Selecting multiple lipids with different head groups

[Saleh-OM4R]

Hi,

I've just started using LipPyphilic, and I've been trying to select multiple lipids but with different head groups using this code :

# Find which leaflet each lipid is in at each frame
leaflets = AssignLeaflets(
    universe=u,
    lipid_sel= 'resname POPE POPC PSM BMGP and name P C11 C12','resname CHL1 and name O3 C3' # Select headgroup beads in the MARTINI forcefield
)
# Select which frames to use and perform the analysis
leaflets.run(start=None, stop=None, step=None)  # this will use every frame in the trajectory

but it doesn't work and I get this error:

File "/tmp/ipykernel_22911/1408747556.py", line 4
lipid_sel= 'resname POPE POPC PSM BMGP and name P C11 C12','resname CHL1 and name O3 C3' # Select headgroup beads in the MARTINI forcefield
^
SyntaxError: positional argument follows keyword argument

But, if I use the same selection with u.select_atoms it works fine:

u.select_atoms('resname POPE POPC PSM BMGP and name P C11 C12','resname CHL1 and name O3 C3')

So my question is how does the (lipid_sel=) read the lipid selection? I thought it uses the same selection language as MDAnalysis?or is it different?

Cheers,

[p-j-smith]

Hi @Saleh-OM4R thanks for trying out lipyphilic!

Lipyphilic does indeed use the same selection language as MDAnalysis. The issue is that you have two selection strings that you are passing to lipid_sel.

In MDAnalysis:

u.select_atoms(
    'resname POPE POPC PSM BMGP and name P C11 C12',
    'resname CHL1 and name O3 C3',
)

will create a single atom group that contains all atoms selected by both strings.

If this is indeed what you want, then you need to pass a single string to AssignLeaflets:

    lipid_sel ='(resname POPE POPC PSM BMGP and name P C11 C12) or (resname CHL1 and name O3 C3)'

If you try to pass two separate strings, then Python will assume that you are trying to pass two arguments - one to lipid_sel and another to a different argument. This is why it raises the error positional argument follows keyword argument.

If on the other hand you want to pass 'resname POPE POPC PSM BMGP and name P C11 C12' to lipid_sel and resname CHL1 and name O3 C3 to midplane_sel, then you need to explicitly pass the second string to midplane_sel:

leaflets = AssignLeaflets(
    universe=u,
    lipid_sel= 'resname POPE POPC PSM BMGP and name P C11 C12',
    midplane_sel='resname CHL1 and name O3 C3',
)