visualize_molecule.m
33bba04159d6master

visualize_molecule.m
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			function d = visualize_molecule(coord,thr,figure_num,molecule_name)
			%VISUALIZE_MOLECULE generates a 3D representation of a system of points.
			%
			%Invoked as d=visualize_molecule(coord,thr,molecule_name), coord is the
			%matrix of atomic coordinates, thr is the largest atomic distance to draw a
			%bond and molecule_name is a string containing the title of the plot.
			%
			%Coord has to be a Nx3 matrix with the x,y,z coordinates of each point
			%stored as rows. The function generates a figure, save it as an eps file and gives
			%the distance map of the points d

			%Search for connectivities
			n=size(coord,1);

			d=zeros(n,n);

			nconn=0;

			for i1=1:n
			for i2=i1+1:n
			d(i1,i2)=sum((coord(i1,:)-coord(i2,:)).^2)^(0.5);

			if d(i1,i2) < thr
			nconn=nconn+1;
			conn(nconn,1)=i1; conn(nconn,2)=i2;
			end
			end
			end

			d=d+d';

			figure(figure_num);

			hold on;

			for i1=1:n
			plot3(coord(i1,1),coord(i1,2),coord(i1,3),'-r.','MarkerSize',30);
			end

			for i1=1:nconn
			line([coord(conn(i1,1),1) coord(conn(i1,2),1)],[coord(conn(i1,1),2) coord(conn(i1,2),2)],[coord(conn(i1,1),3) coord(conn(i1,2),3)],'LineWidth',2);
			end

			axis equal;
			grid on;

			xlim([min(coord(:,1))-1 max(coord(:,1))+1]);
			ylim([min(coord(:,2))-1 max(coord(:,2))+1]);
			zlim([min(coord(:,3))-1 max(coord(:,3))+1]);

			xlabel('X (sigma)');
			ylabel('Y (sigma)');
			zlabel('Z (sigma)');

			title(molecule_name);

			view([-60 26]);

			filename=strcat(molecule_name,'.eps');
			print(gcf,'-depsc',filename)


			end