Class PCPRes

  extended by org.strbio.mol.Monomer
      extended by org.strbio.mol.Residue
          extended by org.strbio.mol.ProfRes
              extended by org.strbio.mol.ProfResPSI
                  extended by org.strbio.mol.lib.pred2ary.PCPRes
All Implemented Interfaces:

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

1.2, 6/7/99
See Also:

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
          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


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


public PCPRes(char t)


public PCPRes(java.lang.String s)


public PCPRes(PCPRes q)
Copy another PCPRes.

Method Detail


public void copyDataFrom(Monomer q)
Copy another PCPRes.

copyDataFrom in class ProfResPSI


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

Specified by:
copyNode in interface DLinkedList.Node
copyNode in class ProfResPSI