Basic UsageΒΆ

The analysis tools in lipyphilic all require an MDAnalysis Universe as input, so to use lipyphilic you will also need to import MDAnalysis. The analyses are then performed in the same way as the majority of those in MDAnalysis. For example, to assign each lipid to the upper or lower leaflet at each frame in a trajectory:

import MDAnalysis as mda
from lipyphilic.lib.assign_leaflets import AssignLeaflets

# Load an MDAnalysis Universe
u = mda.Universe('production.tpr','production.xtc')

# Find which leaflet each lipid is in at each frame
leaflets = AssignLeaflets(
    lipid_sel="name PO4 ROH"  # Select headgroup beads in the MARTINI forcefield

# Select which frames to use and perform the analysis, stop=None, step=None)  # this will use every frame in the trajectory

And the results will be available as a NumPy array stored in the leaflets.leaflets attribute.

For more details on how to use lipyphilic, check out our interactive tutorials.