From 156e25ee49d7f359f1a073f2ebb73ddb72aebf63 Mon Sep 17 00:00:00 2001 From: Nuri Jung Date: Mon, 18 Mar 2024 16:21:28 +0900 Subject: [PATCH 1/2] fix(data): join unique a3m results only Fixes seoklab/RoseTTAFold-All-Atom#3. --- rf2aa/data/merge_inputs.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/rf2aa/data/merge_inputs.py b/rf2aa/data/merge_inputs.py index bf12ff8..7917fa1 100644 --- a/rf2aa/data/merge_inputs.py +++ b/rf2aa/data/merge_inputs.py @@ -43,8 +43,8 @@ def merge_protein_inputs(protein_inputs, deterministic: bool = False): if len(unique_a3m) >1: a3m_out = unique_a3m[0] - for i in range(1, len(unique_a3m)): - a3m_out = join_msas_by_taxid(a3m_out, a3m_list[i]) + for unq_a3m in unique_a3m[1:]: + a3m_out = join_msas_by_taxid(a3m_out, unq_a3m) a3m_out = expand_multi_msa(a3m_out, unique_hashes, hash_list, unique_lengths_list, lengths_list) else: a3m = unique_a3m[0] From bd57e106762c00aa6e6c7d8f35366c7ba6f7c6d6 Mon Sep 17 00:00:00 2001 From: Nuri Jung Date: Mon, 18 Mar 2024 16:31:48 +0900 Subject: [PATCH 2/2] fix(data): match input format in multimer prediction Return as dictionary. Closes baker-laboratory/RoseTTAFold-All-Atom#11 (supersedes). Fixes baker-laboratory/RoseTTAFold-All-Atom#12. --- rf2aa/data/data_loader_utils.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/rf2aa/data/data_loader_utils.py b/rf2aa/data/data_loader_utils.py index bd66579..0b3c38a 100644 --- a/rf2aa/data/data_loader_utils.py +++ b/rf2aa/data/data_loader_utils.py @@ -455,7 +455,7 @@ def merge_a3m_homo(msa_orig, ins_orig, nmer, mode="default"): ins[N:, start:start+L] = ins_orig[1:] start += L - return msa, ins + return {"msa": msa, "ins": ins} def merge_msas(a3m_list, L_s): """