Sample code for outputting basepair, basestacking, basephosphate, and baseribose annotations found by FR3D in a PDB file. Get FR3D here: https://github.com/BGSU-RNA/FR3D

annotate_pdb.m

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% Sample code for outputting basepair, basestacking, basephosphate, and
% baseribose annotations found by FR3D in a PDB file.

% Input parameters:
% <pdb_id>          - four-character PDB identifier.
% <output_filename> - optional name of the output file. If not provided, the
%                     output is printed to the screen

% Sample output:
% "1_A_1001_A","cWW","1_A_1040_U"
% "1_A_1002_G","s55","1_A_1040_U"
% "1_A_1039_C","s35","1_A_1040_U"

% FR3D looks in the /PDBFiles folder for <pdb_id>.pdb, if it's not there,
% then it attempts to download the structure from PDB.

% FR3D stores internal representation of the 3D structure in the
% /PrecomputedData folder for faster performance.

% Make sure that /PDBFiles and /PrecomputedData folders are writeable.

% Examples:
% from Matlab or octave command line:
% annotate_pdb('1S72')
% annotate_pdb('1S72', 'output.csv')

% from Unix system command line:
% path/to/matlab -nodisplay -r "setup_path; annotate_pdb('1S72'), quit"
% path/to/matlab -nodisplay -r "setup_path; annotate_pdb('1S72', 'output.csv'), quit"
% path/to/octave --eval "setup_path; annotate_pdb('1S72')"
% path/to/octave --eval "setup_path; annotate_pdb('1S72', 'output.csv')"

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function annotate_pdb(pdb_id, output_filename)

    if nargin == 2
        writeToFile = 1;
        fid = fopen(output_filename, 'w');
    else
        writeToFile = 0;
        fid = -1;
    end

    % create internal FR3D representation of the input file
    File = zAddNTData(pdb_id);

    % first parameter  - function handle for data exporting
    % second parameter - matrix with the interaction data
    outputInteractions(@zEdgeText, File, 'Edge', writeToFile, fid);

    outputInteractions(@zBasePhosphateText, File, 'BasePhosphate', writeToFile, fid);

    outputInteractions(@zBaseRiboseText, File, 'BaseRibose', writeToFile, fid);

    if writeToFile, fclose(fid); end

end


function outputInteractions(functionHandle, File, field_name, writeToFile, fid)

    interaction_matrix = getfield(File, field_name);
    interactions = find(interaction_matrix);
    dimensions = size(interaction_matrix);
    N = length(interactions);

    for i = 1:N
        [nt1, nt2] = ind2sub(dimensions, interactions(i));

        % convert internal interaction label to its text representation
        annotation = strtrim(functionHandle(interaction_matrix(nt1, nt2)));

        if strcmp(annotation, '----'), continue; end

        % edit this line to change the output format
        output = sprintf('"%i_%s_%s_%s","%s","%i_%s_%s_%s"\n',      ...
                                             File.NT(nt1).ModelNum, ...
                                             File.NT(nt1).Chain,    ...
                                             File.NT(nt1).Number,   ...
                                             File.NT(nt1).Base,     ...
                                             annotation,            ...
                                             File.NT(nt1).ModelNum, ...
                                             File.NT(nt2).Chain,    ...
                                             File.NT(nt2).Number,   ...
                                             File.NT(nt2).Base);
        if writeToFile
            fprintf(fid, output);
        else
            fprintf(output);
        end
    end

end

Tested with Matlab R2007b and octave 3.2.3

Tested with Matlab R2007b and octave 3.6.3

Tested with Matlab R2007b and octave 3.8.0

Tested with the following Docker image: https://hub.docker.com/r/schickling/octave/