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java.lang.ObjectRdcPanda.RotaPattern
public class RotaPattern
This class implements data structures and functions that deal with the rotamer properties. Written by Jianyang (Michael) Zeng (2005-2009).
Nested Class Summary | |
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static class |
RotaPattern.scoreComparator
The Class scoreComparator. |
Constructor Summary | |
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RotaPattern()
Instantiates a new rota pattern. |
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RotaPattern(double[] coordTemp,
double dbSc)
Instantiates a new rota pattern. |
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RotaPattern(int res_no,
double dbSc)
Instantiates a new rota pattern. |
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RotaPattern(int no,
java.lang.String resName,
java.util.Vector hdistVec,
java.util.Vector NoeVec)
Instantiates a new rota pattern. |
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RotaPattern(int no,
java.lang.String resName,
java.util.Vector hdistVec,
java.util.Vector NoeVec,
java.util.Vector pVec)
Instantiates a new rota pattern. |
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RotaPattern(Pdb pdbRot,
double dbSc)
Instantiates a new rota pattern. |
Method Summary | |
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java.util.Vector |
BackCompNoePattern(java.util.Vector asgVec,
int resNo,
java.lang.String resName,
java.util.Vector vecHDist)
Back compute all NOE peaks from given pairs of NOE distance patterns for a rotamer. |
BackNoe |
BackCompNOEPeak(java.util.Vector asgVec,
Hdist hdist)
Back compute an NOE peak from a given pair of NOE distance. |
java.util.Vector |
getBackNoeVec()
Gets the back noe vec. |
double[] |
getCoord()
Gets the coord. |
java.util.Vector |
getHdistVec()
Gets the hdist vec. |
Pdb |
getPdb()
Gets the pdb. |
int |
getResNo()
Gets the res no. |
java.lang.String |
getResType()
Gets the res type. |
double |
getScore()
Gets the score. |
java.util.Vector |
RefineRotLib(double csErrH,
double csErrN,
double csErrCA,
java.util.Vector vecRot,
java.util.Vector vecBB,
java.util.Vector assignVec,
java.util.Vector NoesyVec,
int resNo,
double distBound,
int pickNum,
double[] maxScore)
Refined function for general case: calculate the score of each rotamer, and choose rotamers with highest scores. |
java.util.Vector |
RefineRotLib(double csErrH,
double csErrN,
double csErrCA,
java.util.Vector vecRot,
java.util.Vector vecBB,
java.util.Vector assignVec,
java.util.Vector NoesyVec,
int resNo,
double distBound,
int pickNum,
int[] maxInd)
Refined function for general case: calculate the score of each rotamer, and choose rotamers with highest scores. |
java.util.Vector |
RefineRotLib(java.util.Vector vecRot,
java.util.Vector vecBB,
java.util.Vector assignVec,
java.util.Vector hnNoeVec,
java.util.Vector cnoeVec,
int resNo,
double distBound,
int pickNum,
int[] maxInd,
java.util.Vector vecXrayBB)
calculate the score of each rotamer, and choose rotamers with highest scores. |
java.util.Vector |
RefineRotLibNew(double csErrH,
double csErrN,
double csErrCA,
java.util.Vector vecRot,
java.util.Vector vecBB,
java.util.Vector assignVec,
java.util.Vector NoesyVec,
int resNo,
double distBound,
int pickNum,
java.util.Vector vecRotStr,
double constant)
Refined function for general case: calculate the score of each rotamer, and return ensemble of rotamers with highest scores. |
java.util.Vector |
RefineRotLibNewUsingBins(double csErrH,
double csErrN,
double csErrCA,
java.util.Vector vecRot,
java.util.Vector vecBB,
java.util.Vector assignVec,
java.util.Vector NoesyVec,
int resNo,
double distBound,
int pickNum,
java.util.Vector vecRotStr)
calibration scheme: using bin scheme. |
void |
setScore(double sc)
Sets the score. |
BackNoe |
SimulateBackCompNOEPeak(java.util.Vector asgVec,
Hdist hdist)
for simulate ca NOEs, Back compute an NOE peak from a given pair of NOE distance. |
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 RotaPattern(double[] coordTemp, double dbSc)
coordTemp
- the coord tempdbSc
- the db scpublic RotaPattern(Pdb pdbRot, double dbSc)
pdbRot
- the pdb rotdbSc
