RdcPanda
Class Peak

java.lang.Object
  extended by RdcPanda.Peak

public class Peak
extends java.lang.Object

This class is modified from LW's original one, and some functions might be redundant with other classes. This class hasn't been completely cleaned. Written by Lincong Wang (2001-2005) and Jianyang (Michael) Zeng (2005-2009).


Nested Class Summary
static class Peak.csComparator
          The Class csComparator.
 
Constructor Summary
Peak()
          Instantiates a new peak.
Peak(double csV)
          A constructor designed specifically for the Comparator class used for the Sort and BinarySearch.
Peak(java.lang.String type, double no)
          Instantiates a new peak.
Peak(java.lang.String type, double no, boolean isAsg)
          Instantiates a new peak.
Peak(java.lang.String type, double no, double inten)
          Instantiates a new peak.
Peak(java.lang.String type, double no, double inten, boolean isAsg)
          Instantiates a new peak.
 
Method Summary
 java.util.Vector allNoes(java.util.Vector pdbVec, java.util.Vector asgVec, double[] coordA, double noeLimit, double methylCorrection)
          Compute all the possible NOE peaks from the nucleus with coordA to all other nuclei in a PDB structure, the.
 java.util.Vector allProtonSorted_old(java.util.Vector asgVec)
          A method to extract all the protons and convert the Assign object to Peak object Please note that the returned Peak has special identification for the nucleus element.
 java.util.Vector allProtonSorted(java.util.Vector asgVec)
          A method to extract all the protons and convert the Assign object to Peak object Please note that the returned Peak has special identification for the nucleus element.
 java.util.Vector BackCSGenerate(java.util.Vector allCSVec, int resNo1, java.lang.String resName1, java.lang.String atomName1, int resNo2, java.lang.String resName2, java.lang.String atomName2, java.lang.String heavyName2, double csSigma)
          A function to generate and check back NOE chemical shifts.
 void BackNOEGenerate(java.util.Vector h1Vec, java.util.Vector asgVec, java.util.Vector pdbVecXray, java.util.Vector allCSVec, java.util.Vector allHnVec, java.util.Vector allHaVec)
          generate the back noes from assignment based on x-ray structure.
 boolean CheckBackNOE(java.util.Vector hnNoeVec, java.util.Vector haNoeVec, java.util.Vector csAllAsg, int resNo1, java.lang.String resName1, java.lang.String atomName1, int resNo2, java.lang.String resName2, java.lang.String atomName2, double chkErr)
          check whether there exists a back Noe from H2 to H1.
 java.util.Vector CheckLongRangNOE(java.util.Vector vecNoe, int Threshold)
          for long-range noes, check whether number of neighboring noes is larger than some bound.
 boolean checkNoe_old(java.util.Vector pdbVec, java.util.Vector asgVec, int no, java.lang.String nucleus, int no2, java.lang.String nucleus2, double noeLimit, double methylCorrection, double[] noe)
          Compute all the possible NOE peaks from the nucleus with coordA to all other nuclei in a PDB structure, the.
 boolean checkNoe(java.util.Vector pdbVec, int no, java.lang.String nucleus, int no2, java.lang.String nucleus2, double noeLimit, double methylCorrection, double[] noe)
          Refined function: for the general case.
 boolean checkNoe2(java.util.Vector pdbVec, int no, java.lang.String nucleus, int no2, java.lang.String nucleus2, double noeLimit, double methylCorrection, double[] noe)
          Compute all the possible NOE peaks from the nucleus with coordA to all other nuclei in a PDB structure, the.
 boolean checkNoeNew(java.util.Vector pdbVec, int no, java.lang.String nucleus, int no2, java.lang.String nucleus2, double noeLimit, double methylCorrection, double[] noe)
          better version of "checkNoe" Refined function: for the general case.
 boolean checkNoeNew2(java.util.Vector pdbVec, int no, java.lang.String nucleus, int no2, java.lang.String nucleus2, double noeLimit, double methylCorrection, double[] noe)
          similar to checkNoeNew, with additional0.5 A
 java.util.Vector CheckNoeSym(java.util.Vector vecNoe)
          refine NOEs and only keep those NOE with symmetry property, for C13 NOESY and sidechain N15 NOESY.
