機能別コマンド一覧

提供: Eospedia
2012年9月23日 (日) 04:26時点におけるAdmin (トーク | 投稿記録)による版

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ここでは、機能別に少しずつ整理をしています。まだまだ整理が終わっていません。すこしずつ進めていますので、ご容赦下さい。

統合環境

  • Display2: ２Ｄ画像もしくは３Ｄ画像のセクションの表示、処理など
  • Display3: ３Ｄ画像の表示
  • ctfDisplay: For CTF Correlation
  • Visualmake: Easy and automatics GUI generator for Makefile
  • Eos: Eos on Tcl/Tk, CUI
  • smolet:　トモグラフィーのためのGUIソフトウェア（傾斜シリーズの表示）

molvieシリーズ

開発環境　

コマンドリスト　

CheckCommonLineData CheckOfOrientation CheckOrientationByDegree CommonLineCalculation CommonLineRankCalc_k Descartes2Polar

EvaluateCorrelationMapwithCommonLine

FETOrientationSearchByAnnealing FETOrientationSearchByFeatureAlignment FETmapOrientationSearchBySimultaneousFitting FETsmallMapSetCreate_forSimultaneousMinimization

LCalculationForOrientationSearch

Polar2Descartes ProjectionDirectionMapCreate

TestForLcalculationOfOrientationSearchBySimultaneousMinimization

WeightCalculationOfCommonLineSearch WeightCalculationOfCommonLineSearchByAllSinogram WeigthCaluculationOfCommonLineCalculation

angleMatchTest_k anglediffcalc anglediffchk

calcCommonLine


coordRotation

ＣＴＦ関係のコマンド群　

CTF決定のためのプログラム群

CTFの関数に関するプログラム

CTF補正に関するプログラム群

DCDフォーマットのファイルに関する取り扱い

dcdFilePrint dcdInfo dcdSelectAtoms dcdSerectAtom dcdTest dcdTimeSeriesBehavior

cufft dataAnalysis_kayabuki

defocusDeterminationFromThonRing

electronWaveLength energyTransferModelCheck energyTransferModelResultCheck fft2d geogeoge gmolvie homology2PG hostCondition imageView imagesClustering imagesView


khorosFilterGenerate largeIPInfo

らせん対称性を用いた3次元再構成

空間の変換

llExtractのサポートプログラム群

llExtractCtfinfFileCreate llExtractCtrlFileCreate llExtractWithLayerSeparation llExtractWithLayerSeparationCtrlFileCreate llExtractWithLayerSeparationCtrlFileCreateMyosin llExtractWithLayerSeparationFilamentInfo llExtractWithLayerSeparationServer llExtractWithLayerSeparationSingle

G(R, THETA, Z)空間の取り扱い

llDataAverage llDataAxisSearch llDataCTFCompensate llDataCompare llDataContributionCalcDifferentN llDataDump llDataEquatorAdd llDataExtract llDataFit llDataFitServer llDataInfo llDataLowPassFiltering llDataMultiCTFCompensation llDataNEstimation llDataNormalization llDataPrint llDataRescaling llDataResolutionCheck llDataRotation llDataSelectionEstimation llDataSeparate llDataWeightSet llDatarMaxLimit

