< Master index Index for FR3DSource >

Index for FR3DSource

Matlab files in this directory:

 FR3DFR3D is the graphical user interaface to Find RNA 3D
 FR3D_DisplayExemplarszDisplayExamplars(Paircode,Cateogry) displays the best known
 FR3D_InteractionMapFR3D_InteractionMap(File) puts a dot at the center of each nucleotide
 mCreateMatrixmCreateMatrix is a script that sets up the interaction matrix for FR3D_GUI
 mCreateMatrix_LoadedmCreateMatrix_Loaded
 mEditBoxWrapmEditbox(text,title,button) creates a text window
 mEditboxmEditbox(text,title,button) creates a text window
 mGetPDBFilenamesmGetPDBfilenames %By Ali Mokdad - April 14 2006
 mSetLoadedParametersmSetLoadedParameters.m fills in entries in the GUI from a saved search file
 mSpecifyQueryforGUImSpecifyQueryforGUI reads the entries in the GUI to set query constraints
 mSynListmSynList.m %By Ali Mokdad %April 21, 2006
 sFindPermutationxFindPermutation(b);
 xAddFiletoSearchxAddFiletoSearch(File,Search) adds data on nucleotides found in Search. It assumes that File is in the proper order for the index in Candidates
 xAddNucleotidexAddNucleotide adds a nucleotide according to the screen matrices S
 xAlignCandidatesxAlignCandidates(File,Search,Direction) shows a multiple sequence
 xConstructQueryxConstructQuery(Query,File) fills in details of Query from File
 xDescribeDistance
 xDescribeInteraction
 xDescribeMask
 xDiscrepancyFastxDiscrepancy(Model,Cand) calculates the discrepancy between Model and
 xDisplayCandidatesxDisplayCandidates(File,Search,Level) displays candidates
 xExcludeOverlapxExcludeOverlap(Candidates) removes candidates which overlap with one
 xExcludeOverlap2xExcludeOverlap(Candidates) removes candidates which overlap with one
 xFR3DSearchxFR3DSearch conducts the search given in xSpecifyQuery in the PDB files
 xFindCandidatesxFindCandidates finds and ranks candidate fits to Model
 xFindPolyhedraxFindHexahedra.m returns a list of indices (i,j,k,m) for which
 xFlankingPairsxFlankingPairs identifies nucleotides on the same strand which make
 xGetDiffSpecxGetDiffSpec parses the text for nucleotide differences
 xGetEdgeNumsxGetEdgeNums parses the entries in the GUI concerning base-base interactions
 xGetNuclSpecxGetNuclSpec parses the text for nucleotide mask, angle weight, location weight
 xListCandidatesxListCandidates(Search) prints a candidate list to the screen
 xListPairszListPairs lists pair data in columns
 xMutualDiscrepancyxMutualDiscrepancy computes the mutual distances between candidates
 xNeighborhoodxNeighborhood(File,Indices,v,MaxDiff,MaxInsert) returns indices "near"
 xPairwiseScreenxPairwiseScreen returns a sparse matrix with non-zero entries corresponding to pairs of bases which satisfy all given constraints
 xPrecomputeForDiscrepancyxPrecomputeForDiscrepancy(c) computes a few things that are needed for
 xRankCandidatesxRankCandidates(File,Model,Candidates) calculates the discrepancy for
 xReduceOverlap
 xScatterPairsxScatterPairs displays multiple 3d scatter plots of pair parameters, with a menu that allows one to color points in different orders, or display different nucleotides from the candidates
 xSpecifyQueryxSpecifyQuery returns the description of a model motif
 xSuperimposeCandidatesxSuperimposeCandidates(Model,Cand) returns the rotation matrix R and
 xWriteCandidatePDBxWriteCandidatePDB(File,Search) writes a single PDB file, named after
 zAddNTDatazAddNTData(Filenames,ReadCode,File,Verbose,PDBStart) reads RNA structure
 zAnalyzePairzAnalyzePair(N1,N2,CL) computes distances, angles, and classification
 zAnglezAngle(A,B,C) computes the angle at B made by vectors BA and BC
