I want to plot a xyz graph and also get clusters from the array of my data; can someone help please. Atoms are linked by indices. (attaching the sheet for reference)

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ANINDYA GANGULY
ANINDYA GANGULY 2021-9-11
回答： Chetan 2024-5-2
I have combined the information from the bonds file and xyz file and want to plot a graph with various clusters (based on how the indices are connected). Is there a code to get this done with?
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ANINDYA GANGULY
ANINDYA GANGULY 2021-9-11
4000 rows are the 4000 atoms (2000 C and 2000 H) and the 23 columns have the position of the atoms along the x, y and z coordinates, then the heading of the 4000 atoms listed; how the indices are connected to each other (defining clusters); bond order (bo) values, bond order of the indexed atom; charge of the atom; lone pair of the atom.
If you open the .xlsx file; all the informatiom is provided in the topmost row.
Regards
J
ANINDYA GANGULY
ANINDYA GANGULY 2021-9-11
And id refers to the indices of the atoms. Some indices (C) are connected 1, some with 2, some with 3 atoms (can be H/C) and so on.
Regards
J

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Chetan
Chetan 2024-5-2
Hi @ANINDYA GANGULY
I understand you wish to plot a 3D graph for clusters from an array of data. To visualize a 3D graph of atoms and identify clusters based on the connectivity defined by indices, MATLAB's graph and clustering functions can be utilized.
Step 1: Import Data
filename = 'Testfile3.xlsx'; % Update this with the actual file name
data = readtable(filename);
Step 2: Create Graph
Assuming the `id` columns represent the atom indices and `id_1` to `id_5` signify connections (with zeros indicating no connections), you can construct an edge list and create a graph.
% Initialize an empty array for edges
edges = [];
% Assuming 'id_of_atom' is the unique identifier for atoms
% and connections are in 'id_1' to 'id_5' columns
for i = 1:30
atomId = data.idOfAtom(i);
for j = 11:15 % Assuming id_1 to id_5 are in columns 11 to 15
connectedAtomId = data{i,j};
if ~isnan(connectedAtomId) % Check if there is a connection
edges = [edges; atomId, connectedAtomId];
end
end
end
% Create the graph
G = graph(edges(:,1),edges(:,2));
Step 3: Plotting
To plot the graph in 3D, the x, y, and z coordinates of each atom are required.
figure;
hold on;
% Plot edges
for i = 1:size(edges,1)
atomIndex1 = find(data.idOfAtom == edges(i,1));
atomIndex2 = find(data.idOfAtom == edges(i,2));
x = [data.x_axis(atomIndex1); data.x_axis(atomIndex2)];
y = [data.y_axis(atomIndex1); data.y_axis(atomIndex2)];
z = [data.z_axis(atomIndex1); data.z_axis(atomIndex2)];
plot3(x, y, z, 'k-'); % 'k-' for black lines
end
% Plot atoms on top of the edges
scatter3(data.x_axis, data.y_axis, data.z_axis, 36, 'filled');
xlabel('X-axis');
ylabel('Y-axis');
zlabel('Z-axis');
title('3D Graph of Atoms and Bonds');
hold off;
Step 4: Clustering
To identify clusters based on connectivity:
% Find connected components (clusters)
clusters = conncomp(G);
% Number of clusters
numClusters = max(clusters);
% Display number of clusters
disp(['Number of clusters: ', num2str(numClusters)]);
For further information, refer to the following documentation:
Thanks
Chetan

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