RdcPanda
Class Assign

java.lang.Object
  extended by RdcPanda.Assign

public class Assign
extends java.lang.Object

This class provides functions that involves NOE assignment, such initial NOE assignment using only chemical shift information, pruning ambiguous NOE assignments using given structural information,etc. Written by Lincong Wang (2001-2005) and Jianyang (Michael) Zeng (2005-2009).


Nested Class Summary
static class Assign.assignComparator
          The Class assignComparator.
static class Assign.caComparator
          The Class caComparator.
static class Assign.haComparator
          The Class haComparator.
static class Assign.hnComparator
          The Class hnComparator.
 
Constructor Summary
Assign()
          Instantiates a new assign.
Assign(int no)
          Instantiates a new assign.
Assign(int no, java.lang.String type)
          Instantiates a new assign.
Assign(int no, java.lang.String type, java.util.Map aMap)
          Instantiates a new assign.
Assign(int no, java.lang.String type, java.util.Map aMap, java.util.Vector hnVec, java.util.Vector haVec)
          Instantiates a new assign.
Assign(int no, java.lang.String type, java.util.Map aMap, java.util.Vector hnVec, java.util.Vector haVec, java.util.Vector h1Vec)
          Instantiates a new assign.
 
Method Summary
 java.util.Vector asgReader3(java.lang.String filename)
          Written by Lincong, only used in his previous functions.
 void assignHsqc(java.util.Vector assignVec, java.util.Vector hsqcVec)
          Written by Lincong, only used in his previous functions.
 java.util.Vector assignReader(java.lang.String pdbFile, double h1Ref)
          Read the resonance assignment.
 java.util.Vector assignReader2(java.lang.String hncacbFile, java.util.Vector assignVec, java.util.Vector chsqcVec)
          Read the resonance assignment, meanwhile update the residue name for each chemical shift.
 java.util.Vector BackNoeDeleteRepeat(java.util.Vector vecBackNoe)
          delete repeated back noes, mainly from methyl groups.
 void CompMaxMatchScore_old(java.util.Vector vecBackNoe, double preMisPenalty, double preMatchScore, int depth, int finalDepth, int[] missingIndex)
          recursively compute the max matching score.
 java.util.Vector deleteRepeat(java.util.Vector allVec, double epsH, double epsN, double epsH1)
          Delete repeated chemical shifts.
 void doCompareTwoNOETables(java.lang.String src, java.lang.String strOut, java.lang.String strInput)
          compare two NOE table and output the summary.
 void doExtractNOEs(java.lang.String src, java.lang.String strOut, java.lang.String strInput)
          extract NOEs in certain regions.
 void doHANANOEAsg(java.lang.String src, java.lang.String strOut, java.lang.String strInput)
          HANA algorithm for the NOE assignment and output the NOE table.
 void doLongNOEsAsgWOStructure(java.lang.String src, java.lang.String strOut, java.lang.String strInput)
          refine the long-range NOE assignment without structure information.
 void doLongNOEsAsgWOStructureNew(java.lang.String src, java.lang.String strOut, java.lang.String strInput)
          refine the long-range NOE assignment without structure information, better version of doLongNOEsAsgWOStructure.
 void doRefineNOEsWBB(java.lang.String src, java.lang.String strOut, java.lang.String strInput)
          note: randomStructureSlect..need to be fixed, refine the NOE assignment using given the backbone and output the refine NOE table.
 java.util.Vector getH1NoeVec()
          Gets the h1 noe vec.
 java.util.Vector getHaNoeVec()
          Gets the ha noe vec.
 java.util.Vector getHnNoeVec()
          Gets the hn noe vec.
 java.util.Map getMap()
          Gets the map.
 double getMaxValue()
          Gets the max value.
 int[] getMissingIndex()
          Gets the missing index.
 java.util.Vector getOrder(java.lang.String strSSES)
          A very simple reader for secondary structure identification file.
 int getResidueNo()
          Gets the residue no.
 java.lang.String getResidueType()
          Gets the residue type.
 java.util.Vector InitAmbiAssignment(double nErr, double cErr, double hnErr, double haErr, double h2Err, java.util.Vector vecAsg, java.util.Vector vecAllH1, java.util.Vector vecNoesy)
          Compute the intiial NOE assignments using only chemcial shift information.
 java.util.Vector InitAmbiAssignment4D(double nErr, double cErr, double hnErr, double haErr, double h2Err, java.util.Vector vecAsg, java.util.Vector vecAllH1, java.util.Vector vecNoesy)
          Initial NOE assignment for 4D NOESY.
