Hey guys! Much help needed here! I am a student doing a protein structure alignment algorithm which is my final year project, using various forms of translation, rotation & computing the RMSD.

From line 164:

This is my loop calculation, basically it computes the Root Mean Square Deviation (RMSD) of my X, Y & Z coordinates.

An example of how it looks in a **text file** that I will be reading from & storing in my 2D arrays. (NOTE: I'll be playing round with 2 diff PROTEIN files: File 1- coordinates1[][], File 2- coordinates2 [][]. 1 file has approx. 1000+ - 3000+ LINES, depending on the size of the protein)

ATOM 1 N VAL A 1 -4.040 15.048 13.602 1.00 37.04 N

ATOM 2 CA VAL A 1 -3.621 15.574 14.908 1.00 25.44 C

ATOM 3 C VAL A 1 -2.766 14.564 15.637 1.00 24.20 C

I'll be **extracting** these values(X,Y & Z respectively) from the files and will be **storing in my 2D array**.

**Extracted coordinates:****X Y Z**

-4.040 15.048 13.602

-3.621 15.574 14.908

-2.766 14.564 15.637

I have a couple of problems here:

When I do: RMSD_Final = R2 / coordinatesRotZ.length;

It literally divides by the size of the coordinates, which is 3000.

Here's an example of my declaration of my 2D array:

public static double [][] coordinatesRotZ = new double [3000][1000];

so I guess for my loops and all, it goes on and on for 3000 times, which i don't want that. I want it to go according to the number of rows that has numbers in it. Please note that I do not know the amount of rows which I will be using for the file reading part, that's why I put 3000. because I might be using diff files each time with diff number of rows each time.

please do advise:

1. Is there any possibility of getting back the number of rows that i've used so that I can use that as my .length & my denominator during the division?

2. The logic of the computation part from line 164 : I want to 'accumulate' all my R1s so that I can divide it by the total no. of coordinates of that particular file. Is it correct? Or perhaps is there any other better way of doing it? I wish to keep it simple as my java knowledge is limited.

