Differences

This shows you the differences between two versions of the page.

@@ Line 1: / Line 1: @@
+====== Function Reference ======
+===== How to get help about function options =====
+Functions implemented in LFMPro are designed to accept their required and optional arguments in the following style: functionname('requiredvalue1', 'requiredvalue2',..., 'option1','value1', 'option2','value2',...);
+If you pass 'help' as one of the options, you will be given the list of available options for that function, and also a synopsis, if one is available. For example, here are the available options and their default values for draw_backbone function:
+<code>
+>> draw_backbone('1irda','help')
+default options are:
+simple: 1
+LineWidth: 1
+useSphere: 0
+sphereRadius: 0.4000
+sphereDetails: 6
+cylinderDetail: 8
+color: 0.2000    0.2000    0.2000
+withLabels: 0
+labelShift: 0.3000
+R:
+T:
+</code>
+LFMPro uses a caching mechanism to avoid recalculation of some of the steps. Among the common options to functions is ''recache'' parameter which when set to 1, triggers recalculation of the function value.
+===== src/* Matlab scripts =====
+==== Protein Classification ====
+[ cs,feated ] = classify_proteins ( ptns, feats,scores,borderDs, feats_,scores_,borderDs_, prior,varargin )
+   binary-classify proteins using representative feature sets of families
+==== Data handling functions ====
+[ pdbs,families,cacheOpts ] = data_astral_family ( varargin )
+   get the list of pdbs in a given SCOP family, using a representative
+   ASTRAL file.
+[ pdbs,families,cacheOpts ] = data_culled_family ( varargin )
+   get the list of pdbs in a given SCOP family, selected from similarity-
+   reduced culled-pdb set.
+[ pdbs ] = data_culled_parse ( varargin )
+   reads in list of pdb/chain identifiers from a culledPDB list.
+[ pdbs ] = data_pdbs_cleanup ( varargin )
+   filters pdbs using desired criteria. filtering based on length of chain,
+   or whether broken-backbones exist are possible.
+data_prepare_batch ( varargin )
+   automates preprocessing of a list of pdbs. Resume/Continue using an
+   external file is possible.
+[ ptns,families ] = data_prepare_experiment ( varargin )
+   prepare an experiment dataset. reads in an external file of family pdbs
+   and loads families and proteins.
+[ s ] = data_rand_family ( varargin )
+   prints a random permutation of family members, which can be pasted to
+   families.txt file for use in experiments.
+[ pdbs,families,cacheOpts ] = data_scop_family ( varargin )
+   get the list of pdbs in a given SCOP family
+[ families ] = data_scop_findFamily ( pdb )
+   finds the scop family of a given pdb.
+==== 3D display functions ====
+signatures_show ( p,feats,scores,varargin )
+   show the mapping of features onto a protein
+draw_backbone ( coords, varargin )
+   draws the protein backbone in 3D
+   coords can be pdb file name, a protein struct, or a list of coords.
+[ handles ] = draw_centers ( centers,varargin )
+   draws critical points. use this together with draw_backbone.
+[ X, Y, Z ] = draw_cylinder ( R, N,r1,r2 )
+   draw a N-sided cylinder based on the generator curve in the vector R.
+==== Experimentation batch scripts ====
+[ stats ] = experiment_G ( ptns, family_inds, varargin )
+   run experiments for varying family/background size.
+[ thestats ] = experiment_Gs ( ptns, families, fams, nonfams, varargin )
+   run experiments for varying family/background size
+[ feateds ] = experiment_classification ( ptns, family_inds, varargin )
+   run experiments for classification, and collect results.
+==== Family-specific functions ====
+[ triads ] = family_triad_find ( p,varargin )
+   find the location of catalytic triad (approximate)
+[ minmax ] = features_getMinMax ( ptns, varargin )
+   finds min,max of features, which can later be used for normalization.
+==== Environment setup ====
+globals_aksu (  )
+   setup the global paths and variables.
+globals_garip (  )
+   setup the global paths and variables.
+globals_set (  )
+   setup the global paths and variables. determines which machine we are on,
+   and calls the appropriate globals_* configuration file.
+==== Geometric utility functions ====
+[ bins,binSize ] = lib_3D_hashing ( coords, varargin )
+   uniform hashing of the coordinates. which can be used to speed-up the
+   nearest neighbor or range calculations.
+[ ret ] = lib_points_within_spheres ( centers, atomCoords, varargin )
+   finds points within the centers.
+[ center, r ] = lib_tetra_center ( tetra )
+   finds the center of the sphere that passes through a tetrahedra
+[ r,rind,nextind,firstDist ] = matches_rank_triad ( feats,p,varargin )
+   find the rank of the triad among the features.
+[ sum_writhe ] = writhe_edges ( edgeList, coor, exact )
+   calculate writhe of the given list of edges.