 java.util.Vector InitAmbiAssignmentUnique(double nErr, double cErr, double hnErr, double haErr, double h2Err, java.util.Vector vecAsg, java.util.Vector vecAllH1, java.util.Vector vecNoesy)
          The same as InitAmbiAssignment, but only output those unique noe assignments.
 void matchC13Hsqc(java.util.Vector foldHsqcVec, java.util.Vector hsqcVec)
          Written by Lincong, only used in his previous functions.
 java.util.Vector mergeAll(java.util.Vector allVec, java.util.Vector hcchVec, double haErr, double c13Err)
          Written by Lincong.
 java.util.Vector mergeAll3(java.util.Vector allVec, java.util.Vector hcchVec)
          written by LW.
 java.util.Vector mergeAll4(java.util.Vector allHcchVec)
          written by LW.
 java.util.Vector mergeAssignAndNoe(java.util.Vector asgVec, java.util.Vector hnNoeVec, java.util.Vector cNoeVec, double hnErr, double nErr, double haErr, double cErr)
          Written by Lincong, only used in his previous functions.
 java.util.Vector mergeC13Noe(java.util.Vector hcchVec, java.util.Vector hsqcVec, double haErr, double cErr)
          Written by Lincong, only used in his previous functions.
 java.util.Vector mergeNoe(java.util.Vector hnNoeVec, java.util.Vector hsqcVec, double hnErr, double nErr)
          Written by Lincong, only used in his previous functions.
 java.util.Vector mergeNoeAndAssign(java.util.Vector hnNoeVec, java.util.Vector hsqcVec, java.util.Vector assignVec, double hnErr, double nErr)
          Written by Lincong, only used in his previous functions.
 void NOEAsgFromCS(java.lang.String src, java.lang.String strOut, java.lang.String strInput)
          NOE assignment only based on the chemical shift information, and output the NOE table.
 double NoePatternMatchScore_old2(double csErrH, double csErrN, double csErrCA, java.util.Vector vecBackNoe, java.util.Vector vecNoesy, int[] numPeaks)
          This is an old function, and can be deleted.
 double NoePatternMatchScore(double csErrH, double csErrN, double csErrCA, java.util.Vector vecBackNoe, java.util.Vector vecNoesy, int[] numPeaks, boolean isSkipIntensity)
          Refined function for the general case: Compute the matching score between back-computed NOE pattern and original NOE list.
 double NoePatternMatchScore(java.util.Vector vecBackNoe, java.util.Vector vecHnNoe, java.util.Vector vecCaNoe, int[] numPeaks)
          Compute the matching score between backcomputed NOE pattern and original NOE list.
 double NoePatternMatchScoreWCali(double csErrH, double csErrN, double csErrCA, java.util.Vector vecBackNoe, java.util.Vector vecNoesy, int[] numPeaks, boolean isSkipIntensity, double constant)
          This is an old function with adding the calibration lines in the code.
 double NoePatternMatchScoreWCaliHdphic(double csErrH, double csErrN, double csErrCA, java.util.Vector vecBackNoe, java.util.Vector vecNoesy, int[] numPeaks, boolean isSkipIntensity, double constant)
          This is an old function, for hydrophilic residues.
 double NoePatternMatchScoreWCaliTestJBNMR1(double csErrH, double csErrN, double csErrCA, java.util.Vector vecBackNoe, java.util.Vector vecNoesy, int[] numPeaks, boolean isSkipIntensity, double constant)
          This is a test in order to address the comments from the second reviewer (point 4) from the JBNMR09 submission.
 double NoePatternMatchScoreWCaliTestJBNMR2(double csErrH, double csErrN, double csErrCA, java.util.Vector vecBackNoe, java.util.Vector vecNoesy, int[] numPeaks, boolean isSkipIntensity, double constant)
          This is a test in order to address the comments from the second reviewer (point 4) from the JBNMR09 submission.
 java.util.Vector<java.util.Map<java.lang.String,java.lang.String>> ParamReader(java.lang.String fileName)
          Read the parameters such as the number of refinement cycle etc for running the program.
 java.util.Vector PrunAmbgNoeAsg(java.util.Vector pdbVec, java.util.Vector vecNoe, double noeLimit, double methylCorrection, int nIsoriginalUp)
          Prune ambiguous NOE assignment using given structural information.
 java.util.Vector ReaderSeq(java.lang.String filename)
          Read protein sequence.
 void setMaxValue(double maxval)
          Sets the max value.
 void setMissingIndex(int[] index)
          Sets the missing index.
 java.util.Vector sortAssign(java.util.Vector allVec)
          Written by Lincong.
 java.util.Vector StereospecificNoeAsg(java.util.Vector vecNoe)
          consider the stereospecific assignments.
 java.util.Vector SwapStereoAsg(java.util.Vector vecAsg, int resNo)
          swap the stereospecific assignment for a given residue we assume the atom naming scheme is PDB-New.
 java.lang.String toString()
           
