function [inchi, metList] = sdf2inchi(sdfFileName, options)
% Converts metabolite structures in an SDF to a cell array of InChI
% strings with OpenBabel.
%
% USAGE:
%
%    [inchi, metList] = sdf2inchi(sdfFileName, options)
%
% INPUT:
%    sdfFileName:    Path to SDF file.
%
% OPTIONAL INPUTS:
%    options:        Write options for InChI strings. See InChI documentation
%                    for details. If no options are specified the function will
%                    output standard InChI.
%
% OUTPUTS:
%    inchi:          Cell array of InChI strings for metabolites in the SDF file.
%    metList:        Cell array of metabolite identifiers (first line of each
%                    molfile in SDF). Will be empty unless write option `t` is
%                    used (i.e., options >= '-xt').
%
% .. Author: - Hulda SH, Nov. 2012

if ~strcmp(sdfFileName(end-3:end),'.sdf') % Check inputs
    sdfFileName = [sdfFileName '.sdf'];
end

if ~exist('options','var')
    options = [];
end
if ~isempty(options)
   options = [' ' strtrim(options)];
end

babelcmd = 'babel';

% Convert to InChI with OpenBabel
[success,result] = system([babelcmd ' ' sdfFileName ' -oinchi' options]);

% Parse output from OpenBabel
if success == 0
    result = regexp(result,'InChI=[^\n]*\n','match');
    result = result';
    result = strtrim(result);

    [inchi,metList] = strtok(result);
    inchi = strtrim(inchi);
    metList = strtrim(metList);
else
    [success,result] = system([babelcmd ' ' sdfFileName ' -oinchi' options])
    fprintf('%s\n','If you get a ''not found'' message from the call to Babel, make sure that Matlab''s LD_LIBRARY_PATH is edited to include correct system libraries. See initVonBertylanffy')
    error('Conversion to InChI not successful. Make sure OpenBabel is installed correctly.\n')
end

if size(inchi,2) > size(inchi,1)
    inchi = inchi';
end
if size(metList,2) > size(metList,1)
    metList = metList';
end
