org.strbio.mol
Class ProfResPSI

java.lang.Object
  extended by org.strbio.mol.Monomer
      extended by org.strbio.mol.Residue
          extended by org.strbio.mol.ProfRes
              extended by org.strbio.mol.ProfResPSI
All Implemented Interfaces:
DLinkedList.Node
Direct Known Subclasses:
PCPRes

public class ProfResPSI
extends ProfRes

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
  

Version:
1.2, 6/7/99
Author:
JMC
See Also:
ProfilePSI

Field Summary
 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
frequency, nonZeroFrequency, oneLetterHSSP, seq, weight
 
Fields inherited from class org.strbio.mol.Residue
aaMolecularWeight, cAlpha, cPhi, cPsi, cTau, env, exposedArea, oneLetter, oneLetterBLAST, oneLetterDefay, pctExposed, predE, predH, predStructure, structure, threeLetter
 
Fields inherited from class org.strbio.mol.Monomer
atoms, n, type
 
Constructor Summary
ProfResPSI()
          Most constructors just call the superclass one.
ProfResPSI(char t)
           
ProfResPSI(ProfResPSI q)
          copy another residue, including the atoms.
ProfResPSI(java.lang.String s)
           
 
Method Summary
 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
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
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
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
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

JMCPhiPsi

public DMatrix JMCPhiPsi
JMC's phi/psi potential matrix for this postion.

See Also:
BackbonePotential

JMCAlphaTau

public DMatrix JMCAlphaTau
JMC's alpha/tau potential matrix.

See Also:
BackbonePotential

posScore

public DVector posScore
Position dependent alignment score, as in PSI-BLAST.

Constructor Detail

ProfResPSI

public ProfResPSI()
Most constructors just call the superclass one.


ProfResPSI

public ProfResPSI(char t)

ProfResPSI

public ProfResPSI(java.lang.String s)

ProfResPSI

public ProfResPSI(ProfResPSI q)
copy another residue, including the atoms. This makes another copy of the data.

Method Detail

copyDataFrom

public void copyDataFrom(Monomer q)
Copy another ProfResPSI.

Overrides:
copyDataFrom in class ProfRes

copyNode

public DLinkedList.Node copyNode()
copy contents of a ProfResPSI.

Specified by:
copyNode in interface DLinkedList.Node
Overrides:
copyNode in class ProfRes

positionSpecificScore

public final double positionSpecificScore(char type)
Return the position specific score for aligning this position to a certain type of residue.


positionSpecificScore

public final double positionSpecificScore(int n)
Return the position specific score for aligning this position to a certain type (1-20) of residue.


readPSIBlastRecord

public void readPSIBlastRecord(java.lang.String buffer)
                        throws java.io.IOException
Read PSI-BLAST info out of YAPF file.

Throws:
java.io.IOException

writePSIBlastRecord

public void writePSIBlastRecord(Printf outfile)
                         throws java.io.IOException
Write PSIBLAST record to YAPF file.

Throws:
java.io.IOException

scoreBackbonePhiPsi

public final double scoreBackbonePhiPsi(double phi,
                                        double psi)
the BackbonePotential score for putting this residue into a given phi/psi. Throws IllegalArgumentException if uninitialized.


scoreBackboneAlphaTau

public final double scoreBackboneAlphaTau(double alpha,
                                          double tau)
the BackbonePotential score for putting this residue into a given alpha/tau. Throws IllegalArgumentException if uninitialized.


setupBackbonePotential

public final void setupBackbonePotential(boolean alpha,
                                         BackbonePotential pot,
                                         double offset,
                                         double scale)
set up the BackbonePotential scoring matrices

Parameters:
alpha - true if you want alpha/tau, false if you want phi/psi
pot - an initialized BackbonePotential
offset - how much to offset the potential?
scale - how much to scale the potential?

setupBackbonePotential

public final void setupBackbonePotential(boolean alpha,
                                         BackbonePotential pot)
set up the BackbonePotential scoring matrices

Parameters:
alpha - true if you want alpha/tau, false if you want phi/psi
pot - an initialized BackbonePotential

deleteBackbonePotential

public final void deleteBackbonePotential(boolean alpha)
delete the BackbonePotential scoring matrices

Parameters:
alpha - true if you want alpha/tau, false if you want phi/psi