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Constructor Detail

Assign

public Assign()
Instantiates a new assign.


Assign

public Assign(int no)
Instantiates a new assign.

Parameters:
no - the no

Assign

public Assign(int no,
              java.lang.String type)
Instantiates a new assign.

Parameters:
no - the no
type - the type

Assign

public Assign(int no,
              java.lang.String type,
              java.util.Map aMap)
Instantiates a new assign.

Parameters:
no - the no
type - the type
aMap - the map

Assign

public Assign(int no,
              java.lang.String type,
              java.util.Map aMap,
              java.util.Vector hnVec,
              java.util.Vector haVec)
Instantiates a new assign.

Parameters:
no - the no
type - the type
aMap - the a map
hnVec - the hn vec
haVec - the ha vec

Assign

public Assign(int no,
              java.lang.String type,
              java.util.Map aMap,
              java.util.Vector hnVec,
              java.util.Vector haVec,
              java.util.Vector h1Vec)
Instantiates a new assign.

Parameters:
no - the no
type - the type
aMap - the a map
hnVec - the hn vec
haVec - the ha vec
h1Vec - the h1 vec
Method Detail

setMaxValue

public void setMaxValue(double maxval)
Sets the max value.

Parameters:
maxval - the new max value

setMissingIndex

public void setMissingIndex(int[] index)
Sets the missing index.

Parameters:
index - the new missing index

getMissingIndex

public int[] getMissingIndex()
Gets the missing index.

Returns:
the missing index

getMaxValue

public double getMaxValue()
Gets the max value.

Returns:
the max value

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

getMap

public java.util.Map getMap()
Gets the map.

Returns:
the map

getHnNoeVec

public java.util.Vector getHnNoeVec()
Gets the hn noe vec.

Returns:
the hn noe vec

getHaNoeVec

public java.util.Vector getHaNoeVec()
Gets the ha noe vec.

Returns:
the ha noe vec

getH1NoeVec

public java.util.Vector getH1NoeVec()
Gets the h1 noe vec.

Returns:
the h1 noe vec

toString

public java.lang.String toString()
Overrides:
toString in class java.lang.Object

getOrder

public java.util.Vector getOrder(java.lang.String strSSES)
A very simple reader for secondary structure identification file.

Parameters:
strSSES - the str sses
Returns:
a vector of IDof2aryStructure objects

assignReader

public java.util.Vector assignReader(java.lang.String pdbFile,
                                     double h1Ref)
Read the resonance assignment.

Parameters:
pdbFile - the pdb file
h1Ref - the chemical shift correction (?)
Returns:
a vector of Assign object

assignReader2

public java.util.Vector assignReader2(java.lang.String hncacbFile,
                                      java.util.Vector assignVec,
                                      java.util.Vector chsqcVec)
Read the resonance assignment, meanwhile update the residue name for each chemical shift.

Parameters:
hncacbFile - the hncacb file
assignVec - the assign vec
chsqcVec - the chsqc vec
Returns:
a vector of Assign object

ReaderSeq

public java.util.Vector ReaderSeq(java.lang.String filename)
Read protein sequence.

