomains (domains);
}
else if (maximum_valuem > PDPParameters.CUT_OFF_VALUE1M) {
/*
avd=(domains[Sim].avd+domains[Sjm].avd)/2;
*/
if(verbose) System.out.println(" Criteria 2 matched");
if(verbose) System.out.println(String.format(" maximum_values = %f", maximum_valuem));
if(verbose) System.out.println(String.format(" Sim = %d Sjm = %d", Sim, Sjm));
domains = combine(domains, Sim, Sjm, maximum_valuem);
maximum_value = PDPParameters.CUT_OFF_VALUE1-.1;
maximum_values = PDPParameters.CUT_OFF_VALUE1S-.1;
maximum_valuem = PDPParameters.CUT_OFF_VALUE1M-.1;
/*
domains[Sim].avd=domcont(domains[Sim]);
domains[Sjm].avd=domcont(domains[Sjm]);
*/
if(verbose) System.out.println(String.format(" Listing the domains after combining..."));
if(verbose) listdomains (domains);
}
else if (maximum_values > PDPParameters.CUT_OFF_VALUE1S) {
/*
avd=(domains[Sis].avd+domains[Sjs].avd)/2;
*/
if(verbose) System.out.println(" Criteria 3 matched");
if(verbose) System.out.println(String.format(" maximum_values = %f", maximum_values));
if(verbose) System.out.println(String.format(" Sis = %d Sjs = %d", Sis, Sjs));
domains = combine(domains, Sis, Sjs, maximum_values);
maximum_value = PDPParameters.CUT_OFF_VALUE1-.1;
maximum_values = PDPParameters.CUT_OFF_VALUE1S-.1;
maximum_valuem = PDPParameters.CUT_OFF_VALUE1M-.1;
/*
domains[Sis].avd=domcont(domains[Sis]);
domains[Sjs].avd=domcont(domains[Sjs]);
*/
if(verbose) System.out.println(String.format(" Listing the domains after combining..."));
if(verbose) listdomains(domains);
}
else {
if(verbose) System.out.println(String.format(" Maximum value is less than cut off value. (max:" + maximum_value+")" ));
maximum_value = -1.0;
maximum_values = -1.0;
maximum_valuem = -1.0;
}
} while ( maximum_value > 0.0||maximum_values>0.0||maximum_valuem>0.0);
if(verbose) System.out.println(String.format(" The domains are:"));
if(verbose) listdomains(domains);
return domains;
}
private static long getTotalContacts(List domains,
PDPDistanceMatrix pdpDistMatrix, Domain i, Domain j) {
long total_contacts=0;
for(int k=0;k combine(List domains,int Si, int Sj, double maximum_value) {
if ( verbose)
System.out.println(" +++ combining domains " + Si + " " + Sj);
List newdoms = new ArrayList();
//int ndom = domains.size();
for(int i=0;i domains){
int i = -1;
for ( Domain dom : domains){
i++;
System.out.println("DOMAIN:" + i + " size:" + dom.size + " " + dom.score);
List segments = dom.getSegments();
for ( Segment s : segments){
System.out.println(" Segment: " + s);
}
}
}
}
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