 boolean checkSymmetry(java.util.Vector scNoe, double csBbH, double csScH, double winErr)
          check whether there exists a symmetric Noe from side-chains to other protons.
 double getCS()
          Gets the cS.
 double getCSFromList(java.util.Vector vecAsg, int resNo, java.lang.String atom)
          Gets the cS from list.
 java.lang.String GetHeavyAtomFromProton(java.lang.String resName, java.lang.String protonName)
          Gets the heavy atom from proton.
 boolean getIsAssg()
          Gets the checks if is assg.
 java.lang.String getNucleus()
          Gets the nucleus.
 void intensityVsDistance(java.util.Vector h1Vec, java.util.Vector asgVec, java.util.Vector pdbVec)
          A temporary method to relate NOE intensity with distance,.
 double[] internuclearVec(double[] n1, double[] n2)
          Compute the internuclear vector between two atoms.
 boolean isCharged(java.lang.String resName)
          check whether a residue is a charged amino acid.
 boolean isHydrophobic(java.lang.String resName)
          check whether a residue is a hydrophobic amino acid.
 double length(double[] v1)
          Length.
 void noeAssign1st(java.util.Vector h1Vec, java.util.Vector asgVec)
          This is an earlier version of NOE assignment method, not filtered by Structure.
 void noeAssign2nd(java.util.Vector h1Vec, java.util.Vector asgVec, java.util.Vector pdbVec, java.util.Vector pdbVecXray, java.util.Vector hnNoeVec, java.util.Vector cNoeVec)
          an NOE assignment method, filtered by Structure.
 void noeAssign2ndLW(java.util.Vector h1Vec, java.util.Vector asgVec, java.util.Vector pdbVec, java.util.Vector pdbVecXray)
          Lw's original + rotamer library an NOE assignment method, filtered by Structure.
 void noeAssign3rd(java.util.Vector h1Vec, java.util.Vector asgVec, java.util.Vector pdbVec, java.util.Vector pdbVecXray, java.util.Vector hnNoeVec, java.util.Vector cNoeVec)
          an NOE assignment method, filtered by Structure.
 void noeAssign3rdLW(java.util.Vector h1Vec, java.util.Vector asgVec, java.util.Vector pdbVec, java.util.Vector pdbVecXray, java.util.Vector hnNoeVec, java.util.Vector cNoeVec)
          Lincong's original + rotamer library an NOE assignment method, filtered by Structure.
 Matrix noeAssignMat(java.util.Vector h1Vec, java.util.Vector asgVec)
          Compute the possbile NOE assignment matrix, an idea not further pursued.
 void noeBackCompute(java.util.Vector pdbVec, java.util.Vector asgVec)
          A method for back-computing NOEs, in the current implementation only compute the NOEs from amide protons ("H" in the Pdb file).
 double[] noeLimit(double dis)
          Noe limit.
 boolean noeSearch(java.util.Vector h1Vec, java.util.Vector asgVec, int no1, java.lang.String nucleus1, int no2, java.lang.String nucleus2, double[] noe)
          return NOEs between the two nuclei specified in the input if exists.
 java.util.Vector rangeSearch(java.util.Vector sortedH1Vec, double csValue, double h1Err)
          Range Search: search all the protons with in the range [CS-h1Err, CS + h1Err].
 java.util.Vector rangeSearchScNoeCS1(java.util.Vector sortedH1Vec, double csValue, double h1Err)
          Range Search: search all the protons with in the range [CS-h1Err, CS + h1Err].
 java.util.Vector rangeSearchScNoeCS2(java.util.Vector sortedH1Vec, double csValue, double h1Err)
          Range Search: search all the protons with in the range [CS-h1Err, CS + h1Err].
 java.util.Vector ringResonanceAsg(double csValue, double hErr)
          ringResonaceAsg: search all the protons with in the range [CS-Err, CS + Err] and assign the H resonance.
 java.util.Vector scNoeGenerate(java.util.Vector h1CSVec, int resNo1, java.lang.String nucleus1, double csH1Err, java.util.Vector pdbVecXray)
          A function to generate NOEs from side-chains to HN or HA, //no longer used.
 void setCS(double R)
          Sets the cS.
 void setNucleus(java.lang.String R)
          Sets the nucleus.
 java.util.Vector SimulatedCaNoe(java.util.Vector pdbVecXray, java.util.Vector asgVec, double distBound)
          generate the simulated ca noes from x-ray structure.
 java.lang.String toString()
           