Parameters:
filename - the name of the file
Returns:
a vector of residues and corresponding residue numbers (IDs)

ParamReader

public java.util.Vector<java.util.Map<java.lang.String,java.lang.String>> ParamReader(java.lang.String fileName)
Read the parameters such as the number of refinement cycle etc for running the program. This function was only used in Lincong's previous code.

Parameters:
fileName - the name of the parameter file
Returns:
an array of Map with the name of the parameter and the corresponding value

asgReader3

public java.util.Vector asgReader3(java.lang.String filename)
Written by Lincong, only used in his previous functions. Read peak list generated by NMRView, just for ubq peaks picked by Lincong

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

assignHsqc

public void assignHsqc(java.util.Vector assignVec,
                       java.util.Vector hsqcVec)
Written by Lincong, only used in his previous functions.

Parameters:
assignVec - the assign vec
hsqcVec - the hsqc vec

matchC13Hsqc

public void matchC13Hsqc(java.util.Vector foldHsqcVec,
                         java.util.Vector hsqcVec)
Written by Lincong, only used in his previous functions.

Parameters:
foldHsqcVec - the fold hsqc vec
hsqcVec - the hsqc vec

mergeNoe

public java.util.Vector mergeNoe(java.util.Vector hnNoeVec,
                                 java.util.Vector hsqcVec,
                                 double hnErr,
                                 double nErr)
Written by Lincong, only used in his previous functions.

Parameters:
hnNoeVec - the hn noe vec
hsqcVec - the hsqc vec
hnErr - the hn err
nErr - the n err
Returns:
the vector

mergeC13Noe

public java.util.Vector mergeC13Noe(java.util.Vector hcchVec,
                                    java.util.Vector hsqcVec,
                                    double haErr,
                                    double cErr)
Written by Lincong, only used in his previous functions.

Parameters:
hcchVec - a C13 NOE vector which has the same members as HcchTocsy object
hsqcVec - the assigned C13 Hsqc vector (in fact, the folded one since C13 NOESY is folded)
haErr - the ha err
cErr - the c err
Returns:
the vector

mergeNoeAndAssign

public java.util.Vector mergeNoeAndAssign(java.util.Vector hnNoeVec,
                                          java.util.Vector hsqcVec,
                                          java.util.Vector assignVec,
                                          double hnErr,
                                          double nErr)
Written by Lincong, only used in his previous functions.

Parameters:
hnNoeVec - the hn noe vec
hsqcVec - the hsqc vec
assignVec - the assign vec
hnErr - the hn err
nErr - the n err
Returns:
the vector

mergeAssignAndNoe

public java.util.Vector mergeAssignAndNoe(java.util.Vector asgVec,
                                          java.util.Vector hnNoeVec,
                                          java.util.Vector cNoeVec,
                                          double hnErr,
                                          double nErr,
                                          double haErr,
                                          double cErr)
Written by Lincong, only used in his previous functions.

Parameters:
asgVec - the asg vec
hnNoeVec - the hn noe vec
cNoeVec - the c noe vec
hnErr - the hn err
nErr - the n err
haErr - the ha err
cErr - the c err
Returns:
the vector

deleteRepeat

public java.util.Vector deleteRepeat(java.util.Vector allVec,
                                     double epsH,
                                     double epsN,
                                     double epsH1)
Delete repeated chemical shifts.

Parameters:
allVec - original chemical shift list;
epsH - the eps h
epsN - the eps n
epsH1 - the eps h1
Returns:
new list of chemical shifts

sortAssign

public java.util.Vector sortAssign(java.util.Vector allVec)
Written by Lincong. Please note that in order to sort the map structure we first converted it into a vector IT's a stupid ans slow but I am in a hurry

Parameters:
allVec - the all vec
Returns:
the vector

mergeAll

public java.util.Vector mergeAll(java.util.Vector allVec,
                                 java.util.Vector hcchVec,
                                 double haErr,
                                 double c13Err)
Written by Lincong. Please note that in order to sort the map structure we first converted it into a vector IT's a stupid ans slow but I am in a hurry

Parameters:
allVec - the all vec
hcchVec - the hcch vec
haErr - the ha err
c13Err - the c13 err
Returns:
the vector

BackNoeDeleteRepeat

public java.util.Vector BackNoeDeleteRepeat(java.util.Vector vecBackNoe)
delete repeated back noes, mainly from methyl groups.

