機能別コマンド一覧
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。
目次
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
CTF関係のコマンド群
CTF決定のためのプログラム群
- ctfDisplay: CTFの決定のためのプログラム(GUI)
- ctfDeterminationFromMultiImage
- ctfDeterminationFromPhaseComparison
- ctfDeterminationFromThonRing
- ctfDetermine
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
- ctfInfoSet
- ctfMultiFunction
- ctfWeightMapCreation
- mrcImageCTFCompensation
- mrcImageCTFCompensationForTiltImage
- mrcImageCTFDetermination
- mrcImageCTFObservation
- mrcImageCTFSN
3次元再構成
汎用3次元再構成
ラドン空間(シノグラム)を用いた解析
ラドン空間の変換
コモンラインの探索
- mrcImageSinogramCorrelation
- commonLinesSearchByVoting
- WeightCalculationOfCommonLineSearch
- WeightCalculationOfCommonLineSearchByAllSinogram
- WeigthCaluculationOfCommonLineCalculation
- CommonLineCalculation
- CommonLineRankCalc_k
特徴量を用いたシノグラム解析
- mrcSinogramFET
- mrcSinogramFETcalcSDforNormalize
- mrcSinogramFETcalcWeight
- mrcSinogramFETcorrelationMap
- mrcSinogramFETnormalizedMap
- mrcSinogramFETreferredCorrelation
- mrcSinogramFETsmoothParameterMatching
特徴量を用いた3次元再構成
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: G(R, THETA, Z)空間の表示
- llDataRescaling
- llDataResolutionCheck
- llDataRotation
- llDataSelectionEstimation
- llDataSeparate
- llDataWeightSet
- llDatarMaxLimit
g(r, theta, Z) の取り扱い
mrcImageフォーマットに対するコマンド群
- mrc3DExtractZ
- 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
- 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
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
defocusDeterminationFromThonRing
electronWaveLength energyTransferModelCheck energyTransferModelResultCheck fft2d gmolvie homology2PG hostCondition imageView imagesClustering imagesView
khorosFilterGenerate
largeIPInfo
mrcFFT(フーリエ空間)を処理するためのコマンド群
- mrcFTMeridianEquatorRedece
- mrcFFTBandPassFilter
- mrcFFTCTFCompensation
- mrcFFTDigitize
- mrcFFTExpression
- mrcFFTFibreDiagram
- mrcFFTFiltering
- mrcFFTIQEstimation
- mrcFFTInfo
- mrcFFTLayerLineCheck
- mrcFFTMedianFilter
- mrcFFTProjection
- mrcFFTResampling
- mrcFFTShellInfo
- mrcFFTSizeChange
- mrcFFTSpectrum
- mrcFFTXFiltering
- mrcFFTplainreduce
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
クラスター解析に関するツール
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
tiltInfoDetermine vectorImageNearestNeighborMethod
画像フォーマット等のフィルター
他のファイルフォーマットからMRC形式へ変換
MRC形式から他のフォーマットへの変換
pgFormat方のファイルに対するプログラム
- pgDataBaseSelectServer
- pgJournalSelect
- pgJournalSelectCORBAClient
- pgJournalSelectCORBAServer
- pgMemoSelectCORBAServer
- pgSelect
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
DCDフォーマットのファイルに関する取り扱い
- dcdAtomChangeDistanceFromAtom
- dcdAtomDistanceDistribution
- dcdCompareCA
- dcdDistanceAtomBetweenAtom
- dcdFilePrint
- dcdInfo
- dcdSelectAtoms
- dcdSerectAtom
- dcdTest
- dcdTimeSeriesBehavior
その他
コマンドリスト
CheckCommonLineData CheckOfOrientation CheckOrientationByDegree
EvaluateCorrelationMapwithCommonLine
FETOrientationSearchByAnnealing FETOrientationSearchByFeatureAlignment FETmapOrientationSearchBySimultaneousFitting FETsmallMapSetCreate_forSimultaneousMinimization
LCalculationForOrientationSearch
Polar2Descartes ProjectionDirectionMapCreate
TestForLcalculationOfOrientationSearchBySimultaneousMinimization
angleMatchTest_k
anglediffcalc
anglediffchk
その他
分子の取り扱い
matrix3Dの取り扱い(3次元空間変換用4x4行列)
乱数の発生
- randomUniformGet:一様乱数
- randomNormalGet:正規分布に従う乱数