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java.lang.ObjectRdcPanda.Noe
public class Noe
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 | |
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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 | |
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Noe()
Constructors. |
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Noe(int NoA,
int noB)
Instantiates a new noe. |
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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. |
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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. |
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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. |
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Noe(int Ano,
java.lang.String atom1,
int Bno,
java.lang.String atom2,
double low,
double up)
Instantiates a new noe. |
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Noe(int pkID,
java.util.Vector vec1,
java.util.Vector vec2,
double low,
double up)
Instantiates a new noe. |
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Noe(int pkID,
java.util.Vector vec1,
java.util.Vector vec2,
Noe noe)
Instantiates a new noe. |
Method Summary | |
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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 |
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equals, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
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public Noe()
public Noe(int NoA, int noB)
NoA
- the no anoB
- the no bpublic 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)
Ano
- the anoBno
- the bnores1
- the res1res2
- the res2atom1
- the atom1atom2
- the atom2low
- the lowup
- the uppublic 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)
pkID
- the pk idAno
- the anoBno
- the bnores1
- the res1res2
- the res2atom1
- the atom1atom2
- the atom2low
- the lowup
- the uppublic 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)
pkID
- the pk idAno
- the anoBno
- the bnores1
- the res1res2
- the res2atom1
- the atom1atom2
- the atom2low
- the lowup
- the upr
- the rpublic Noe(int Ano, java.lang.String atom1, int Bno, java.lang.String atom2, double low, double up)
Ano
- the anoatom1
- the atom1Bno
- the bnoatom2
- the atom2low
- the lowup
- the uppublic Noe(int pkID, java.util.Vector vec1, java.util.Vector vec2, double low, double up)
pkID
- the pk idvec1
- the vec1vec2
- the vec2low
- the lowup
- the uppublic Noe(int pkID, java.util.Vector vec1, java.util.Vector vec2, Noe noe)
pkID
- the pk idvec1
- the vec1vec2
- the vec2noe
- the noeMethod Detail |
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public int getResidueNoA()
public int getResidueNoB()
public java.lang.String getResidueA()
public java.lang.String getResidueB()
public java.lang.String getAtomA()
public java.lang.String getAtomB()
public double getRatioEnsemb()
public double[] getRange()
public double getLower()
public int getPeakID()
public double getUpper()
public java.util.Vector getVecH_A()
public java.util.Vector getVecH_B()
public void setDistUpper(double up)
up
- the new dist upperpublic void setDistLower(double lw)
lw
- the new dist lowerpublic void setRatioEnsemb(double ratio)
ratio
- the new ratio ensembpublic void setResNameA(java.lang.String res1)
res1
- the new res name apublic void setResNameB(java.lang.String res2)
res2
- the new res name bpublic void setAtom1Name(java.lang.String atom1)
atom1
- the new atom1 namepublic void setAtom2Name(java.lang.String atom2)
atom2
- the new atom2 namepublic void setPeakID(int id)
id
- the new peak idpublic void setResNoA(int n1)
n1
- the new res no apublic void setResNoB(int n2)
n2
- the new res no bpublic void setVecH_A(java.util.Vector vec1)
vec1
- the new vec h_ apublic void setVecH_B(java.util.Vector vec2)
vec2
- the new vec h_ bpublic void addH_A(H1CS h1csA)
h1csA
- the h1cs apublic void addH_B(H1CS h1csB)
h1csB
- the h1cs bpublic void addProtons(Noe noe)
noe
- the noepublic java.lang.String toString()
toString
in class java.lang.Object
public java.util.Vector ConvertMultiToSingleAsg(java.util.Vector vecMultiNoe)
vecMultiNoe
- original multiple NOE assignment vector
public java.util.Vector ConvertSingleToMultiAsg(java.util.Vector vecSingleNoe)
vecSingleNoe
- original signle NOE assignment vector
public void OutputMultiNOEAsg(java.util.Vector vecMultiNoe, java.lang.String strOutName)
vecMultiNoe
- multiple NOE assignmentstrOutName
- output path namepublic void CompareAsgToRefStr(java.util.Vector vecNoe, java.util.Vector vecPdbRef, double noeLimit, double methylCorrection, double[] number)
vecPdbRef
- referernce pdb structurenumber
- number[0]: number of correct assignments, number[1]: number of wrong assignmentsvecNoe
- the vec noenoeLimit
- the noe limitmethylCorrection
- the methyl correctionpublic java.util.Vector NoeMethylCorrection(java.util.Vector vecNoeOld, double metCorrection) throws JampackException
vecNoeOld
- original NOEs before correctionmetCorrection
- metyl correction
JampackException
- the jampack exceptionpublic void doCheckNoeByEnsemble(java.lang.String src, java.lang.String strOut, java.lang.String strInput) throws JampackException
