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SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.ObjectRdcPanda.Nasca
public class Nasca
Nested Class Summary | |
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class |
Nasca.Node
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Constructor Summary | |
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Nasca()
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Method Summary | |
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void |
AddProtonCoordinates(int resID,
java.lang.String resName,
java.lang.String atomName,
Cartesian coord,
java.util.Vector vecOldGraph)
add the coordinates of a proton into the graph |
java.util.Vector |
AddResonanceNode(java.util.Vector vecOldGraph,
double csH,
double csHeavy,
double csErrH,
double csErrC,
double csErrN)
add the reosnance node into the graph |
java.util.Vector |
AStarSearchForSCAsgs(java.util.Vector vecResonGraph,
java.util.Vector vecHPositions,
int[][] Map,
double[][] MapScore,
java.util.Vector vecNewNoesy,
java.util.Vector vecBMRBNew)
Apply the A* search algorithm to find the optimal side-chain resonances. |
void |
CompOneToOneMapBtwInterval(java.util.Vector vecResonGraph,
java.util.Vector vecStructGraph,
int[][] Map,
double intvLower,
double intvUpper)
compute all possible one-to-one mapping for all resonances within an interval |
double |
ComputeAStarEstimatedCost(java.util.Vector vecResonGraph,
java.util.Vector vecGraph,
java.util.Vector vecBMRBNew,
int curIndex)
compute the estimated cost in A* search. |
java.util.Vector |
ConstructProtonPositions(java.util.Vector pdbBBVec,
java.lang.String rotSrc,
double noeUp)
put all rotamers at each redidue, and construct the label set (i.e. |
java.util.Vector |
ConstructResonGraph(java.util.Vector vecNodeSet,
java.util.Vector vecNoesy,
double errH1,
double errH3,
double errC,
double errN)
add the reosnance node into the graph from given assigned resonance list |
java.util.Vector |
ConstructResonGraphFromAsgedList(java.util.Vector vecAsged,
java.util.Vector vecUnAsged)
add the reosnance node into the graph from given assigned resonance list |
void |
ConstructResonGraphSymmetry(java.util.Vector vecResonGraph,
java.util.Vector vecNoesy,
double errH1,
double errH3,
double errC,
double errN)
add the reosnance node into the graph from given assigned resonance list |
static void |
copyfile(java.lang.String srFile,
java.lang.String dtFile)
|
void |
doNasca(java.lang.String src,
java.lang.String strOut,
java.lang.String strInput)
Implement the NOE assignment (NASCA) algorithm without using the side-chain resonance infomration. |
java.util.Vector |
EnumAllScAsg(java.util.Vector vecStructGraph)
enumerate all possible for assignment for sidechain protons in a residue |
java.util.Vector |
EnumAllScAsgSaveIntoFile(java.util.Vector vecSCProtons,
java.util.Vector vecResonGraph,
java.util.Vector vecStructGraph)
compute all possible one-to-one mapping for all resonances within an interval |
void |
ExactSubgraphIsomorphism(java.util.Vector vecResonGraph,
java.util.Vector vecStructGraph,
int[][] Map)
compute the exact one-to-one mapping between two graph |
java.util.Vector |
ExtractAllResonFromNOESY(java.util.Vector vecNOESY,
double csErrH,
double csErrC,
double csErrN)
exact the backbone resonance assignment |
java.util.Vector |
ExtractBackboneAsignment(java.util.Vector vecAsg)
exact the backbone resonance assignment |
java.util.Vector |
ExtractSideChainAsignment(java.util.Vector vecAsg)
|
java.util.Vector |
GreedyGraphMatching(java.util.Vector vecResonGraph,
java.util.Vector vecGraph,
int[][] Map,
double[][] MapScore,
java.util.Vector vecNewNoesy,
java.util.Vector vecBMRBNew)
at each step, choose the most confident assignment for one proton node. |
java.util.Vector |
GreedyGraphMatchingAstar(java.util.Vector vecResonGraph,
java.util.Vector vecGraphOld,
int[][] Map,
double[][] MapScore,
java.util.Vector vecNewNoesy,
java.util.Vector vecBMRBNew,
java.util.Vector vecBBAsg,
java.util.Vector vecBBPdb,
java.lang.String strRot,
double caliConstant)
Not used now at each step, choose the most confident assignment for one proton node. |
