====== 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 )