Exporting lipid assignment data

You can configure gorder to export leaflet assignment data into an external file. This can be useful for verifying leaflet assignments, reusing them for additional analyses, or ensuring reproducibility.

To export the lipid assignment data, add the export keyword to the leaflets section of your configuration file and specify the path to the output file:

leaflets: !Global
  membrane: "@membrane"
  heads: "name P"
  frequency: !Every 5
  export: "leaflet_assignment.yaml"  # or collect: "leaflet_assignment.yaml"

Alternatively, you can use the collect keyword instead of export.

Leaflet classification will be performed using the global method for every 5th analyzed frame (frequency: !Every 5). Once the trajectory has been processed, the assignment data will be written to leaflet_assignment.yaml. The data are exported in a condensed leaflet assignment file format. This means that you can directly reuse the exported YAML file in a subsequent gorder run by requesting manual leaflet classification. Since the output file is a valid YAML, you an also easily process it using other software.

Note that exporting lipid assignment data is only supported for automatic leaflet classification methods: global, local, individual, and clustering. Exporting lipid assignments is not supported for manual lipid assignment, as it is effectively pointless.

Below is an example of an exported leaflet assignment file for a very short trajectory:

# Leaflet assignment file generated by 'gorder v1.2.0' using a trajectory file 'md.xtc'.
POPE:
# Frame index 1
  - [1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]
# Frame index 6
  - [1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]
# Frame index 11
  - [1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0]
POPC:
# Frame index 1
  - [1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]
# Frame index 6
  - [1,1,1,1,1,1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]
# Frame index 11
  - [1,1,1,1,1,1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]
POPG:
# Frame index 1
  - [0,0,0,0,0,1,1,1,1,1]
# Frame index 6
  - [0,0,0,0,0,1,1,1,1,1]
# Frame index 11
  - [0,0,0,0,0,1,1,1,1,1]

Data are written separately for each molecule type. Within each block, every line beginning with - corresponds to a single trajectory frame for which leaflet classification was performed.

Each number in the line represents the leaflet assignment of an individual lipid molecule of the specified type in the given trajectory frame:

1 indicates the Upper leaflet
0 indicates the Lower leaflet

Molecules are listed in the order in which their first atom appears in the input structure file.

Note that the frame index refers to the sequential index of a frame in the input trajectory file, with the first analyzed frame assigned index 1. If your analysis begins later in the trajectory (using the begin keyword), frame 1 will not correspond to the very first frame of the trajectory.

gorder manual

Exporting lipid assignment data