 java.util.Vector ubqNoeGenerate(java.util.Vector h1CSVec, double csH1Err, java.util.Vector pdbVecXray)
          A function to generate ubq NOEs from side-chains to HN or HA,.
 java.lang.String xplorNoeStatement_old(int no1, java.lang.String nucleus1, int no2, java.lang.String resid, java.lang.String nucleus2, double dis, double[] disUp)
          Xplor noe statement_old.
 java.lang.String xplorNoeStatement(int no1, java.lang.String nucleus1, int no2, java.lang.String nucleus2, double dis)
          Xplor noe statement.
 java.lang.String xplorNoeStatement(int no1, java.lang.String resid1, java.lang.String nucleus1, int no2, java.lang.String resid, java.lang.String nucleus2, double dis, double[] disUp)
          Xplor noe statement.
 java.lang.String xplorNoeStatementNew(int no1, java.lang.String resid1, java.lang.String nucleus1, int no2, java.lang.String resid, java.lang.String nucleus2, double dis)
          Xplor noe statement new.
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Constructor Detail

Peak

public Peak()
Instantiates a new peak.


Peak

public Peak(double csV)
A constructor designed specifically for the Comparator class used for the Sort and BinarySearch.

Parameters:
csV - the cs v

Peak

public Peak(java.lang.String type,
            double no)
Instantiates a new peak.

Parameters:
type - the type
no - the no

Peak

public Peak(java.lang.String type,
            double no,
            boolean isAsg)
Instantiates a new peak.

Parameters:
type - the type
no - the no
isAsg - the is asg

Peak

public Peak(java.lang.String type,
            double no,
            double inten)
Instantiates a new peak.

Parameters:
type - the type
no - the no
inten - the inten

Peak

public Peak(java.lang.String type,
            double no,
            double inten,
            boolean isAsg)
Instantiates a new peak.

Parameters:
type - the type
no - the no
inten - the inten
isAsg - the is asg
Method Detail

getCS

public double getCS()
Gets the cS.

Returns:
the cS

getIsAssg

public boolean getIsAssg()
Gets the checks if is assg.

Returns:
the checks if is assg

getNucleus

public java.lang.String getNucleus()
Gets the nucleus.

Returns:
the nucleus

setCS

public void setCS(double R)
Sets the cS.

Parameters:
R - the new cS

setNucleus

public void setNucleus(java.lang.String R)
Sets the nucleus.

Parameters:
R - the new nucleus

toString

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

GetHeavyAtomFromProton

public java.lang.String GetHeavyAtomFromProton(java.lang.String resName,
                                               java.lang.String protonName)
Gets the heavy atom from proton.

Parameters:
resName - the res name
protonName - the proton name
Returns:
the string

xplorNoeStatement

public java.lang.String xplorNoeStatement(int no1,
                                          java.lang.String nucleus1,
                                          int no2,
                                          java.lang.String nucleus2,
                                          double dis)
Xplor noe statement.

Parameters:
no1 - the no1
nucleus1 - the nucleus1
no2 - the no2
nucleus2 - the nucleus2
dis - the dis
Returns:
the string

noeLimit

public double[] noeLimit(double dis)
Noe limit.

Parameters:
dis - the dis
Returns:
the double[]

xplorNoeStatementNew

public java.lang.String xplorNoeStatementNew(int no1,
                                             java.lang.String resid1,
                                             java.lang.String nucleus1,
                                             int no2,
                                             java.lang.String resid,
                                             java.lang.String nucleus2,
                                             double dis)
Xplor noe statement new.

Parameters:
no1 - the no1
resid1 - the resid1
nucleus1 - the nucleus1
no2 - the no2
resid - the resid
nucleus2 - the nucleus2
dis - the dis
Returns:
the string

xplorNoeStatement

public java.lang.String xplorNoeStatement(int no1,
                                          java.lang.String resid1,
                                          java.lang.String nucleus1,
                                          int no2,
                                          java.lang.String resid,
                                          java.lang.String nucleus2,
                                          double dis,
                                          double[] disUp)
Xplor noe statement.

