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java.lang.ObjectRdcPanda.Assign
public class Assign
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 | |
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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 | |
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Assign()
Instantiates a new assign. |
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Assign(int no)
Instantiates a new assign. |
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Assign(int no,
java.lang.String type)
Instantiates a new assign. |
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Assign(int no,
java.lang.String type,
java.util.Map aMap)
Instantiates a new assign. |
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Assign(int no,
java.lang.String type,
java.util.Map aMap,
java.util.Vector hnVec,
java.util.Vector haVec)
Instantiates a new assign. |
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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 | |
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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()
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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 Assign()
public Assign(int no)
no
- the nopublic Assign(int no, java.lang.String type)
no
- the notype
- the typepublic Assign(int no, java.lang.String type, java.util.Map aMap)
no
- the notype
- the typeaMap
- the mappublic Assign(int no, java.lang.String type, java.util.Map aMap, java.util.Vector hnVec, java.util.Vector haVec)
no
- the notype
- the typeaMap
- the a maphnVec
- the hn vechaVec
- the ha vecpublic Assign(int no, java.lang.String type, java.util.Map aMap, java.util.Vector hnVec, java.util.Vector haVec, java.util.Vector h1Vec)
no
- the notype
- the typeaMap
- the a maphnVec
- the hn vechaVec
- the ha vech1Vec
- the h1 vecMethod Detail |
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public void setMaxValue(double maxval)
maxval
- the new max valuepublic void setMissingIndex(int[] index)
index
- the new missing indexpublic int[] getMissingIndex()
public double getMaxValue()
public int getResidueNo()
public java.lang.String getResidueType()
public java.util.Map getMap()
public java.util.Vector getHnNoeVec()
public java.util.Vector getHaNoeVec()
public java.util.Vector getH1NoeVec()
public java.lang.String toString()
toString
in class java.lang.Object
public java.util.Vector getOrder(java.lang.String strSSES)
strSSES
- the str sses
public java.util.Vector assignReader(java.lang.String pdbFile, double h1Ref)
pdbFile
- the pdb fileh1Ref
- the chemical shift correction (?)
public java.util.Vector assignReader2(java.lang.String hncacbFile, java.util.Vector assignVec, java.util.Vector chsqcVec)
hncacbFile
- the hncacb fileassignVec
- the assign vecchsqcVec
- the chsqc vec
public java.util.Vector ReaderSeq(java.lang.String filename)
filename
- the name of the file
public java.util.Vector<java.util.Map<java.lang.String,java.lang.String>> ParamReader(java.lang.String fileName)
fileName
- the name of the parameter file
public java.util.Vector asgReader3(java.lang.String filename)
filename
- the name of the file
public void assignHsqc(java.util.Vector assignVec, java.util.Vector hsqcVec)
assignVec
- the assign vechsqcVec
- the hsqc vecpublic void matchC13Hsqc(java.util.Vector foldHsqcVec, java.util.Vector hsqcVec)
foldHsqcVec
- the fold hsqc vechsqcVec
- the hsqc vecpublic java.util.Vector mergeNoe(java.util.Vector hnNoeVec, java.util.Vector hsqcVec, double hnErr, double nErr)
hnNoeVec
- the hn noe vechsqcVec
- the hsqc vechnErr
- the hn errnErr
- the n err
public java.util.Vector mergeC13Noe(java.util.Vector hcchVec, java.util.Vector hsqcVec, double haErr, double cErr)
hcchVec
- a C13 NOE vector which has the same members as HcchTocsy objecthsqcVec
- the assigned C13 Hsqc vector (in fact, the folded one since C13 NOESY is folded)haErr
- the ha errcErr
- the c err
public java.util.Vector mergeNoeAndAssign(java.util.Vector hnNoeVec, java.util.Vector hsqcVec, java.util.Vector assignVec, double hnErr, double nErr)
hnNoeVec
- the hn noe vechsqcVec
- the hsqc vecassignVec
- the assign vechnErr
- the hn errnErr
- the n err
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)
asgVec
- the asg vechnNoeVec
- the hn noe veccNoeVec
- the c noe vechnErr
- the hn errnErr
- the n errhaErr
- the ha errcErr
- the c err
public java.util.Vector deleteRepeat(java.util.Vector allVec, double epsH, double epsN, double epsH1)
allVec
- original chemical shift list;epsH
- the eps hepsN
- the eps nepsH1
- the eps h1
public java.util.Vector sortAssign(java.util.Vector allVec)
allVec
- the all vec
public java.util.Vector mergeAll(java.util.Vector allVec, java.util.Vector hcchVec, double haErr, double c13Err)
allVec
- the all vechcchVec
- the hcch vechaErr
- the ha errc13Err
- the c13 err
public java.util.Vector BackNoeDeleteRepeat(java.util.Vector vecBackNoe)
vecBackNoe
- back computed NOE patterns.
