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java.lang.ObjectRdcPanda.Noesy
public class Noesy
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 | |
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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 | |
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Noesy()
Instantiates a new noesy. |
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Noesy(int no)
Instantiates a new noesy. |
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Noesy(int no,
java.lang.String resid,
double H1,
double Heavy,
double H2,
double inten)
Instantiates a new noesy. |
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Noesy(int no,
java.lang.String resid,
double H1,
double Heavy,
double H2,
double inten,
double uncn)
Instantiates a new noesy. |
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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 | |
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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 |
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equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public Noesy()
public Noesy(int no)
no
- the nopublic Noesy(int no, java.lang.String resid, double H1, double Heavy, double H2, double inten)
no
- the noresid
- the residH1
- the h1Heavy
- the heavyH2
- the h2inten
- the intenpublic Noesy(int no, java.lang.String resid, double H1, double Heavy, double H2, double inten, double uncn)
no
- the noresid
- the residH1
- the h1Heavy
- the heavyH2
- the h2inten
- the intenuncn
- the uncnpublic Noesy(int no, java.lang.String resid, double H1, double Heavy1, double H2, double Heavy2, double inten, double uncn)
no
- the noresid
- the residH1
- the h1Heavy1
- the heavy1H2
- the h2Heavy2
- the heavy2inten
- the intenuncn
- the uncnMethod Detail |
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public int getResidueNo()
public java.lang.String getResidueType()
public double getH1()
public double getHeavy()
public double getHeavy1()
public double getHeavy2()
public double getH2()
public double getIntensity()
public double getUncertainty()
public double getUpperDist()
public int getBinIndex()
public void setResidueNo(int R)
R
- the new residue nopublic void setResidueType(java.lang.String R)
R
- the new residue typepublic void setUpperDist(double dist)
dist
- the new upper distpublic void setBinIndex(int i)
i
- the new bin indexpublic java.util.Vector SetCalibration(java.util.Vector vecNoesy)
vecNoesy
- before volume calibration
public java.util.Vector SetCalibration2(java.util.Vector vecNoesy)
vecNoesy
- before volume calibration
public java.util.Vector SetCalibrationC13(java.util.Vector vecNoesy, java.util.Vector vecAsg)
vecNoesy
- before volume calibrationvecAsg
- resonance assignment list
public java.util.Vector SetCalibrationCyana(java.util.Vector vecNoe, java.util.Vector vecNoesy, double constant)
vecNoe
- initial NOE assignmentsvecNoesy
- noesy peak listconstant
- constant from sse backbone
public double SetCalibrationOneCyana(BackNoe bkNoe, Noesy noesy, double constant)
constant
- constant from sse backbonebkNoe
- the bk noenoesy
- the noesy
public java.util.Vector SetCalibrationC13Sec(java.util.Vector vecNoesy, java.util.Vector vecSeq, java.util.Vector vecAsg)
vecNoesy
- before volume calibrationvecSeq
- sse backbonevecAsg
- resonance assignment list
public java.util.Vector SetCalibrationN15(java.util.Vector vecNoesy, java.util.Vector vecSSEBB, java.util.Vector vecAsg, double[] constantK)
vecNoesy
- before volume calibrationvecSSEBB
- sse backbonevecAsg
- resonance assignment listconstantK
- the constant k
public java.util.Vector DeleteRepeatedNoesy3D(java.util.Vector vecOldNoesy)
vecOldNoesy
- the vec old noesy
public java.util.Vector NoesyReaderNMRView(java.lang.String filename)
filename
- the name of the file
public java.util.Vector NoesyReaderNMRView4D(java.lang.String filename)
filename
- the name of the file
public java.util.Vector NoesyReader(java.lang.String filename)
filename
- the name of the file
public java.util.Vector rangeSearch(java.lang.String nucType, double a, double b, java.util.Vector pkVec)
nucType
- the type of nucleus: H1 or N15a
- the lower limit of the rangeb
- the up limit of the rangepkVec
- an array of NOE peaks.
public java.util.Vector mergeHnNoe(java.util.Vector pkVec, double epsH, double epsN)
pkVec
- the pk vecepsH
- the eps hepsN
- the eps n
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