g(r, theta, Z) の取り扱い

ltlg2ps ltlgDataInfo


mrc3DExtractZ


3次元再構成

mrcImageフォーマットに対するコマンド群

mrcFTMeridianEquatorRedece mrcImage1DProjectionfrom2D mrcImage1dAverageByCorrelation mrcImage1dCutAverage mrcImage1dShiftAverageByAnnealing mrcImage1dShiftByCorrelation mrcImage2DBackProjection mrcImage2DProjection mrcImage2pdb mrcImage3DHighResoEmphasis mrcImage3DPad mrcImage3DPad2 mrcImage3DSymmetryFind mrcImage3DWindowing mrcImageAbnormalValueRemove mrcImageActinSingleParticleAnalysis mrcImageAdaptiveBinalization mrcImageAdd mrcImageAddValue mrcImageAreaCalc mrcImageAssignedToTFofPDB mrcImageAutoCorrelationWithWindowing mrcImageAutoFilamentExtract mrcImageAutoFilamentExtractResultAnalysis mrcImageAutoRotationCorrelation mrcImageAutoRotationCorrelation3D mrcImageAutoRotationCorrelationResultPrint mrcImageAverage mrcImageBandPassFilter mrcImageBinalization mrcImageBlockMerge mrcImageBoundaryInfo mrcImageBtest mrcImageCCDNoiseRemove mrcImageCTFCompensation mrcImageCTFCompensationForTiltImage mrcImageCTFDetermination mrcImageCTFObservation mrcImageCTFSN mrcImageCVE mrcImageCenterDensityChange mrcImageCenterGet mrcImageCenterOfMassCalculate mrcImageCircumferentialProjection mrcImageColoring mrcImageCommonLineSearch mrcImageConnection mrcImageConnectivityNumberCalc mrcImageContourSurfaceCreate mrcImageCoordinateChange mrcImageCoreImageCalc mrcImageCorrelation mrcImageCorrelationInFourierSpace mrcImageCorrelationServer mrcImageCorrelationWithCTFCompensation mrcImageCrystalCreate mrcImageCutAndSetInArray mrcImageCylinderSection mrcImageDeadPixelCorrection mrcImageDensityChangeEstimation mrcImageDensityInfo mrcImageDensityNormalization mrcImageDensityNormalizationByImage mrcImageDisplayDensityAsTempFactor mrcImageDistanceConversion mrcImageDivideInfoForTomography mrcImageDivideIntoTwoImages mrcImageEdgeImageGet mrcImageEnhancementWithFuzzySets mrcImageEstimateTiltImage mrcImageExpression mrcImageFFT mrcImageFFTLayerLineExtraction mrcImageFOMCalc mrcImageFTest mrcImageFeatureExtraction mrcImageFilamentSearch mrcImageFilterCreate mrcImageFilteringbyFile mrcImageFilteringbyFileForVariance mrcImageFourierPowerSpectrum mrcImageFourierShellCorrelation mrcImageFractalFourierShellCorrelation mrcImageFractalFrourierShellCorrelation mrcImageGaussDisc mrcImageGaussSphere mrcImageHeaderChange mrcImageHelicalAveraging mrcImageHelicalConvolution mrcImageHelicalMappingFrom2DImage mrcImageHelicalMasking mrcImageHelicalMaskingBy2DImage mrcImageHelicalProjection mrcImageHighPassFilter mrcImageHighlighting mrcImageInfo mrcImageInverseRadonTransform mrcImageLabeling mrcImageLowPassFilter mrcImageMagnificationChange mrcImageMake2DArrayImage mrcImageMakeCylinder mrcImageMakeDump mrcImageMakeFromTextFile mrcImageMakeSphere mrcImageMappingtoPdb mrcImageMasking mrcImageMaskingByImage mrcImageMergebyside mrcImageMirroring mrcImageModeChange mrcImageModelCreate mrcImageModelSubfilamentsCreate mrcImageMontageCreate mrcImageMove mrcImageMultiCTFCompensation mrcImageMultiCTFDetermination mrcImageMultiplying mrcImageMultiplyingbyFile mrcImageNLMeansFilter mrcImageNeuralNetParticleExtraction mrcImageNeuralNetParticleLearning mrcImageNfoldAxisSearch mrcImageNoiseAdd mrcImageNoiseCreate mrcImageNoiseReductionByRelaxation mrcImageNormalDistributionTest mrcImageNormalizedSubtraction mrcImageNormalizing mrcImageNullImageCreate mrcImageOddBoxel mrcImageOneLineSimilarityCalc mrcImageOrientationSearch mrcImageOrientationSearchByHigherSelection mrcImageOrientationSearchByHybridization mrcImageOrientationSearchBySimultaneousMinimization mrcImagePCA mrcImagePad mrcImageParticleCandidateExtract mrcImagePeakSearch mrcImagePhaseCTFCompensationFromCTFINFO mrcImagePixelDataGet mrcImagePolyROI mrcImagePosterization mrcImagePrint mrcImagePrint3D mrcImageProjection mrcImagePut3D mrcImageROI mrcImageROI3D mrcImageROIs mrcImageROItoPCAoutputImage mrcImageRadialDistribution mrcImageRadonTransform mrcImageRealValueAdd mrcImageRectangleGet mrcImageRectangleGetByCorrelation mrcImageRefConv2D mrcImageRefCreate mrcImageRefFFTConv2D mrcImageRefScaleChangeWithPad mrcImageResolutionEstimateForFilaments mrcImageReverse mrcImageRotation mrcImageRotation3D mrcImageSN mrcImageSamplingUnitChange mrcImageScalarAdd mrcImageSectionGet mrcImageSetFunction mrcImageShapePCA mrcImageShift mrcImageShiftFollowingGC mrcImageShrink mrcImageSiemensStar mrcImageSimilarImageSearch mrcImageSimilarityEstimate mrcImageSmoothing mrcImageSolventFlattening mrcImageSphere mrcImageSplit mrcImageSquare mrcImageStack mrcImageStandardDeviation mrcImageSubtraction mrcImageSuperResolution mrcImageSymmetryAverage mrcImageSymmetryCentreFind mrcImageSymmetryFind

