[Biojava-l] sturcture.io

I've got an ArrayList object containing a PDB file's information.How may I feed it to the structure parser? As far as I could see, it onlyaccepts BufferdReader or imputStream... ___ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mai

Re: [Biojava-l] sturcture.io

> to parse it in.>> Cheers,> Andreas>>> String filename = "path/to/pdbfile.ent" ;>> PDBFileReader pdbreader = new PDBFileReader();>> try{> Structure struc = pdbreader.getStructure(filename);> System.out.println(struc);> } cat

Re: [Biojava-l] sturcture.io

= new PDBFileParser(); try { if (pdb_inputstream != null) structure = pdbfileparser.parsePDBFile(pdb_inputstream); } catch (IOException ioe) {System.out.println(ioe);} return structure; } On 11/30/05, Tamas Horvath <[EMAIL PROTECTED]> wrote:&g

[Biojava-l] modify structure

Is there any way to modify a protein structure by modifying the contents ofthe Structure object?In short, I have a Structure object, parsed from a pdb file, and I want tointroduce point mutations to it, and save the modified structure to a pdbfile for further analysis... (I intend to use gromacs

Re: [Biojava-l] Install question: classpath and use of jar files in compiling TestEmbl.java

the easiest way is to put the jar files to the jdkxxx/jre/lib/extU may have to link them to your jre's same directory (shuld u use differentjre then the jdk's) On 11/30/05, Travis Rodkey <[EMAIL PROTECTED]> wrote:>> Hi - I am new to biojava and am trying to get it set up on Red Hat EE 3> running

Re: [Biojava-l] modify structure

lines to implement.>> Cheers,> Andreas>> On 30 Nov 2005, at 16:21, Tamas Horvath wrote:>> > Is there any way to modify a protein structure by modifying the> > contents ofthe Structure object?In short, I have a Structure object,> > parsed from a pdb file, and I

Re: [Biojava-l] modify structure

If I've got a Group , which is an amino acid, and I want to shift it by a 3Dvector (or 3 2D vectors), how may I do it?Similarly, if i want to rotate the same structure, how may I do it?If you just can show me a very short sample code, I'd really appreciate it!Thanks! On 12/1/05, Tam

Re: [Biojava-l] modify structure

Thanks for the codes! I've noticed the methods in Calc, but my main questionis the following. Let's say I've got a primitive library of AminoAcides.They stored as a group, they have all the atoms. When I'm mutating thechain, I want to keep the backbone atoms in place, so as far as your mutatemet

Re: [Biojava-l] modify structure

s the structure. On 12/2/05, Tamas Horvath <[EMAIL PROTECTED]> wrote:>> Thanks for the codes! I've noticed the methods in Calc, but my main> question is the following. Let's say I've got a primitive library of> AminoAcides. They stored as a group, they have all th

[Biojava-l] cvs ant build failure

ant package-biojavaBuildfile: build.xml init: [echo] Building biojava-live [echo] Java Home:/home/hota/programs/java/jdk1.5.0/jre [echo] JUnit present: ${junit.present} [echo] JUnit supported by Ant: true [echo] HSQLDB driver present: ${sq

[Biojava-l] 3d structure rotation code

I'd like to show u the following 2 functions that may be valuable in theCalc class: /**Returns a rotated Structure object (the rotation is around the origo) ** @param ostructure Structure -- the stucture to be rotated* @param from Atom-- the reference Atom's originalcoo

[Biojava-l] parsePDB

I have some very plane pdb files (Coordinates only), and if I try to parsethem, it throws: java.lang.StringIndexOutOfBoundsException: String index out of range: 6at java.lang.String.substring(String.java:1765)at org.biojava.bio.structure.io.PDBFileParser.parsePDBFile(PDBFileParser.java:7

[Biojava-l] gromacs shell script

I know this is not strictly BioJava, but here's my problem: I create a shell script file that would run a GROMACS MD simulationI generate the necessary input and config files I can make the generated shell script runnable I cannot actually run the script from the Java application. The script works

Re: [Biojava-l] gromacs shell script

I tried the ProcessTools method and nothing happens there either... On 12/8/05, Thomas Down <[EMAIL PROTECTED]> wrote:>>> On 8 Dec 2005, at 14:16, Tamas Horvath wrote:>> > I know this is not strictly BioJava, but here's my problem:> > I create a shell scri

Re: [Biojava-l] gromacs shell script

On 12/8/05, Tamas Horvath <[EMAIL PROTECTED]> wrote:>> Runtime rtime = Runtime.getRuntime();> Process child = rtime.exec("/bin/sh");>>> BufferedWriter outCommand = new BufferedWriter(new> Outp

[Biojava-l] Re: strange pdb

ve so far seen, these altlocs reallyrefer to alternative sidechain conformations. In this case there would be aTYR A and TYR B conformation. On 1/12/06, Tamas Horvath <[EMAIL PROTECTED]> wrote:>> Hi!> I've just stubled upon a strange pdb parsing fenomenon. Look at the> follo

[Biojava-l] strange pdb

Hi!I've just stubled upon a strange pdb parsing fenomenon. Look at thefollowing pdb file:ATOM 1 N GLU 326 14.783 14.947 -11.793 1.00 46.17NATOM 2 CA GLU 326 15.471 16.220 -11.447 1.00 39.29CATOM 3 C GLU 326 14.978 16.646 -10.075 1.00 37.04CATOM

[Biojava-l] Re: structureNMRImpl

I forgot to mention, that I use a not yet published modified version ofStructureImpl, which can parse an ArrayList. It has a newconstructor for it, and the old BufferedReader method was changed so itgenerates the ArrayList for the parser method... On 2/8/06, Tamas Horvath <[EMAIL PROTEC

[Biojava-l] warnings, errors, comments

> What do u think about making a givewarning flag for PDBFileParser? that would be nice - I would suggest to do it using the java -loggingtool - - actually that applies to all of biojava and should be suggested tothe list -I find java.util.logging very helpful. > By default it would be true, but

Re: [Biojava-l] Newbie struggling with secondary structure

. alternatively I can send u my compiledbiojava.jaras well. It's not the most current cvs, but not too lateeither... On 2/13/06, Tamas Horvath <[EMAIL PROTECTED]> wrote:>> You are right the secondary structure is not yet parsed. But it's> quite easy, so if Andreas is

[Biojava-l] structureNMRImpl

Hi! The structureNMRImpl class, I've been working on is finally working. It is far from ready to be incorporated into BioJava just yet. It's a bit messy, lacks documentation, there are some naming convention issues with it, nevertheless I'd be happy to hear suggestions about it. In theory in the fu