java.util.Vector |
GreedyGraphMatchingResidue(java.util.Vector vecResonGraph,
java.util.Vector vecGraph,
int[][] Map,
double[][] MapScore,
java.util.Vector vecNewNoesy,
java.util.Vector vecBMRBNew)
at each step, choose the most confident assignment for one proton node. |
void |
Initialization(java.util.Vector vecResonGraph,
java.util.Vector vecGraph,
int[][] Map,
double[][] MapScore,
java.util.Vector vecBBAsg)
Initialization. |
boolean |
isInCloseAdj(Nasca.Node nodeSrc,
Nasca.Node nodeObj)
check whether one node is in another node's close neighbors |
boolean |
isInStereoSet(Nasca.Node nodeSrc,
Nasca.Node nodeObj)
check whether one node is in another node's stereo set |
boolean |
isMappedBetwTwoSets(java.util.Vector vecNodeSetA,
java.util.Vector vecNodeSetB,
int[][] M,
boolean isConsiderAssigned,
int threshold,
double[] Score)
check whether there exists at least one mapping between two node sets |
boolean |
isMappedBetwTwoSetsCalScore(Nasca.Node nodeReson,
Nasca.Node nodeStruct,
java.util.Vector vecNodeSetA,
java.util.Vector vecNodeSetB,
int[][] M,
boolean isConsiderAssigned,
int threshold,
double[] Score,
java.util.Vector vecNoesy)
check whether there exists at least one mapping between two node sets |
java.util.Vector |
myVectorCopy(java.util.Vector vecSrc)
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java.util.Vector |
myVectorCopyOneLayer(java.util.Vector vecSrc)
|
void |
PrintAllPossibleMappings(java.util.Vector vecResonGraph,
java.util.Vector vecGraph,
int[][] Map)
print out all possible for proton nodes |
java.util.Vector |
RandomGraphMatching(java.util.Vector vecResonGraph,
java.util.Vector vecGraph,
int[][] Map,
double[][] MapScore,
java.util.Vector vecNewNoesy,
java.util.Vector vecBMRBNew)
random graph matching algorithm. |
void |
RefineMappingBasedAsg(java.util.Vector vecResonGraph,
java.util.Vector vecGraph,
int[][] Map,
double[][] MapScore,
java.util.Vector vecNewNoesy,
java.util.Vector vecBMRBNew)
refine mapping based on backbone assignment |
void |
RefineMappingBasedBMRBOutliers(java.util.Vector vecResonGraph,
java.util.Vector vecGraph,
int[][] Map,
java.util.Vector vecBMRBNew)
refine mapping based on BMRB outliers |
void |
RefineMappingBasedNeighbor(java.util.Vector vecResonGraph,
java.util.Vector vecGraph,
int[][] Map)
refine mapping based on neighboring information |
void |
RefineMappingBasedRestrained(java.util.Vector vecResonGraph,
java.util.Vector vecGraph,
int[][] Map,
double[][] MapScore,
java.util.Vector vecNewNoesy,
java.util.Vector vecBMRBNew)
refine mapping based on previous restrained mapping sets, modified from "RefineMappingBasedAsg" |
void |
RefineMappingBasedRotPattern(java.util.Vector vecResonGraph,
java.util.Vector vecGraph,
int[][] Map)
refine mapping based on intra NOE patterns Note: Sysmetry-only when distance<3.0A, and sidechain protons |
void |
RefineMappingDeeCut(java.util.Vector vecResonGraph,
java.util.Vector vecHPositions,
int[][] Map,
double[][] MapScore,
java.util.Vector vecNewNoesy,
java.util.Vector vecBMRBNew)
Use the DEE algorithm to prune possible side-chain resonance assignments. |
void |
RefineMappingDeeCutGoldstein(java.util.Vector vecResonGraph,
java.util.Vector vecGraph,
int[][] Map,
double[][] MapScore,
java.util.Vector vecNewNoesy,
java.util.Vector vecBMRBNew)
Use the DEE algorithm to prune possible mapping. |
void |
RefineMappingForHG(java.util.Vector vecResonGraph,
java.util.Vector vecGraph,
int[][] Map,
double[][] MapScore,
java.util.Vector vecNewNoesy,
java.util.Vector vecBMRBNew)
refine mapping for HG protons modified from "RefineMappingBasedAsg" |
void |
RefineResonGraph(java.util.Vector vecResonGraph,
java.util.Vector vecStructGraph,
int[][] Map)
refine resonance graph based currrent possible mapping set |
java.util.Vector |
RefineRotLibWOSCAsg(double csErrH,
double csErrN,
double csErrCA,
java.util.Vector vecRot,
java.util.Vector vecBB,
java.util.Vector assignBBVec,
java.util.Vector NoesyVec,
int resNo,
double distBound,
int pickNum,
java.util.Vector vecRotStr,
java.util.Vector vecResonGraph,
java.util.Vector vecStructGraph,
