RdcPanda
Class Model

java.lang.Object
  extended by RdcPanda.Model

public class Model
extends java.lang.Object

This class provides functions that compute backbone from RDC-EXACT algorithm. Written by Lincong Wang (2001-2005) and Jianyang (Michael) Zeng (2005-2009)


Constructor Summary
Model()
          Instantiates a new model.
 
Method Summary
 java.util.Vector BackonbeRotation(java.util.Vector pdbAll, java.util.Vector pdbBB)
          rotate the whole protein according to the reference backbone such that the backbone coordinates are the same (both should have the same residues).
 java.util.Vector BackonbeRotationAtResidue(java.util.Vector pdbAll, java.util.Vector pdbBB, int resNo)
          rotate the whole protein according to the reference backbone at specific residue, such that the backbone coordinates are the same (both should have the same residues).
 void doRdcExactSheet(java.lang.String src, java.lang.String strOut, java.lang.String strInput)
          compute the beta sheet using RDC-EXACT.
static void main(java.lang.String[] argv)
          The main method for testing.
static void main1(java.lang.String[] argv)
          Main function for testing.
 java.util.Vector parameterReader(java.lang.String fileName)
          Parameter reader.
 java.util.Vector sheetModel(java.util.Vector eRdc1Vec, java.util.Vector eRdc2Vec, double Syy, double Szz, java.util.Vector HbondVec, java.util.Vector paraVec, java.util.Vector[] orderVec, boolean printEulerSearch)
          Compute s beta-sheet with the order specified by orderVec.
 java.util.Vector sheetModel2(java.util.Vector pdbVec, java.util.Vector eRdc1Vec, java.util.Vector eRdc2Vec, double Syy, double Szz, java.util.Vector HbondVec, java.util.Vector paraVec, java.util.Vector[] orderVec, boolean printEulerSearch)
          Compute s beta-sheet with the order specified by orderVec.
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

Model

public Model()
Instantiates a new model.

Method Detail

parameterReader

public java.util.Vector parameterReader(java.lang.String fileName)
Parameter reader.

Parameters:
fileName - the file name
Returns:
the vector

BackonbeRotation

public java.util.Vector BackonbeRotation(java.util.Vector pdbAll,
                                         java.util.Vector pdbBB)
                                  throws JampackException
rotate the whole protein according to the reference backbone such that the backbone coordinates are the same (both should have the same residues).

Parameters:
pdbAll - pdb to be rotated
pdbBB - reference backbone pdb
Returns:
the pdb vector after rotated.
Throws:
JampackException - the jampack exception

BackonbeRotationAtResidue

public java.util.Vector BackonbeRotationAtResidue(java.util.Vector pdbAll,
                                                  java.util.Vector pdbBB,
                                                  int resNo)
                                           throws JampackException
rotate the whole protein according to the reference backbone at specific residue, such that the backbone coordinates are the same (both should have the same residues).

Parameters:
pdbAll - pdb to be rotated
pdbBB - reference backbone pdb
resNo - the res no
Returns:
the pdb vector after rotated.
Throws:
JampackException - the jampack exception

doRdcExactSheet

public void doRdcExactSheet(java.lang.String src,
                            java.lang.String strOut,
                            java.lang.String strInput)
                     throws JampackException
compute the beta sheet using RDC-EXACT.

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

sheetModel

public java.util.Vector sheetModel(java.util.Vector eRdc1Vec,
                                   java.util.Vector eRdc2Vec,
                                   double Syy,
                                   double Szz,
                                   java.util.Vector HbondVec,
                                   java.util.Vector paraVec,
                                   java.util.Vector[] orderVec,
                                   boolean printEulerSearch)
Compute s beta-sheet with the order specified by orderVec.

Parameters:
eRdc1Vec - RDC of medium 1 for all the strands of the sheet
eRdc2Vec - RDC of medium 2 for all the strands of the sheet
HbondVec - the Hbonds between the strands
paraVec - the set of parameters used to compute each strands including the 1st one
printEulerSearch - if true it will print out the the detail of rotation search
Syy - the syy
Szz - the szz
orderVec - the order vec
Returns:
the computed sheet Pdb vector

sheetModel2

public java.util.Vector sheetModel2(java.util.Vector pdbVec,
                                    java.util.Vector eRdc1Vec,
                                    java.util.Vector eRdc2Vec,
                                    double Syy,
                                    double Szz,
                                    java.util.Vector HbondVec,
                                    java.util.Vector paraVec,
                                    java.util.Vector[] orderVec,
                                    boolean printEulerSearch)
Compute s beta-sheet with the order specified by orderVec.

Parameters:
eRdc1Vec - RDC of medium 1 for all the strands of the sheet
eRdc2Vec - RDC of medium 2 for all the strands of the sheet
HbondVec - the Hbonds between the strands
paraVec - the set of parameters used to compute each strands including the 1st one
printEulerSearch - if true it will print out the the detail of rotation search
pdbVec - the pdb vec
Syy - the syy
Szz - the szz
orderVec - the order vec
Returns:
the computed sheet Pdb vector

main

public static void main(java.lang.String[] argv)
                 throws JampackException
The main method for testing.

Parameters:
argv - the arguments
Throws:
JampackException - the jampack exception

main1

public static void main1(java.lang.String[] argv)
                  throws JampackException
Main function for testing.

Parameters:
argv - the argv
Throws:
JampackException - the jampack exception