RdcPanda
Class RdcPanda

java.lang.Object
  extended by RdcPanda.RdcPanda

public class RdcPanda
extends java.lang.Object

This class implements the main function of RDC-Panda. Written by Jianyang (Michael) Zeng (2005-2009)


Field Summary
 java.lang.String rotLibName
          The path of rot lib location.
 
Constructor Summary
RdcPanda()
           
 
Method Summary
static boolean deleteDir(java.io.File dir)
          Delete a directory.
 void doAddRandomLoops(java.lang.String src, java.lang.String strOut, java.lang.String strInput)
          add random loops to an ensemble of packed SSE structures (i.e.
 void doAddSideChains(java.lang.String src, java.lang.String strOut, java.lang.String strInput)
          * add the side chains and prune steic clahes.
 void doCalAlignmentTensor(java.lang.String src, java.lang.String strOut, java.lang.String strInput)
          calculate the alignment tensor.
 void doCheckPackingSym(java.lang.String src, java.lang.String strOut, java.lang.String strInput)
          check the packing symmetry that best fit the noe restraints (namely with minimum NOE RMSD).
 void doMergeNCluster(java.lang.String src, java.lang.String strOut, java.lang.String strInput)
          * merge all structures in previous ensemble into one enemble (with the same pdb name) and cluster them according to given resolution.
 void doMergeNClusterAll(java.lang.String src, java.lang.String strOut, java.lang.String strInput)
          * merge all structures in previous ensemble into one enemble (with the same pdb name) and cluster them according to given resolution.
 void doRdcExactHelix(java.lang.String src, java.lang.String strOut, java.lang.String strInput)
          RDC-EXACT for two RDCs (CH and NH RDCs), and for long helix Co-Ca and Co-N RDCs are optional.
 void doRdcExactHelixWOAT(java.lang.String src, java.lang.String strOut, java.lang.String strInput)
          RDC-EXACT without alignment tensor for two RDCs (CH and NH RDCs), and for long helix.
 void doReadPDBEnergy(java.lang.String src, java.lang.String strOut, java.lang.String strInput)
          Read the engergy value from xplor PDB, and output the top structures with lowest energies.
 void doRefineRdcExact(java.lang.String src, java.lang.String strOut, java.lang.String strInput)
          refine the half start and end residues of pdb backbone solved from RDC-EXACT.
 void doRefineRdcExactMiddle(java.lang.String src, java.lang.String strOut, java.lang.String strInput)
          refine the middle residues of pdb backbone solved from RDC-EXACT.
 void doRunXplor(java.lang.String src, java.lang.String strOut, java.lang.String strInput)
          call Xplor as a subroutine given a script file.
 void doSSEPacking(java.lang.String src, java.lang.String strOut, java.lang.String strInput)
          Pack SSEs using sparse inter-SSE NOE restraints.
static void main(java.lang.String[] args)
          The main method.
 void outputProgInfo()
          Output prog info.
 void parse(java.lang.String[] args)
          Parses the.
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

rotLibName

public java.lang.String rotLibName
The path of rot lib location.

Constructor Detail

RdcPanda

public RdcPanda()
Method Detail

main

public static void main(java.lang.String[] args)
                 throws JampackException,
                        java.lang.InterruptedException
The main method.

Parameters:
args - the arguments
Throws:
JampackException - the jampack exception
java.lang.InterruptedException - the interrupted exception

parse

public void parse(java.lang.String[] args)
           throws JampackException,
                  java.lang.InterruptedException
Parses the.

Parameters:
args - the args
Throws:
JampackException - the jampack exception
java.lang.InterruptedException - the interrupted exception

doRunXplor

public void doRunXplor(java.lang.String src,
                       java.lang.String strOut,
                       java.lang.String strInput)
                throws JampackException,
                       java.lang.InterruptedException
call Xplor as a subroutine given a script file.

Parameters:
src - location of the input file
strOut - location of the output file
strInput - input file name
Throws:
JampackException - the jampack exception
java.lang.InterruptedException - the interrupted exception

doSSEPacking

public void doSSEPacking(java.lang.String src,
                         java.lang.String strOut,
                         java.lang.String strInput)
                  throws JampackException
Pack SSEs using sparse inter-SSE NOE restraints.

Parameters:
src - location of the input file
strOut - location of the output file
strInput - input file name
Throws:
JampackException - the jampack exception

doMergeNCluster

public void doMergeNCluster(java.lang.String src,
                            java.lang.String strOut,
                            java.lang.String strInput)
                     throws JampackException
* merge all structures in previous ensemble into one enemble (with the same pdb name) and cluster them according to given resolution.