int[][] Map,
java.util.Vector vecAsgBMRB)
rotamer selection without sidechain resonance assignment: calculate the score of each rotamer, and return ensemble of rotamers with highest scores |
java.util.Vector |
RotamSelectWOSCAsg(java.util.Vector pdbBBVec,
java.util.Vector asgBBVec,
java.util.Vector NoesyVec,
java.util.Vector vecResonGraph,
java.util.Vector vecStructGraph,
int[][] Map,
java.util.Vector vecAsgBMRB)
Compute a structure without sidechain resonances, given the backbone and rotamers at all residue positions |
void |
StatisticsAllSCAssignment(java.util.Vector vecResonGraph,
java.util.Vector vecStructGraph,
int[][] Map,
java.util.Vector vecRefAsg)
New: compute the statistical information of the sidechain assignment |
void |
StatisticsAllSCAssignmentOld(java.util.Vector vecResonGraph,
java.util.Vector vecStructGraph,
int[][] Map,
java.util.Vector vecRefAsg)
This is an old function. |
void |
UpdateIsRestrained(java.util.Vector vecResonGraph,
java.util.Vector vecGraph,
int[][] Map)
update the mapping set based on the mapping matrix |
void |
UpdateMappingSet(java.util.Vector vecResonGraph,
java.util.Vector vecGraph,
int[][] Map)
update the mapping set based on the mapping matrix |
void |
UpdateStereoSymSet(java.util.Vector vecResonGraph,
java.util.Vector vecGraph,
int[][] Map)
update stereo symmetry |
java.util.Vector |
UpdateStructGraphAdj(java.util.Vector pdbVec,
java.util.Vector vecGraphOld,
double noeUp,
double[][] distMatrix)
update the neighborhood of the structure graph, given a pdb including both bb and sc (i.e. |
Methods inherited from class java.lang.Object |
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equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public Nasca()
Method Detail |
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public java.util.Vector RefineRotLibWOSCAsg(double csErrH, double csErrN, double csErrCA, java.util.Vector vecRot, java.util.Vector vecBB, java.util.Vector assignBBVec, java.util.Vector NoesyVec, int resNo, double distBound, int pickNum, java.util.Vector vecRotStr, java.util.Vector vecResonGraph, java.util.Vector vecStructGraph, int[][] Map, java.util.Vector vecAsgBMRB)
vecRot
- rotamersassignVec
- resonance assignmentvecBB
- backbone structurehnNoeVec
- hn Noe peak listcnoeVec
- ca noe peak listresNo
- residue numberdistBound
- distance bound to define noe distancepcikNum
- number of chosen rotamers with highest scoresvecRotStr
- rotamer vectors in the structure format.vecAsgBMRB:
- BMRB statistical information
public java.util.Vector RotamSelectWOSCAsg(java.util.Vector pdbBBVec, java.util.Vector asgBBVec, java.util.Vector NoesyVec, java.util.Vector vecResonGraph, java.util.Vector vecStructGraph, int[][] Map, java.util.Vector vecAsgBMRB)
csErrH
- csErrN csErrCA error window size at each dimensionpdbBBVec
- the PDB backbone structureasgVec
- resonace listrotSrc
- the path of rotmaer libraryNoesyVec
- Noe vector including both ha and hn noesdistBound
- the distance bound for back computing distance pattern for each rotamerpickNum
- the best number of rotamers picked for computation
public void PrintAllPossibleMappings(java.util.Vector vecResonGraph, java.util.Vector vecGraph, int[][] Map)
vecResonGraph
- resonance graphvecStructGraph
- structure graphMap
- mapping matrix between two graphspublic void UpdateStereoSymSet(java.util.Vector vecResonGraph, java.util.Vector vecGraph, int[][] Map)
vecResonGraph
- resonance graphvecStructGraph
- structure graphMap
- mapping matrix between two graphspublic void UpdateIsRestrained(java.util.Vector vecResonGraph, java.util.Vector vecGraph, int[][] Map)
vecResonGraph
- resonance graphvecStructGraph
- structure graphMap
- mapping matrix between two graphs
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- public void UpdateMappingSet(java.util.Vector vecResonGraph, java.util.Vector vecGraph, int[][] Map)
vecResonGraph
- resonance graphvecStructGraph
- structure graphMap
- mapping matrix between two graphs
-
- public void RefineMappingBasedNeighbor(java.util.Vector vecResonGraph, java.util.Vector vecGraph, int[][] Map)
vecResonGraph
