org.strbio.raf
Class RAFProtein

java.lang.Object
  org.strbio.mol.Molecule
      org.strbio.mol.Polymer
          org.strbio.mol.Protein
              org.strbio.raf.RAFProtein

public class RAFProtein
extends Protein

Modified version of org.strbio.mol.Protein... part of this might might be ported back to Protein. Changes that had to be made: 1) it works in cases where a residue in atom/seqres don't match, 2) it can independently read atom and seqres, and 3) handles modified aa and aa that are in HETATM.

Version:

1.0, 11/2/01

Author:

JMC

Field Summary

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

RAFProtein()

Method Summary

static ProteinSet	readAtom(java.lang.String filename, Printf outfile)
void	readPDBAtomRAF(java.io.BufferedReader infile, Printf outfile) read a protein out of a PDB file ATOM records.
void	readPDBSeqresRAF(java.io.BufferedReader infile, Printf outfile) read a protein out of a PDB SEQRES records
static ProteinSet	readSeqres(java.lang.String filename, Printf outfile)

Methods inherited from class org.strbio.mol.Protein

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

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, writeFasta, 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

RAFProtein

public RAFProtein()

Method Detail

readPDBSeqresRAF

public final void readPDBSeqresRAF(java.io.BufferedReader infile,
                                   Printf outfile)
                            throws java.io.IOException

read a protein out of a PDB SEQRES records

Parameters:

infile - an open PDB file

outfile - if non-null, will print info on what's going on

Throws:

java.io.IOException

See Also:

Polymer.read(java.io.BufferedReader, org.strbio.io.Printf, boolean)

readPDBAtomRAF

public final void readPDBAtomRAF(java.io.BufferedReader infile,
                                 Printf outfile)
                          throws java.io.IOException

read a protein out of a PDB file ATOM records. insertion code stored in residue 'structure' fields.

Parameters:

infile - an open PDB file

outfile - if non-null, will print info on what's going on

Throws:

java.io.IOException

readAtom

public static ProteinSet readAtom(java.lang.String filename,
                                  Printf outfile)
                           throws java.io.IOException

Throws:

java.io.IOException

readSeqres

public static ProteinSet readSeqres(java.lang.String filename,
                                    Printf outfile)
                             throws java.io.IOException

Throws:

java.io.IOException