RdcPanda
Class Noe

java.lang.Object
  extended by RdcPanda.Noe
All Implemented Interfaces:
java.lang.Cloneable

public class Noe
extends java.lang.Object
implements java.lang.Cloneable

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


Nested Class Summary
static class Noe.NoeComparator
          The Class NoeComparator.
static class Noe.noeComparatorA
          The Class noeComparatorA.
static class Noe.noeComparatorB
          The Class noeComparatorB.
static class Noe.noeComparatorC
          The Class noeComparatorC.
 
Constructor Summary
Noe()
          Constructors.
Noe(int NoA, int noB)
          Instantiates a new noe.
Noe(int pkID, int Ano, int Bno, java.lang.String res1, java.lang.String res2, java.lang.String atom1, java.lang.String atom2, double low, double up)
          Instantiates a new noe.
Noe(int pkID, int Ano, int Bno, java.lang.String res1, java.lang.String res2, java.lang.String atom1, java.lang.String atom2, double low, double up, double r)
          Instantiates a new noe.
Noe(int Ano, int Bno, java.lang.String res1, java.lang.String res2, java.lang.String atom1, java.lang.String atom2, double low, double up)
          Instantiates a new noe.
Noe(int Ano, java.lang.String atom1, int Bno, java.lang.String atom2, double low, double up)
          Instantiates a new noe.
Noe(int pkID, java.util.Vector vec1, java.util.Vector vec2, double low, double up)
          Instantiates a new noe.
Noe(int pkID, java.util.Vector vec1, java.util.Vector vec2, Noe noe)
          Instantiates a new noe.
 