- resonance graphvecStructGraph
- structure graphMap
- mapping matrix between two graphs
-
- public void Initialization(java.util.Vector vecResonGraph, java.util.Vector vecGraph, int[][] Map, double[][] MapScore, java.util.Vector vecBBAsg)
vecResonGraph
- resonance graphvecStructGraph
- structure graphMap
- mapping matrix between two graphsMapScore
- mapping score matrixvecBBAsg
- backbone resonance assignment list
-
- public void RefineMappingBasedBMRBOutliers(java.util.Vector vecResonGraph, java.util.Vector vecGraph, int[][] Map, java.util.Vector vecBMRBNew)
vecResonGraph
- resonance graphvecStructGraph
- structure graphMap
- mapping matrix between two graphsMapScore
- mapping score matrixvecNewNoesy
- noesy cross peak listvecBMRBNew
- BMRB information
- public void RefineMappingBasedRotPattern(java.util.Vector vecResonGraph, java.util.Vector vecGraph, int[][] Map)
vecResonGraph
- resonance graphvecStructGraph
- structure graphMap
- mapping matrix between two graphsvecSeq
- sequence listvecNewNoesy
- noesy cross peak listvecBMRBNew
- BMRB information
- public void RefineMappingBasedAsg(java.util.Vector vecResonGraph, java.util.Vector vecGraph, int[][] Map, double[][] MapScore, java.util.Vector vecNewNoesy, java.util.Vector vecBMRBNew)
vecResonGraph
- resonance graphvecStructGraph
- structure graphMap
- mapping matrix between two graphsMapScore
- mapping score matrixvecNewNoesy
- noesy cross peak listvecBMRBNew
- BMRB information
- public void RefineMappingBasedRestrained(java.util.Vector vecResonGraph, java.util.Vector vecGraph, int[][] Map, double[][] MapScore, java.util.Vector vecNewNoesy, java.util.Vector vecBMRBNew)
vecResonGraph
- resonance graphvecStructGraph
- structure graphMap
- mapping matrix between two graphsMapScore
- mapping score matrixvecNewNoesy
- noesy cross peak listvecBMRBNew
- BMRB information
- public java.util.Vector RandomGraphMatching(java.util.Vector vecResonGraph, java.util.Vector vecGraph, int[][] Map, double[][] MapScore, java.util.Vector vecNewNoesy, java.util.Vector vecBMRBNew)
vecResonGraph
- resonance graphvecStructGraph
- structure graphMap
- mapping matrix between two graphsMapScore
- mapping score matrixvecNewNoesy
- noesy cross peak listvecBMRBNew
- BMRB information
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public java.util.Vector GreedyGraphMatchingResidue(java.util.Vector vecResonGraph, java.util.Vector vecGraph, int[][] Map, double[][] MapScore, java.util.Vector vecNewNoesy, java.util.Vector vecBMRBNew)
vecResonGraph
- resonance graphvecStructGraph
- structure graphMap
- mapping matrix between two graphsMapScore
- mapping score matrixvecNewNoesy
- noesy cross peak listvecBMRBNew
- BMRB information
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public void RefineMappingDeeCut(java.util.Vector vecResonGraph, java.util.Vector vecHPositions, int[][] Map, double[][] MapScore, java.util.Vector vecNewNoesy, java.util.Vector vecBMRBNew)
vecResonGraph
- resonance graphvecHPositions
- structure graphMap
- mapping matrix between two graphsMapScore
- mapping score matrixvecNewNoesy
- noesy cross peak listvecBMRBNew
- BMRB information
- public void RefineMappingDeeCutGoldstein(java.util.Vector vecResonGraph, java.util.Vector vecGraph, int[][] Map, double[][] MapScore, java.util.Vector vecNewNoesy, java.util.Vector vecBMRBNew)
vecResonGraph
- resonance graphvecStructGraph
- structure graphMap
- mapping matrix between two graphsMapScore
- mapping score matrixvecNewNoesy
- noesy cross peak listvecBMRBNew
- BMRB information
- public java.util.Vector GreedyGraphMatchingAstar(java.util.Vector vecResonGraph, java.util.Vector vecGraphOld, int[][] Map, double[][] MapScore, java.util.Vector vecNewNoesy, java.util.Vector vecBMRBNew, java.util.Vector vecBBAsg, java.util.Vector vecBBPdb, java.lang.String strRot, double caliConstant)
vecResonGraph
- resonance graphvecBBAsg
- backbone resonance listMap
- mapping matrix between two graphsMapScore
- mapping score matrixvecNewNoesy
- noesy cross peak listvecBMRBNew
- BMRB informationvecBBPdb
- bb pdbstrRot
- rotamer lib file namecaliConstant
- constant for calibration.
