| 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 |
System.out.println("Calculating difference distance map..."); |
| 38 |
HashMap<Pair<Integer>,Double> diffDistMap = pdb1.getDiffDistMap("Ca", pdb2, "Ca"); |
| 39 |
assert(diffDistMap != null); |
| 40 |
assert(diffDistMap.size() == distMap1.size()); |
| 41 |
assert(diffDistMap.size() == distMap2.size()); |
| 42 |
|
| 43 |
System.out.print("Missing matrix values (dim=" + pdb1.getFullLength() + "): "); |
| 44 |
int mis = 0; |
| 45 |
for(int i=1; i<=pdb1.getFullLength();i++) { |
| 46 |
for(int j=1; j<i;j++) { |
| 47 |
if(!diffDistMap.containsKey(new Pair<Integer>(j,i))) { |
| 48 |
//System.out.print("(" + i + "," + j + ") "); |
| 49 |
mis++; |
| 50 |
} |
| 51 |
} |
| 52 |
} |
| 53 |
System.out.println(mis); |
| 54 |
|
| 55 |
Pair<Integer> e = new Pair<Integer>(27,30); |
| 56 |
|
| 57 |
double dist1 = distMap1.get(e); |
| 58 |
double dist2 = distMap2.get(e); |
| 59 |
double diffDist = diffDistMap.get(e); |
| 60 |
assert(diffDist == Math.abs(dist1 - dist2)); |
| 61 |
double min = Collections.min(diffDistMap.values()); |
| 62 |
double max = Collections.max(diffDistMap.values()); |
| 63 |
|
| 64 |
System.out.println("Checking difference distance map for " + pdbCode1 + chainCode1 + " and " + pdbCode2 + chainCode2); |
| 65 |
System.out.println("size=" + diffDistMap.size() + " min=" + min + " max= " + max); |
| 66 |
} |
| 67 |
catch(Exception e) { |
| 68 |
e.printStackTrace(); |
| 69 |
|
| 70 |
} |
| 71 |
|
| 72 |
} |
| 73 |
|
| 74 |
} |
