In what direction should we move in the implementation of this program?

Question

Counts

the following task
is given a file, for example h2s molecules:
input.txt
3
S1 0.000000 0.000000 0.000000
H2 1 1.290404 0.000000 0.000000
H3 1 1.290393 2 93.512189 0.000000
Where 1 line is the number of atoms n. Then n lines, each containing the following entry:
substance_number(0-n), then the number of the element with which it is associated, the distance from this element, then the number of element1, the angle from this element1, the number of element2, the angle from this element2.
In this example, the molecule is built from sulfur.
The user chooses where to start building the substance and the program rebuilds the table, putting the new substance in the first place, restoring all connections.
For example, the user enters
H.output.txt
3
H1 0.000000 0.000000 0.000000
S2 1 1.290404 0.000000 0.000000 H3
2 1.290393 1
93.512189 0.000000

Answer 1

There are 2 main ways to represent a graph:
1) adjacency matrix
Normal NxN matrix, where 0 are unconnected vertices, 1 are connected
2) connectivity table
Hashtable, where array[i] is a vertex and array[i]->obj->obj these are the vertices with which they are connected.
I think adjacency matrix is ​​better.
---s1 h2 h3
s1 - 1 1
h2 1 - 0
h3 1 0 -