Skip to content

Doc Improvement for generate_lomap_network #89

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Closed
beitom wants to merge 3 commits into from
Closed

Doc Improvement for generate_lomap_network #89

Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
231a210
added missing docs + improved doc clarity of generate_lomap_network …
beitom Nov 13, 2025
6506ee7
Update lomap/gufe_bindings/network_generation.py
IAlibay Nov 21, 2025
ab5439e
Update lomap/gufe_bindings/network_generation.py
IAlibay Nov 21, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
8 changes: 4 additions & 4 deletions lomap/gufe_bindings/network_generation.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -44,13 +44,13 @@ def generate_lomap_network(
to 0.0 (worst). These values are use as the "distance" between two molecules, and compared against the
'distance_cutoff' parameter
distance_cutoff : float
the maximum distance/dissimilarity between two molecules for an edge to be accepted
edges with a score < 1 - distance_cutoff will be rejected. Default is 0.4.
max_path_length : int
maximum distance between any two molecules in the resulting network
maximum distance between any two molecules in the resulting network. Default is 6.
actives : list[bool]
for each molecule, if it is tagged as an active molecule
for each molecule, if it is tagged as an active molecule
max_dist_from_active
when 'actives' is given, constrains the resulting map to
when 'actives' is given, constrains the resulting map to be within this this number of edges (e.g. distance) from an active molecule. Default is 2.
require_cycle_covering : bool
add cycles into the network
radial : bool
Expand Down