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%
% CS321 Project1: Main program
%
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% Add relevant directories to Matlab PATH
addpath align
addpath clusters


% The proteins used in the project, and other definitions
proteins = {'1MBC','1DO1','1A6G','1VXH','1BZ6','1MBO','1BZR', ...
	    '1YMB','1YOI','4MBN','1LH1'};
numprot  = length(proteins);

pdbdir = 'proteins/';                   % Directory where pdb files are stored
alignfile = 'align/alignments.txt';     % File containing sequence alignments


% Read the CA coordinates of each protein
allcrd = cell(1, numprot);
for i=1:numprot
   pdbfile = strcat(pdbdir, proteins{i}, '.pdb');
   allcrd{i} = pickAtom(pdbfile, 'CA');
end

% Extract sequence alignments
M = loadAlignments(alignfile);

% Compute pairwise distances
dist = zeros(numprot, numprot);
for i=1:numprot
   for j=i+1:numprot
      [Si, Sj] = getAlignment(M, i, j); 
      [crdi, crdj] = alignCoords(allcrd{i}, Si, allcrd{j}, Sj);
      dist(i, j) = getDistance(crdi, crdj);
      dist(j, i) = dist(i, j);
   end
end

% Display the distance matrix 
disp(dist);

% Perform clustering, and draw the output
drawCluster(clusterProteins(dist));