RdcPanda
Class RotaPattern

java.lang.Object
  extended by RdcPanda.RotaPattern

public class RotaPattern
extends java.lang.Object

This class implements data structures and functions that deal with the rotamer properties. Written by Jianyang (Michael) Zeng (2005-2009).


Nested Class Summary
static class RotaPattern.scoreComparator
          The Class scoreComparator.
 
Constructor Summary
RotaPattern()
          Instantiates a new rota pattern.
RotaPattern(double[] coordTemp, double dbSc)
          Instantiates a new rota pattern.
RotaPattern(int res_no, double dbSc)
          Instantiates a new rota pattern.
RotaPattern(int no, java.lang.String resName, java.util.Vector hdistVec, java.util.Vector NoeVec)
          Instantiates a new rota pattern.
RotaPattern(int no, java.lang.String resName, java.util.Vector hdistVec, java.util.Vector NoeVec, java.util.Vector pVec)
          Instantiates a new rota pattern.
RotaPattern(Pdb pdbRot, double dbSc)
          Instantiates a new rota pattern.
 
Method Summary
 java.util.Vector BackCompNoePattern(java.util.Vector asgVec, int resNo, java.lang.String resName, java.util.Vector vecHDist)
          Back compute all NOE peaks from given pairs of NOE distance patterns for a rotamer.
 BackNoe BackCompNOEPeak(java.util.Vector asgVec, Hdist hdist)
          Back compute an NOE peak from a given pair of NOE distance.
 java.util.Vector getBackNoeVec()
          Gets the back noe vec.
 double[] getCoord()
          Gets the coord.
 java.util.Vector getHdistVec()
          Gets the hdist vec.
 Pdb getPdb()
          Gets the pdb.
 int getResNo()
          Gets the res no.
 java.lang.String getResType()
          Gets the res type.
 double getScore()
          Gets the score.
 java.util.Vector RefineRotLib(double csErrH, double csErrN, double csErrCA, java.util.Vector vecRot, java.util.Vector vecBB, java.util.Vector assignVec, java.util.Vector NoesyVec, int resNo, double distBound, int pickNum, double[] maxScore)
          Refined function for general case: calculate the score of each rotamer, and choose rotamers with highest scores.
 java.util.Vector RefineRotLib(double csErrH, double csErrN, double csErrCA, java.util.Vector vecRot, java.util.Vector vecBB, java.util.Vector assignVec, java.util.Vector NoesyVec, int resNo, double distBound, int pickNum, int[] maxInd)
          Refined function for general case: calculate the score of each rotamer, and choose rotamers with highest scores.
 java.util.Vector RefineRotLib(java.util.Vector vecRot, java.util.Vector vecBB, java.util.Vector assignVec, java.util.Vector hnNoeVec, java.util.Vector cnoeVec, int resNo, double distBound, int pickNum, int[] maxInd, java.util.Vector vecXrayBB)
          calculate the score of each rotamer, and choose rotamers with highest scores.
 java.util.Vector RefineRotLibNew(double csErrH, double csErrN, double csErrCA, java.util.Vector vecRot, java.util.Vector vecBB, java.util.Vector assignVec, java.util.Vector NoesyVec, int resNo, double distBound, int pickNum, java.util.Vector vecRotStr, double constant)
          Refined function for general case: calculate the score of each rotamer, and return ensemble of rotamers with highest scores.
 java.util.Vector RefineRotLibNewUsingBins(double csErrH, double csErrN, double csErrCA, java.util.Vector vecRot, java.util.Vector vecBB, java.util.Vector assignVec, java.util.Vector NoesyVec, int resNo, double distBound, int pickNum, java.util.Vector vecRotStr)
          calibration scheme: using bin scheme.
 void setScore(double sc)
          Sets the score.
 BackNoe SimulateBackCompNOEPeak(java.util.Vector asgVec, Hdist hdist)
          for simulate ca NOEs, Back compute an NOE peak from a given pair of NOE distance.
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

RotaPattern

public RotaPattern(double[] coordTemp,
                   double dbSc)
Instantiates a new rota pattern.