 zAngleOfRotationzAngleOfRotation calculates the angle of rotation from a rotation matrix R
 zAxisAnglezAxisAngle(R) computes the axis and angle of rotation in an orthogonal
 zAxisAngleRadianszAxisAngleRadians computes the axis and angle of rotation in an
 zBackboneCodeszBackboneCodes defines a list of backbone conformation codes from Richardson et al
 zBackboneConformation
 zBackboneContinuity
 zBackboneText
 zBasePhosphateTablezBasePhosphateTable(File,NTList) displays a table of interactions
 zBasePhosphateTextzBasePhosphateText(e) converts internal code e for a base-phosphate interaction to text for human use. If edge = 1, it lists the active edge as well
 zBestRotationzBestRotation(X,Y) finds the least squares rotation
 zBestTransformationzBestTransformation(X,Y) finds the least squares translation and rotation
 zCheckCutoffszCheckCutoffs(D,Normal,Ang,Gap,B) finds the categories whose cutoffs
 zCheckHydrogenThis program is generated by zGenerateCheckHydrogen.m
 zClassLimitszClassLimits stores the cutoffs for the computer classification of pairs
 zClassifyPairzClassifyPair(N1,N2) calculates the rotation matrix, axis, angle, and shift
 zClassifyPairszClassifyPairs(File) calculates the rotation matrix, axis, angle, and shift
 zDisplayNTzDisplayNT(File,NTList,ViewParam) is a general-purpose nucleotide plotting program. It can be called in several ways, for example,
 zDistancezDistance(A,B) finds the Euclidean distances between the rows of A and of B
 zDistanceToExemplarszDistanceToExemplars(Exemplar,Pair) computes the distance to each
 zEdgeTextzEdgeText converts internal codes for pair interactions into text
 zExtractAtomsPDBzExtractAtomsPDB(Filename) reads Filename and writes out lines
 zGetNTDatazGetNTData(Filenames,ReadCode,Verbose) reads data files, depending on ReadCode
 zGetPDBInfozGetPDBInfo(File) reads a data file about PDB files and extracts
 zGraphDistanceMatrixzClusterGraph(D,Lab,W) treats D as the distances between instances with labels given by Lab. It displays the distances graphically. W is the number of characters of Lab to use.
 zIndexLookupzIndexLookup(File,Num,Chain) finds the base index for base having nucleotide
 zInteractionRangezInteractionRange(File) returns a sparse matrix S which indicates
 zMutualDistancezMutalDistance(A,L) finds the mutual distances between the rows of A and
 zOrderbySimilarityzOrderbySimilarity uses the result of a cluster analysis and puts the
 zPhosphateInteractionszPhosphateInteractions checks all nearby pairs of bases for base-phosphate
 zPlotOneNT
 zPlotOneNTRotatedzPlotOneNTRotated(NT,ViewParam,R,S) rotates NT and displays with ViewParam
 zPlotStandardBasezPlotStandardBase(code,textoption) plots base with code,
 zReadPDBListzReadPDBList(Filename) reads Filename.pdb for a list of PDB file names
 zReadPDBTextRead
 zReadandAnalyzezReadandAnalyze.m read a _mod.pdb file, then
 zSaveNTDatazSaveNTData saves File in File.Filename.analyzed
 zShowInteractionTablezShowInteractionTable(File,NTList) displays a table of interactions
 zSquarezBox(X,Y,color) plots a rectangular box with lower left corner X and
 zStackingOverlapzStackingOverlap(N1,N2) computes a measure of overlap between nucleotides
 zStandardBasezStandardBase returns QM optimized base geometries
 zStandardBaseszStandardBases reads optimized bases, then centers and rotates them
 zStoreO3
 zWriteNucleotidePDBzWriteNucleotidePDB(fid,NT,a,c,R,Sh) writes the atoms of nucleotide NT, with

Other Matlab-specific files in this directory:

Dependency Graph


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