Parameters:
vecBackNoe - back computed NOE patterns.
Returns:
new back noes

CompMaxMatchScore_old

public void CompMaxMatchScore_old(java.util.Vector vecBackNoe,
                                  double preMisPenalty,
                                  double preMatchScore,
                                  int depth,
                                  int finalDepth,
                                  int[] missingIndex)
recursively compute the max matching score. This is an old function. Need to be careful if this is used again.

Parameters:
vecBackNoe - back computed NOE patterns
preMisPenalty - the pre mis penalty
preMatchScore - the pre match score
depth - the depth
finalDepth - the final depth
missingIndex - the missing index

NoePatternMatchScore_old2

public double NoePatternMatchScore_old2(double csErrH,
                                        double csErrN,
                                        double csErrCA,
                                        java.util.Vector vecBackNoe,
                                        java.util.Vector vecNoesy,
                                        int[] numPeaks)
This is an old function, and can be deleted. Compute the matching score between backcomputed NOE pattern and original NOE list

Parameters:
csErrH - the cs err h
csErrN - the cs err n
numPeaks - number of non-missing peaks
csErrCA - the cs err ca
vecBackNoe - the vec back noe
vecNoesy - the vec noesy
Returns:
matching score

NoePatternMatchScoreWCali

public double NoePatternMatchScoreWCali(double csErrH,
                                        double csErrN,
                                        double csErrCA,
                                        java.util.Vector vecBackNoe,
                                        java.util.Vector vecNoesy,
                                        int[] numPeaks,
                                        boolean isSkipIntensity,
                                        double constant)
This is an old function with adding the calibration lines in the code. Compute the matching score between backcomputed NOE pattern and original NOE list

Parameters:
csErrH - error window of the first proton attached to the heavy atom (indirect proton)
csErrN - the cs err n
numPeaks - number of non-missing peaks
csErrCA - the cs err ca
vecBackNoe - the vec back noe
vecNoesy - the vec noesy
isSkipIntensity - the is skip intensity
constant - the constant
Returns:
matching score

NoePatternMatchScoreWCaliTestJBNMR1

public double NoePatternMatchScoreWCaliTestJBNMR1(double csErrH,
                                                  double csErrN,
                                                  double csErrCA,
                                                  java.util.Vector vecBackNoe,
                                                  java.util.Vector vecNoesy,
                                                  int[] numPeaks,
                                                  boolean isSkipIntensity,
                                                  double constant)
This is a test in order to address the comments from the second reviewer (point 4) from the JBNMR09 submission. Basically change the current Hausdorff-based measure to Bayesian metric and RMSD-based metric. This function is to test the Bayesian metric. This is an old function with adding the calibration lines in the code. Compute the matching score between backcomputed NOE pattern and original NOE list

Parameters:
csErrH - error window of the first proton attached to the heavy atom (indirect proton)
csErrN - the cs err n
numPeaks - number of non-missing peaks
csErrCA - the cs err ca
vecBackNoe - the vec back noe
vecNoesy - the vec noesy
isSkipIntensity - the is skip intensity
constant - the constant
Returns:
matching score

NoePatternMatchScoreWCaliTestJBNMR2

public double NoePatternMatchScoreWCaliTestJBNMR2(double csErrH,
                                                  double csErrN,
                                                  double csErrCA,
                                                  java.util.Vector vecBackNoe,
                                                  java.util.Vector vecNoesy,
                                                  int[] numPeaks,
                                                  boolean isSkipIntensity,
                                                  double constant)
This is a test in order to address the comments from the second reviewer (point 4) from the JBNMR09 submission. Basically change the current Hausdorff-based measure to Bayesian metric and RMSD-based metric. This function is to test the RMSD-based metric. This is an old function with adding the calibration lines in the code. Compute the matching score between backcomputed NOE pattern and original NOE list

Parameters:
csErrH - error window of the first proton attached to the heavy atom (indirect proton)
csErrN - the cs err n
numPeaks - number of non-missing peaks
csErrCA - the cs err ca
vecBackNoe - the vec back noe
vecNoesy - the vec noesy
isSkipIntensity - the is skip intensity
constant - the constant
Returns:
matching score

NoePatternMatchScoreWCaliHdphic

public double NoePatternMatchScoreWCaliHdphic(double csErrH,
                                              double csErrN,
                                              double csErrCA,
                                              java.util.Vector vecBackNoe,
                                              java.util.Vector vecNoesy,
                                              int[] numPeaks,
                                              boolean isSkipIntensity,
                                              double constant)
This is an old function, for hydrophilic residues.

