org.strbio.mol
Class ProfilePSI

java.lang.Object
  org.strbio.mol.Molecule
      org.strbio.mol.Polymer
          org.strbio.mol.Protein
              org.strbio.mol.Profile
                  org.strbio.mol.ProfilePSI

Direct Known Subclasses:

PredClassProfile

public class ProfilePSI
extends Profile

Class to represent a profile with position specific information (PSI), such as PSI-BLAST info and JMC's backbone potential.

  Version 1.4, 7/13/00 - added getPSIBlastMatrix
  Version 1.3, 6/7/99 - changed name from JMCProtein to ProfilePSI,
    documented things more
  Version 1.2, 6/4/99 - added constructor from ProfilePSI
  Version 1.1, 1/28/99 - added positionSpecificScore
  Version 1.0, 4/22/98 - original version
  

Version:

1.4, 7/13/00

Author:

JMC

See Also:

ProfResPSI

Field Summary

Fields inherited from class org.strbio.mol.Profile

blastBits, blastLog10E, seqName

Fields inherited from class org.strbio.mol.Polymer

chainID, includeFile, includingFile, monDistance, monomers, properties

Fields inherited from class org.strbio.mol.Molecule

atoms, data, MAX_NAME_LENGTH, name

Constructor Summary

ProfilePSI()
Default constructor.

ProfilePSI(Profile q)
Create from a regular profile.

ProfilePSI(Protein q)
Create from a single protein.

ProfilePSI(ProteinSet q)
Create from a set of proteins.

Method Summary

void	blast(Printf outfile, Blast blastServer) Run BLAST on this profile, using a specified server.
Polymer	copy() Return a copy of yourself.
void	deleteBackbonePotential(boolean alpha) delete the BackbonePotential scoring matrices for all residues.
void	deletePSIBlastMatrix() Delete PSI-blast matrices at each position.
PSIBlastMatrices	getPSIBlastMatrix() Get the psi-blast matrix back from this profile.
Monomer	newMonomer() This returns a new ProfResPSI.
Monomer	newMonomer(char t) This returns a new ProfResPSI.
Monomer	newMonomer(java.lang.String s) This returns a new ProfResPSI.
void	processYAPF(java.lang.String buffer) Process a line from a YAPF file... this should ignore the line if it doesn't know what it is.
void	setupBackbonePotential(boolean alpha, BackbonePotential pot) set up the BackbonePotential scoring matrices for all residues.
void	setupBackbonePotential(boolean alpha, BackbonePotential pot, double offset, double scale) set up the BackbonePotential scoring matrices for all residues
void	setupFakePSIBlastMatrix() Set up fake PSI-blast matrices at each position, using the BLAST (blosum62) matrix.
void	setupPSIBlastMatrix(PSIBlastMatrices p) Set up PSI-blast matrices at each position.
protected Polymer	splitCopy() When a Profile is split, sequence names should go to each child.
protected void	writeYAPFInfo(Printf outfile) Write applicable sections of YAPF info.

Methods inherited from class org.strbio.mol.Profile

addKeySeq, addSeq, addSeqsDirectlyFrom, addSeqsFrom, allocSeqs, allocSeqsRes, blast, choose, clearSeqs, copySeqsDirectlyFrom, copySeqsFrom, doVarTom, ensureUniqueNames, ensureUniqueNames, findConsensus, findConservationWeights, findFrequencies, findNonZeroFrequencies, findSeqByName, firstNonGap, getSeqName, lastNonGap, printProfile, printProfile, readBLAST, readClustal, readHSSP, readMSF, recognizeAndRead, removeRedundantSequences, removeSeq, removeSpacesInNames, seqPctCoverage, seqPctID, sequence, sequences, setSeqName, setSequence, splitCopy, truncateNames, writeClustal, writeFasta, writeMSF, writeProf, writeSAF, writeTDP

Methods inherited from class org.strbio.mol.Protein

AA, actualAccuracy, copyPredSSFrom, expectedAccuracy, filterPred, filterPred, filterReal, filterReal, findAccess, findDSSP, findDSSPResult, findPDB, firstRes, fixDistanceGaps, getDSSPResults, getInfo, hasGaps, isCATHMatch, makeMonDistance, makeMonDistanceCB, makeVirtualCB, molecularWeight, preCalculateAlphaTau, preCalculateAngles, preCalculatePhiPsi, predictSS, predictSS, readAccess, readCASP, readConv, readDSSP, readEA, readPDB, readPDBAtom, readProf, readSwissProt, readVar, readVar2, residues, reverse, runDSSP, showGaps, smoothHE, stripAllButCA, thread, thread, translateEA, writeCASP, writeConv, writeEA, writePDB, writePDB, writeVar2

