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https://github.com/baker-laboratory/RoseTTAFold-All-Atom.git
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72 lines
2.7 KiB
Python
72 lines
2.7 KiB
Python
import torch
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import torch.nn as nn
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import numpy as np
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from contextlib import ExitStack
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from rf2aa.chemical import ChemicalData as ChemData
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def recycle_step_legacy(ddp_model, input, n_cycle, use_amp, nograds=False, force_device=None):
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if force_device is not None:
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gpu = force_device
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else:
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gpu = ddp_model.device
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xyz_prev, alpha_prev, mask_recycle = \
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input["xyz_prev"], input["alpha_prev"], input["mask_recycle"]
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output_i = (None, None, xyz_prev, alpha_prev, mask_recycle)
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for i_cycle in range(n_cycle):
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with ExitStack() as stack:
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stack.enter_context(torch.cuda.amp.autocast(enabled=use_amp))
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if i_cycle < n_cycle -1 or nograds is True:
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stack.enter_context(torch.no_grad())
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if force_device is None:
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stack.enter_context(ddp_model.no_sync())
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return_raw = (i_cycle < n_cycle -1)
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use_checkpoint = not nograds and (i_cycle == n_cycle -1)
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input_i = add_recycle_inputs(input, output_i, i_cycle, gpu, return_raw=return_raw, use_checkpoint=use_checkpoint)
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output_i = ddp_model(**input_i)
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return output_i
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def run_model_forward_legacy(model, network_input, device="cpu"):
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""" run model forward pass, no recycling or ddp with legacy model (for tests)"""
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gpu = device
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xyz_prev, alpha_prev, mask_recycle = \
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network_input["xyz_prev"], network_input["alpha_prev"], network_input["mask_recycle"]
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output_i = (None, None, xyz_prev, alpha_prev, mask_recycle)
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input_i = add_recycle_inputs(network_input, output_i, 0, gpu, return_raw=False, use_checkpoint=False)
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input_i["seq_unmasked"] = input_i["seq_unmasked"].to(gpu)
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input_i["sctors"] = input_i["sctors"].to(gpu)
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model.eval()
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with torch.no_grad():
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output_i = model(**input_i)
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return output_i
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def add_recycle_inputs(network_input, output_i, i_cycle, gpu, return_raw=False, use_checkpoint=False):
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input_i = {}
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for key in network_input:
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if key in ['msa_latent', 'msa_full', 'seq']:
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input_i[key] = network_input[key][:,i_cycle].to(gpu, non_blocking=True)
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else:
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input_i[key] = network_input[key]
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L = input_i["msa_latent"].shape[2]
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msa_prev, pair_prev, _, alpha, mask_recycle = output_i
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xyz_prev = ChemData().INIT_CRDS.reshape(1,1,ChemData().NTOTAL,3).repeat(1,L,1,1).to(gpu, non_blocking=True)
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input_i['msa_prev'] = msa_prev
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input_i['pair_prev'] = pair_prev
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input_i['xyz'] = xyz_prev
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input_i['mask_recycle'] = mask_recycle
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input_i['sctors'] = alpha
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input_i['return_raw'] = return_raw
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input_i['use_checkpoint'] = use_checkpoint
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input_i.pop('xyz_prev')
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input_i.pop('alpha_prev')
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return input_i
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