hazeeel

Hi guys! I need help here, When ever I write onto my text file, i get null and then the value.Please help me! I don't want the "null"! Here is how it looks like in Notepad++: null1: 0.22056311934213296 2: 3.017771771149946 null3: 1.508399104807777 4: 0.07575171145562612 null5: 5.187081012091999 6: 2.049001095182013 null null …

How do I overwrite the 7th, 8th and 9th column of the text file with new values? What can I use? [CODE] ATOM 1 N ASN A 1 12.844 -5.008 -17.071 1.00 0.00 N ATOM 2 CA ASN A 1 12.377 -4.399 -15.793 1.00 0.00 C ATOM 3 C ASN …

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 …

Hey guys, I seriously need some help here. I have no idea why but after undergoing the Rotation phase I lost coordinatesRotZ[a][0],coordinatesRotZ[a][1]. The value appears to be 0.0 However coordinatesRotZ[a][2] has values stored in it. so the output looks something like that after printing: coordinatesRotZ[a][0] coordinatesRotZ[a][1] coordinatesRotZ[a][2]: 0.0 0.0 13.44 …

Hey guys How do I do a calculation of coordinates X,Y,Z between 2 files. Eg. File 1 has about 1000 lines and so does File 2 I have done the pre processing for the coordinates that are needed to be extracted out. They are kept in my 2D arrays. This …

How do I calculate my RMSD(root mean square deviation) score for my PDB protein structures, atom by atom. I wish to calculate it line by line. But I do not know how to go about it? I was thinking of using a for loop but as you can see, I've …

hi all!! I need some help here. It's the Translation matrix. I can't seem to get the output. I wonder if my conditions are right cause I've been changing them. Please do take a look from line 125 onwards. Thanks much! [CODE]import java.io.*; import java.util.*; import java.text.*; public class KateAug24{ …

Please help me to solve the error: coordinates2T[a][b]=-3.7830557977332173 coordinates2T[a][b]=-3.7830557977332173 coordinates2T[a][b]=-3.7830557977332173 Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 3 at KateAug24.main(KateAug24.java:137) Press any key to continue... Thanks is adv! [CODE]import java.io.*; import java.util.*; import java.text.*; public class KateAug24{ private static StringBuffer buffer; private static BufferedReader input1=null; public static String [] arrayM1 = new …

[CODE] import java.io.*; import java.util.*; import java.text.*; //-------------------------------------------------------------------------------------------------------------------------------------------------- public class KateAug17{ private static StringBuffer buffer; private static BufferedReader input1=null; public static String [] arrayM1 = new String [10000]; public static Double [][] coordinates1 = new Double [10000][4]; public static Double [][] coordinates2 = new Double [10000][10]; public static String [] …

Hi all, I need to do a translation using 2D arrays for my Superposition algorithm. Translation: I plan to use the CA(Alpha carbon) as my invariant point which is usually the 2nd line in the pdb.txt file. So how go about doing that? Must I use an orthogonal matrix? Or …

Hi all! I really really need your advice here! So please do reply me. Your help is greatly appreciated!! I need to do a translation here: X Y Z -3.621 15.574 14.908 (file1 - 2nd row) -3.441 15.678 14.859 (file2 - 2nd row) I need to move file 2 coordinates …

[CODE] 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 [/CODE] Can I do this: coordinates2[i][j]= coordinates2[i][0]+ coordinates2[i][1]+ coordinates2[i][2]; Is it possible to add them all together ?

[CODE] coordinates1[i][0]= Double.parseDouble(text2.substring(30,38));//X coordinates1[i][1]= Double.parseDouble(text2.substring(38,46));//Y coordinates1[i][2]= Double.parseDouble(text2.substring(46,56));//Z [/CODE] How do I combine the above 3 into 1 2D array?

Hi guys, For multi dimentional arrays, i know the amount of columns- 3. But I do not know the amount of rows because each input file has a diff. no. of rows(which can go up to a few thousands). So how do I make an array out of it? Thank …

Hey there! How do i read 2 files, one after another and then storing it into 2 seperate array? This is the code for reading 1 file. So, how do I read 2 files? The array would be a 3x3 2D array. [CODE]File dir = new File("1A6G.pdb"); //set file String …

ATOM 1430 CB ASP A 187 [B]54.776 12.063 20.348[/B] 1.00 50.88 C How do I store the above in bold into a 1x3 arrray after using StringSplit?

Greetings! The below is an example of a text file from PDB. ATOM 2 CA ASP E 423 [B]-50.931 46.011 -16.062[/B] 1.00153.24 C ATOM 3 C ASP E 423 [B]-51.314 44.692 -15.381[/B] 1.00152.70 C ATOM 4 O ASP E 423 [B]-52.175 44.673 -14.497[/B] 1.00153.08 O ATOM 5 CB ASP E …

I have to read the co-ordinates of a 3D object from the txt file and store it in an array. But I need to store it in a JAR file so that I can view the final product in my visualizer (Jmol). How do I get about in doing that?

How do I integrate a visualizer(Jmol) with my java(JCreator)? Can anybody give me the codes or explain it to me as I'm very new to the world of java. Thanks~!

What is BioJava? Is it an application? Can it work with Jcreator to create my own program?

Hi all, I am a student doing a project on the superposition algorithm. I have to rotate 1 protein on top of the other protein after translation to match it as closey as possible. In order to do that, I need to write the codes in java and also, to …

I am a student, doing a project on superposition(bioinformatics). I am doing the part on rotation using matrices and I'm stuck. I need to open a visualizer (jmol) and adjust the angles of my protein structure at the same time via java codes. So I need to have 2 protein …