src
- location of the input filestrOut
- location of the output filestrInput
- input file name
JampackException
- the jampack exceptionpublic void doNoeStatistics(java.lang.String src, java.lang.String strOut, java.lang.String strInput) throws JampackException
src
- location of the input filestrOut
- location of the output filestrInput
- input file name
JampackException
- the jampack exceptionpublic java.util.Vector NameConvertFromPDBNewToPDBNew(java.util.Vector vecNoe)
vecNoe
- the vec noe
public java.util.Vector NameConvertFromBMRBNewToPDBNew(java.util.Vector vecNoe)
vecNoe
- the vec noe
public void CompareAsgToManualAsg(java.util.Vector vecAsg, java.util.Vector vecManualAsg, double[] number)
vecAsg
- final noe resonance assignmentvecManualAsg
- manual noe resonance assignmentnumber
- number[0]: number of correct assignments, number[1]: number of wrong assignmentspublic java.lang.String getResNameFromSequence(java.util.Vector vecSeq, int resNo)
vecSeq
- the vec seqresNo
- the res no
public boolean[] identifyNoeResidues(java.util.Vector vecSseSeq, java.util.Vector vecNoeAll, int sseIndex)
vecSseSeq
- the sequence of sse structuresvecNoeAll
- the vector all Noe retraintssseIndex
- the index of SSE to be determined
public java.util.Vector<Noe> noeReader_old_fromLW(java.lang.String noeFile)
noeFile
- the name of the file
public java.util.Vector noeReader(java.lang.String noeFile, double upCorrection)
noeFile
- the name of the fileupCorrection
- the up correction
public java.util.Vector noeReaderMultiAsg(java.lang.String noeFile, java.util.Vector vecSeq)
noeFile
- the name of the filevecSeq
- vector of sequence
public java.util.Vector noeReader(java.lang.String noeFile, double upCorrection, java.util.Vector vecSeq)
noeFile
- the name of the fileupCorrection
- the up correctionvecSeq
- vector of sequence
public java.lang.String UpdateNOEAtomName(java.lang.String resName, java.lang.String atomName)
resName
- the res nameatomName
- the atom name
public java.lang.String UpdateNOEAtomName2(java.lang.String resName, java.lang.String atomName)
resName
- the res nameatomName
- the atom name
public java.util.Vector noeReader2(java.lang.String noeFile, double upCorrection)
noeFile
- the name of the fileupCorrection
- correction for the nOE upper bound
public boolean CheckNoeHInPdb(java.util.Vector vecNoe, java.util.Vector vecPdb)
vecNoe
- the vec noevecPdb
- the vec pdb
public java.util.Vector UpdatePseudoProton(java.lang.String resName, java.lang.String atomName)
resName
- the res nameatomName
- the atom name
public java.util.Vector setSameUpperBounds4All(java.util.Vector vecOldNOE, double dbUpper)
vecOldNOE
- old noe constraints with pseudo protonsdbUpper
- NOE upper bound
public java.util.Vector DeleteRepeatNOEs(java.util.Vector vecOldNOE)
vecOldNOE
- old noe constraints with pseudo protons
public void PrintNOE(java.util.Vector vecNOE)
vecNOE
- the vec noepublic java.util.Vector UpdateNOE(java.util.Vector vecOldNOE, java.util.Vector vecSSEOrder)
vecOldNOE
- old noe constraints with pseudo protonsvecSSEOrder
- the vec sse order
public java.util.Vector LongRangeNoeReaderTestLW(java.lang.String noeFile)
noeFile
- the name of the file
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)
no1
- the no1resid1
- the resid1nucleus1
- the nucleus1no2
- the no2resid
- the residnucleus2
- the nucleus2lower
- the lowerupper
- the upper
public static void main(java.lang.String[] argv)
argv
- the argumentspublic java.util.Vector ConvertAllNoeToBBNoe(java.util.Vector vecNoeAll, java.util.Vector vecSeq)
vecNoeAll
- the vec noe allvecSeq
- the vec seq
public java.util.Vector ConvertXplorAsgToUplFormat(java.util.Vector vecNoeXplor, java.util.Vector vecSeq, java.lang.String nameScheme)
nameScheme
- naming scheme, defult "PDB-NEW"; if using "BMRB-NEW", change to "PDB-NEW"vecNoeXplor
- the vec noe xplorvecSeq
- the vec seq
public java.util.Vector ConvertXplorAsgToUplFormatFF2(java.util.Vector vecNoeXplor, java.util.Vector vecSeq)
vecNoeXplor
- the vec noe xplorvecSeq
- the vec seq
public void ConvertCyanNoeAsgToXplor(java.lang.String noeFile, java.io.PrintWriter out)
noeFile
- the name of the fileout
- the outpublic boolean noeSatisfiedScore(java.util.Vector noeVec, java.util.Vector vecPdb, double[] noeRmsd, double[] noeHarmScore, int[] numConflicts)
noeVec
- the noe vecvecPdb
- the vec pdbnoeRmsd
- the noe rmsdnoeHarmScore
- the noe harm scorenumConflicts
- the num conflicts
public boolean noeSatisfiedScoreFF2(java.util.Vector noeVec, java.util.Vector vecPdb, double[] noeRmsd, double[] noeHarmScore, int[] numConflicts)
noeVec
- the noe vecvecPdb
- the vec pdbnoeRmsd
- the noe rmsdnoeHarmScore
- the noe harm scorenumConflicts
- the num conflicts
public java.util.Vector ConvertNoeFromBMRMToPDB(java.util.Vector vecNoeBMRB)
vecNoeBMRB
- original NOE vector
public java.util.Vector LongRangeNoeReader(java.lang.String noeFile, double upCorrection, java.lang.String nameScheme)
noeFile
- the name of the fileupCorrection
- correction of NOE upper bound,
use 6A if upCorrection<0nameScheme
- the name scheme
public java.util.Vector LongRangeNoeReader2(java.lang.String noeFile)
noeFile
- the name of the file
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