Interacting atom names from prolif.ifp?

[Erikna00]

Hi Prolif,

Thank you for writing such a useful piece of code. It has really earned its place in my MD workflows.
Is there any "easy" way to revise plf.ifp or its dataframe so in addition to residue it also reports what atom name in the residue/ligand the interactions is made from? Is this a feature/option which could be added? Eg residue: (Ca, PHE, 17, A)

Furthermore, i had a hard time finding docs on the exact structure of the plf.ifp dictionary and how to get useful information out of it, have i missed something in the docs or is this something you could explain/add to the docs? I´m currently interested in monitoring H-bond donor atom, acceptor atom, distance and angle for many binding poses in many proteins but in the future this will be extended to most interactions.

[cbouy]

Hi @Erikna00,

For the dataframe with atom names, you may find this thread useful. It only saves the protein atom name, if you want the ligand you'll have to add it with the same logic.

So the structure of the ifp dictionary is a dict[<frame number>, IFP] where IFP is described here in the docs:

• indices corresponds to the atom indices at the residue level
• parent_indices is the same but at the molecule level. For molecules built from an MDAnalysis object, this will correspond to the indices in the AtomGroup selection, not the indices in the entire Universe.
• other metadata: all interactions expose a distance value, and then some of them have one or more angle (the exact name for the angle varies between interactions, HBond has DHA_angle, XBond has both AXD_angle and XAR_angle, CationPi is just angle, PiStacking will have plane_angle and normal_to_centroid_angle) and other things depending on the interaction type (the PiStacking ones may have an intersect_distance if it's an edge-to-face interaction, but not for face-to-face). Ideally I should specify the metadata available in each interaction class, and also what these all mean...