Rename main directory

README.md

@@ -5,7 +5,7 @@ A faithful PyTorch reproduction of DeepMind's
 
 ## Installation
 
-1. Install Python 3.9 and install dependencies.
+1. Having installed Python 3.9, install dependencies.
 
 ```bash
 pip3 install -r requirements.txt

config.py

@@ -199,12 +199,12 @@ config = mlc.ConfigDict({
                 "clamp_distance": 10.,
                 "loss_unit_distance": 10.,
                 "weight": 0.5,
-            }
+            },
             "sidechain": {
                 "clamp_distance": 10.,
                 "length_scale": 10.,
                 "weight": 0.5,
-            }
+            },
             "weight": 1.0,
         },
         "lddt": {

alphafold/model/embedders.py → openfold/model/embedders.py

@@ -17,8 +17,8 @@ import torch
 import torch.nn as nn
 from typing import Tuple
 
-from alphafold.model.primitives import Linear
-from alphafold.utils.tensor_utils import one_hot
+from openfold.model.primitives import Linear
+from openfold.utils.tensor_utils import one_hot
 
 
 class InputEmbedder(nn.Module):

alphafold/model/evoformer.py → openfold/model/evoformer.py

@@ -18,25 +18,25 @@ import torch.nn as nn
 from typing import Tuple, Optional
 from functools import partial
 
-from alphafold.model.primitives import Linear
-from alphafold.utils.deepspeed import checkpoint_blocks 
-from alphafold.model.dropout import DropoutRowwise, DropoutColumnwise
-from alphafold.model.msa import (
+from openfold.model.primitives import Linear
+from openfold.utils.deepspeed import checkpoint_blocks 
+from openfold.model.dropout import DropoutRowwise, DropoutColumnwise
+from openfold.model.msa import (
     MSARowAttentionWithPairBias,
     MSAColumnAttention,
     MSAColumnGlobalAttention,
 )
-from alphafold.model.outer_product_mean import OuterProductMean
-from alphafold.model.pair_transition import PairTransition
-from alphafold.model.triangular_attention import (
+from openfold.model.outer_product_mean import OuterProductMean
+from openfold.model.pair_transition import PairTransition
+from openfold.model.triangular_attention import (
     TriangleAttentionStartingNode,
     TriangleAttentionEndingNode,
 )
-from alphafold.model.triangular_multiplicative_update import (
+from openfold.model.triangular_multiplicative_update import (
     TriangleMultiplicationOutgoing,
     TriangleMultiplicationIncoming,
 )
-from alphafold.utils.tensor_utils import chunk_layer
+from openfold.utils.tensor_utils import chunk_layer
 
 
 class MSATransition(nn.Module):

alphafold/model/heads.py → openfold/model/heads.py

@@ -16,8 +16,8 @@
 import torch
 import torch.nn as nn
 
-from alphafold.model.primitives import Linear
-from alphafold.utils.loss import compute_plddt
+from openfold.model.primitives import Linear
+from openfold.utils.loss import compute_plddt
 
 
 class AuxiliaryHeads(nn.Module):

alphafold/model/model.py → openfold/model/model.py

@@ -16,7 +16,7 @@
 import torch
 import torch.nn as nn
 
-from alphafold.utils.feats import (
+from openfold.utils.feats import (
     pseudo_beta_fn,
     atom37_to_torsion_angles,
     build_extra_msa_feat,
@@ -24,26 +24,26 @@ from alphafold.utils.feats import (
     build_template_pair_feat,
     atom14_to_atom37,
 )
-from alphafold.model.embedders import (
+from openfold.model.embedders import (
     InputEmbedder, 
     RecyclingEmbedder,
     TemplateAngleEmbedder,
     TemplatePairEmbedder,
     ExtraMSAEmbedder,
 )
-from alphafold.model.evoformer import EvoformerStack, ExtraMSAStack
-from alphafold.model.heads import AuxiliaryHeads
-import alphafold.np.residue_constants as residue_constants
-from alphafold.model.structure_module import StructureModule
-from alphafold.model.template import (
+from openfold.model.evoformer import EvoformerStack, ExtraMSAStack
+from openfold.model.heads import AuxiliaryHeads
+import openfold.np.residue_constants as residue_constants
+from openfold.model.structure_module import StructureModule
+from openfold.model.template import (
     TemplatePairStack, 
     TemplatePointwiseAttention,
 )
-from alphafold.utils.loss import (
+from openfold.utils.loss import (
     compute_plddt,
 )
 
-from alphafold.utils.tensor_utils import (
+from openfold.utils.tensor_utils import (
     tensor_tree_map,
 )
         

alphafold/model/msa.py → openfold/model/msa.py

@@ -17,8 +17,8 @@ import math
 import torch
 import torch.nn as nn
 
-from alphafold.model.primitives import Linear, Attention
-from alphafold.utils.tensor_utils import (
+from openfold.model.primitives import Linear, Attention
+from openfold.utils.tensor_utils import (
     chunk_layer,
     permute_final_dims, 