Methods inherited from class org.strbio.mol.Polymer

alignToArray, alignToInverseArray, autoSplit, centerOfMass, centerOfMass, clear, clearProperties, clearProperty, copyAtoms, correctAlignFold, correctAlignSeq, deleteMonDistance, firstMon, getGlobalAlignment, getMonomers, getNonGapMonomers, getProperty, getValidNonGapMonomers, globalAlign, globalAlign, globalCompare, globalCompare, keepMonomers, kludgeChainID, lastMon, length, makeMonDistanceAllAtomMin, minareaSuperimpose, monomer, nMonomers, nMonomers, nonGapMonomers, pad, printSequence, quickAlign, quickAlign, quickCompare, quickCompare, read, read, read, readFasta, readList, readSequence, readYAPF, renumberMonomers, renumberValidNonGapMonomers, reverseCopy, rotate, sequence, sequenceNonGap, sequenceValidNonGap, setProperty, stripAllAtoms, stripAllBut, stripAllButFirstAtom, stripAtomsByName, stripCommonGaps, stripGaps, stripInvalidAndGaps, stripNoAtoms, stripType, transform, translate, trimEnds, validNonGapMonomers, writePDBAtom, writePDBSeqres, writePTS, writeYAPF, writeYAPFAtom, YAPFGetNextMonomer

Methods inherited from class org.strbio.mol.Molecule

atomSearch, copyAtoms

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ProfilePSI

public ProfilePSI()

Default constructor.

ProfilePSI

public ProfilePSI(Protein q)

Create from a single protein.

ProfilePSI

public ProfilePSI(Profile q)

Create from a regular profile.

ProfilePSI

public ProfilePSI(ProteinSet q)

Create from a set of proteins.

Method Detail

newMonomer

public Monomer newMonomer()

This returns a new ProfResPSI.

Overrides:

newMonomer in class Profile

newMonomer

public Monomer newMonomer(char t)

This returns a new ProfResPSI.

Overrides:

newMonomer in class Profile

newMonomer

public Monomer newMonomer(java.lang.String s)

This returns a new ProfResPSI.

Overrides:

newMonomer in class Profile

splitCopy

protected Polymer splitCopy()

Description copied from class: Profile

When a Profile is split, sequence names should go to each child.

Overrides:

splitCopy in class Profile

copy

public Polymer copy()

Return a copy of yourself.

Overrides:

copy in class Profile

setupPSIBlastMatrix

public final void setupPSIBlastMatrix(PSIBlastMatrices p)

Set up PSI-blast matrices at each position. Does not check to make sure the right matrices are being used!

setupFakePSIBlastMatrix

public final void setupFakePSIBlastMatrix()

Set up fake PSI-blast matrices at each position, using the BLAST (blosum62) matrix.

getPSIBlastMatrix

public final PSIBlastMatrices getPSIBlastMatrix()

Get the psi-blast matrix back from this profile.

deletePSIBlastMatrix

public final void deletePSIBlastMatrix()

Delete PSI-blast matrices at each position.

setupBackbonePotential

public final void setupBackbonePotential(boolean alpha,
                                         BackbonePotential pot,
                                         double offset,
                                         double scale)

set up the BackbonePotential scoring matrices for all residues

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 for all residues. offset and scale are set to make the potential average 0.0 with stdev 1.0 over all sampled values.

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 for all residues.

Parameters:

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

writeYAPFInfo

protected void writeYAPFInfo(Printf outfile)
                      throws java.io.IOException

Write applicable sections of YAPF info.

Overrides:

writeYAPFInfo in class Profile

Throws:

java.io.IOException

blast

public void blast(Printf outfile,
                  Blast blastServer)

Run BLAST on this profile, using a specified server. Keeps the PSI-BLAST info if there is any.

Overrides:

blast in class Profile

processYAPF

public void processYAPF(java.lang.String buffer)
                 throws java.io.IOException

Process a line from a YAPF file... this should ignore the line if it doesn't know what it is.

Overrides:

processYAPF in class Profile

Throws:

java.io.IOException