Hydrophobic patch areas appear to be low by a factor of two

[DavidBJaffe]

The areas outputted to stdout by pep_patch_hydrophobic appear to be low by a factor of two. My reasoning for this is two-fold:

1. When I compute the areas myself, from the .ply file, I get a number which is twice as large.
2. By eye, the patches appear to be assigned too small an area.

Obviously this is not proof. I only mention it because I think there might be an error.

[fwaibl]

Hi. Thanks for bringing this up. Could you specify a bit more precisely what you did? E.g., could you share the code you used to compute the areas from the .ply file?

Best,
Franz

[DavidBJaffe]

What my code does is read the ply file outputted by pep_patch_hydrophobic, extract the triangles, and assign an area to each vertex by distributing the area of each triangle equally across its vertices, thus mimicking pep_patch_electrostatic.

It gets the patch identifiers from the same file. Then for each patch, it adds up the vertex areas as computed above.

I would share the actual code, but it's in Rust, and not standalone at present.

[fwaibl]

Hi. I've added some unittests doing basic triangle areas in #52, and so far it seems correct. Could you run some similar tests (or the same ones) through your code to see if they give the same results?

Best,
Franz

[DavidBJaffe]

I added a test for that triangle, and it passes in my code.

There are other ways I could have made a mistake, and not see it. At some point we'll likely go through your code in detail and perhaps resolve the seeming discrepancy. Thank you for investigating!