     flatten_final_dims,

alphafold/model/outer_product_mean.py → openfold/model/outer_product_mean.py

@@ -17,8 +17,8 @@ from functools import partial
 import torch
 import torch.nn as nn
 
-from alphafold.model.primitives import Linear
-from alphafold.utils.tensor_utils import chunk_layer
+from openfold.model.primitives import Linear
+from openfold.utils.tensor_utils import chunk_layer
 
 
 class OuterProductMean(nn.Module):

alphafold/model/pair_transition.py → openfold/model/pair_transition.py

@@ -16,8 +16,8 @@
 import torch
 import torch.nn as nn
 
-from alphafold.model.primitives import Linear
-from alphafold.utils.tensor_utils import chunk_layer
+from openfold.model.primitives import Linear
+from openfold.utils.tensor_utils import chunk_layer
 
 
 class PairTransition(nn.Module):

alphafold/model/primitives.py → openfold/model/primitives.py

@@ -21,7 +21,7 @@ import torch
 import torch.nn as nn
 from scipy.stats import truncnorm
 
-from alphafold.utils.tensor_utils import (
+from openfold.utils.tensor_utils import (
     permute_final_dims, 
     flatten_final_dims,
 )

alphafold/model/structure_module.py → openfold/model/structure_module.py

@@ -18,15 +18,15 @@ import torch
 import torch.nn as nn
 from typing import Optional
 
-from alphafold.model.primitives import Linear, ipa_point_weights_init_
-from alphafold.np.residue_constants import (
+from openfold.model.primitives import Linear, ipa_point_weights_init_
+from openfold.np.residue_constants import (
     restype_rigid_group_default_frame,
     restype_atom14_to_rigid_group,
     restype_atom14_mask,
     restype_atom14_rigid_group_positions,
 )
-from alphafold.utils.affine_utils import T, quat_to_rot 
-from alphafold.utils.tensor_utils import (
+from openfold.utils.affine_utils import T, quat_to_rot 
+from openfold.utils.tensor_utils import (
     stack_tensor_dicts, 
     permute_final_dims, 
     flatten_final_dims,
@@ -739,7 +739,7 @@ class StructureModule(nn.Module):
             preds = {
                 "frames": 
                     t.scale_translation(self.trans_scale_factor).to_4x4(),
-                "sidechain_frames": all_frames_to_global,
+                "sidechain_frames": all_frames_to_global.to_4x4(),
                 "unnormalized_angles": unnormalized_a,
                 "angles": a,
                 "positions": pred_xyz,

alphafold/model/template.py → openfold/model/template.py

@@ -18,22 +18,22 @@ import math
 import torch
 import torch.nn as nn
 
-from alphafold.model.primitives import Linear, Attention
-from alphafold.utils.deepspeed import checkpoint_blocks
-from alphafold.model.dropout import  (
+from openfold.model.primitives import Linear, Attention
+from openfold.utils.deepspeed import checkpoint_blocks
+from openfold.model.dropout import  (
     DropoutRowwise,
     DropoutColumnwise,
 )
-from alphafold.model.pair_transition import PairTransition
-from alphafold.model.triangular_attention import (
+from openfold.model.pair_transition import PairTransition
+from openfold.model.triangular_attention import (
     TriangleAttentionStartingNode,
     TriangleAttentionEndingNode,
 )
-from alphafold.model.triangular_multiplicative_update import (
+from openfold.model.triangular_multiplicative_update import (
     TriangleMultiplicationOutgoing,
     TriangleMultiplicationIncoming,
 )
-from alphafold.utils.tensor_utils import (
+from openfold.utils.tensor_utils import (
     chunk_layer,
     permute_final_dims, 
     flatten_final_dims,

alphafold/model/triangular_attention.py → openfold/model/triangular_attention.py

@@ -18,8 +18,8 @@ import math
 import torch
 import torch.nn as nn
 
-from alphafold.model.primitives import Linear, Attention
-from alphafold.utils.tensor_utils import (
+from openfold.model.primitives import Linear, Attention
+from openfold.utils.tensor_utils import (
     chunk_layer, 
     permute_final_dims, 
     flatten_final_dims,

alphafold/model/triangular_multiplicative_update.py → openfold/model/triangular_multiplicative_update.py

@@ -17,8 +17,8 @@ from functools import partialmethod
 import torch
 import torch.nn as nn
 
-from alphafold.model.primitives import Linear
-from alphafold.utils.tensor_utils import permute_final_dims
+from openfold.model.primitives import Linear
+from openfold.utils.tensor_utils import permute_final_dims
 
 
 class TriangleMultiplicativeUpdate(nn.Module):

alphafold/np/protein.py → openfold/np/protein.py

@@ -17,7 +17,7 @@
 import dataclasses
 import io
 from typing import Any, Mapping, Optional
-from alphafold.np import residue_constants
+from openfold.np import residue_constants
 from Bio.PDB import PDBParser
 import numpy as np