Indexing Using Serial ID

[HamiltonGeorge]

It seems that, while the documentation says the attachment ID is selected via the serial ID of an atom rather than atom index (https://rna-fretools.github.io/fretraj/getting_started/acv_calculation.html?highlight=serial), in the Volume class of cloud.py the atom index is used, leading to issues if the mdtraj atom_slice method is used or atoms are deleted from the trajectory and then AVs are calculated after, as the number of atoms changes.

For my purposes as a quick fix to make cloud.py use the serial IDs (which are maintained when doing atom_slice, while atom index is not), I edited line 823 of cloud.py to pull the atom index of the existing atom with atom.serial equal the supplied labels["Position"][site]["attach_id"]+1, and changed line 887 to this index-1. Without this change, ft.cloud.Volume returns an index error when the given serial ID is greater than the number of atoms in the atom_slice.

self.attach_id = [i.index for i in self.structure.top.atoms if i.serial == labels["Position"][site]["attach_id"]][0]+1