Parameters:
coordTemp - the coord temp
dbSc - the db sc

RotaPattern

public RotaPattern(Pdb pdbRot,
                   double dbSc)
Instantiates a new rota pattern.

Parameters:
pdbRot - the pdb rot
dbSc - the db sc

RotaPattern

public RotaPattern(int res_no,
                   double dbSc)
Instantiates a new rota pattern.

Parameters:
res_no - the res_no
dbSc - the db sc

RotaPattern

public RotaPattern()
Instantiates a new rota pattern.


RotaPattern

public RotaPattern(int no,
                   java.lang.String resName,
                   java.util.Vector hdistVec,
                   java.util.Vector NoeVec)
Instantiates a new rota pattern.

Parameters:
no - the no
resName - the res name
hdistVec - the hdist vec
NoeVec - the noe vec

RotaPattern

public RotaPattern(int no,
                   java.lang.String resName,
                   java.util.Vector hdistVec,
                   java.util.Vector NoeVec,
                   java.util.Vector pVec)
Instantiates a new rota pattern.

Parameters:
no - the no
resName - the res name
hdistVec - the hdist vec
NoeVec - the noe vec
pVec - the vec
Method Detail

getResNo

public int getResNo()
Gets the res no.

Returns:
the res no

getResType

public java.lang.String getResType()
Gets the res type.

Returns:
the res type

getHdistVec

public java.util.Vector getHdistVec()
Gets the hdist vec.

Returns:
the hdist vec

getBackNoeVec

public java.util.Vector getBackNoeVec()
Gets the back noe vec.

Returns:
the back noe vec

getPdb

public Pdb getPdb()
Gets the pdb.

Returns:
the pdb

getCoord

public double[] getCoord()
Gets the coord.

Returns:
the coord

getScore

public double getScore()
Gets the score.

Returns:
the score

setScore

public void setScore(double sc)
Sets the score.

Parameters:
sc - the new score

RefineRotLib

public java.util.Vector RefineRotLib(java.util.Vector vecRot,
                                     java.util.Vector vecBB,
                                     java.util.Vector assignVec,
                                     java.util.Vector hnNoeVec,
                                     java.util.Vector cnoeVec,
                                     int resNo,
                                     double distBound,
                                     int pickNum,
                                     int[] maxInd,
                                     java.util.Vector vecXrayBB)
calculate the score of each rotamer, and choose rotamers with highest scores.

Parameters:
vecRot - rotamers
assignVec - resonance assignment
vecBB - backbone structure
hnNoeVec - hn Noe peak list
cnoeVec - ca noe peak list
resNo - residue number
distBound - distance bound to define noe distance
vecXrayBB - xray backbone for computing rmsd
pickNum - the pick num
maxInd - the max ind
Returns:
refined rotamer positions

RefineRotLib

public java.util.Vector RefineRotLib(double csErrH,
                                     double csErrN,
                                     double csErrCA,
                                     java.util.Vector vecRot,
                                     java.util.Vector vecBB,
                                     java.util.Vector assignVec,
                                     java.util.Vector NoesyVec,
                                     int resNo,
                                     double distBound,
                                     int pickNum,
                                     int[] maxInd)
Refined function for general case: calculate the score of each rotamer, and choose rotamers with highest scores.

Parameters:
vecRot - rotamers
assignVec - resonance assignment
vecBB - backbone structure
resNo - residue number
distBound - distance bound to define noe distance
csErrH - the cs err h
csErrN - the cs err n
csErrCA - the cs err ca
NoesyVec - the noesy vec
pickNum - the pick num
maxInd - the max ind
Returns:
refined rotamer positions

RefineRotLibNew

public java.util.Vector RefineRotLibNew(double csErrH,
                                        double csErrN,
                                        double csErrCA,
                                        java.util.Vector vecRot,
                                        java.util.Vector vecBB,
                                        java.util.Vector assignVec,
                                        java.util.Vector NoesyVec,
                                        int resNo,
                                        double distBound,
                                        int pickNum,
                                        java.util.Vector vecRotStr,
                                        double constant)
Refined function for general case: calculate the score of each rotamer, and return ensemble of rotamers with highest scores.

