__init__() got an unexpected keyword argument 'structure_module_type'

[fromeast]

When I run

import torch
from alphafold2_pytorch import Alphafold2

model = Alphafold2(
    dim = 256,
    depth = 2,
    heads = 8,
    dim_head = 64,
    predict_coords = True,
    structure_module_type = 'se3',          # use SE3 Transformer - if set to False, will use E(n)-Transformer, Victor and Max Welling's new paper
    structure_module_dim = 4,               # se3 transformer dimension
    structure_module_depth = 1,             # depth
    structure_module_heads = 1,             # heads
    structure_module_dim_head = 16,         # dimension of heads
    structure_module_refinement_iters = 2,  # number of equivariant coordinate refinement iterations
    structure_num_global_nodes = 1          # number of global nodes for the structure module, only works with SE3 transformer
)

I will get ERROR that TypeError: __init__() got an unexpected keyword argument 'structure_module_type'.
and I found that MSA have to be the same length as primary sequence.

[Youqing Xiaozhua]

the same error here

[了无歌]

me too

[了无歌]

@youqingxiaozhua, @ifromeast
I got it! you can annotate those paras which don't appear in "alphafold2_pytorch.Alphafold2", and then, modify the definition of seq to make sure that seq and msa have the same length. your code should like:

import torch
from alphafold2_pytorch import Alphafold2

model = Alphafold2(
    dim=256,
    depth=2,
    heads=8,
    dim_head=64,
    predict_coords=True,
    # structure_module_type='se3',
    # use SE3 Transformer - if set to False, will use E(n)-Transformer, Victor and Max Welling's new paper
    # structure_module_dim=4,  # se3 transformer dimension
    structure_module_depth=1,  # depth
    structure_module_heads=1,  # heads
    structure_module_dim_head=16,  # dimension of heads
    # structure_module_refinement_iters=2  # number of equivariant coordinate refinement iterations
    # structure_num_global_nodes=1  # number of global nodes for the structure module, only works with SE3 transformer
).cuda()

seq = torch.randint(0, 21, (2, 60)).cuda()
msa = torch.randint(0, 21, (2, 5, 60)).cuda()
mask = torch.ones_like(seq).bool().cuda()
msa_mask = torch.ones_like(msa).bool().cuda()

coords = model(
    seq,
    msa,
    mask=mask,
    msa_mask=msa_mask
)  # (2, 64 * 3, 3)  <-- 3 atoms per residue

print(coords)

[chungongyu]

ki mskk