Parameters:
src - location of the input file
strOut - location of the output file
strInput - input file name
Throws:
JampackException - the jampack exception

doAddSideChains

public void doAddSideChains(java.lang.String src,
                            java.lang.String strOut,
                            java.lang.String strInput)
                     throws JampackException
* add the side chains and prune steic clahes.

Parameters:
src - location of the input file
strOut - location of the output file
strInput - input file name
Throws:
JampackException - the jampack exception

doMergeNClusterAll

public void doMergeNClusterAll(java.lang.String src,
                               java.lang.String strOut,
                               java.lang.String strInput)
                        throws JampackException
* merge all structures in previous ensemble into one enemble (with the same pdb name) and cluster them according to given resolution. similar to "doMergeNCluster", but clustering all structures in one directory as an ensemble

Parameters:
src - location of the input file
strOut - location of the output file
strInput - input file name
Throws:
JampackException - the jampack exception

doAddRandomLoops

public void doAddRandomLoops(java.lang.String src,
                             java.lang.String strOut,
                             java.lang.String strInput)
                      throws JampackException
add random loops to an ensemble of packed SSE structures (i.e. core structures). It is quite simple: just merging two PDB files and not caring about the translations, rotation, etc.

Parameters:
src - location of the input file
strOut - location of the output file
strInput - input file name
Throws:
JampackException - the jampack exception

doReadPDBEnergy

public void doReadPDBEnergy(java.lang.String src,
                            java.lang.String strOut,
                            java.lang.String strInput)
                     throws JampackException
Read the engergy value from xplor PDB, and output the top structures with lowest energies.

Parameters:
src - location of the input file
strOut - location of the output file
strInput - input file name
Throws:
JampackException - the jampack exception

doCheckPackingSym

public void doCheckPackingSym(java.lang.String src,
                              java.lang.String strOut,
                              java.lang.String strInput)
                       throws JampackException
check the packing symmetry that best fit the noe restraints (namely with minimum NOE RMSD). This function is the same as the begining part of doSSEPacking function. Note: Currently we consider all possible rotamer states for pruning packing symmetry degenarcies. This might not be the best stragy. It might require more thoughts about this step.

Parameters:
src - location of the input file
strOut - location of the output file
strInput - input file name
Throws:
JampackException - the jampack exception

doCalAlignmentTensor

public void doCalAlignmentTensor(java.lang.String src,
                                 java.lang.String strOut,
                                 java.lang.String strInput)
                          throws JampackException
calculate the alignment tensor.

Parameters:
src - location of the input file
strOut - location of the output file
strInput - input file name
Throws:
JampackException - the jampack exception

doRefineRdcExact

public void doRefineRdcExact(java.lang.String src,
                             java.lang.String strOut,
                             java.lang.String strInput)
                      throws JampackException
refine the half start and end residues of pdb backbone solved from RDC-EXACT.

Parameters:
src - location of the input file
strOut - location of the output file
strInput - input file name
Throws:
JampackException - the jampack exception

doRefineRdcExactMiddle

public void doRefineRdcExactMiddle(java.lang.String src,
                                   java.lang.String strOut,
                                   java.lang.String strInput)
                            throws JampackException
refine the middle residues of pdb backbone solved from RDC-EXACT.

Parameters:
src - location of the input file
strOut - location of the output file
strInput - input file name
Throws:
JampackException - the jampack exception

doRdcExactHelix

public void doRdcExactHelix(java.lang.String src,
                            java.lang.String strOut,
                            java.lang.String strInput)
                     throws JampackException
RDC-EXACT for two RDCs (CH and NH RDCs), and for long helix Co-Ca and Co-N RDCs are optional.

Parameters:
src - location of the input file
strOut - location of the output file
strInput - input file name
Throws:
JampackException - the jampack exception

doRdcExactHelixWOAT

public void doRdcExactHelixWOAT(java.lang.String src,
                                java.lang.String strOut,
                                java.lang.String strInput)
                         throws JampackException
RDC-EXACT without alignment tensor for two RDCs (CH and NH RDCs), and for long helix. Co-Ca and Co-N RDCs are optional.

Parameters:
src - location of the input file
strOut - location of the output file
strInput - input file name
Throws:
JampackException - the jampack exception

outputProgInfo

public void outputProgInfo()
Output prog info.


deleteDir

public static boolean deleteDir(java.io.File dir)
Delete a directory.

Parameters:
dir - the dir
Returns:
true, if successful