 FR3D | FR3D is the graphical user interaface to Find RNA 3D |
| FR3D_DisplayExemplars | zDisplayExamplars(Paircode,Cateogry) displays the best known |
| FR3D_InteractionMap | FR3D_InteractionMap(File) puts a dot at the center of each nucleotide |
| mCreateMatrix | mCreateMatrix is a script that sets up the interaction matrix for FR3D_GUI |
| mCreateMatrix_Loaded | mCreateMatrix_Loaded |
| mEditBoxWrap | mEditbox(text,title,button) creates a text window |
| mEditbox | mEditbox(text,title,button) creates a text window |
| mGetPDBFilenames | mGetPDBfilenames %By Ali Mokdad - April 14 2006 |
| mSetLoadedParameters | mSetLoadedParameters.m fills in entries in the GUI from a saved search file |
| mSpecifyQueryforGUI | mSpecifyQueryforGUI reads the entries in the GUI to set query constraints |
| mSynList | mSynList.m %By Ali Mokdad %April 21, 2006 |
| sFindPermutation | xFindPermutation(b); |
| xAddFiletoSearch | xAddFiletoSearch(File,Search) adds data on nucleotides found in Search. It assumes that File is in the proper order for the index in Candidates |
| xAddNucleotide | xAddNucleotide adds a nucleotide according to the screen matrices S |
| xAlignCandidates | xAlignCandidates(File,Search,Direction) shows a multiple sequence |
| xConstructQuery | xConstructQuery(Query,File) fills in details of Query from File |
| xDescribeDistance | |
| xDescribeInteraction | |
| xDescribeMask | |
| xDiscrepancyFast | xDiscrepancy(Model,Cand) calculates the discrepancy between Model and |
| xDisplayCandidates | xDisplayCandidates(File,Search,Level) displays candidates |
| xExcludeOverlap | xExcludeOverlap(Candidates) removes candidates which overlap with one |
| xExcludeOverlap2 | xExcludeOverlap(Candidates) removes candidates which overlap with one |
| xFR3DSearch | xFR3DSearch conducts the search given in xSpecifyQuery in the PDB files |
| xFindCandidates | xFindCandidates finds and ranks candidate fits to Model |
| xFindPolyhedra | xFindHexahedra.m returns a list of indices (i,j,k,m) for which |
| xFlankingPairs | xFlankingPairs identifies nucleotides on the same strand which make |
| xGetDiffSpec | xGetDiffSpec parses the text for nucleotide differences |
| xGetEdgeNums | xGetEdgeNums parses the entries in the GUI concerning base-base interactions |
| xGetNuclSpec | xGetNuclSpec parses the text for nucleotide mask, angle weight, location weight |
| xListCandidates | xListCandidates(Search) prints a candidate list to the screen |
| xListPairs | zListPairs lists pair data in columns |
| xMutualDiscrepancy | xMutualDiscrepancy computes the mutual distances between candidates |
| xNeighborhood | xNeighborhood(File,Indices,v,MaxDiff,MaxInsert) returns indices "near" |
| xPairwiseScreen | xPairwiseScreen returns a sparse matrix with non-zero entries corresponding to pairs of bases which satisfy all given constraints |
| xPrecomputeForDiscrepancy | xPrecomputeForDiscrepancy(c) computes a few things that are needed for |
| xRankCandidates | xRankCandidates(File,Model,Candidates) calculates the discrepancy for |
| xReduceOverlap | |
| xScatterPairs | xScatterPairs 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 |
| xSpecifyQuery | xSpecifyQuery returns the description of a model motif |
| xSuperimposeCandidates | xSuperimposeCandidates(Model,Cand) returns the rotation matrix R and |
| xWriteCandidatePDB | xWriteCandidatePDB(File,Search) writes a single PDB file, named after |
| zAddNTData | zAddNTData(Filenames,ReadCode,File,Verbose,PDBStart) reads RNA structure |
| zAnalyzePair | zAnalyzePair(N1,N2,CL) computes distances, angles, and classification |
