owl/trunk/testDeltaDistanceMap.java

import proteinstructure.*;
import java.util.*;

import edu.uci.ics.jung.graph.util.Pair;

/**
 * Calculate a matrix containing the element-wise differences between the distance maps of two proteins
 * @author stehr
 *
 */
public class testDeltaDistanceMap {
        
        /**
         * Run tests
         */
        public static void main(String[] args) {
                try {
                        String pdbCode1 = "12as";
                        String chainCode1 = "A";
                        String pdbCode2 = "12as";
                        String chainCode2 = "B";
                        
                        System.out.println("Loading pdb objects...");
                        Pdb pdb1 = new PdbasePdb("12as");
                        pdb1.load("B");
                        assert(pdb1 != null);
                        Pdb pdb2 = new PdbasePdb("12as");
                        pdb2.load("A");
                        assert(pdb2 != null);
                        
                        System.out.println("Calculating distance maps...");
                        HashMap<Pair<Integer>,Double> distMap1 = pdb1.calculate_dist_matrix("Ca");
                        assert(distMap1 != null);
                        HashMap<Pair<Integer>,Double> distMap2 = pdb2.calculate_dist_matrix("Ca");
                        assert(distMap2 != null);
                        
                        // create an alignment
                        String name1 = pdbCode1+chainCode1;
                        String name2 = pdbCode2+chainCode2;
                        String[] tags = {name1, name2};
                        String[] seqs = {pdb1.getSequence(), pdb2.getSequence()};
                        Alignment ali = new Alignment(tags, seqs);
                        
                        System.out.println("Calculating difference distance map...");
                        HashMap<Pair<Integer>,Double> diffDistMap = pdb1.getDiffDistMap("Ca", pdb2, "Ca", ali, name1, name2);
                        assert(diffDistMap != null);
                        assert(diffDistMap.size() == distMap1.size());
                        assert(diffDistMap.size() == distMap2.size());
                        
                        System.out.print("Missing matrix values (dim=" + pdb1.getFullLength() + "): ");
                        int mis = 0;
                        for(int i=1; i<=pdb1.getFullLength();i++) {
                                for(int j=1; j<i;j++) {
                                        if(!diffDistMap.containsKey(new Pair<Integer>(j,i))) {
                                                //System.out.print("(" + i + "," + j + ") ");
                                                mis++;
                                        }
                                }
                        }
                        System.out.println(mis);
                        
                        Pair<Integer> e = new Pair<Integer>(27,30);

                        double dist1 = distMap1.get(e);
                        double dist2 = distMap2.get(e);
                        double diffDist = diffDistMap.get(e);
                        assert(diffDist == Math.abs(dist1 - dist2));
                        double min = Collections.min(diffDistMap.values());
                        double max = Collections.max(diffDistMap.values());
                        
                        System.out.println("Checking difference distance map for " + pdbCode1 + chainCode1 + " and " + pdbCode2 + chainCode2);
                        System.out.println("size=" + diffDistMap.size() + " min=" + min + " max= " + max);
                }
                catch(Exception e) {
                        e.printStackTrace();

                }

        }

}
Revision:	517
Committed:	Tue Jan 15 13:19:36 2008 UTC (16 years, 8 months ago) by duarte
File size:	2437 byte(s)
Log Message:	Changed Alignment class so that both alignment and sequence indexing are starting at 1 (before alignment indices were starting at 0). Also mapping is now done through arrays not maps. Changed all other classes using Alignment to accommodate this. NOTE: graph averaging hasn't been tested after the change
Line	File contents
1	import proteinstructure.*;
2	import java.util.*;
3
4	import edu.uci.ics.jung.graph.util.Pair;
5
6	/**
7	* Calculate a matrix containing the element-wise differences between the distance maps of two proteins
8	* @author stehr
9	*
10	*/
11	public class testDeltaDistanceMap {
12
13	/**
14	* Run tests
15	*/
16	public static void main(String[] args) {
17	try {
18	String pdbCode1 = "12as";
19	String chainCode1 = "A";
20	String pdbCode2 = "12as";
21	String chainCode2 = "B";
22
23	System.out.println("Loading pdb objects...");
24	Pdb pdb1 = new PdbasePdb("12as");
25	pdb1.load("B");
26	assert(pdb1 != null);
27	Pdb pdb2 = new PdbasePdb("12as");
28	pdb2.load("A");
29	assert(pdb2 != null);
30
31	System.out.println("Calculating distance maps...");
32	HashMap<Pair<Integer>,Double> distMap1 = pdb1.calculate_dist_matrix("Ca");
33	assert(distMap1 != null);
34	HashMap<Pair<Integer>,Double> distMap2 = pdb2.calculate_dist_matrix("Ca");
35	assert(distMap2 != null);
36
37	// create an alignment
38	String name1 = pdbCode1+chainCode1;
39	String name2 = pdbCode2+chainCode2;
40	String[] tags = {name1, name2};
41	String[] seqs = {pdb1.getSequence(), pdb2.getSequence()};
42	Alignment ali = new Alignment(tags, seqs);
43
44	System.out.println("Calculating difference distance map...");
45	HashMap<Pair<Integer>,Double> diffDistMap = pdb1.getDiffDistMap("Ca", pdb2, "Ca", ali, name1, name2);
46	assert(diffDistMap != null);
47	assert(diffDistMap.size() == distMap1.size());
48	assert(diffDistMap.size() == distMap2.size());
49
50	System.out.print("Missing matrix values (dim=" + pdb1.getFullLength() + "): ");
51	int mis = 0;
52	for(int i=1; i<=pdb1.getFullLength();i++) {
53	for(int j=1; j<i;j++) {
54	if(!diffDistMap.containsKey(new Pair<Integer>(j,i))) {
55	//System.out.print("(" + i + "," + j + ") ");
56	mis++;
57	}
58	}
59	}
60	System.out.println(mis);
61
62	Pair<Integer> e = new Pair<Integer>(27,30);
63
64	double dist1 = distMap1.get(e);
65	double dist2 = distMap2.get(e);
66	double diffDist = diffDistMap.get(e);
67	assert(diffDist == Math.abs(dist1 - dist2));
68	double min = Collections.min(diffDistMap.values());
69	double max = Collections.max(diffDistMap.values());
70
71	System.out.println("Checking difference distance map for " + pdbCode1 + chainCode1 + " and " + pdbCode2 + chainCode2);
72	System.out.println("size=" + diffDistMap.size() + " min=" + min + " max= " + max);
73	}
74	catch(Exception e) {
75	e.printStackTrace();
76
77	}
78
79	}
80
81	}