From f81055a88607b66b5463592135b65dc992e1a53b Mon Sep 17 00:00:00 2001 From: lucidrains Date: Fri, 27 Sep 2024 10:13:27 -0700 Subject: [PATCH] prepare the radiuses, to customize radius based on atom type for rsa --- alphafold3_pytorch/alphafold3.py | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/alphafold3_pytorch/alphafold3.py b/alphafold3_pytorch/alphafold3.py index e7ce5328..9fe43e7a 100644 --- a/alphafold3_pytorch/alphafold3.py +++ b/alphafold3_pytorch/alphafold3.py @@ -5286,8 +5286,19 @@ def __init__( self.register_buffer('lddt_thresholds', torch.tensor([0.5, 1.0, 2.0, 4.0])) self.dssp_path = dssp_path + self.use_inhouse_rsa_calculation = use_inhouse_rsa_calculation + atom_type_radii = tensor([ + 1.65, # 0 - nitrogen + 1.87, # 1 - carbon alpha + 1.76, # 2 - carbon + 1.4, # 3 - oxygen + 1.8, # 4 - side atoms + 1.4 # 5 - water + ]) + + self.register_buffer('atom_radii', atom_type_radii) @property def is_mkdssp_available(self):