mirror of
https://github.com/baker-laboratory/RoseTTAFold-All-Atom.git
synced 2024-11-04 22:25:42 +00:00
100 lines
4.3 KiB
Python
100 lines
4.3 KiB
Python
import torch
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import torch.nn as nn
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from icecream import ic
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import inspect
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import sys, os
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#script_dir = os.path.dirname(os.path.realpath(__file__))+'/'
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#sys.path.insert(0,script_dir+'SE3Transformer')
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from rf2aa.util import xyz_frame_from_rotation_mask
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from rf2aa.util_module import init_lecun_normal_param, \
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make_full_graph, rbf, init_lecun_normal
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from rf2aa.loss.loss import calc_chiral_grads
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from rf2aa.model.layers.Attention_module import FeedForwardLayer
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from rf2aa.SE3Transformer.se3_transformer.model import SE3Transformer
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from rf2aa.SE3Transformer.se3_transformer.model.fiber import Fiber
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from rf2aa.util_module import get_seqsep_protein_sm
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se3_transformer_path = inspect.getfile(SE3Transformer)
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se3_fiber_path = inspect.getfile(Fiber)
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assert 'rf2aa' in se3_transformer_path
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class SE3TransformerWrapper(nn.Module):
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"""SE(3) equivariant GCN with attention"""
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def __init__(self, num_layers=2, num_channels=32, num_degrees=3, n_heads=4, div=4,
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l0_in_features=32, l0_out_features=32,
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l1_in_features=3, l1_out_features=2,
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num_edge_features=32):
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super().__init__()
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# Build the network
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self.l1_in = l1_in_features
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self.l1_out = l1_out_features
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#
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fiber_edge = Fiber({0: num_edge_features})
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if l1_out_features > 0:
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if l1_in_features > 0:
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fiber_in = Fiber({0: l0_in_features, 1: l1_in_features})
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fiber_hidden = Fiber.create(num_degrees, num_channels)
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fiber_out = Fiber({0: l0_out_features, 1: l1_out_features})
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else:
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fiber_in = Fiber({0: l0_in_features})
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fiber_hidden = Fiber.create(num_degrees, num_channels)
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fiber_out = Fiber({0: l0_out_features, 1: l1_out_features})
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else:
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if l1_in_features > 0:
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fiber_in = Fiber({0: l0_in_features, 1: l1_in_features})
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fiber_hidden = Fiber.create(num_degrees, num_channels)
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fiber_out = Fiber({0: l0_out_features})
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else:
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fiber_in = Fiber({0: l0_in_features})
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fiber_hidden = Fiber.create(num_degrees, num_channels)
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fiber_out = Fiber({0: l0_out_features})
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self.se3 = SE3Transformer(num_layers=num_layers,
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fiber_in=fiber_in,
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fiber_hidden=fiber_hidden,
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fiber_out = fiber_out,
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num_heads=n_heads,
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channels_div=div,
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fiber_edge=fiber_edge,
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populate_edge="arcsin",
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final_layer="lin",
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use_layer_norm=True)
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self.reset_parameter()
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def reset_parameter(self):
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# make sure linear layer before ReLu are initialized with kaiming_normal_
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for n, p in self.se3.named_parameters():
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if "bias" in n:
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nn.init.zeros_(p)
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elif len(p.shape) == 1:
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continue
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else:
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if "radial_func" not in n:
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p = init_lecun_normal_param(p)
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else:
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if "net.6" in n:
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nn.init.zeros_(p)
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else:
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nn.init.kaiming_normal_(p, nonlinearity='relu')
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# make last layers to be zero-initialized
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#self.se3.graph_modules[-1].to_kernel_self['0'] = init_lecun_normal_param(self.se3.graph_modules[-1].to_kernel_self['0'])
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#self.se3.graph_modules[-1].to_kernel_self['1'] = init_lecun_normal_param(self.se3.graph_modules[-1].to_kernel_self['1'])
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#nn.init.zeros_(self.se3.graph_modules[-1].to_kernel_self['0'])
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#nn.init.zeros_(self.se3.graph_modules[-1].to_kernel_self['1'])
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nn.init.zeros_(self.se3.graph_modules[-1].weights['0'])
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if self.l1_out > 0:
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nn.init.zeros_(self.se3.graph_modules[-1].weights['1'])
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def forward(self, G, type_0_features, type_1_features=None, edge_features=None):
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if self.l1_in > 0:
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node_features = {'0': type_0_features, '1': type_1_features}
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else:
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node_features = {'0': type_0_features}
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edge_features = {'0': edge_features}
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return self.se3(G, node_features, edge_features)
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