public void CompMaxMatchScore_old(java.util.Vector vecBackNoe, double preMisPenalty, double preMatchScore, int depth, int finalDepth, int[] missingIndex)
vecBackNoe
- back computed NOE patternspreMisPenalty
- the pre mis penaltypreMatchScore
- the pre match scoredepth
- the depthfinalDepth
- the final depthmissingIndex
- the missing indexpublic double NoePatternMatchScore_old2(double csErrH, double csErrN, double csErrCA, java.util.Vector vecBackNoe, java.util.Vector vecNoesy, int[] numPeaks)
csErrH
- the cs err hcsErrN
- the cs err nnumPeaks
- number of non-missing peakscsErrCA
- the cs err cavecBackNoe
- the vec back noevecNoesy
- the vec noesy
public double NoePatternMatchScoreWCali(double csErrH, double csErrN, double csErrCA, java.util.Vector vecBackNoe, java.util.Vector vecNoesy, int[] numPeaks, boolean isSkipIntensity, double constant)
csErrH
- error window of the first proton attached to the heavy atom (indirect proton)csErrN
- the cs err nnumPeaks
- number of non-missing peakscsErrCA
- the cs err cavecBackNoe
- the vec back noevecNoesy
- the vec noesyisSkipIntensity
- the is skip intensityconstant
- the constant
public double NoePatternMatchScoreWCaliTestJBNMR1(double csErrH, double csErrN, double csErrCA, java.util.Vector vecBackNoe, java.util.Vector vecNoesy, int[] numPeaks, boolean isSkipIntensity, double constant)
csErrH
- error window of the first proton attached to the heavy atom (indirect proton)csErrN
- the cs err nnumPeaks
- number of non-missing peakscsErrCA
- the cs err cavecBackNoe
- the vec back noevecNoesy
- the vec noesyisSkipIntensity
- the is skip intensityconstant
- the constant
public double NoePatternMatchScoreWCaliTestJBNMR2(double csErrH, double csErrN, double csErrCA, java.util.Vector vecBackNoe, java.util.Vector vecNoesy, int[] numPeaks, boolean isSkipIntensity, double constant)
csErrH
- error window of the first proton attached to the heavy atom (indirect proton)csErrN
- the cs err nnumPeaks
- number of non-missing peakscsErrCA
- the cs err cavecBackNoe
- the vec back noevecNoesy
- the vec noesyisSkipIntensity
- the is skip intensityconstant
- the constant
public double NoePatternMatchScoreWCaliHdphic(double csErrH, double csErrN, double csErrCA, java.util.Vector vecBackNoe, java.util.Vector vecNoesy, int[] numPeaks, boolean isSkipIntensity, double constant)
csErrH
- error window of the first proton attached to the heavy atom (indirect proton)csErrN
- the cs err nnumPeaks
- number of non-missing peakscsErrCA
- the cs err cavecBackNoe
- the vec back noevecNoesy
- the vec noesyisSkipIntensity
- the is skip intensityconstant
- the constant
public double NoePatternMatchScore(double csErrH, double csErrN, double csErrCA, java.util.Vector vecBackNoe, java.util.Vector vecNoesy, int[] numPeaks, boolean isSkipIntensity)
csErrH
- error window of the first proton attached to the heavy atom (indirect proton)csErrN
- the cs err nnumPeaks
- number of non-missing peakscsErrCA
- the cs err cavecBackNoe
- the vec back noevecNoesy
- the vec noesyisSkipIntensity
- the is skip intensity
public double NoePatternMatchScore(java.util.Vector vecBackNoe, java.util.Vector vecHnNoe, java.util.Vector vecCaNoe, int[] numPeaks)
vecBackNoe
- back computed NOE patternsvecHnNoe
- HnNOE peak listvecCaNoe
- CA NOE peak listnumPeaks
- number of non-missing peaks