Parameters:
csErrH - error window of the first proton attached to the heavy atom (indirect proton)
csErrN - the cs err n
numPeaks - number of non-missing peaks
csErrCA - the cs err ca
vecBackNoe - the vec back noe
vecNoesy - the vec noesy
isSkipIntensity - the is skip intensity
constant - the constant
Returns:
matching score

NoePatternMatchScore

public double NoePatternMatchScore(double csErrH,
                                   double csErrN,
                                   double csErrCA,
                                   java.util.Vector vecBackNoe,
                                   java.util.Vector vecNoesy,
                                   int[] numPeaks,
                                   boolean isSkipIntensity)
Refined function for the general case: Compute the matching score between back-computed NOE pattern and original NOE list.

Parameters:
csErrH - error window of the first proton attached to the heavy atom (indirect proton)
csErrN - the cs err n
numPeaks - number of non-missing peaks
csErrCA - the cs err ca
vecBackNoe - the vec back noe
vecNoesy - the vec noesy
isSkipIntensity - the is skip intensity
Returns:
matching score

NoePatternMatchScore

public double NoePatternMatchScore(java.util.Vector vecBackNoe,
                                   java.util.Vector vecHnNoe,
                                   java.util.Vector vecCaNoe,
                                   int[] numPeaks)
Compute the matching score between backcomputed NOE pattern and original NOE list.

Parameters:
vecBackNoe - back computed NOE patterns
vecHnNoe - HnNOE peak list
vecCaNoe - CA NOE peak list
numPeaks - number of non-missing peaks
Returns:
matching score

SwapStereoAsg

public java.util.Vector SwapStereoAsg(java.util.Vector vecAsg,
                                      int resNo)
swap the stereospecific assignment for a given residue we assume the atom naming scheme is PDB-New.

Parameters:
vecAsg - vector of resonance assignments
resNo - the res no
Returns:
new resonance assignments

StereospecificNoeAsg

public java.util.Vector StereospecificNoeAsg(java.util.Vector vecNoe)
consider the stereospecific assignments.

Parameters:
vecNoe - vector of original noe assignments
Returns:
new noe assignments

PrunAmbgNoeAsg

public java.util.Vector PrunAmbgNoeAsg(java.util.Vector pdbVec,
                                       java.util.Vector vecNoe,
                                       double noeLimit,
                                       double methylCorrection,
                                       int nIsoriginalUp)
Prune ambiguous NOE assignment using given structural information.

Parameters:
pdbVec - the pdb structure after combining selected rotamers and backbone
vecNoe - vector of ambiguous noe assignments
noeLimit - noe upper limit to prune ambiguous noes
methylCorrection - always 0 in new verstion.
nIsoriginalUp - whether keep the original noe upper bound, 1 for yes, 0 for using distance information
Returns:
noe assignments after filtration

InitAmbiAssignmentUnique

public java.util.Vector InitAmbiAssignmentUnique(double nErr,
                                                 double cErr,
                                                 double hnErr,
                                                 double haErr,
                                                 double h2Err,
                                                 java.util.Vector vecAsg,
                                                 java.util.Vector vecAllH1,
                                                 java.util.Vector vecNoesy)
The same as InitAmbiAssignment, but only output those unique noe assignments.

Parameters:
nErr - error tolerance in the N dimension
cErr - error tolerance in the c dimension
hnErr - error tolerance in the hn dimension
haErr - error tolerance in the ha dimension
vecAsg - assigned resonance list
vecAllH1 - all sorted protons
vecNoesy - NOESY peaks, including both c13 and n15 noesy peaks
h2Err - the h2 err
Returns:
ambiguous noe assignments (vector of Noe)

InitAmbiAssignment

public java.util.Vector InitAmbiAssignment(double nErr,
                                           double cErr,
                                           double hnErr,
                                           double haErr,
                                           double h2Err,
                                           java.util.Vector vecAsg,
                                           java.util.Vector vecAllH1,
                                           java.util.Vector vecNoesy)
Compute the intiial NOE assignments using only chemcial shift information.

