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:
>> 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:
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.
[ cs,feated ] = classify_proteins ( ptns, feats,scores,borderDs, feats_,scores_,borderDs_, prior,varargin )
binary-classify proteins using representative feature sets of families
[ 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.
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.
[ 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.
[ 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.
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.
[ 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]
[ feats,scores,border_ds,varargout ] = mine_Sites ( ptns, family_inds, varargin )
mines representative feature set, ordered by discriminative scores.
[ 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.
[ 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
[ 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.
[ 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 )
[ ret ] = myEuclidean ( X, Y )
[ mins, inds ] = myEuclidean_closest ( X, Y )
[ hist ] = myHistogram ( V,varargin )
[ 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 )
[ fid ] = myFile_open ( filename,mode )
[ s ] = myImplode ( d, a )
[ str ] = myTime_pretty ( secs )