Method Summary
 void addH_A(H1CS h1csA)
          Adds the h_ a.
 void addH_B(H1CS h1csB)
          Adds the h_ b.
 void addProtons(Noe noe)
          Adds the protons.
 boolean CheckNoeHInPdb(java.util.Vector vecNoe, java.util.Vector vecPdb)
          check whether there is a atom name in noe talbe which is not in pdb.
 void CompareAsgToManualAsg(java.util.Vector vecAsg, java.util.Vector vecManualAsg, double[] number)
          Compare assignment results with manual assignments.
 void CompareAsgToRefStr(java.util.Vector vecNoe, java.util.Vector vecPdbRef, double noeLimit, double methylCorrection, double[] number)
          Compare assignment results with manual assignments.
 java.util.Vector ConvertAllNoeToBBNoe(java.util.Vector vecNoeAll, java.util.Vector vecSeq)
          convert genaral noe into noes between backbones.
 void ConvertCyanNoeAsgToXplor(java.lang.String noeFile, java.io.PrintWriter out)
          long reange noe read from cyana format.
 java.util.Vector ConvertMultiToSingleAsg(java.util.Vector vecMultiNoe)
          convert all multiple NOE assignments into single assignment format.
 java.util.Vector ConvertNoeFromBMRMToPDB(java.util.Vector vecNoeBMRB)
          convert an NOE set from BMRB-NEW to PDB-NEW format.
 java.util.Vector ConvertSingleToMultiAsg(java.util.Vector vecSingleNoe)
          convert all NOE assignments into multiple assignment format.
 java.util.Vector ConvertXplorAsgToUplFormat(java.util.Vector vecNoeXplor, java.util.Vector vecSeq, java.lang.String nameScheme)
          convert from the xplor noe format to cyna upl format.
 java.util.Vector ConvertXplorAsgToUplFormatFF2(java.util.Vector vecNoeXplor, java.util.Vector vecSeq)
          convert from the xplor noe format to cyna upl format.
 java.util.Vector DeleteRepeatNOEs(java.util.Vector vecOldNOE)
          delete repeated NOEs.
 void doCheckNoeByEnsemble(java.lang.String src, java.lang.String strOut, java.lang.String strInput)
          check the NOE table by an ensemble of structures, and output the statistical information.
 void doNoeStatistics(java.lang.String src, java.lang.String strOut, java.lang.String strInput)
          output the NOE statistics.
 java.lang.String getAtomA()
          Gets the atom a.
 java.lang.String getAtomB()
          Gets the atom b.
 double getLower()
          Gets the lower.
 int getPeakID()
          Gets the peak id.
 double[] getRange()
          Gets the range.
 double getRatioEnsemb()
          Gets the ratio ensemb.
 java.lang.String getResidueA()
          Gets the residue a.
 java.lang.String getResidueB()
          Gets the residue b.
 int getResidueNoA()
          Gets the residue no a.
 int getResidueNoB()
          Gets the residue no b.
 java.lang.String getResNameFromSequence(java.util.Vector vecSeq, int resNo)
          get the residue name from the sequence vector.
 double getUpper()
          Gets the upper.
 java.util.Vector getVecH_A()
          Gets the vec h_ a.
 java.util.Vector getVecH_B()
          Gets the vec h_ b.
 boolean[] identifyNoeResidues(java.util.Vector vecSseSeq, java.util.Vector vecNoeAll, int sseIndex)
          identify NOE residues for a sse.
 java.util.Vector LongRangeNoeReader(java.lang.String noeFile, double upCorrection, java.lang.String nameScheme)
          long reange noe read from cyana format.
 java.util.Vector LongRangeNoeReader2(java.lang.String noeFile)
          long reange noe read from cyana format.
 java.util.Vector LongRangeNoeReaderTestLW(java.lang.String noeFile)
          This is an old function.
static void main(java.lang.String[] argv)
          The main method.
 java.util.Vector NameConvertFromBMRBNewToPDBNew(java.util.Vector vecNoe)
          Convert naming scheme From BMRBNew To PDBNew, including pseudo protons of methyl groups.
 java.util.Vector NameConvertFromPDBNewToPDBNew(java.util.Vector vecNoe)
          Convert naming scheme From PDBNew To PDBNew, just do the changes of pseudo protons of methyl groups (eg.HB#)
 java.util.Vector NoeMethylCorrection(java.util.Vector vecNoeOld, double metCorrection)
          correct the NOE upper distance for an methyl NOE we assume that the pseudo methyl atoms of all old NOEs are labeled with "#" or "##".
 java.util.Vector<Noe> noeReader_old_fromLW(java.lang.String noeFile)
          A very simple reader for NOE data, see the file format.
 java.util.Vector noeReader(java.lang.String noeFile, double upCorrection)
          A very simple reader for NOE data, see the file format.
 java.util.Vector noeReader(java.lang.String noeFile, double upCorrection, java.util.Vector vecSeq)
          A very simple reader for NOE data, see the file format.
 java.util.Vector noeReader2(java.lang.String noeFile, double upCorrection)
          A very simple reader for NOE data, see the file format.
 java.util.Vector noeReaderMultiAsg(java.lang.String noeFile, java.util.Vector vecSeq)
          read the NOE assignment in mutiple format.
 boolean noeSatisfiedScore(java.util.Vector noeVec, java.util.Vector vecPdb, double[] noeRmsd, double[] noeHarmScore, int[] numConflicts)
          calculate the NOE satisfiation score.
 boolean noeSatisfiedScoreFF2(java.util.Vector noeVec, java.util.Vector vecPdb, double[] noeRmsd, double[] noeHarmScore, int[] numConflicts)
          Special for ff2 // only consider noes in between two SSEs calculate the NOE satisfiation score.
 void OutputMultiNOEAsg(java.util.Vector vecMultiNoe, java.lang.String strOutName)
          output the noe assignment in multple format.
 void PrintNOE(java.util.Vector vecNOE)
          print noe.
 void setAtom1Name(java.lang.String atom1)
          Sets the atom1 name.
 void setAtom2Name(java.lang.String atom2)
          Sets the atom2 name.
 void setDistLower(double lw)
          Sets the dist lower.
 void setDistUpper(double up)
          Sets the dist upper.
 void setPeakID(int id)
          Sets the peak id.
 void setRatioEnsemb(double ratio)
          Sets the ratio ensemb.
 void setResNameA(java.lang.String res1)
          Sets the res name a.
 void setResNameB(java.lang.String res2)
          Sets the res name b.
 void setResNoA(int n1)
          Sets the res no a.
 void setResNoB(int n2)
          Sets the res no b.
 java.util.Vector setSameUpperBounds4All(java.util.Vector vecOldNOE, double dbUpper)
          set the same upper bound for all NOEs.
 void setVecH_A(java.util.Vector vec1)
          Sets the vec h_ a.
 void setVecH_B(java.util.Vector vec2)
          Sets the vec h_ b.
 java.lang.String toString()
           
