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java.lang.Objectorg.strbio.mol.Monomer
org.strbio.mol.Residue
org.strbio.mol.ProfRes
org.strbio.mol.ProfResPSI
public class ProfResPSI
Class to represent a single residue in a profile, with position specific information (PSI) added.
Version 1.2, 6/7/99 - changed name from ProfResPSI to ProfResPSI, documented things more Version 1.1, 1/28/99 - added positionSpecificScore Version 1.0, 4/22/98 - original version
ProfilePSI
Field Summary | |
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DMatrix |
JMCAlphaTau
JMC's alpha/tau potential matrix. |
DMatrix |
JMCPhiPsi
JMC's phi/psi potential matrix for this postion. |
DVector |
posScore
Position dependent alignment score, as in PSI-BLAST. |
Fields inherited from class org.strbio.mol.ProfRes |
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frequency, nonZeroFrequency, oneLetterHSSP, seq, weight |
Fields inherited from class org.strbio.mol.Residue |
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aaMolecularWeight, cAlpha, cPhi, cPsi, cTau, env, exposedArea, oneLetter, oneLetterBLAST, oneLetterDefay, pctExposed, predE, predH, predStructure, structure, threeLetter |
Fields inherited from class org.strbio.mol.Monomer |
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atoms, n, type |
Constructor Summary | |
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ProfResPSI()
Most constructors just call the superclass one. |
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ProfResPSI(char t)
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ProfResPSI(ProfResPSI q)
copy another residue, including the atoms. |
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ProfResPSI(java.lang.String s)
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Method Summary | |
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void |
copyDataFrom(Monomer q)
Copy another ProfResPSI. |
DLinkedList.Node |
copyNode()
copy contents of a ProfResPSI. |
void |
deleteBackbonePotential(boolean alpha)
delete the BackbonePotential scoring matrices |
double |
positionSpecificScore(char type)
Return the position specific score for aligning this position to a certain type of residue. |
double |
positionSpecificScore(int n)
Return the position specific score for aligning this position to a certain type (1-20) of residue. |
void |
readPSIBlastRecord(java.lang.String buffer)
Read PSI-BLAST info out of YAPF file. |
double |
scoreBackboneAlphaTau(double alpha,
double tau)
the BackbonePotential score for putting this residue into a given alpha/tau. |
double |
scoreBackbonePhiPsi(double phi,
double psi)
the BackbonePotential score for putting this residue into a given phi/psi. |
void |
setupBackbonePotential(boolean alpha,
BackbonePotential pot)
set up the BackbonePotential scoring matrices |
void |
setupBackbonePotential(boolean alpha,
BackbonePotential pot,
double offset,
double scale)
set up the BackbonePotential scoring matrices |
void |
writePSIBlastRecord(Printf outfile)
Write PSIBLAST record to YAPF file. |
Methods inherited from class org.strbio.mol.ProfRes |
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allocSeqs, clearSeqs, findFrequencies, findNonZeroFrequencies, frequencies2Consensus, HSSPnum2Num, readCWRecord, readFREQRecord, readHSSPSeqs, readProf, readSeqRecord, removeSeq, sequences, writeCWRecord, writeFREQRecord, writeProf, writeSeqRecord |
Methods inherited from class org.strbio.mol.Residue |
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alpha, is3Res, isGap, isGap, isRes, isValidType, makeVirtualCB, molecularWeight, num2Res, num2ResDefay, one2Three, phi, psi, readAccess, readAccessRecord, readAngleRecord, readConv, readDSSP, readDSSPRecord, readEA, readJMCSTR, readPredSSRecord, readVar, readVar2, readVarTomRecord, res2Num, res2NumDefay, stripAllButCA, tau, three2One, translateEA, typeName, writeAccessRecord, writeAngleRecord, writeCASP, writeConv, writeDSSPRecord, writeEA, writePDBStr, writePredSSRecord, writeVar2, writeVarTomRecord |
Methods inherited from class org.strbio.mol.Monomer |
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atomSearch, centerOfMass, centerOfMass, copyAtoms, isValidNonGap, nAtoms, nAtomsWithCoord, next, prev, readAtomRecord, readFasta, rotate, setNext, setPrev, stripAllAtoms, stripAllBut, stripAllButFirstAtom, stripAtomsByName, transform, translate, writePDBAtom, writePts, writeYAPFAtom |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public DMatrix JMCPhiPsi
BackbonePotential
public DMatrix JMCAlphaTau
BackbonePotential
public DVector posScore
Constructor Detail |
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public ProfResPSI()
public ProfResPSI(char t)
public ProfResPSI(java.lang.String s)
public ProfResPSI(ProfResPSI q)
Method Detail |
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public void copyDataFrom(Monomer q)
copyDataFrom
in class ProfRes
public DLinkedList.Node copyNode()
copyNode
in interface DLinkedList.Node
copyNode
in class ProfRes
public final double positionSpecificScore(char type)
public final double positionSpecificScore(int n)
public void readPSIBlastRecord(java.lang.String buffer) throws java.io.IOException
java.io.IOException
public void writePSIBlastRecord(Printf outfile) throws java.io.IOException
java.io.IOException
public final double scoreBackbonePhiPsi(double phi, double psi)
public final double scoreBackboneAlphaTau(double alpha, double tau)
public final void setupBackbonePotential(boolean alpha, BackbonePotential pot, double offset, double scale)
alpha
- true if you want alpha/tau, false if you want phi/psipot
- an initialized BackbonePotentialoffset
- how much to offset the potential?scale
- how much to scale the potential?public final void setupBackbonePotential(boolean alpha, BackbonePotential pot)
alpha
- true if you want alpha/tau, false if you want phi/psipot
- an initialized BackbonePotentialpublic final void deleteBackbonePotential(boolean alpha)
alpha
- true if you want alpha/tau, false if you want phi/psi
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