public java.util.Vector GreedyGraphMatching(java.util.Vector vecResonGraph, java.util.Vector vecGraph, int[][] Map, double[][] MapScore, java.util.Vector vecNewNoesy, java.util.Vector vecBMRBNew)
vecResonGraph
- resonance graphvecStructGraph
- structure graphMap
- mapping matrix between two graphsMapScore
- mapping score matrixvecNewNoesy
- noesy cross peak listvecBMRBNew
- BMRB information
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public double ComputeAStarEstimatedCost(java.util.Vector vecResonGraph, java.util.Vector vecGraph, java.util.Vector vecBMRBNew, int curIndex)
vecResonGraph
- resonance graph.vecStructGraph
- structure graph.vecBMRBNew
- BMRB information.curIndex
- current index.
public java.util.Vector AStarSearchForSCAsgs(java.util.Vector vecResonGraph, java.util.Vector vecHPositions, int[][] Map, double[][] MapScore, java.util.Vector vecNewNoesy, java.util.Vector vecBMRBNew)
vecResonGraph
- resonance graphvecHPositions
- structure graphMap
- mapping matrix between two graphsMapScore
- mapping score matrixvecNewNoesy
- noesy cross peak listvecBMRBNew
- BMRB information
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public void RefineMappingForHG(java.util.Vector vecResonGraph, java.util.Vector vecGraph, int[][] Map, double[][] MapScore, java.util.Vector vecNewNoesy, java.util.Vector vecBMRBNew)
vecResonGraph
- resonance graphvecStructGraph
- structure graphMap
- mapping matrix between two graphsMapScore
- mapping score matrixvecNewNoesy
- noesy cross peak listvecBMRBNew
- BMRB information
- public void RefineResonGraph(java.util.Vector vecResonGraph, java.util.Vector vecStructGraph, int[][] Map)
vecResonGraph
- resonance graphvecStructGraph
- structure graphMap
- mapping matrix between two graphs
-
- public void ExactSubgraphIsomorphism(java.util.Vector vecResonGraph, java.util.Vector vecStructGraph, int[][] Map)
vecResonGraph
- resonance graphvecStructGraph
- structure graphMap
- mapping matrix between two graphs
-
- public java.util.Vector myVectorCopy(java.util.Vector vecSrc)
public java.util.Vector myVectorCopyOneLayer(java.util.Vector vecSrc)
public java.util.Vector EnumAllScAsg(java.util.Vector vecStructGraph)
vecStructGraph
- structure graph, in which the mapping sets are givenMap
- mapping matrix between two graphsintvLower,
- intvUpper: bounds of interval
-
public void CompOneToOneMapBtwInterval(java.util.Vector vecResonGraph, java.util.Vector vecStructGraph, int[][] Map, double intvLower, double intvUpper)
vecResonGraph
- resonance graphvecStructGraph
- structure graphMap
- mapping matrix between two graphsintvLower,
- intvUpper: bounds of interval
- public java.util.Vector EnumAllScAsgSaveIntoFile(java.util.Vector vecSCProtons, java.util.Vector vecResonGraph, java.util.Vector vecStructGraph)
vecResonGraph
- resonance graphvecStructGraph
- structure graphMap
- mapping matrix between two graphsintvLower,
- intvUpper: bounds of interval
-
public static void copyfile(java.lang.String srFile, java.lang.String dtFile)
public void StatisticsAllSCAssignment(java.util.Vector vecResonGraph, java.util.Vector vecStructGraph, int[][] Map, java.util.Vector vecRefAsg)
vecResonGraph
- resonance graphvecStructGraph
- structure graphMap
- mapping matrix between two graphsvecRefAsg
- reference assignment table
- public void StatisticsAllSCAssignmentOld(java.util.Vector vecResonGraph, java.util.Vector vecStructGraph, int[][] Map, java.util.Vector vecRefAsg)
