diff --git a/models/rfd3/src/rfd3/constants.py b/models/rfd3/src/rfd3/constants.py index c7d43c6..3ec144c 100644 --- a/models/rfd3/src/rfd3/constants.py +++ b/models/rfd3/src/rfd3/constants.py @@ -398,6 +398,7 @@ association_schemes["atom23"]["X"] = ( ATOM23_ATOM_NAMES_RNA = np.array( [item.strip() for item in backbone_atomscheme_RNA] + [f"V{i}" for i in range(23 - len(backbone_atomscheme_RNA))] +) """Atom23 atom names (e.g. CA, V1)""" ATOM23_ATOM_ELEMENTS_RNA = np.array( diff --git a/models/rfd3/src/rfd3/transforms/design_transforms.py b/models/rfd3/src/rfd3/transforms/design_transforms.py index 04f1500..aeadcc2 100644 --- a/models/rfd3/src/rfd3/transforms/design_transforms.py +++ b/models/rfd3/src/rfd3/transforms/design_transforms.py @@ -758,18 +758,6 @@ class AddAdditional1dFeaturesToFeats(Transform): if "feats" not in data.keys(): data["feats"] = {} - if association_scheme == 'atom23': - data['atom_array'].set_annotation('is_protein_token', data['atom_array'].is_protein) - data['atom_array'].set_annotation('is_dna_token', data['atom_array'].is_dna) - data['atom_array'].set_annotation('is_rna_token', data['atom_array'].is_rna) - - if self.association_scheme == "atom23": - data["atom_array"].set_annotation( - "is_protein_token", data["atom_array"].is_protein - ) - data["atom_array"].set_annotation("is_dna_token", data["atom_array"].is_dna) - data["atom_array"].set_annotation("is_rna_token", data["atom_array"].is_rna) - if self.association_scheme == "atom23": data["atom_array"].set_annotation( "is_protein_token", data["atom_array"].is_protein