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
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 java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
RAFProtein
public RAFProtein()
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 fileoutfile
- 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 fileoutfile
- 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