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    <p>EDIT Well, you're leaking memory left and right, but not quite in the way I was thinking. Fixed sequence below:</p> <p>Specifically, when you do:</p> <pre><code>atoms = (struct Atom *) malloc(sizeof(struct Atom) * numAtoms); // 1 atoms = (*amino).atoms; // 2 // ... atoms = (struct Atom *) malloc(sizeof(struct Atom)); // 3 free(atoms); // 4 </code></pre> <p>What is happening is that you are allocating some memory and putting the address in <code>atoms</code> in step(1). Then, you toss away that address and instead point <code>atoms</code> at part of the inside of your <code>amino</code> structure in (2). Then you allocate a <em>second</em> pointer with a single atom. Finally, you call <code>free</code> on that. You treat <code>bonds</code> the same way. You probably mean something like this:</p> <pre><code>atoms = (struct Atom *) malloc(sizeof(struct Atom) * numAtoms); // 1 memcpy(atoms, (*amino).atoms, sizeof(struct Atom) * numAtoms); // 2 // ... // delete 3 free(atoms); // 4 </code></pre> <p>Note that if an Atom has any pointer components you might want to do a <code>for</code> loop and copy the atoms individually along with their contents, which you would then have to individually <code>free</code> at the return point.</p> <p>...or maybe just this if you are only wanting to read the atoms data from the structure:</p> <pre><code>atoms = (*amino).atoms; // delete 1, 3, 4 entirely and just read directly from the structure </code></pre> <p>Other answers talking about the amount of space in <code>diff</code> and other issues are probably also worth investigating.</p> <p>EDIT: fixed the sequence of calls to match the code sample.</p>
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    1. COI don't think the `free()` calls are the problem (though they are confusing the issue). The `free()` call is being made after `atom` is set to the result of another (useless) `malloc()`, so it is freeing memory returned from a `malloc()` call. However, all the calls to `malloc()` and `free()` in the function do seem to be pointless.
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    2. COI think you're right. I've edited my post to indicate that memory is leaking without claiming that the free calls are the real issue.
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