mrcImageTTest

mrcImageTfunction mrcImageTiltAxisSearch mrcImageTiltAxisSearchHelp mrcImageToNAMDConstantForces mrcImageTrans mrcImageTransformDescartesIntoPolar mrcImageTransformSign mrcImageTranspose mrcImageTwoImageTest mrcImageUnbentROI mrcImageUnexpectedMassFromPDB mrcImageUntwist mrcImageVarianceAnalysis mrcImageVarianceMap mrcImageVolumeCalc mrcImageWindowing mrcImageZPad mrcImagepdbFileReduce mrcImagesSinogramCorrelation mrcImagestoRef mrcInfo mrcInfoSet mrcManipulate_kaya mrcMask mrcMeanYlinePos mrcMirrorImageCreate

mrcFFT（フーリエ空間）を処理するためのコマンド群　


mrcRef関連

mrcRefCorEstimate mrcRefCorModify mrcRefCoreGet mrcRefCorrelation mrcRefCorrelationConv mrcRefEstimate mrcRefFFTConvert mrcRefHeaderCreate mrcRefHighPassFilter mrcRefImageCorrelation mrcRefImageOmegaCorrelation mrcRefImagepwzCorEstimate mrcRefImagepwzCorModify mrcRefImagepwzCorPeakFind mrcRefImagepwzCorSmoothing mrcRefImagepwzCorrelation mrcRefImagepwzCorrelationByFFT mrcRefImagexaFit mrcRefLowPassFilter mrcRefNoiseAdd mrcRefNormalizing mrcRefPhaseImageCreate mrcRefSmoothing mrcRefz1ImageCorrelation

　ラドン空間（シノグラム）を用いた解析

特徴量を用いたシノグラム解析

特徴量を用いた３次元再構成


PDB関係のコマンド群　

pdb2SketchMacro pdb2bender pdb2mrc pdb2mrc2d pdb2mrc2dWithCTF pdb2ucd pdbAtomSection pdbCAOnly pdbChargeFit pdbCoordAdd pdbCrystalCreate pdbDisplay pdbFileMerge pdbHelix pdbHomologySearch pdbInfo pdbListRMSDCalc pdbMatrixCreate pdbMolecularInterfaceFind pdbMove pdbNAMDRestraintCreate pdbNearAtomListShow pdbOneProteinGet pdbPCA pdbProteinIDSet pdbRhoFit pdbRhoFitCoiledCoil pdbRhoFitTm pdbRotation pdbSecondaryStructurePrint pdbShapeFit pdbSurface pdbTempFactorSet pdbTrans pdbTwoProteinFit pdbView pdbWaterAdd

pgFormat方のファイルに対するプログラム

pgDataBaseSelectServer pgJournalSelect pgJournalSelectCORBAClient pgJournalSelectCORBAServer pgMemoSelectCORBAServer pgSelect


pointAffineTransform

ポストスクリプトファイルの取り扱いに関するプログラム

psFileMerge psFilePageMerge


rasmonyo


tiltInfoDetermine vectorImageNearestNeighborMethod

クラスター解析に関するツール

mrcImageClusterAnalysis clusterLog2ToLog clusterLogASCII2Binary clusterShow


　画像フォーマット等のフィルター

tgaInfo tiff2mrc vector2pdb dos2unix imodst2mrc ip2mrc emData2mrc moi2mrc array2mrc bin2mrc mrc2dsn6 mrc2fld mrc2gif mrc2hdf mrc2lattice mrc2map mrc2pov mrc2tiff mrc2viff

その他

分子の取り扱い

molecularEnvelopeResampling molecularWeightCalc

matrix3Dの取り扱い（3次元空間変換用4x4行列)

matrix3DEulerAngleTransform matrix3DFromEulerAngle matrix3DInverse matrix3DToEulerAngle

乱数の発生

電子顕微鏡制御

テストのためのプラグラム

その他　


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