RdcPanda
Class Rotamer

java.lang.Object
  extended by RdcPanda.Rotamer

public class Rotamer
extends java.lang.Object

This class provides data structures and functions related to rotamers. Written by Lincong Wang (2001-2005) and Jianyang (Michael) Zeng (2005-2009).


Constructor Summary
Rotamer()
          Instantiates a new rotamer.
Rotamer(java.lang.String res)
          Instantiates a new rotamer.
Rotamer(java.lang.String res, java.util.Vector aa)
          Instantiates a new rotamer.
 
Method Summary
 java.lang.String getAAName()
          Gets the aA name.
 java.util.Vector getPdbVec()
          Gets the pdb vec.
static void main(java.lang.String[] argv)
          The main method.
 boolean pruneRotamers(java.util.Vector vecPdb, java.lang.String rotSrc, java.util.Vector noeVec, int curNo, int lastNo, java.util.Vector vecEmsemblePdbSave)
          prune rotamers based on: 1: collisions with backbone atoms; 2: collisions between pairwise rotamer atoms; 3: NOE constraints, including pairwise and local NOEs Note: a recurrsive approach is used.
 java.util.Vector readRotamer(java.lang.String rtamerFile)
          Read rotamer.
 void setAAName(java.lang.String res)
          Sets the aA name.
 void setAtomVec(java.util.Vector aVec)
          Sets the atom vec.
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

Rotamer

public Rotamer()
Instantiates a new rotamer.


Rotamer

public Rotamer(java.lang.String res)
Instantiates a new rotamer.

Parameters:
res - the res

Rotamer

public Rotamer(java.lang.String res,
               java.util.Vector aa)
Instantiates a new rotamer.

Parameters:
res - the res
aa - the aa
Method Detail

getAAName

public java.lang.String getAAName()
Gets the aA name.

Returns:
the aA name

getPdbVec

public java.util.Vector getPdbVec()
Gets the pdb vec.

Returns:
the pdb vec

setAAName

public void setAAName(java.lang.String res)
Sets the aA name.

Parameters:
res - the new aA name

setAtomVec

public void setAtomVec(java.util.Vector aVec)
Sets the atom vec.

Parameters:
aVec - the new atom vec

pruneRotamers

public boolean pruneRotamers(java.util.Vector vecPdb,
                             java.lang.String rotSrc,
                             java.util.Vector noeVec,
                             int curNo,
                             int lastNo,
                             java.util.Vector vecEmsemblePdbSave)
                      throws JampackException
prune rotamers based on: 1: collisions with backbone atoms; 2: collisions between pairwise rotamer atoms; 3: NOE constraints, including pairwise and local NOEs Note: a recurrsive approach is used.

Parameters:
vecPdb - the pdb structure including backbone and those residue in which rotamers have been decided.
rotSrc - the file path of the rotamer library
noeVec - vector of ALL NOE restraints
curNo - the cur no
lastNo - the last no
vecEmsemblePdbSave - the vec emsemble pdb save
Returns:
true, if prune rotamers
Throws:
JampackException - the jampack exception

readRotamer

public java.util.Vector readRotamer(java.lang.String rtamerFile)
Read rotamer.

Parameters:
rtamerFile - the rtamer file
Returns:
the vector

main

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

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