From 9ed50646838134e98d46a0a3f999a3bf0d3e34b5 Mon Sep 17 00:00:00 2001 From: teddygroves Date: Wed, 14 Aug 2024 15:19:37 +0200 Subject: [PATCH 1/2] Fix allostery free enzyme ratio bug It sounds like it should be a per-enzyme vector, but it's a per-edge one. Oops! --- maud/stan/functions.stan | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/maud/stan/functions.stan b/maud/stan/functions.stan index 5e1f8ffc..74566178 100644 --- a/maud/stan/functions.stan +++ b/maud/stan/functions.stan @@ -242,7 +242,7 @@ functions { } out[f] = inv(1 + tc_edge - * (free_enzyme_ratio[edge_to_enzyme[f]] * Q_num / Q_denom) ^ subunits[edge_to_enzyme[f]]); + * (free_enzyme_ratio[f] * Q_num / Q_denom) ^ subunits[edge_to_enzyme[f]]); } return out; } @@ -680,7 +680,7 @@ functions { out[f] = 1 / (1 + tc_edge - * (free_enzyme_ratio[edge_to_enzyme[f]] * Q_num / Q_denom) ^ subunits[edge_to_enzyme[f]]); + * (free_enzyme_ratio[f] * Q_num / Q_denom) ^ subunits[edge_to_enzyme[f]]); } return out; } From 3e3f7254f698a8d39f529a6cde57068886ffe0e1 Mon Sep 17 00:00:00 2001 From: teddygroves Date: Wed, 14 Aug 2024 15:20:46 +0200 Subject: [PATCH 2/2] Ignore safety warning 70612 This is because Maud has jinja2 as a dependency. See https://data.safetycli.com/v/70612/97c/. I think it's not a serious problem because Maud doesn't provide access to any templates. --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 9429d75c..78734d3f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -184,5 +184,5 @@ legacy_tox_ini = """ safety commands= pip install --upgrade pip - safety check -i 44715 -i 51549 + safety check -i 44715 -i 51549 -i 70612 """