Parameters:
vecRot - rotamers
assignVec - resonance assignment
vecBB - backbone structure
resNo - residue number
distBound - distance bound to define noe distance
vecRotStr - rotamer vectors in the structure format.
csErrH - the cs err h
csErrN - the cs err n
csErrCA - the cs err ca
NoesyVec - the noesy vec
pickNum - the pick num
constant - the constant
Returns:
refined rotamer positions

RefineRotLibNewUsingBins

public java.util.Vector RefineRotLibNewUsingBins(double csErrH,
                                                 double csErrN,
                                                 double csErrCA,
                                                 java.util.Vector vecRot,
                                                 java.util.Vector vecBB,
                                                 java.util.Vector assignVec,
                                                 java.util.Vector NoesyVec,
                                                 int resNo,
                                                 double distBound,
                                                 int pickNum,
                                                 java.util.Vector vecRotStr)
calibration scheme: using bin scheme. Refined function for general case: calculate the score of each rotamer, and return ensemble of rotamers with highest scores

Parameters:
vecRot - rotamers
assignVec - resonance assignment
vecBB - backbone structure
resNo - residue number
distBound - distance bound to define noe distance
vecRotStr - rotamer vectors in the structure format.
csErrH - the cs err h
csErrN - the cs err n
csErrCA - the cs err ca
NoesyVec - the noesy vec
pickNum - the pick num
Returns:
refined rotamer positions

RefineRotLib

public java.util.Vector RefineRotLib(double csErrH,
                                     double csErrN,
                                     double csErrCA,
                                     java.util.Vector vecRot,
                                     java.util.Vector vecBB,
                                     java.util.Vector assignVec,
                                     java.util.Vector NoesyVec,
                                     int resNo,
                                     double distBound,
                                     int pickNum,
                                     double[] maxScore)
Refined function for general case: calculate the score of each rotamer, and choose rotamers with highest scores.

Parameters:
vecRot - rotamers
assignVec - resonance assignment
vecBB - backbone structure
resNo - residue number
distBound - distance bound to define noe distance
csErrH - the cs err h
csErrN - the cs err n
csErrCA - the cs err ca
NoesyVec - the noesy vec
pickNum - the pick num
maxScore - the max score
Returns:
refined rotamer positions

SimulateBackCompNOEPeak

public BackNoe SimulateBackCompNOEPeak(java.util.Vector asgVec,
                                       Hdist hdist)
for simulate ca NOEs, Back compute an NOE peak from a given pair of NOE distance.

Parameters:
asgVec - resonance assignment
hdist - the hdist
Returns:
the NOE peak

BackCompNOEPeak

public BackNoe BackCompNOEPeak(java.util.Vector asgVec,
                               Hdist hdist)
Back compute an NOE peak from a given pair of NOE distance.

Parameters:
asgVec - resonance assignment
hdist - the hdist
Returns:
the NOE peak

BackCompNoePattern

public java.util.Vector BackCompNoePattern(java.util.Vector asgVec,
                                           int resNo,
                                           java.lang.String resName,
                                           java.util.Vector vecHDist)
Back compute all NOE peaks from given pairs of NOE distance patterns for a rotamer.

Parameters:
asgVec - resonance assignment
resNo - residue No of the rotamer
resName - residue name of the rotamer
vecHDist - all pairs of NOE distances from rotamer protons to backbone protons, namely HN/HA/HB
Returns:
the HNOE vector that stores all pairs of bakc-computed NOE peaks