RdcPanda
Class Noesy

java.lang.Object
  extended by RdcPanda.Noesy

public class Noesy
extends java.lang.Object

This class provides data structures and functions for processing NOESY spectra. Written by Lincong Wang (2001-2005) and Jianyang (Michael) Zeng (2005-2009).


Nested Class Summary
static class Noesy.h1Comparator
          The Class h1Comparator.
static class Noesy.h2Comparator
          The Class h2Comparator.
static class Noesy.heavyComparator
          The Class heavyComparator.
static class Noesy.IntensityComparator
          The Class IntensityComparator.
static class Noesy.resNoComparator
          The Class resNoComparator.
 
Constructor Summary
Noesy()
          Instantiates a new noesy.
Noesy(int no)
          Instantiates a new noesy.
Noesy(int no, java.lang.String resid, double H1, double Heavy, double H2, double inten)
          Instantiates a new noesy.
Noesy(int no, java.lang.String resid, double H1, double Heavy, double H2, double inten, double uncn)
          Instantiates a new noesy.
Noesy(int no, java.lang.String resid, double H1, double Heavy1, double H2, double Heavy2, double inten, double uncn)
          Instantiates a new noesy.
 
Method Summary
 java.util.Vector DeleteRepeatedNoesy3D(java.util.Vector vecOldNoesy)
          delete repeated NOE peaks.
 int getBinIndex()
          Gets the bin index.
 double getH1()
          Gets the h1.
 double getH2()
          Gets the h2.
 double getHeavy()
          Gets the heavy.
 double getHeavy1()
          Gets the heavy1.
 double getHeavy2()
          Gets the heavy2.
 double getIntensity()
          Gets the intensity.
 int getResidueNo()
          Gets the residue no.
 java.lang.String getResidueType()
          Gets the residue type.
 double getUncertainty()
          Gets the uncertainty.
 double getUpperDist()
          Gets the upper dist.
 java.util.Vector mergeHnNoe(java.util.Vector pkVec, double epsH, double epsN)
          a method to merge NOE peaks since some NOE peaks are picked with a lightly different CS more than once.
 java.util.Vector NoesyReader(java.lang.String filename)
          Read NOESY peaks in xeasy format The required file format is:.
 java.util.Vector NoesyReaderNMRView(java.lang.String filename)
          Read NOESY peaks in NMRView format The required file format is:.
 java.util.Vector NoesyReaderNMRView4D(java.lang.String filename)
          Read 4D NOESY peaks in NMRView format The required file format is:.
 java.util.Vector rangeSearch(java.lang.String nucType, double a, double b, java.util.Vector pkVec)
          Extract all the HnNoe objects with proton CS or N15 CS in the range of [a, b] from an array of NOE peaks.
 void setBinIndex(int i)
          Sets the bin index.
 java.util.Vector SetCalibration(java.util.Vector vecNoesy)
          calibration of intensity: using xplor-NIH method The required file format is:.
 java.util.Vector SetCalibration2(java.util.Vector vecNoesy)
          calibration of intensity: using -3 The required file format is:.
 java.util.Vector SetCalibrationC13(java.util.Vector vecNoesy, java.util.Vector vecAsg)
          the following rules are used to calibrate the constant k 1.
 java.util.Vector SetCalibrationC13Sec(java.util.Vector vecNoesy, java.util.Vector vecSeq, java.util.Vector vecAsg)
          incompleted..., this function can be delested...
 java.util.Vector SetCalibrationCyana(java.util.Vector vecNoe, java.util.Vector vecNoesy, double constant)
          calibrate one NOE peak, using a calibration strategy similar to CYANA.
 java.util.Vector SetCalibrationN15(java.util.Vector vecNoesy, java.util.Vector vecSSEBB, java.util.Vector vecAsg, double[] constantK)
          we use the HN(i)-HA(i-1) in SSE regions to calibrate distance from peak intensity (dist<2.5A).
 double SetCalibrationOneCyana(BackNoe bkNoe, Noesy noesy, double constant)
          calibrate one NOE peak, using a calibration strategy similar to CYANA.
 void setResidueNo(int R)
          Sets the residue no.
 void setResidueType(java.lang.String R)
          Sets the residue type.
 void setUpperDist(double dist)
          Sets the upper dist.
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

Noesy

public Noesy()
Instantiates a new noesy.


Noesy

public Noesy(int no)
Instantiates a new noesy.

Parameters:
no - the no

Noesy

public Noesy(int no,
             java.lang.String resid,
             double H1,
             double Heavy,
             double H2,
             double inten)
Instantiates a new noesy.

Parameters:
no - the no
resid - the resid
H1 - the h1
Heavy - the heavy
H2 - the h2
inten - the inten

Noesy

public Noesy(int no,
             java.lang.String resid,
             double H1,
             double Heavy,
             double H2,
             double inten,
             double uncn)
Instantiates a new noesy.

Parameters:
no - the no
resid - the resid
H1 - the h1
Heavy - the heavy
H2 - the h2
inten - the inten
uncn - the uncn

Noesy

public Noesy(int no,
             java.lang.String resid,
             double H1,
             double Heavy1,
             double H2,
             double Heavy2,
             double inten,
             double uncn)
Instantiates a new noesy.

Parameters:
no - the no
resid - the resid
H1 - the h1
Heavy1 - the heavy1
H2 - the h2
Heavy2 - the heavy2
inten - the inten
uncn - the uncn
Method Detail

getResidueNo

public int getResidueNo()
Gets the residue no.

Returns:
the residue no

getResidueType

public java.lang.String getResidueType()
Gets the residue type.

Returns:
the residue type

getH1

public double getH1()
Gets the h1.

Returns:
the h1

getHeavy

public double getHeavy()
Gets the heavy.