vecResonGraph
- resonance graphvecStructGraph
- structure graphMap
- mapping matrix between two graphsvecRefAsg
- reference assignment table
- public void AddProtonCoordinates(int resID, java.lang.String resName, java.lang.String atomName, Cartesian coord, java.util.Vector vecOldGraph)
resID
- resName
- atomName
- coord
- coordiante of the protonvecOldGraph
- old graphpublic java.util.Vector ConstructProtonPositions(java.util.Vector pdbBBVec, java.lang.String rotSrc, double noeUp)
pdbBBVec
- the PDB backbone structurerotSrc
- the path of rotmaer librarynoeUp
- upper limit for noe interaction, default:6A
public java.util.Vector UpdateStructGraphAdj(java.util.Vector pdbVec, java.util.Vector vecGraphOld, double noeUp, double[][] distMatrix)
pdbVec
- the PDB structure,including both bb and scrotSrc
- the path of rotmaer librarynoeUp
- upper limit for noe interaction, default:6AdistMatrix
- distance matrix
public boolean isInStereoSet(Nasca.Node nodeSrc, Nasca.Node nodeObj)
vecAsg
- all resonance assignments
-
public boolean isInCloseAdj(Nasca.Node nodeSrc, Nasca.Node nodeObj)
vecAsg
- all resonance assignments
-
public java.util.Vector ExtractBackboneAsignment(java.util.Vector vecAsg)
vecAsg
- all resonance assignments
-
public java.util.Vector ExtractSideChainAsignment(java.util.Vector vecAsg)
public java.util.Vector ConstructResonGraph(java.util.Vector vecNodeSet, java.util.Vector vecNoesy, double errH1, double errH3, double errC, double errN)
vecNodeSet
- all resonance nodesvecNoesy
- Noesy peak list
-
-
-
public void ConstructResonGraphSymmetry(java.util.Vector vecResonGraph, java.util.Vector vecNoesy, double errH1, double errH3, double errC, double errN)
vecNodeSet
- all resonance nodesvecNoesy
- Noesy peak list
-
-
- public java.util.Vector ConstructResonGraphFromAsgedList(java.util.Vector vecAsged, java.util.Vector vecUnAsged)
csH,csHeavy:
- chemical shifts of proton and heavy atom attached to it, -999.9 if it is unkowncsErrH,csErrC,csErrN:
- eror windows.vecUnAsged
- unassigned resonance list
- vecOldGraph
- old graph
public java.util.Vector AddResonanceNode(java.util.Vector vecOldGraph, double csH, double csHeavy, double csErrH, double csErrC, double csErrN)
csH,csHeavy:
- chemical shifts of proton and heavy atom attached to it, -999.9 if it is unkowncsErrH,csErrC,csErrN:
- eror windows.
-
- vecOldGraph
- old graph
public boolean isMappedBetwTwoSetsCalScore(Nasca.Node nodeReson, Nasca.Node nodeStruct, java.util.Vector vecNodeSetA, java.util.Vector vecNodeSetB, int[][] M, boolean isConsiderAssigned, int threshold, double[] Score, java.util.Vector vecNoesy)
vecNodeSetA:
- adj set for resonance nodevecNodeSetB:
- adj set of proton nodeM
- previous mapping matrixisAssigned
- whether only consider the assigned backbone resonance nodes
public boolean isMappedBetwTwoSets(java.util.Vector vecNodeSetA, java.util.Vector vecNodeSetB, int[][] M, boolean isConsiderAssigned, int threshold, double[] Score)
vecNodeSetB:
- node setsM
- previous mapping matrixisAssigned
- whether only consider the assigned backbone resonance nodes
public java.util.Vector ExtractAllResonFromNOESY(java.util.Vector vecNOESY, double csErrH, double csErrC, double csErrN)
vecNOESY
- NOESY peak listcsErrH,csErrC,csErrN:
- error windows
public void doNasca(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
|
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PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |