charite.christo.strap.extensions
Class Superimpose_CE

java.lang.Object
  charite.christo.strap.AbstractAligner
      charite.christo.strap.extensions.Superimpose_CE

All Implemented Interfaces:

CanBeStopped, Disposable, HasControlPanel, HasNativeExec, HasPropertyMap, HasScore, IsEnabled, NeedsProteins, SequenceAligner, SequenceAligner3D, Superimpose3D

public class Superimpose_CE
extends AbstractAligner
implements HasScore, SequenceAligner3D, Superimpose3D

HELP
Publication: PUBMED:11125099 , PUBMED:9796821 This is the Java based implementation of CE/CL superposition. Ported from C++ to Java by Andreas Prlic.

Nested Class Summary

Nested classes/interfaces inherited from interface charite.christo.protein.Superimpose3D

Superimpose3D.Result

Field Summary

Fields inherited from class charite.christo.strap.AbstractAligner

MFA_FILE, PFX_DPKG, RPLC_WIN_DOT_EXE

Fields inherited from interface charite.christo.protein.SequenceAligner

OPTION_CHECK_PERFECT_MATCH, OPTION_NOT_TO_SECURITY_LIST, OPTION_USE_SECONDARY_STRUCTURE, PROPERTY_LOCAL_ALIGNMENT, PROPERTY_ONLY_TWO_SEQUENCES, SCORE_FOR_PERFECT_MATCH

Fields inherited from interface charite.christo.protein.Superimpose3D

COLUMN_SEQUENCE, NO_BYTE, PARSE_ALIGNMENT, PARSE_MATRIX, PARSE_MSA_START_S, PARSE_SCORE, PRINT_HUMAN_READABLE

Fields inherited from interface charite.christo.Disposable

NONE

Fields inherited from interface charite.christo.CanBeStopped

vALIGNMENTS

Constructor Summary

Superimpose_CE()

Method Summary

Superimpose3D.Result	computeResult(byte[][] ssNotNeeded, Protein[] proteins)
static org.biojava.bio.structure.StructureImpl	toBiojavaStructureCA(Protein p, boolean[] selectedAminos, boolean original)

Methods inherited from class charite.christo.strap.AbstractAligner

addProfile, cbCommutative, compute, defineParameters, dirTemp, dispose, getAlignedSequences, getControlPanel, getIndicesOfSequences, getMaxNumberOfProfiles, getNativeExec, getOptions, getPrgParas, getProfiles, getPropertyFlags, getPropertyMap, getProteins, getResult, getRmsd, getScore, getSequences, getSharedInstance, initX, insertWhereNoCoordinates, isEnabled, mfaInFile, parse, pdbFile, setOptions, setPropertyFlags, setProteins, setSequences, setSharedInstance, stop

Methods inherited from class java.lang.Object

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

Methods inherited from interface charite.christo.HasScore

getScore

Methods inherited from interface charite.christo.protein.SequenceAligner

compute, getAlignedSequences, getOptions, getPropertyFlags, getSequences, setOptions, setSequences

Methods inherited from interface charite.christo.protein.Superimpose3D

compute, getOptions, getProteins, getResult, setOptions

Methods inherited from interface charite.christo.protein.NeedsProteins

setProteins

Constructor Detail

Superimpose_CE

public Superimpose_CE()

Method Detail

computeResult

public Superimpose3D.Result computeResult(byte[][] ssNotNeeded,
                                          Protein[] proteins)

Specified by:

computeResult in class AbstractAligner

toBiojavaStructureCA

public static org.biojava.bio.structure.StructureImpl toBiojavaStructureCA(Protein p,
                                                                           boolean[] selectedAminos,
                                                                           boolean original)