adding config

paper_algs/configuration_alphafold.py

@@ -0,0 +1,72 @@
+from transformers import PretrainedConfig
+
+
+class AlphaFoldConfig(PretrainedConfig):
+    def __init__(
+            self,
+            # model
+            N_cycle=4,
+            dim_single=384,
+            dim_pair=128,
+            c_atom=384,
+            c_atompair=128,
+            c_token=256,
+            # pos emb
+            r_max=32,
+            s_max=2,
+            # msa
+            msa_depth=4,
+            dim_msa=64,
+            dim_msa_input=None,
+            outer_product_dim=32,
+            msa_pwa_dropout_row_prob=0.15,
+            msa_pwa_heads=8,
+            msa_pwa_dim_head=32,
+            # pairformer
+            pairformer_depth=48,
+            pair_bais_attn_dim_head=64,
+            pair_bias_attn_heads=16,
+            dropout_row_prob=0.25,
+            tri_mult_dim_hidden=None,
+            tri_attn_dim_head=32,
+            tri_attn_heads=4,
+            dropout_col_prob=0.25,
+            # confidence head
+            dim_single_inputs=256,
+            atompair_dist_bins=64,
+            num_plddt_bins=50,
+            num_pde_bins=64,
+            num_pae_bins=64,
+            confidence_depth=4,
+            **kwargs,
+    ):
+        super().__init__(**kwargs)
+        self.N_cycle = N_cycle
+        self.dim_single = dim_single
+        self.dim_pair = dim_pair
+        self.c_atom = c_atom
+        self.c_atompair = c_atompair
+        self.c_token = c_token
+        self.r_max = r_max
+        self.s_max = s_max
+        self.msa_depth = msa_depth
+        self.dim_msa = dim_msa
+        self.dim_msa_input = dim_msa_input
+        self.outer_product_dim = outer_product_dim
+        self.msa_pwa_dropout_row_prob = msa_pwa_dropout_row_prob
+        self.msa_pwa_heads = msa_pwa_heads
+        self.msa_pwa_dim_head = msa_pwa_dim_head
+        self.pairformer_depth = pairformer_depth
+        self.pair_bais_attn_dim_head = pair_bais_attn_dim_head
+        self.pair_bias_attn_heads = pair_bias_attn_heads
+        self.dropout_row_prob = dropout_row_prob
+        self.tri_mult_dim_hidden = tri_mult_dim_hidden
+        self.tri_attn_dim_head = tri_attn_dim_head
+        self.tri_attn_heads = tri_attn_heads
+        self.dropout_col_prob = dropout_col_prob
+        self.dim_single_inputs = dim_single_inputs
+        self.atompair_dist_bins = atompair_dist_bins
+        self.num_plddt_bins = num_plddt_bins
+        self.num_pde_bins = num_pde_bins
+        self.num_pae_bins = num_pae_bins
+        self.confidence_depth = confidence_depth