 java.util.Vector UpdateNOE(java.util.Vector vecOldNOE, java.util.Vector vecSSEOrder)
          update noe constraint, for pseudo atoms.
 java.lang.String UpdateNOEAtomName(java.lang.String resName, java.lang.String atomName)
          update the atom name in NOEs: we assume that all noes use PDB-NEW scheme.
 java.lang.String UpdateNOEAtomName2(java.lang.String resName, java.lang.String atomName)
          update the atom name in NOEs: we assume that all noes use PDB-NEW scheme.
 java.util.Vector UpdatePseudoProton(java.lang.String resName, java.lang.String atomName)
          update proton name from pseudo atoms.
 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 lower, double upper)
          Xplor noe statement.
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Constructor Detail

Noe

public Noe()
Constructors.


Noe

public Noe(int NoA,
           int noB)
Instantiates a new noe.

Parameters:
NoA - the no a
noB - the no b

Noe

public Noe(int Ano,
           int Bno,
           java.lang.String res1,
           java.lang.String res2,
           java.lang.String atom1,
           java.lang.String atom2,
           double low,
           double up)
Instantiates a new noe.

Parameters:
Ano - the ano
Bno - the bno
res1 - the res1
res2 - the res2
atom1 - the atom1
atom2 - the atom2
low - the low
up - the up

Noe

public Noe(int pkID,
           int Ano,
           int Bno,
           java.lang.String res1,
           java.lang.String res2,
           java.lang.String atom1,
           java.lang.String atom2,
           double low,
           double up)
Instantiates a new noe.

Parameters:
pkID - the pk id
Ano - the ano
Bno - the bno
res1 - the res1
res2 - the res2
atom1 - the atom1
atom2 - the atom2
low - the low
up - the up

Noe

public Noe(int pkID,
           int Ano,
           int Bno,
           java.lang.String res1,
           java.lang.String res2,
           java.lang.String atom1,
           java.lang.String atom2,
           double low,
           double up,
           double r)
Instantiates a new noe.

Parameters:
pkID - the pk id
Ano - the ano
Bno - the bno
res1 - the res1
res2 - the res2
atom1 - the atom1
atom2 - the atom2
low - the low
up - the up
r - the r

Noe

public Noe(int Ano,
           java.lang.String atom1,
           int Bno,
           java.lang.String atom2,
           double low,
           double up)
Instantiates a new noe.

Parameters:
Ano - the ano
atom1 - the atom1
Bno - the bno
atom2 - the atom2
low - the low
up - the up

Noe

public Noe(int pkID,
           java.util.Vector vec1,
           java.util.Vector vec2,
           double low,
           double up)
Instantiates a new noe.

Parameters:
pkID - the pk id
vec1 - the vec1
vec2 - the vec2
low - the low
up - the up

Noe

public Noe(int pkID,
           java.util.Vector vec1,
           java.util.Vector vec2,
           Noe noe)
Instantiates a new noe.

Parameters:
pkID - the pk id
vec1 - the vec1
vec2 - the vec2
noe - the noe
Method Detail

getResidueNoA

public int getResidueNoA()
Gets the residue no a.