| zAngle | zAngle(A,B,C) computes the angle at B made by vectors BA and BC |
| zAngleOfRotation | zAngleOfRotation calculates the angle of rotation from a rotation matrix R |
| zAxisAngle | zAxisAngle(R) computes the axis and angle of rotation in an orthogonal |
| zAxisAngleRadians | zAxisAngleRadians computes the axis and angle of rotation in an |
| zBackboneCodes | zBackboneCodes defines a list of backbone conformation codes from Richardson et al |
| zBackboneConformation | |
| zBackboneContinuity | |
| zBackboneText | |
| zBasePhosphateTable | zBasePhosphateTable(File,NTList) displays a table of interactions |
| zBasePhosphateText | zBasePhosphateText(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 |
| zBestRotation | zBestRotation(X,Y) finds the least squares rotation |
| zBestTransformation | zBestTransformation(X,Y) finds the least squares translation and rotation |
| zCheckCutoffs | zCheckCutoffs(D,Normal,Ang,Gap,B) finds the categories whose cutoffs |
| zCheckHydrogen | This program is generated by zGenerateCheckHydrogen.m |
| zClassLimits | zClassLimits stores the cutoffs for the computer classification of pairs |
| zClassifyPair | zClassifyPair(N1,N2) calculates the rotation matrix, axis, angle, and shift |
| zClassifyPairs | zClassifyPairs(File) calculates the rotation matrix, axis, angle, and shift |
| zDisplayNT | zDisplayNT(File,NTList,ViewParam) is a general-purpose nucleotide plotting program. It can be called in several ways, for example, |
| zDistance | zDistance(A,B) finds the Euclidean distances between the rows of A and of B |
| zDistanceToExemplars | zDistanceToExemplars(Exemplar,Pair) computes the distance to each |
| zEdgeText | zEdgeText converts internal codes for pair interactions into text |
| zExtractAtomsPDB | zExtractAtomsPDB(Filename) reads Filename and writes out lines |
| zGetNTData | zGetNTData(Filenames,ReadCode,Verbose) reads data files, depending on ReadCode |
| zGetPDBInfo | zGetPDBInfo(File) reads a data file about PDB files and extracts |
| zGraphDistanceMatrix | zClusterGraph(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. |
| zIndexLookup | zIndexLookup(File,Num,Chain) finds the base index for base having nucleotide |
| zInteractionRange | zInteractionRange(File) returns a sparse matrix S which indicates |
| zMutualDistance | zMutalDistance(A,L) finds the mutual distances between the rows of A and |
| zOrderbySimilarity | zOrderbySimilarity uses the result of a cluster analysis and puts the |
| zPhosphateInteractions | zPhosphateInteractions checks all nearby pairs of bases for base-phosphate |
| zPlotOneNT | |
| zPlotOneNTRotated | zPlotOneNTRotated(NT,ViewParam,R,S) rotates NT and displays with ViewParam |
| zPlotStandardBase | zPlotStandardBase(code,textoption) plots base with code, |
| zReadPDBList | zReadPDBList(Filename) reads Filename.pdb for a list of PDB file names |
| zReadPDBTextRead | |
| zReadandAnalyze | zReadandAnalyze.m read a _mod.pdb file, then |
| zSaveNTData | zSaveNTData saves File in File.Filename.analyzed |
| zShowInteractionTable | zShowInteractionTable(File,NTList) displays a table of interactions |
| zSquare | zBox(X,Y,color) plots a rectangular box with lower left corner X and |
| zStackingOverlap | zStackingOverlap(N1,N2) computes a measure of overlap between nucleotides |
| zStandardBase | zStandardBase returns QM optimized base geometries |
| zStandardBases | zStandardBases reads optimized bases, then centers and rotates them |
| zStoreO3 | |
| zWriteNucleotidePDB | zWriteNucleotidePDB(fid,NT,a,c,R,Sh) writes the atoms of nucleotide NT, with |
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