org.strbio.mol.lib.pred2ary
Class PCPRes

java.lang.Object
  org.strbio.mol.Monomer
      org.strbio.mol.Residue
          org.strbio.mol.ProfRes
              org.strbio.mol.ProfResPSI
                  org.strbio.mol.lib.pred2ary.PCPRes

All Implemented Interfaces:

DLinkedList.Node

public class PCPRes
extends ProfResPSI

ProfRes with a couple extras useful for 2ary structure prediction.

  Version 1.2, 6/7/99 - moved to org.strbio.mol.lib.pred2ary, changed
    name from PredRes to PCPRes
  Version 1.1, 5/28/99 - made a child of JMCResidue
  Version 1.0, 5/12/98 - original version
  

Version:

1.2, 6/7/99

Author:

JMC

See Also:

PredClassProfile

Field Summary

Fields inherited from class org.strbio.mol.ProfResPSI

JMCAlphaTau, JMCPhiPsi, posScore

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

PCPRes()
Most constructors just call the superclass one.

PCPRes(char t)

PCPRes(PCPRes q)
Copy another PCPRes.

PCPRes(java.lang.String s)

Method Summary

void	copyDataFrom(Monomer q) Copy another PCPRes.
DLinkedList.Node	copyNode() copy contents of a residue

Methods inherited from class org.strbio.mol.ProfResPSI

deleteBackbonePotential, positionSpecificScore, positionSpecificScore, readPSIBlastRecord, scoreBackboneAlphaTau, scoreBackbonePhiPsi, setupBackbonePotential, setupBackbonePotential, writePSIBlastRecord

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

Constructor Detail

PCPRes

public PCPRes()

Most constructors just call the superclass one. A new ProfRes has 1.0 weight and 0.0 frequencies.

PCPRes

public PCPRes(char t)

PCPRes

public PCPRes(java.lang.String s)

PCPRes

public PCPRes(PCPRes q)

Copy another PCPRes.

Method Detail

copyDataFrom

public void copyDataFrom(Monomer q)

Copy another PCPRes.

Overrides:

copyDataFrom in class ProfResPSI

copyNode

public DLinkedList.Node copyNode()

copy contents of a residue

Specified by:

copyNode in interface DLinkedList.Node

Overrides:

copyNode in class ProfResPSI