From 07e9ace4711546a3062f2709b072fd1683600317 Mon Sep 17 00:00:00 2001 From: Raktim Mitra Date: Sat, 23 May 2026 05:25:13 -0700 Subject: [PATCH] Fix: stop dropping nucleic acid residues in partial diffusion (#281) * stop dropping nucleic acid residues in partial diffusion * stop dropping nucleic acids in partial diffusion rfd3na * ruff format * Update input_parsing.py ruff format --- models/rfd3/src/rfd3/inference/input_parsing.py | 4 +++- models/rfd3na/src/rfd3na/inference/input_parsing.py | 4 +++- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/models/rfd3/src/rfd3/inference/input_parsing.py b/models/rfd3/src/rfd3/inference/input_parsing.py index f8b9021..5826de7 100644 --- a/models/rfd3/src/rfd3/inference/input_parsing.py +++ b/models/rfd3/src/rfd3/inference/input_parsing.py @@ -611,7 +611,9 @@ class DesignInputSpecification(BaseModel): ).astype(int) # ... Subset to residues only - atom_array_in = atom_array_in[atom_array_in.is_protein] + atom_array_in = atom_array_in[ + atom_array_in.is_protein | atom_array_in.is_dna | atom_array_in.is_rna + ] # ... Set chain ID for unindexed residues as whatever the input has start_resid = np.max(atom_array_in.res_id) + 1 diff --git a/models/rfd3na/src/rfd3na/inference/input_parsing.py b/models/rfd3na/src/rfd3na/inference/input_parsing.py index ad3deb9..aaa91f0 100644 --- a/models/rfd3na/src/rfd3na/inference/input_parsing.py +++ b/models/rfd3na/src/rfd3na/inference/input_parsing.py @@ -640,7 +640,9 @@ class DesignInputSpecification(BaseModel): ).astype(int) # ... Subset to residues only - atom_array_in = atom_array_in[atom_array_in.is_protein] + atom_array_in = atom_array_in[ + atom_array_in.is_protein | atom_array_in.is_dna | atom_array_in.is_rna + ] # ... Set chain ID for unindexed residues as whatever the input has start_resid = np.max(atom_array_in.res_id) + 1