Thank you all in advance! Please do help me as I am stuck on this for days and weeks.

```
public class testest{
private static StringBuffer buffer;
private static BufferedReader input1=null;
private static String st[]= new String[20000]; //keep at 20000, initially 1000
public static String [] arrayM1 = new String [3000];
public static String [] arrayM2 = new String [3000];
public static double [][] coordinates1 = new double [3000][1000];
public static double [][] coordinates2 = new double [3000][1000];
public static double [][] coordinates2T = new double [3000][1000];
public static double [] Translate = new double [10];
//public static double [] R1 = new double [3];
public static double [][] coordinatesDiff = new double [3000][1000];
public static double [][] coordinatesRotz = new double [3000][1000];
public static double [][] coordinatesRotX = new double [3000][1000];
public static double [][] coordinatesRotZ = new double [3000][1000];
static DecimalFormat fmt= new DecimalFormat("0.000"); //3 D.P
public static void main(String args[]) {
int i=0,j=0;
String text1;
String text2;
double X=0.0;
double Y=0.0;
double Z=0.0;
double alpha=0.0;
double beta =0.0;
double theta=0.0;
double R1 = 0.0;
double R2 = 0.0;
double R3 = 0.0;
double RMSD_Final = 0.0;
GetFilenameWithoutExtension example=new GetFilenameWithoutExtension(); //new instance of class
int counter2=0;
String line2="";
int counter1=0;
String line1="";
try{
FileInputStream fstream1 = new FileInputStream("C:\\Users\\Hazel\\Documents\\Desktop\\MPSIP\\proteintest1.txt");
FileInputStream fstream2 = new FileInputStream("C:\\Users\\Hazel\\Documents\\Desktop\\MPSIP\\proteintest2.txt");
DataInputStream in1 = new DataInputStream(fstream1); // Get the object of DataInputStream
DataInputStream in2 = new DataInputStream(fstream2); // Get the object of DataInputStream
BufferedReader br1 = new BufferedReader(new InputStreamReader(in1));
BufferedReader br2 = new BufferedReader(new InputStreamReader(in2));
// to get protein ID
while ((text1 = br1.readLine()) != null) { //Read File Line By Line
if(text1.trim().startsWith("ATOM")) {
StringTokenizer s1 = new StringTokenizer(text1," ");
while(s1.hasMoreTokens()) {
String ss1 = s1.nextToken();
counter1++;
if(counter1 == 3){
line1 += ss1;
arrayM1[i] = ss1;
}
}
coordinates1[i][0]= Double.parseDouble(text1.substring(30,38));//X
coordinates1[i][1]= Double.parseDouble(text1.substring(38,46));//Y
coordinates1[i][2]= Double.parseDouble(text1.substring(46,56));//Z
i+=1;
}//end of if
} //end of while.
i=0;
while ((text2 = br2.readLine()) != null) { //Read File Line By Line
if(text2.trim().startsWith("ATOM")) {
StringTokenizer s2 = new StringTokenizer(text2," ");
while(s2.hasMoreTokens()) {
String ss2 = s2.nextToken();
counter2++;
if(counter2 == 3){
line2 += ss2;
arrayM2[i] = ss2;
}
}
coordinates2[i][0]= Double.parseDouble(text2.substring(30,38));//X
coordinates2[i][1]= Double.parseDouble(text2.substring(38,46));//Y
coordinates2[i][2]= Double.parseDouble(text2.substring(46,56));//Z
i+=1;
}//end of if
} //end of while.
}//end of try
catch( IOException e) {
e.printStackTrace();
}//end of catch
//------------------------------Translation-------------------------------------
for(int a=0; a<3; a++) {
for(int b=0; b<3; b++){
for(int c=0; c<3; c++){
X = coordinates1[1][0]/coordinates2[1][0]; //alpha c coordinate
Y = coordinates1[1][1]/coordinates2[1][1];
Z = coordinates1[1][2]/coordinates2[1][2];
double [][] Translation1={ {X,0.0,0.0}, {0.0,Y,0.0}, {0.0,0.0,Z} };
coordinates2T[a][b] += coordinates2[a][c]*Translation1[c][b];
//-------------------------Rotation & RMSD Cal----------------------------------
//Uses Leohard Euler's angle of rotation theorem
//5 degrees in rad.
double [][] Rotz={ {Math.cos(0.087266463), Math.sin(-0.087266463), 0.0},
{Math.sin(0.087266463), Math.cos(0.087266463), 0.0},
{0.0, 0.0 , 1.0} };
double [][] RotX={ {1.0,0.0,0.0},
{0.0,Math.cos(0.087266463), Math.sin(-0.087266463)},
{0.0,Math.sin(0.087266463), Math.cos(0.087266463)} };
double [][] RotZ={ {Math.cos(0.087266463), Math.sin(0.087266463), 0.0},
{Math.sin(-0.087266463), Math.cos(0.087266463), 0.0},
{0.0, 0.0 , 1.0} };
coordinatesRotz[a][b]+= coordinates2T[a][c]*Rotz[c][b];
coordinatesRotX[a][b]+= coordinatesRotz[a][c]*RotX[c][b];
coordinatesRotZ[a][b]+= coordinatesRotX[a][c]*RotZ[c][b];
}
}
}
for(int a=0; a<coordinates1.length; a++){
for(int b=0; b<coordinatesRotZ; b++){
R1 =Math.sqrt((Math.pow((coordinates1[a][0]-coordinatesRotZ[b][0]),2.0) //computes X
+Math.pow((coordinates1[a][1]-coordinatesRotZ[b][1]),2.0)// computes Y
+Math.pow((coordinates1[a][2]-coordinatesRotZ[b][2]),2.0)));//computes Z
R2 += R1; //Store R1 for every loop into R2
}
}
RMSD_Final = R2 / coordinatesRotZ.length;
if( RMSD_Final!= 0.0)
System.out.println("RMSD="+fmt.format(RMSD_Final));
}
}
```