Parameters:
no1 - the no1
resid1 - the resid1
nucleus1 - the nucleus1
no2 - the no2
resid - the resid
nucleus2 - the nucleus2
dis - the dis
disUp - the dis up
Returns:
the string

xplorNoeStatement_old

public java.lang.String xplorNoeStatement_old(int no1,
                                              java.lang.String nucleus1,
                                              int no2,
                                              java.lang.String resid,
                                              java.lang.String nucleus2,
                                              double dis,
                                              double[] disUp)
Xplor noe statement_old.

Parameters:
no1 - the no1
nucleus1 - the nucleus1
no2 - the no2
resid - the resid
nucleus2 - the nucleus2
dis - the dis
disUp - the dis up
Returns:
the string

length

public double length(double[] v1)
Length.

Parameters:
v1 - the v1
Returns:
the double

internuclearVec

public double[] internuclearVec(double[] n1,
                                double[] n2)
Compute the internuclear vector between two atoms.

Parameters:
n1 - the coordinate for atom 1
n2 - the coordinate for atom 2
Returns:
a vector from n1->n2

allProtonSorted_old

public java.util.Vector allProtonSorted_old(java.util.Vector asgVec)
A method to extract all the protons and convert the Assign object to Peak object Please note that the returned Peak has special identification for the nucleus element.

Parameters:
asgVec - the asg vec
Returns:
the vector

allProtonSorted

public java.util.Vector allProtonSorted(java.util.Vector asgVec)
A method to extract all the protons and convert the Assign object to Peak object Please note that the returned Peak has special identification for the nucleus element.

Parameters:
asgVec - the asg vec
Returns:
the vector

ringResonanceAsg

public java.util.Vector ringResonanceAsg(double csValue,
                                         double hErr)
ringResonaceAsg: search all the protons with in the range [CS-Err, CS + Err] and assign the H resonance.

Parameters:
csValue - the middle value of cs value
hErr - error range for the csValue
Returns:
a vector of Peak objects

scNoeGenerate

public java.util.Vector scNoeGenerate(java.util.Vector h1CSVec,
                                      int resNo1,
                                      java.lang.String nucleus1,
                                      double csH1Err,
                                      java.util.Vector pdbVecXray)
A function to generate NOEs from side-chains to HN or HA, //no longer used.

Parameters:
csH1Err - the cs h1 err
pdbVecXray - the x-ray Pdb file
h1CSVec - the h1 cs vec
resNo1 - the res no1
nucleus1 - the nucleus1
Returns:
the vector

BackCSGenerate

public java.util.Vector BackCSGenerate(java.util.Vector allCSVec,
                                       int resNo1,
                                       java.lang.String resName1,
                                       java.lang.String atomName1,
                                       int resNo2,
                                       java.lang.String resName2,
                                       java.lang.String atomName2,
                                       java.lang.String heavyName2,
                                       double csSigma)
A function to generate and check back NOE chemical shifts.

Parameters:
allCSVec - the all cs vec
resNo1 - the res no1
resName1 - the res name1
atomName1 - the atom name1
resNo2 - the res no2
resName2 - the res name2
atomName2 - the atom name2
heavyName2 - the heavy name2
csSigma - the cs sigma
Returns:
the vector

ubqNoeGenerate

public java.util.Vector ubqNoeGenerate(java.util.Vector h1CSVec,
                                       double csH1Err,
                                       java.util.Vector pdbVecXray)
A function to generate ubq NOEs from side-chains to HN or HA,.

Parameters:
csH1Err - the cs h1 err
pdbVecXray - the x-ray Pdb file
h1CSVec - the h1 cs vec
Returns:
the vector

rangeSearch

public java.util.Vector rangeSearch(java.util.Vector sortedH1Vec,
                                    double csValue,
                                    double h1Err)
Range Search: search all the protons with in the range [CS-h1Err, CS + h1Err].

Parameters:
sortedH1Vec - is a sorted resonance assignment vector with monotone increasing sequence number.
csValue - the middle value of cs value
h1Err - error range for the csValue
Returns:
a vector of Peak objects

rangeSearchScNoeCS1

public java.util.Vector rangeSearchScNoeCS1(java.util.Vector sortedH1Vec,
                                            double csValue,
                                            double h1Err)
Range Search: search all the protons with in the range [CS-h1Err, CS + h1Err].