Parameters:
nErr - error tolerance in the N dimension
cErr - error tolerance in the c dimension
hnErr - error tolerance in the hn dimension
haErr - error tolerance in the ha dimension
vecAsg - assigned resonance list
vecAllH1 - all sorted protons
vecNoesy - NOESY peaks, including both c13 and n15 noesy peaks
h2Err - the h2 err
Returns:
ambiguous noe assignments (vector of Noe)

InitAmbiAssignment4D

public java.util.Vector InitAmbiAssignment4D(double nErr,
                                             double cErr,
                                             double hnErr,
                                             double haErr,
                                             double h2Err,
                                             java.util.Vector vecAsg,
                                             java.util.Vector vecAllH1,
                                             java.util.Vector vecNoesy)
Initial NOE assignment for 4D NOESY.

Parameters:
nErr - error tolerance in the N dimension
cErr - error tolerance in the c dimension
hnErr - error tolerance in the hn dimension
haErr - error tolerance in the ha dimension
vecAsg - assigned resonance list
vecAllH1 - all sorted protons
vecNoesy - 4d NOESY peaks, including both c13 and n15 noesy peaks
h2Err - the h2 err
Returns:
ambiguous noe assignments (vector of Noe)

mergeAll3

public java.util.Vector mergeAll3(java.util.Vector allVec,
                                  java.util.Vector hcchVec)
written by LW. Please note that in order to sort the map structure we first converted it into a vector IT's a stupid ans slow but I am in a hurry

Parameters:
allVec - the all vec
hcchVec - the hcch vec
Returns:
the vector

mergeAll4

public java.util.Vector mergeAll4(java.util.Vector allHcchVec)
written by LW. Please note that in order to sort the map structure we first converted it into a vector IT's a stupid ans slow but I am in a hurry

Parameters:
allHcchVec - the all hcch vec
Returns:
the vector

NOEAsgFromCS

public void NOEAsgFromCS(java.lang.String src,
                         java.lang.String strOut,
                         java.lang.String strInput)
NOE assignment only based on the chemical shift information, and output the NOE table.

Parameters:
src - location of the input file
strOut - location of the output file
strInput - input file name

doHANANOEAsg

public void doHANANOEAsg(java.lang.String src,
                         java.lang.String strOut,
                         java.lang.String strInput)
                  throws JampackException
HANA algorithm for the NOE assignment and output the NOE table.

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

doCompareTwoNOETables

public void doCompareTwoNOETables(java.lang.String src,
                                  java.lang.String strOut,
                                  java.lang.String strInput)
compare two NOE table and output the summary.

Parameters:
src - location of the input file
strOut - location of the output file
strInput - input file name

doExtractNOEs

public void doExtractNOEs(java.lang.String src,
                          java.lang.String strOut,
                          java.lang.String strInput)
extract NOEs in certain regions.

Parameters:
src - location of the input file
strOut - location of the output file
strInput - input file name

doLongNOEsAsgWOStructureNew

public void doLongNOEsAsgWOStructureNew(java.lang.String src,
                                        java.lang.String strOut,
                                        java.lang.String strInput)
refine the long-range NOE assignment without structure information, better version of doLongNOEsAsgWOStructure.

Parameters:
src - location of the input file
strOut - location of the output file
strInput - input file name

doLongNOEsAsgWOStructure

public void doLongNOEsAsgWOStructure(java.lang.String src,
                                     java.lang.String strOut,
                                     java.lang.String strInput)
refine the long-range NOE assignment without structure information.

Parameters:
src - location of the input file
strOut - location of the output file
strInput - input file name

doRefineNOEsWBB

public void doRefineNOEsWBB(java.lang.String src,
                            java.lang.String strOut,
                            java.lang.String strInput)
note: randomStructureSlect..need to be fixed, refine the NOE assignment using given the backbone and output the refine NOE table.

Parameters:
src - location of the input file
strOut - location of the output file
strInput - input file name