Merge pull request #14 from hpcaitech/inference_pipeline

add inference pipeline from openfold/alphafold

Merge pull request #14 from hpcaitech/inference_pipeline
add inference pipeline from openfold/alphafold
eecadd36 · shenggan · GitHub · b3b3b445 · 42427a1c · eecadd36
Unverified Commit eecadd36 authored Apr 18, 2022 by shenggan Committed by GitHub Apr 18, 2022
20 changed files
--- a/fastfold/data/tools/jackhmmer.py
+++ b/fastfold/data/tools/jackhmmer.py
--- a/fastfold/data/tools/kalign.py
+++ b/fastfold/data/tools/kalign.py
--- a/fastfold/data/tools/utils.py
+++ b/fastfold/data/tools/utils.py
--- a/fastfold/model/__init__.py
+++ b/fastfold/model/__init__.py
-from .msa import MSAStack
-from .ops import OutProductMean
-from .triangle import PairStack
-from .evoformer import Evoformer
-__all__ = ['MSAStack', 'OutProductMean', 'PairStack', 'Evoformer']
--- a/fastfold/model/fastnn/__init__.py
+++ b/fastfold/model/fastnn/__init__.py
--- a/fastfold/model/evoformer.py
+++ b/fastfold/model/evoformer.py
--- a/fastfold/model/initializer.py
+++ b/fastfold/model/initializer.py
--- a/fastfold/model/kernel/__init__.py
+++ b/fastfold/model/kernel/__init__.py
--- a/fastfold/model/fastnn/kernel/cuda_native/__init__.py
+++ b/fastfold/model/fastnn/kernel/cuda_native/__init__.py
--- a/fastfold/model/kernel/cuda_native/csrc/compat.h
+++ b/fastfold/model/kernel/cuda_native/csrc/compat.h
--- a/fastfold/model/kernel/cuda_native/csrc/layer_norm_cuda.cpp
+++ b/fastfold/model/kernel/cuda_native/csrc/layer_norm_cuda.cpp
--- a/fastfold/model/kernel/cuda_native/csrc/layer_norm_cuda_kernel.cu
+++ b/fastfold/model/kernel/cuda_native/csrc/layer_norm_cuda_kernel.cu
--- a/fastfold/model/kernel/cuda_native/csrc/softmax_cuda.cpp
+++ b/fastfold/model/kernel/cuda_native/csrc/softmax_cuda.cpp
--- a/fastfold/model/kernel/cuda_native/csrc/softmax_cuda_kernel.cu
+++ b/fastfold/model/kernel/cuda_native/csrc/softmax_cuda_kernel.cu
--- a/fastfold/model/kernel/cuda_native/csrc/type_shim.h
+++ b/fastfold/model/kernel/cuda_native/csrc/type_shim.h
--- a/fastfold/model/kernel/cuda_native/layer_norm.py
+++ b/fastfold/model/kernel/cuda_native/layer_norm.py
--- a/fastfold/model/kernel/cuda_native/softmax.py
+++ b/fastfold/model/kernel/cuda_native/softmax.py
--- a/fastfold/model/kernel/jit/__init__.py
+++ b/fastfold/model/kernel/jit/__init__.py
--- a/fastfold/model/kernel/jit/fused_ops.py
+++ b/fastfold/model/kernel/jit/fused_ops.py
--- a/fastfold/model/kernel/jit/options.py
+++ b/fastfold/model/kernel/jit/options.py