Parameters:
sortedH1Vec - is a sorted resonance assignment vector with monotone increasing sequence number.
csValue - the middle value of cs value
h1Err - error range for the csValue
Returns:
a vector of Peak objects

rangeSearchScNoeCS2

public java.util.Vector rangeSearchScNoeCS2(java.util.Vector sortedH1Vec,
                                            double csValue,
                                            double h1Err)
Range Search: search all the protons with in the range [CS-h1Err, CS + h1Err].

Parameters:
sortedH1Vec - is a sorted resonance assignment vector with monotone increasing sequence number.
csValue - the middle value of cs value
h1Err - error range for the csValue
Returns:
a vector of Peak objects

noeAssign1st

public void noeAssign1st(java.util.Vector h1Vec,
                         java.util.Vector asgVec)
This is an earlier version of NOE assignment method, not filtered by Structure.

Parameters:
h1Vec - a sorted array of all protons
asgVec - an array of Assign object for all the residues

SimulatedCaNoe

public java.util.Vector SimulatedCaNoe(java.util.Vector pdbVecXray,
                                       java.util.Vector asgVec,
                                       double distBound)
generate the simulated ca noes from x-ray structure.

Parameters:
asgVec - an array of Assign object for all the residues
pdbVecXray - the Xray structure of ubiquitin
distBound - the dist bound
Returns:
the vector

BackNOEGenerate

public void BackNOEGenerate(java.util.Vector h1Vec,
                            java.util.Vector asgVec,
                            java.util.Vector pdbVecXray,
                            java.util.Vector allCSVec,
                            java.util.Vector allHnVec,
                            java.util.Vector allHaVec)
generate the back noes from assignment based on x-ray structure.

Parameters:
h1Vec - a sorted array of all protons
asgVec - an array of Assign object for all the residues
allCSVec - an array saving all chemical shifts
pdbVecXray - the Xray structure of ubiquitin
allHnVec - returning parameter, saving all Hn NOEs inlucding previous and backNOEs
allHaVec - returning parameter, saving all Ha NOEs inlucding previous and backNOEs

noeAssign2ndLW

public void noeAssign2ndLW(java.util.Vector h1Vec,
                           java.util.Vector asgVec,
                           java.util.Vector pdbVec,
                           java.util.Vector pdbVecXray)
Lw's original + rotamer library an NOE assignment method, filtered by Structure.

Parameters:
h1Vec - a sorted array of all protons
asgVec - an array of Assign object for all the residues
pdbVec - the backbone structure used to filter the assignment
pdbVecXray - the Xray structure of ubiquitin

noeAssign2nd

public void noeAssign2nd(java.util.Vector h1Vec,
                         java.util.Vector asgVec,
                         java.util.Vector pdbVec,
                         java.util.Vector pdbVecXray,
                         java.util.Vector hnNoeVec,
                         java.util.Vector cNoeVec)
an NOE assignment method, filtered by Structure.

Parameters:
h1Vec - a sorted array of all protons
asgVec - an array of Assign object for all the residues
pdbVec - the backbone structure used to filter the assignment
pdbVecXray - the Xray structure of ubiquitin
hnNoeVec - the hn noe vec
cNoeVec - the c noe vec

noeAssign3rdLW

public void noeAssign3rdLW(java.util.Vector h1Vec,
                           java.util.Vector asgVec,
                           java.util.Vector pdbVec,
                           java.util.Vector pdbVecXray,
                           java.util.Vector hnNoeVec,
                           java.util.Vector cNoeVec)
Lincong's original + rotamer library an NOE assignment method, filtered by Structure.

Parameters:
h1Vec - a sorted array of all protons
asgVec - an array of Assign object for all the residues
pdbVec - the backbone structure used to filter the assignment
pdbVecXray - the Xray structure of ubiquitin
hnNoeVec - the hn noe vec
cNoeVec - the c noe vec

noeAssign3rd

public void noeAssign3rd(java.util.Vector h1Vec,
                         java.util.Vector asgVec,
                         java.util.Vector pdbVec,
                         java.util.Vector pdbVecXray,
                         java.util.Vector hnNoeVec,
                         java.util.Vector cNoeVec)
an NOE assignment method, filtered by Structure.