+    synopsis:
+    moleculeCoor=load('../data/1aus.mol')
+    writhe=sum_writhe_volume([1:438;2:439]',moleculeCoor(:,2:4))
+   exact=[1|0] [exact|volume]
+==== Mining for significant sites ====
+[ feats,scores,border_ds,varargout ] = mine_Sites ( ptns, family_inds, varargin )
+   mines representative feature set, ordered by discriminative scores.
+==== pdb reading and features processing ====
+[ PDB_struct ] = my_pdbread ( pdbfile )
+   read in a pdb file.
+[ obje ] = pdbname_parse ( pdb )
+   parse a pdb name into pdb,chain,range parts.
+[ pdb ] = pdbname_unparse ( obje )
+   combine pdb,chain,range parts into a pdb name.
+[ ptn,gotwhat ] = ptn_get ( ptn,varargin )
+   an interface to read/extract/calculate various properties (e.g., atoms,
+    CA-atoms) of a protein. keeps track of caching, so properties are not
+    calculated each time.
+[ centerOfMass ] = ptn_get_atomCenterOfMass ( atoms,atomsWithinSpheres,atomCount,centers,varargin )
+   subfunction of ptn_get. not intended for direct call.
+    calculates individual centerofmasses within the spheres, for each atom-type.
+    note on code-synchronization: this function is similar to
+    ptn_get_atomCount
+[ atomCounts ] = ptn_get_atomCount ( atomsWithinSpheres,atoms,varargin )
+   subfunction of ptn_get. not intended for direct call.
+    calculates individual atom-atomCounts within the spheres, for each atom-type.
+    note on code-synchronization: this function is similar to
+    ptn_get_atom_centerOfMass
+[ cps ] = ptn_get_criticalPoints ( ptn,varargin )
+   subfunction of ptn_get. not intended for direct call.
+    wrapper for criticalPoint executable
+    finds the critical points in pairs.
+[ f ] = ptn_get_features ( p,type )
+   subfunction of ptn_get. not intended for direct call.
+    combines various features into a vector..
+[ features ] = ptn_get_features_normalized ( features,which )
+   subfunction of ptn_get. not intended for direct call.
+    normalizes features between [0-1]
+[ numPieces ] = ptn_get_numPieces ( cas )
+   subfunction of ptn_get. not intended for direct call.
+    calculates the number of backbone pieces that make up the center..
+[ ptn ] = ptn_get_protein ( ptn,varargin )
+   subfunction of ptn_get. not intended for direct call.
+    reads a protein from pdb, takes care of chain-selection
+    and examines broken-chains (missing residues)
+[ ptn ] = ptn_get_tetra ( ptn,varargin )
+   subfunction of ptn_get. not intended for direct call.
+    wrapper for AD-tetrahedra executable.
+    finds the AD-tetrahedra for a given set of points and thresholds.
+[ writhe ] = ptn_get_writhe ( cas, caCoords )
+   subfunction of ptn_get. not intended for direct call.
+    calculates writhing number for centers..
+[ ret ] = ptn_get_x ( ptn,which )
+   helper function to unify accessing a protein's property.
+==== Weight setup and optimization ====
+[ bestWeights,bestWeightsHistory ] = weights_optimize ( ptns,families,family_inds,varargin )
+   optimize the weights of the Euclidean using a simulated annealing approach
+[ weights,varargout ] = weights_get ( varargin )
+   get the weights to be used in Euclidean distance
+[ W ] = weights_set ( o_weights,FEAT_SIZE )
+   set the weights used in Euclidean
+[ feats ] = weights_use ( W, feats )
+   multiply feats with weights to use in distance function
+==== Utility functions ====
+[ varargout ] = myFuncs ( func, varargin )
+   provides a place to store various temporary functions.
+    these are small scripts that don't quite make it into
+    their own function file.
+===== myLibrary/* Matlab scripts =====
+==== Caching mechanism ====
+[ opts ] = myCache_getOptions ( varargin )
+   not intended for direct use. iscalled from myCache_load/save
+[ recache, cachevar, varargout ] = myCache_load ( varargin )
+   synopsis: myCache_load('identifier', struct('extension','branch'))
+myCache_save ( variable, varargin )
+[ ret ] = myCache_test ( varargin )
+==== Optimized geometric operations ====
+[ ret ] = myEuclidean ( X, Y )
+[ mins, inds ] = myEuclidean_closest ( X, Y )
+[ hist ] = myHistogram ( V,varargin )
+==== Setting up Function arguments and options ====
+[ varargin ] = myFix_varargin ( varargin )
+   varargin passed down to function calls gets encapsulated
+    with another layer of {} cell'ation with each call.
+    this function fixes the problem by extracting the innermost
+    cell content.
+[ defaults ] = myOptions_set ( defaults, varargin )
+   synopsis:
+   opts = myOptions_set(struct('name','ahmet', 'surname','sacan'),varargin);
+   vargin=overrides
+myOptions_test ( varargin )
+==== Other utility functions ====
+[ fid ] = myFile_open ( filename,mode )
+[ s ] = myImplode ( d, a )
+[ str ] = myTime_pretty ( secs )