- the db scpublic RotaPattern(int res_no, double dbSc)
res_no
- the res_nodbSc
- the db scpublic RotaPattern()
public RotaPattern(int no, java.lang.String resName, java.util.Vector hdistVec, java.util.Vector NoeVec)
no
- the noresName
- the res namehdistVec
- the hdist vecNoeVec
- the noe vecpublic RotaPattern(int no, java.lang.String resName, java.util.Vector hdistVec, java.util.Vector NoeVec, java.util.Vector pVec)
no
- the noresName
- the res namehdistVec
- the hdist vecNoeVec
- the noe vecpVec
- the vecMethod Detail |
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public int getResNo()
public java.lang.String getResType()
public java.util.Vector getHdistVec()
public java.util.Vector getBackNoeVec()
public Pdb getPdb()
public double[] getCoord()
public double getScore()
public void setScore(double sc)
sc
- the new scorepublic java.util.Vector RefineRotLib(java.util.Vector vecRot, java.util.Vector vecBB, java.util.Vector assignVec, java.util.Vector hnNoeVec, java.util.Vector cnoeVec, int resNo, double distBound, int pickNum, int[] maxInd, java.util.Vector vecXrayBB)
vecRot
- rotamersassignVec
- resonance assignmentvecBB
- backbone structurehnNoeVec
- hn Noe peak listcnoeVec
- ca noe peak listresNo
- residue numberdistBound
- distance bound to define noe distancevecXrayBB
- xray backbone for computing rmsdpickNum
- the pick nummaxInd
- the max ind
public java.util.Vector RefineRotLib(double csErrH, double csErrN, double csErrCA, java.util.Vector vecRot, java.util.Vector vecBB, java.util.Vector assignVec, java.util.Vector NoesyVec, int resNo, double distBound, int pickNum, int[] maxInd)
vecRot
- rotamersassignVec
- resonance assignmentvecBB
- backbone structureresNo
- residue numberdistBound
- distance bound to define noe distancecsErrH
- the cs err hcsErrN
- the cs err ncsErrCA
- the cs err caNoesyVec
- the noesy vecpickNum
- the pick nummaxInd
- the max ind
public java.util.Vector RefineRotLibNew(double csErrH, double csErrN, double csErrCA, java.util.Vector vecRot, java.util.Vector vecBB, java.util.Vector assignVec, java.util.Vector NoesyVec, int resNo, double distBound, int pickNum, java.util.Vector vecRotStr, double constant)
vecRot
- rotamersassignVec
- resonance assignmentvecBB
- backbone structureresNo
- residue numberdistBound
- distance bound to define noe distancevecRotStr
- rotamer vectors in the structure format.csErrH
- the cs err hcsErrN
- the cs err ncsErrCA
- the cs err caNoesyVec
- the noesy vecpickNum
- the pick numconstant
- the constant
public java.util.Vector RefineRotLibNewUsingBins(double csErrH, double csErrN, double csErrCA, java.util.Vector vecRot, java.util.Vector vecBB, java.util.Vector assignVec, java.util.Vector NoesyVec, int resNo, double distBound, int pickNum, java.util.Vector vecRotStr)
vecRot
- rotamersassignVec
- resonance assignmentvecBB
- backbone structureresNo
- residue numberdistBound
- distance bound to define noe distancevecRotStr
- rotamer vectors in the structure format.csErrH
- the cs err hcsErrN
- the cs err ncsErrCA
- the cs err caNoesyVec
- the noesy vecpickNum
- the pick num
public java.util.Vector RefineRotLib(double csErrH, double csErrN, double csErrCA, java.util.Vector vecRot, java.util.Vector vecBB, java.util.Vector assignVec, java.util.Vector NoesyVec, int resNo, double distBound, int pickNum, double[] maxScore)
vecRot
- rotamersassignVec
- resonance assignmentvecBB
- backbone structureresNo
- residue numberdistBound
- distance bound to define noe distancecsErrH
- the cs err hcsErrN
- the cs err ncsErrCA
- the cs err caNoesyVec
- the noesy vecpickNum
- the pick nummaxScore
- the max score
public BackNoe SimulateBackCompNOEPeak(java.util.Vector asgVec, Hdist hdist)
asgVec
- resonance assignmenthdist
- the hdist
public BackNoe BackCompNOEPeak(java.util.Vector asgVec, Hdist hdist)
asgVec
- resonance assignmenthdist
- the hdist
public java.util.Vector BackCompNoePattern(java.util.Vector asgVec, int resNo, java.lang.String resName, java.util.Vector vecHDist)
asgVec
- resonance assignmentresNo
- residue No of the rotamerresName
- residue name of the rotamervecHDist
- all pairs of NOE distances from rotamer protons to backbone protons, namely HN/HA/HB
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