From 231a2108e61a8e916730c0604d84fdf14259233a Mon Sep 17 00:00:00 2001 From: Tom Ginsberg Date: Thu, 13 Nov 2025 20:38:37 +0100 Subject: [PATCH 1/3] added missing docs + improved doc clarity of generate_lomap_network docs --- lomap/gufe_bindings/network_generation.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/lomap/gufe_bindings/network_generation.py b/lomap/gufe_bindings/network_generation.py index c9edc9c..bb5db87 100644 --- a/lomap/gufe_bindings/network_generation.py +++ b/lomap/gufe_bindings/network_generation.py @@ -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 accepted. 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 distance from an active molecule. Default is 2. require_cycle_covering : bool add cycles into the network radial : bool From 6506ee720a83b2de9c4fa9254a42178b92da93e8 Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Fri, 21 Nov 2025 22:31:25 +0000 Subject: [PATCH 2/3] Update lomap/gufe_bindings/network_generation.py --- lomap/gufe_bindings/network_generation.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lomap/gufe_bindings/network_generation.py b/lomap/gufe_bindings/network_generation.py index bb5db87..84b7cf1 100644 --- a/lomap/gufe_bindings/network_generation.py +++ b/lomap/gufe_bindings/network_generation.py @@ -44,7 +44,7 @@ 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 - edges with a score >= 1 - distance_cutoff will be accepted. Default is 0.4. + 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. Default is 6. actives : list[bool] From ab5439eccae1360af7bac8a5ae7e059a085b6318 Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Fri, 21 Nov 2025 22:33:06 +0000 Subject: [PATCH 3/3] Update lomap/gufe_bindings/network_generation.py --- lomap/gufe_bindings/network_generation.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lomap/gufe_bindings/network_generation.py b/lomap/gufe_bindings/network_generation.py index 84b7cf1..33e417d 100644 --- a/lomap/gufe_bindings/network_generation.py +++ b/lomap/gufe_bindings/network_generation.py @@ -50,7 +50,7 @@ def generate_lomap_network( actives : list[bool] for each molecule, if it is tagged as an active molecule max_dist_from_active - when 'actives' is given, constrains the resulting map to be within this distance from an active molecule. Default is 2. + 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