Returns:
the heavy

getHeavy1

public double getHeavy1()
Gets the heavy1.

Returns:
the heavy1

getHeavy2

public double getHeavy2()
Gets the heavy2.

Returns:
the heavy2

getH2

public double getH2()
Gets the h2.

Returns:
the h2

getIntensity

public double getIntensity()
Gets the intensity.

Returns:
the intensity

getUncertainty

public double getUncertainty()
Gets the uncertainty.

Returns:
the uncertainty

getUpperDist

public double getUpperDist()
Gets the upper dist.

Returns:
the upper dist

getBinIndex

public int getBinIndex()
Gets the bin index.

Returns:
the bin index

setResidueNo

public void setResidueNo(int R)
Sets the residue no.

Parameters:
R - the new residue no

setResidueType

public void setResidueType(java.lang.String R)
Sets the residue type.

Parameters:
R - the new residue type

setUpperDist

public void setUpperDist(double dist)
Sets the upper dist.

Parameters:
dist - the new upper dist

setBinIndex

public void setBinIndex(int i)
Sets the bin index.

Parameters:
i - the new bin index

SetCalibration

public java.util.Vector SetCalibration(java.util.Vector vecNoesy)
calibration of intensity: using xplor-NIH method The required file format is:.

Parameters:
vecNoesy - before volume calibration
Returns:
after calibraiton

SetCalibration2

public java.util.Vector SetCalibration2(java.util.Vector vecNoesy)
calibration of intensity: using -3 The required file format is:.

Parameters:
vecNoesy - before volume calibration
Returns:
after calibraiton

SetCalibrationC13

public java.util.Vector SetCalibrationC13(java.util.Vector vecNoesy,
                                          java.util.Vector vecAsg)
the following rules are used to calibrate the constant k 1. distance between HA-HB in ALA is less than 2.5A (unique assignment, peak intensity need to be divided by 3) 2. Methyl-methyl group NOEs (unque NOE asisgnment, divide by 3*3) Note: unique assignment, not close to diagonal line

Parameters:
vecNoesy - before volume calibration
vecAsg - resonance assignment list
Returns:
after calibraiton

SetCalibrationCyana

public java.util.Vector SetCalibrationCyana(java.util.Vector vecNoe,
                                            java.util.Vector vecNoesy,
                                            double constant)
calibrate one NOE peak, using a calibration strategy similar to CYANA.

Parameters:
vecNoe - initial NOE assignments
vecNoesy - noesy peak list
constant - constant from sse backbone
Returns:
after calibraiton

SetCalibrationOneCyana

public double SetCalibrationOneCyana(BackNoe bkNoe,
                                     Noesy noesy,
                                     double constant)
calibrate one NOE peak, using a calibration strategy similar to CYANA.

Parameters:
constant - constant from sse backbone
bkNoe - the bk noe
noesy - the noesy
Returns:
distance after calibraiton

SetCalibrationC13Sec

public java.util.Vector SetCalibrationC13Sec(java.util.Vector vecNoesy,
                                             java.util.Vector vecSeq,
                                             java.util.Vector vecAsg)
incompleted..., this function can be delested... the following rules are used to calibrate the constant k 1. distance between HA-HB in ALA is less than 2.5A (unique assignmen Note: unique assignment, not close to diagonal line

Parameters:
vecNoesy - before volume calibration
vecSeq - sse backbone
vecAsg - resonance assignment list
Returns:
after calibraiton

SetCalibrationN15

public java.util.Vector SetCalibrationN15(java.util.Vector vecNoesy,
                                          java.util.Vector vecSSEBB,
                                          java.util.Vector vecAsg,
                                          double[] constantK)
we use the HN(i)-HA(i-1) in SSE regions to calibrate distance from peak intensity (dist<2.5A). Function: I=kd^(-6)

Parameters:
vecNoesy - before volume calibration
vecSSEBB - sse backbone
vecAsg - resonance assignment list
constantK - the constant k
Returns:
after calibraiton

DeleteRepeatedNoesy3D

public java.util.Vector DeleteRepeatedNoesy3D(java.util.Vector vecOldNoesy)
delete repeated NOE peaks.

Parameters:
vecOldNoesy - the vec old noesy
Returns:
the vector

NoesyReaderNMRView

public java.util.Vector NoesyReaderNMRView(java.lang.String filename)
Read NOESY peaks in NMRView format The required file format is:.

Parameters:
filename - the name of the file
Returns:
a vector of HnNOE object

NoesyReaderNMRView4D

public java.util.Vector NoesyReaderNMRView4D(java.lang.String filename)
Read 4D NOESY peaks in NMRView format The required file format is:.

Parameters:
filename - the name of the file
Returns:
a vector of HnNOE object

NoesyReader

public java.util.Vector NoesyReader(java.lang.String filename)
Read NOESY peaks in xeasy format The required file format is:.

Parameters:
filename - the name of the file
Returns:
a vector of HnNOE object

rangeSearch

public java.util.Vector rangeSearch(java.lang.String nucType,
                                    double a,
                                    double b,
                                    java.util.Vector pkVec)
Extract all the HnNoe objects with proton CS or N15 CS in the range of [a, b] from an array of NOE peaks.

Parameters:
nucType - the type of nucleus: H1 or N15
a - the lower limit of the range
b - the up limit of the range
pkVec - an array of NOE peaks.
Returns:
the vector

mergeHnNoe

public java.util.Vector mergeHnNoe(java.util.Vector pkVec,
                                   double epsH,
                                   double epsN)
a method to merge NOE peaks since some NOE peaks are picked with a lightly different CS more than once.

Parameters:
pkVec - the pk vec
epsH - the eps h
epsN - the eps n
Returns:
the vector