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java.lang.ObjectRdcPanda.GraphCut
public class GraphCut
Nested Class Summary | |
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static class |
GraphCut.ResNoComparator
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class |
GraphCut.RotScore
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static class |
GraphCut.RotScoreComparator
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Constructor Summary | |
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GraphCut()
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GraphCut(int resNO)
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GraphCut(java.lang.String res,
int res_no,
int label,
java.util.Vector vecAllRots)
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GraphCut(java.lang.String res,
int res_no,
int label,
java.util.Vector vecAllRots,
java.util.Vector vecNearPdbs)
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Method Summary | |
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void |
addRotScore(int no,
double sc)
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java.util.Vector |
ComputeScoringFunction(java.util.Vector vecGraphCut,
java.util.Vector vecBB,
java.util.Vector assignVec,
java.util.Vector NoesyVec,
double csErrH,
double csErrN,
double csErrCA,
double distBound)
calculate the scoring function based on NOE patterns |
java.util.Vector |
DEECut(java.util.Vector vecGraphCutPre)
DEE-Cut step in the graph cut algorithm |
java.util.Vector |
getAllRotVec()
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double |
getHomoScore(int nRotLabel)
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boolean |
getIsRemainedLabel(int nID)
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java.util.Vector |
getNeighborVec()
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double |
getPairScore(int rotID,
int neighID,
int neighRotID)
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java.lang.String |
getResidueName()
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int |
getResidueNo()
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int |
getRotLabel()
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java.util.Vector |
getRotScoreVec()
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java.util.Vector |
getTopScoreRots(int pickNum)
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java.util.Vector |
GraphConstruction(java.util.Vector vecPdbBB,
java.lang.String srcRotFile,
double noeLimit)
Construct the residue interation graph |
int |
RandomSelectRot(java.util.Vector vecRotScore)
randomly select a rotamer proportial to its score |
java.util.Vector |
RandomVotingUpdate(java.util.Vector vecGraphCut)
update the match score using random voting scheme |
java.util.Vector |
RotamerSelection(java.util.Vector pdbBBVec,
java.util.Vector vecGraphCut,
int pickNum)
select top rotamers with highest scores |
void |
setHomoScore(double sc,
int nRotID)
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void |
setInitialRotScore()
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void |
setNeighbors(java.util.Vector vecNeigh)
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void |
setPairScore(double sc,
int nRotID,
int nNeighborID,
int nNeighborRotID)
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void |
setPrunedLabel(int nRotLabl)
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void |
setRotlabel(int label)
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java.util.Vector |
ShufflingCut(java.util.Vector vecGraphCutPre)
Shuffling step in the graph cut algorithm |
void |
sortRotScore()
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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 GraphCut()
public GraphCut(int resNO)
public GraphCut(java.lang.String res, int res_no, int label, java.util.Vector vecAllRots)
public GraphCut(java.lang.String res, int res_no, int label, java.util.Vector vecAllRots, java.util.Vector vecNearPdbs)
Method Detail |
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public int getResidueNo()
public java.lang.String getResidueName()
public int getRotLabel()
public java.util.Vector getAllRotVec()
public java.util.Vector getNeighborVec()
public double getHomoScore(int nRotLabel)
public double getPairScore(int rotID, int neighID, int neighRotID)
public boolean getIsRemainedLabel(int nID)
public java.util.Vector getRotScoreVec()
public java.util.Vector getTopScoreRots(int pickNum)
public void setRotlabel(int label)
public void setHomoScore(double sc, int nRotID)
public void setPairScore(double sc, int nRotID, int nNeighborID, int nNeighborRotID)
public void setPrunedLabel(int nRotLabl)
public void setNeighbors(java.util.Vector vecNeigh)
public void setInitialRotScore()
public void sortRotScore()
public void addRotScore(int no, double sc)
public int RandomSelectRot(java.util.Vector vecRotScore)
public java.util.Vector GraphConstruction(java.util.Vector vecPdbBB, java.lang.String srcRotFile, double noeLimit) throws JampackException
vecPdbBB:
- vector of pdb backbonesrcRotFile:
- location of rotamer librarynoeLimit:
- noe distance bound
JampackException
public java.util.Vector ComputeScoringFunction(java.util.Vector vecGraphCut, java.util.Vector vecBB, java.util.Vector assignVec, java.util.Vector NoesyVec, double csErrH, double csErrN, double csErrCA, double distBound)
vecGraphCut:
- vector of GraphCut nodesvecBB:
- backbone pdbassignVec:
- assigned resonance listNoesyVec:
- NOESY peak listcsErrH,
- csErrN, csErrCA: error window at each dimensiondistBound:
- Noe distance bound
public java.util.Vector DEECut(java.util.Vector vecGraphCutPre)
vecGraphCutPre:
- vector of GraphCut nodes before DEE Cut
public java.util.Vector ShufflingCut(java.util.Vector vecGraphCutPre)
vecGraphCutPre:
- vector of GraphCut nodes before DEE Cut
public java.util.Vector RotamerSelection(java.util.Vector pdbBBVec, java.util.Vector vecGraphCut, int pickNum)
pdbBBVec:
- vector of backbone pdbvecGraphCut:
- vector of GraphCut nodesresNo:
- residue IDpickNum:
- number of rotamers to be chosen in the ensemble
public java.util.Vector RandomVotingUpdate(java.util.Vector vecGraphCut)
vecGraphCut:
- vector of GraphCut nodes
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