Returns:
the residue no a

getResidueNoB

public int getResidueNoB()
Gets the residue no b.

Returns:
the residue no b

getResidueA

public java.lang.String getResidueA()
Gets the residue a.

Returns:
the residue a

getResidueB

public java.lang.String getResidueB()
Gets the residue b.

Returns:
the residue b

getAtomA

public java.lang.String getAtomA()
Gets the atom a.

Returns:
the atom a

getAtomB

public java.lang.String getAtomB()
Gets the atom b.

Returns:
the atom b

getRatioEnsemb

public double getRatioEnsemb()
Gets the ratio ensemb.

Returns:
the ratio ensemb

getRange

public double[] getRange()
Gets the range.

Returns:
the range

getLower

public double getLower()
Gets the lower.

Returns:
the lower

getPeakID

public int getPeakID()
Gets the peak id.

Returns:
the peak id

getUpper

public double getUpper()
Gets the upper.

Returns:
the upper

getVecH_A

public java.util.Vector getVecH_A()
Gets the vec h_ a.

Returns:
the vec h_ a

getVecH_B

public java.util.Vector getVecH_B()
Gets the vec h_ b.

Returns:
the vec h_ b

setDistUpper

public void setDistUpper(double up)
Sets the dist upper.

Parameters:
up - the new dist upper

setDistLower

public void setDistLower(double lw)
Sets the dist lower.

Parameters:
lw - the new dist lower

setRatioEnsemb

public void setRatioEnsemb(double ratio)
Sets the ratio ensemb.

Parameters:
ratio - the new ratio ensemb

setResNameA

public void setResNameA(java.lang.String res1)
Sets the res name a.

Parameters:
res1 - the new res name a

setResNameB

public void setResNameB(java.lang.String res2)
Sets the res name b.

Parameters:
res2 - the new res name b

setAtom1Name

public void setAtom1Name(java.lang.String atom1)
Sets the atom1 name.

Parameters:
atom1 - the new atom1 name

setAtom2Name

public void setAtom2Name(java.lang.String atom2)
Sets the atom2 name.

Parameters:
atom2 - the new atom2 name

setPeakID

public void setPeakID(int id)
Sets the peak id.

Parameters:
id - the new peak id

setResNoA

public void setResNoA(int n1)
Sets the res no a.

Parameters:
n1 - the new res no a

setResNoB

public void setResNoB(int n2)
Sets the res no b.

Parameters:
n2 - the new res no b

setVecH_A

public void setVecH_A(java.util.Vector vec1)
Sets the vec h_ a.

Parameters:
vec1 - the new vec h_ a

setVecH_B

public void setVecH_B(java.util.Vector vec2)
Sets the vec h_ b.

Parameters:
vec2 - the new vec h_ b

addH_A

public void addH_A(H1CS h1csA)
Adds the h_ a.

Parameters:
h1csA - the h1cs a

addH_B

public void addH_B(H1CS h1csB)
Adds the h_ b.

Parameters:
h1csB - the h1cs b

addProtons

public void addProtons(Noe noe)
Adds the protons.

Parameters:
noe - the noe

toString

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

ConvertMultiToSingleAsg

public java.util.Vector ConvertMultiToSingleAsg(java.util.Vector vecMultiNoe)
convert all multiple NOE assignments into single assignment format.

Parameters:
vecMultiNoe - original multiple NOE assignment vector
Returns:
vector of multiple NOE assignments.

ConvertSingleToMultiAsg

public java.util.Vector ConvertSingleToMultiAsg(java.util.Vector vecSingleNoe)
convert all NOE assignments into multiple assignment format.

Parameters:
vecSingleNoe - original signle NOE assignment vector
Returns:
vector of multiple NOE assignments.

OutputMultiNOEAsg

public void OutputMultiNOEAsg(java.util.Vector vecMultiNoe,
                              java.lang.String strOutName)
output the noe assignment in multple format.

Parameters:
vecMultiNoe - multiple NOE assignment
strOutName - output path name

CompareAsgToRefStr

public void CompareAsgToRefStr(java.util.Vector vecNoe,
                               java.util.Vector vecPdbRef,
                               double noeLimit,
                               double methylCorrection,
                               double[] number)
Compare assignment results with manual assignments.

Parameters:
vecPdbRef - referernce pdb structure
number - number[0]: number of correct assignments, number[1]: number of wrong assignments
vecNoe - the vec noe
noeLimit - the noe limit
methylCorrection - the methyl correction

NoeMethylCorrection

public java.util.Vector NoeMethylCorrection(java.util.Vector vecNoeOld,
                                            double metCorrection)
                                     throws JampackException
correct the NOE upper distance for an methyl NOE we assume that the pseudo methyl atoms of all old NOEs are labeled with "#" or "##".

Parameters:
vecNoeOld - original NOEs before correction
metCorrection - metyl correction
Returns:
new NOE table after correction Note: created May 29,08.
Throws:
JampackException - the jampack exception

doCheckNoeByEnsemble

public void doCheckNoeByEnsemble(java.lang.String src,
                                 java.lang.String strOut,
                                 java.lang.String strInput)
                          throws JampackException
check the NOE table by an ensemble of structures, and output the statistical information.

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

doNoeStatistics

public void doNoeStatistics(java.lang.String src,
                            java.lang.String strOut,
                            java.lang.String strInput)
                     throws JampackException
output the NOE statistics.

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

NameConvertFromPDBNewToPDBNew

public java.util.Vector NameConvertFromPDBNewToPDBNew(java.util.Vector vecNoe)
Convert naming scheme From PDBNew To PDBNew, just do the changes of pseudo protons of methyl groups (eg.HB#)

Parameters:
vecNoe - the vec noe
Returns:
the vector

NameConvertFromBMRBNewToPDBNew

public java.util.Vector NameConvertFromBMRBNewToPDBNew(java.util.Vector vecNoe)
Convert naming scheme From BMRBNew To PDBNew, including pseudo protons of methyl groups.

Parameters:
vecNoe - the vec noe
Returns:
the vector

CompareAsgToManualAsg

public void CompareAsgToManualAsg(java.util.Vector vecAsg,
                                  java.util.Vector vecManualAsg,
                                  double[] number)
Compare assignment results with manual assignments.

Parameters:
vecAsg - final noe resonance assignment
vecManualAsg - manual noe resonance assignment
number - number[0]: number of correct assignments, number[1]: number of wrong assignments

getResNameFromSequence

public java.lang.String getResNameFromSequence(java.util.Vector vecSeq,
                                               int resNo)
get the residue name from the sequence vector.

Parameters:
vecSeq - the vec seq
resNo - the res no
Returns:
residue name

identifyNoeResidues

public boolean[] identifyNoeResidues(java.util.Vector vecSseSeq,
                                     java.util.Vector vecNoeAll,
                                     int sseIndex)
identify NOE residues for a sse.

Parameters:
vecSseSeq - the sequence of sse structures
vecNoeAll - the vector all Noe retraints
sseIndex - the index of SSE to be determined
Returns:
resIndex residue indexes that involve in NOE restraints

noeReader_old_fromLW

public java.util.Vector<Noe> noeReader_old_fromLW(java.lang.String noeFile)
A very simple reader for NOE data, see the file format.

Parameters:
noeFile - the name of the file
Returns:
a vector of NOE object

noeReader

public java.util.Vector noeReader(java.lang.String noeFile,
                                  double upCorrection)
A very simple reader for NOE data, see the file format.

Parameters:
noeFile - the name of the file
upCorrection - the up correction
Returns:
a vector of NOE object

noeReaderMultiAsg

public java.util.Vector noeReaderMultiAsg(java.lang.String noeFile,
                                          java.util.Vector vecSeq)
read the NOE assignment in mutiple format.

Parameters:
noeFile - the name of the file
vecSeq - vector of sequence
Returns:
a vector of NOE object Note: created May 29, 08.

noeReader

public java.util.Vector noeReader(java.lang.String noeFile,
                                  double upCorrection,
                                  java.util.Vector vecSeq)
A very simple reader for NOE data, see the file format. update the residue name from sequence. check whether the psudo name "#" or "##" has been updated correctly.

Parameters:
noeFile - the name of the file
upCorrection - the up correction
vecSeq - vector of sequence
Returns:
a vector of NOE object Note: created May 29, 08.

UpdateNOEAtomName

public java.lang.String UpdateNOEAtomName(java.lang.String resName,
                                          java.lang.String atomName)
update the atom name in NOEs: we assume that all noes use PDB-NEW scheme. Strictly use "#" and "##" for psuedo-atoms. return new atom name Note: Created May 29, 2008.

Parameters:
resName - the res name
atomName - the atom name
Returns:
the string

UpdateNOEAtomName2

public java.lang.String UpdateNOEAtomName2(java.lang.String resName,
                                           java.lang.String atomName)
update the atom name in NOEs: we assume that all noes use PDB-NEW scheme. convert "#" and "##" of psuedo-atoms into non-"#". return new atom name Note: Created May 29, 2008.

Parameters:
resName - the res name
atomName - the atom name
Returns:
the string

noeReader2

public java.util.Vector noeReader2(java.lang.String noeFile,
                                   double upCorrection)
A very simple reader for NOE data, see the file format. deal with the compact format

Parameters:
noeFile - the name of the file
upCorrection - correction for the nOE upper bound
Returns:
a vector of NOE object

CheckNoeHInPdb

public boolean CheckNoeHInPdb(java.util.Vector vecNoe,
                              java.util.Vector vecPdb)
check whether there is a atom name in noe talbe which is not in pdb.

Parameters:
vecNoe - the vec noe
vecPdb - the vec pdb
Returns:
true, if all noe proton names are in pdb, false else

UpdatePseudoProton

public java.util.Vector UpdatePseudoProton(java.lang.String resName,
                                           java.lang.String atomName)
update proton name from pseudo atoms. notes: may be specific for ff domain

Parameters:
resName - the res name
atomName - the atom name
Returns:
a vector of updated NOE object

setSameUpperBounds4All

public java.util.Vector setSameUpperBounds4All(java.util.Vector vecOldNOE,
                                               double dbUpper)
set the same upper bound for all NOEs.

Parameters:
vecOldNOE - old noe constraints with pseudo protons
dbUpper - NOE upper bound
Returns:
a vector of updated NOE object

DeleteRepeatNOEs

public java.util.Vector DeleteRepeatNOEs(java.util.Vector vecOldNOE)
delete repeated NOEs.

Parameters:
vecOldNOE - old noe constraints with pseudo protons
Returns:
a vector of updated NOE object

PrintNOE

public void PrintNOE(java.util.Vector vecNOE)
print noe.

Parameters:
vecNOE - the vec noe

UpdateNOE

public java.util.Vector UpdateNOE(java.util.Vector vecOldNOE,
                                  java.util.Vector vecSSEOrder)
update noe constraint, for pseudo atoms.

Parameters:
vecOldNOE - old noe constraints with pseudo protons
vecSSEOrder - the vec sse order
Returns:
a vector of updated NOE object

LongRangeNoeReaderTestLW

public java.util.Vector LongRangeNoeReaderTestLW(java.lang.String noeFile)
This is an old function. long reange noe read from cyana format.

Parameters:
noeFile - the name of the file
Returns:
a vector of NOE object

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 lower,
                                          double upper)
Xplor noe statement.

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

main

public static void main(java.lang.String[] argv)
The main method.

Parameters:
argv - the arguments

ConvertAllNoeToBBNoe

public java.util.Vector ConvertAllNoeToBBNoe(java.util.Vector vecNoeAll,
                                             java.util.Vector vecSeq)
convert genaral noe into noes between backbones.

Parameters:
vecNoeAll - the vec noe all
vecSeq - the vec seq
Returns:
a vector of noe in the upl format (bmrb-new)

ConvertXplorAsgToUplFormat

public java.util.Vector ConvertXplorAsgToUplFormat(java.util.Vector vecNoeXplor,
                                                   java.util.Vector vecSeq,
                                                   java.lang.String nameScheme)
convert from the xplor noe format to cyna upl format. Since the xplor is in pdb-new format, we need to change it into BMRB-new format. Also, since the xplor format doesn't include the residue name, we also need to add residue name from the sequence information.

Parameters:
nameScheme - naming scheme, defult "PDB-NEW"; if using "BMRB-NEW", change to "PDB-NEW"
vecNoeXplor - the vec noe xplor
vecSeq - the vec seq
Returns:
a vector of noe in the upl format (bmrb-new)

ConvertXplorAsgToUplFormatFF2

public java.util.Vector ConvertXplorAsgToUplFormatFF2(java.util.Vector vecNoeXplor,
                                                      java.util.Vector vecSeq)
convert from the xplor noe format to cyna upl format. Since the xplor is in pdb-new format, we need to change it into BMRB-new format. Also, since the xplor format doesn't include the residue name, we also need to add residue name from the sequence information.

Parameters:
vecNoeXplor - the vec noe xplor
vecSeq - the vec seq
Returns:
a vector of noe in the upl format (bmrb-new)

ConvertCyanNoeAsgToXplor

public void ConvertCyanNoeAsgToXplor(java.lang.String noeFile,
                                     java.io.PrintWriter out)
long reange noe read from cyana format.

Parameters:
noeFile - the name of the file
out - the out

noeSatisfiedScore

public boolean noeSatisfiedScore(java.util.Vector noeVec,
                                 java.util.Vector vecPdb,
                                 double[] noeRmsd,
                                 double[] noeHarmScore,
                                 int[] numConflicts)
calculate the NOE satisfiation score.

Parameters:
noeVec - the noe vec
vecPdb - the vec pdb
noeRmsd - the noe rmsd
noeHarmScore - the noe harm score
numConflicts - the num conflicts
Returns:
true, if noe satisfied score

noeSatisfiedScoreFF2

public boolean noeSatisfiedScoreFF2(java.util.Vector noeVec,
                                    java.util.Vector vecPdb,
                                    double[] noeRmsd,
                                    double[] noeHarmScore,
                                    int[] numConflicts)
Special for ff2 // only consider noes in between two SSEs calculate the NOE satisfiation score.

Parameters:
noeVec - the noe vec
vecPdb - the vec pdb
noeRmsd - the noe rmsd
noeHarmScore - the noe harm score
numConflicts - the num conflicts
Returns:
true, if noe satisfied score f f2

ConvertNoeFromBMRMToPDB

public java.util.Vector ConvertNoeFromBMRMToPDB(java.util.Vector vecNoeBMRB)
convert an NOE set from BMRB-NEW to PDB-NEW format.

Parameters:
vecNoeBMRB - original NOE vector
Returns:
a vector of new NOE set in PDB-NEW format

LongRangeNoeReader

public java.util.Vector LongRangeNoeReader(java.lang.String noeFile,
                                           double upCorrection,
                                           java.lang.String nameScheme)
long reange noe read from cyana format.

Parameters:
noeFile - the name of the file
upCorrection - correction of NOE upper bound, use 6A if upCorrection<0
nameScheme - the name scheme
Returns:
a vector of NOE object

LongRangeNoeReader2

public java.util.Vector LongRangeNoeReader2(java.lang.String noeFile)
long reange noe read from cyana format.

Parameters:
noeFile - the name of the file
Returns:
a vector of NOE object