Parameters:
h1Vec - a sorted array of all protons
asgVec - an array of Assign object for all the residues
pdbVec - the backbone structure used to filter the assignment
pdbVecXray - the Xray structure of ubiquitin
hnNoeVec - the hn noe vec
cNoeVec - the c noe vec

checkSymmetry

public boolean checkSymmetry(java.util.Vector scNoe,
                             double csBbH,
                             double csScH,
                             double winErr)
check whether there exists a symmetric Noe from side-chains to other protons.

Parameters:
scNoe - the sc noe
csBbH - the cs bb h
csScH - the cs sc h
winErr - the win err
Returns:
all the Peak objects within the specified range

CheckBackNOE

public boolean CheckBackNOE(java.util.Vector hnNoeVec,
                            java.util.Vector haNoeVec,
                            java.util.Vector csAllAsg,
                            int resNo1,
                            java.lang.String resName1,
                            java.lang.String atomName1,
                            int resNo2,
                            java.lang.String resName2,
                            java.lang.String atomName2,
                            double chkErr)
check whether there exists a back Noe from H2 to H1.

Parameters:
hnNoeVec - the hn noe vec
haNoeVec - the ha noe vec
csAllAsg - the cs all asg
resNo1 - the res no1
resName1 - the res name1
atomName1 - the atom name1
resNo2 - the res no2
resName2 - the res name2
atomName2 - the atom name2
chkErr - the chk err
Returns:
all the Peak objects within the specified range

isHydrophobic

public boolean isHydrophobic(java.lang.String resName)
check whether a residue is a hydrophobic amino acid.

Parameters:
resName - the res name
Returns:
yes if distance is less than noe limit, otherwise no

isCharged

public boolean isCharged(java.lang.String resName)
check whether a residue is a charged amino acid.

Parameters:
resName - the res name
Returns:
yes if distance is less than noe limit, otherwise no

checkNoe

public boolean checkNoe(java.util.Vector pdbVec,
                        int no,
                        java.lang.String nucleus,
                        int no2,
                        java.lang.String nucleus2,
                        double noeLimit,
                        double methylCorrection,
                        double[] noe)
Refined function: for the general case. Compute all the possible NOE peaks from the nucleus with coordA to all other nuclei in a PDB structure, the

Parameters:
pdbVec - the pdb coordinates
no - the first reside no.
no2 - the second residue no
noeLimit - the upper limit for NOEs
methylCorrection - the methyl correction
nucleus - the nucleus
nucleus2 - the nucleus2
noe - the noe
Returns:
yes if distance is less than noe limit, otherwise no

checkNoeNew

public boolean checkNoeNew(java.util.Vector pdbVec,
                           int no,
                           java.lang.String nucleus,
                           int no2,
                           java.lang.String nucleus2,
                           double noeLimit,
                           double methylCorrection,
                           double[] noe)
better version of "checkNoe" Refined function: for the general case. Compute all the possible NOE peaks from the nucleus with coordA to all other nuclei in a PDB structure, the

Parameters:
pdbVec - the pdb coordinates
no - the first reside no.
no2 - the second residue no
noeLimit - the upper limit for NOEs
methylCorrection - the methyl correction
nucleus - the nucleus
nucleus2 - the nucleus2
noe - the noe
Returns:
yes if distance is less than noe limit, otherwise no Note: created 08/05/29.

checkNoeNew2

public boolean checkNoeNew2(java.util.Vector pdbVec,
                            int no,
                            java.lang.String nucleus,
                            int no2,
                            java.lang.String nucleus2,
                            double noeLimit,
                            double methylCorrection,
                            double[] noe)
similar to checkNoeNew, with additional0.5 A

Parameters:
pdbVec - the pdb coordinates
no - the first reside no.
no2 - the second residue no
noeLimit - the upper limit for NOEs
methylCorrection - the methyl correction
nucleus - the nucleus
nucleus2 - the nucleus2
noe - the noe
Returns:
yes if distance is less than noe limit, otherwise no Note: created 08/05/29.

getCSFromList

public double getCSFromList(java.util.Vector vecAsg,
                            int resNo,
                            java.lang.String atom)
Gets the cS from list.

Parameters:
vecAsg - the vec asg
resNo - the res no
atom - the atom
Returns:
the cS from list

CheckLongRangNOE

public java.util.Vector CheckLongRangNOE(java.util.Vector vecNoe,
                                         int Threshold)
for long-range noes, check whether number of neighboring noes is larger than some bound.