public java.util.Vector SwapStereoAsg(java.util.Vector vecAsg, int resNo)
vecAsg
- vector of resonance assignmentsresNo
- the res no
public java.util.Vector StereospecificNoeAsg(java.util.Vector vecNoe)
vecNoe
- vector of original noe assignments
public java.util.Vector PrunAmbgNoeAsg(java.util.Vector pdbVec, java.util.Vector vecNoe, double noeLimit, double methylCorrection, int nIsoriginalUp)
pdbVec
- the pdb structure after combining selected rotamers and backbonevecNoe
- vector of ambiguous noe assignmentsnoeLimit
- noe upper limit to prune ambiguous noesmethylCorrection
- always 0 in new verstion.nIsoriginalUp
- whether keep the original noe upper bound, 1 for yes, 0 for using distance information
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)
nErr
- error tolerance in the N dimensioncErr
- error tolerance in the c dimensionhnErr
- error tolerance in the hn dimensionhaErr
- error tolerance in the ha dimensionvecAsg
- assigned resonance listvecAllH1
- all sorted protonsvecNoesy
- NOESY peaks, including both c13 and n15 noesy peaksh2Err
- the h2 err
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)
nErr
- error tolerance in the N dimensioncErr
- error tolerance in the c dimensionhnErr
- error tolerance in the hn dimensionhaErr
- error tolerance in the ha dimensionvecAsg
- assigned resonance listvecAllH1
- all sorted protonsvecNoesy
- NOESY peaks, including both c13 and n15 noesy peaksh2Err
- the h2 err
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)
nErr
- error tolerance in the N dimensioncErr
- error tolerance in the c dimensionhnErr
- error tolerance in the hn dimensionhaErr
- error tolerance in the ha dimensionvecAsg
- assigned resonance listvecAllH1
- all sorted protonsvecNoesy
- 4d NOESY peaks, including both c13 and n15 noesy peaksh2Err
- the h2 err
public java.util.Vector mergeAll3(java.util.Vector allVec, java.util.Vector hcchVec)
allVec
- the all vechcchVec
- the hcch vec
public java.util.Vector mergeAll4(java.util.Vector allHcchVec)
allHcchVec
- the all hcch vec
public void NOEAsgFromCS(java.lang.String src, java.lang.String strOut, java.lang.String strInput)
src
- location of the input filestrOut
- location of the output filestrInput
- input file namepublic void doHANANOEAsg(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 doCompareTwoNOETables(java.lang.String src, java.lang.String strOut, java.lang.String strInput)
src
- location of the input filestrOut
- location of the output filestrInput
- input file namepublic void doExtractNOEs(java.lang.String src, java.lang.String strOut, java.lang.String strInput)
src
- location of the input filestrOut
- location of the output filestrInput
- input file namepublic void doLongNOEsAsgWOStructureNew(java.lang.String src, java.lang.String strOut, java.lang.String strInput)
src
- location of the input filestrOut
- location of the output filestrInput
- input file namepublic void doLongNOEsAsgWOStructure(java.lang.String src, java.lang.String strOut, java.lang.String strInput)
src
- location of the input filestrOut
- location of the output filestrInput
- input file namepublic void doRefineNOEsWBB(java.lang.String src, java.lang.String strOut, java.lang.String strInput)
src
- location of the input filestrOut
- location of the output filestrInput
- input file name
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