Parameters:
vecNoe - previous noe assignment
Threshold - threshold number of neighboring noes
Returns:
refined noe assignments

CheckNoeSym

public java.util.Vector CheckNoeSym(java.util.Vector vecNoe)
refine NOEs and only keep those NOE with symmetry property, for C13 NOESY and sidechain N15 NOESY.

Parameters:
vecNoe - original NOE assignments.
Returns:
new NOE assignment table.

checkNoe_old

public boolean checkNoe_old(java.util.Vector pdbVec,
                            java.util.Vector asgVec,
                            int no,
                            java.lang.String nucleus,
                            int no2,
                            java.lang.String nucleus2,
                            double noeLimit,
                            double methylCorrection,
                            double[] noe)
Compute all the possible NOE peaks from the nucleus with coordA to all other nuclei in a PDB structure, the.

Parameters:
asgVec - the sorted resonance assignment
pdbVec - the pdb coordinates
no - the reside no.
noeLimit - the limitation set for NOEs
nucleus - the nucleus
no2 - the no2
nucleus2 - the nucleus2
methylCorrection - the methyl correction
noe - the noe
Returns:
all the Peak objects within the specified range

checkNoe2

public boolean checkNoe2(java.util.Vector pdbVec,
                         int no,
                         java.lang.String nucleus,
                         int no2,
                         java.lang.String nucleus2,
                         double noeLimit,
                         double methylCorrection,
                         double[] noe)
Compute all the possible NOE peaks from the nucleus with coordA to all other nuclei in a PDB structure, the.

Parameters:
pdbVec - the pdb coordinates
no - the reside no.
noeLimit - the limitation set for NOEs
nucleus - the nucleus
no2 - the no2
nucleus2 - the nucleus2
methylCorrection - the methyl correction
noe - the noe
Returns:
all the Peak objects within the specified range

allNoes

public java.util.Vector allNoes(java.util.Vector pdbVec,
                                java.util.Vector asgVec,
                                double[] coordA,
                                double noeLimit,
                                double methylCorrection)
Compute all the possible NOE peaks from the nucleus with coordA to all other nuclei in a PDB structure, the.

Parameters:
asgVec - the sorted resonance assignment
pdbVec - the pdb coordinates
coordA - the position (coordinate) of nuclues
noeLimit - the limitation set for NOEs
methylCorrection - the methyl correction
Returns:
all the Peak objects within the specified range

noeBackCompute

public void noeBackCompute(java.util.Vector pdbVec,
                           java.util.Vector asgVec)
A method for back-computing NOEs, in the current implementation only compute the NOEs from amide protons ("H" in the Pdb file).

Parameters:
pdbVec - the Pdb structure.
asgVec - the assignment table.

noeSearch

public boolean noeSearch(java.util.Vector h1Vec,
                         java.util.Vector asgVec,
                         int no1,
                         java.lang.String nucleus1,
                         int no2,
                         java.lang.String nucleus2,
                         double[] noe)
return NOEs between the two nuclei specified in the input if exists. Always return the larger one of the two possible NOE intensity. NOTE: We assume that the 1st nucleus is NH, otherwise it is a bug

Parameters:
h1Vec - the sorted all proton CSs
asgVec - resonance assignment table and the NOE peak list
no1 - the first residue
nucleus1 - the nuclues of residue no1, assume to be HN.
no2 - the second residue
nucleus2 - the nuclues of residue no2
noe - for returning the find NOE intensity if exist
Returns:
if found, return the intensity, otherwise, return -1.00;

intensityVsDistance

public void intensityVsDistance(java.util.Vector h1Vec,
                                java.util.Vector asgVec,
                                java.util.Vector pdbVec)
A temporary method to relate NOE intensity with distance,.

Parameters:
h1Vec - a sorted all H1 cs array
asgVec - an assign Vector with assignment tablem and both HN and HA NOEs peak list
pdbVec - the Pdb file

noeAssignMat

public Matrix noeAssignMat(java.util.Vector h1Vec,
                           java.util.Vector asgVec)
Compute the possbile NOE assignment matrix, an idea not further pursued.

Parameters:
h1Vec - the h1 vec
asgVec - the asg vec
Returns:
the matrix