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all_atom_score_model.py
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all_atom_score_model.py
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from e3nn import o3
import torch
from torch import nn
from torch.nn import functional as F
from torch_cluster import radius, radius_graph
from torch_scatter import scatter_mean
import numpy as np
from models.score_model import AtomEncoder, TensorProductConvLayer, GaussianSmearing
from utils import so3, torus
from datasets.process_mols import lig_feature_dims, rec_residue_feature_dims, rec_atom_feature_dims
class TensorProductScoreModel(torch.nn.Module):
def __init__(self, t_to_sigma, device, timestep_emb_func, in_lig_edge_features=4, sigma_embed_dim=32, sh_lmax=2,
ns=16, nv=4, num_conv_layers=2, lig_max_radius=5, rec_max_radius=30, cross_max_distance=250,
center_max_distance=30, distance_embed_dim=32, cross_distance_embed_dim=32, no_torsion=False,
scale_by_sigma=True, use_second_order_repr=False, batch_norm=True,
dynamic_max_cross=False, dropout=0.0, lm_embedding_type=False, confidence_mode=False,
confidence_dropout=0, confidence_no_batchnorm=False, num_confidence_outputs=1):
super(TensorProductScoreModel, self).__init__()
self.t_to_sigma = t_to_sigma
self.in_lig_edge_features = in_lig_edge_features
self.sigma_embed_dim = sigma_embed_dim
self.lig_max_radius = lig_max_radius
self.rec_max_radius = rec_max_radius
self.cross_max_distance = cross_max_distance
self.dynamic_max_cross = dynamic_max_cross
self.center_max_distance = center_max_distance
self.distance_embed_dim = distance_embed_dim
self.cross_distance_embed_dim = cross_distance_embed_dim
self.sh_irreps = o3.Irreps.spherical_harmonics(lmax=sh_lmax)
self.ns, self.nv = ns, nv
self.scale_by_sigma = scale_by_sigma
self.device = device
self.no_torsion = no_torsion
self.num_conv_layers = num_conv_layers
self.timestep_emb_func = timestep_emb_func
self.confidence_mode = confidence_mode
self.num_conv_layers = num_conv_layers
# embedding layers
self.lig_node_embedding = AtomEncoder(emb_dim=ns, feature_dims=lig_feature_dims, sigma_embed_dim=sigma_embed_dim)
self.lig_edge_embedding = nn.Sequential(nn.Linear(in_lig_edge_features + sigma_embed_dim + distance_embed_dim, ns),nn.ReLU(),nn.Dropout(dropout),nn.Linear(ns, ns))
self.rec_node_embedding = AtomEncoder(emb_dim=ns, feature_dims=rec_residue_feature_dims, sigma_embed_dim=sigma_embed_dim, lm_embedding_type=lm_embedding_type)
self.rec_edge_embedding = nn.Sequential(nn.Linear(sigma_embed_dim + distance_embed_dim, ns), nn.ReLU(), nn.Dropout(dropout),nn.Linear(ns, ns))
self.atom_node_embedding = AtomEncoder(emb_dim=ns, feature_dims=rec_atom_feature_dims, sigma_embed_dim=sigma_embed_dim)
self.atom_edge_embedding = nn.Sequential(nn.Linear(sigma_embed_dim + distance_embed_dim, ns), nn.ReLU(), nn.Dropout(dropout),nn.Linear(ns, ns))
self.lr_edge_embedding = nn.Sequential(nn.Linear(sigma_embed_dim + cross_distance_embed_dim, ns), nn.ReLU(), nn.Dropout(dropout),nn.Linear(ns, ns))
self.ar_edge_embedding = nn.Sequential(nn.Linear(sigma_embed_dim + distance_embed_dim, ns), nn.ReLU(), nn.Dropout(dropout),nn.Linear(ns, ns))
self.la_edge_embedding = nn.Sequential(nn.Linear(sigma_embed_dim + cross_distance_embed_dim, ns), nn.ReLU(), nn.Dropout(dropout),nn.Linear(ns, ns))
self.lig_distance_expansion = GaussianSmearing(0.0, lig_max_radius, distance_embed_dim)
self.rec_distance_expansion = GaussianSmearing(0.0, rec_max_radius, distance_embed_dim)
self.cross_distance_expansion = GaussianSmearing(0.0, cross_max_distance, cross_distance_embed_dim)
if use_second_order_repr:
irrep_seq = [
f'{ns}x0e',
f'{ns}x0e + {nv}x1o + {nv}x2e',
f'{ns}x0e + {nv}x1o + {nv}x2e + {nv}x1e + {nv}x2o',
f'{ns}x0e + {nv}x1o + {nv}x2e + {nv}x1e + {nv}x2o + {ns}x0o'
]
else:
irrep_seq = [
f'{ns}x0e',
f'{ns}x0e + {nv}x1o',
f'{ns}x0e + {nv}x1o + {nv}x1e',
f'{ns}x0e + {nv}x1o + {nv}x1e + {ns}x0o'
]
# convolutional layers
conv_layers = []
for i in range(num_conv_layers):
in_irreps = irrep_seq[min(i, len(irrep_seq) - 1)]
out_irreps = irrep_seq[min(i + 1, len(irrep_seq) - 1)]
parameters = {
'in_irreps': in_irreps,
'sh_irreps': self.sh_irreps,
'out_irreps': out_irreps,
'n_edge_features': 3 * ns,
'residual': False,
'batch_norm': batch_norm,
'dropout': dropout
}
for _ in range(9): # 3 intra & 6 inter per each layer
conv_layers.append(TensorProductConvLayer(**parameters))
self.conv_layers = nn.ModuleList(conv_layers)
# confidence and affinity prediction layers
if self.confidence_mode:
output_confidence_dim = num_confidence_outputs
self.confidence_predictor = nn.Sequential(
nn.Linear(2 * self.ns if num_conv_layers >= 3 else self.ns, ns),
nn.BatchNorm1d(ns) if not confidence_no_batchnorm else nn.Identity(),
nn.ReLU(),
nn.Dropout(confidence_dropout),
nn.Linear(ns, ns),
nn.BatchNorm1d(ns) if not confidence_no_batchnorm else nn.Identity(),
nn.ReLU(),
nn.Dropout(confidence_dropout),
nn.Linear(ns, output_confidence_dim)
)
else:
# convolution for translational and rotational scores
self.center_distance_expansion = GaussianSmearing(0.0, center_max_distance, distance_embed_dim)
self.center_edge_embedding = nn.Sequential(
nn.Linear(distance_embed_dim + sigma_embed_dim, ns),
nn.ReLU(),
nn.Dropout(dropout),
nn.Linear(ns, ns)
)
self.final_conv = TensorProductConvLayer(
in_irreps=self.conv_layers[-1].out_irreps,
sh_irreps=self.sh_irreps,
out_irreps=f'2x1o + 2x1e',
n_edge_features=2 * ns,
residual=False,
dropout=dropout,
batch_norm=batch_norm
)
self.tr_final_layer = nn.Sequential(nn.Linear(1 + sigma_embed_dim, ns), nn.Dropout(dropout), nn.ReLU(), nn.Linear(ns, 1))
self.rot_final_layer = nn.Sequential(nn.Linear(1 + sigma_embed_dim, ns), nn.Dropout(dropout), nn.ReLU(), nn.Linear(ns, 1))
if not no_torsion:
# convolution for torsional score
self.final_edge_embedding = nn.Sequential(
nn.Linear(distance_embed_dim, ns),
nn.ReLU(),
nn.Dropout(dropout),
nn.Linear(ns, ns)
)
self.final_tp_tor = o3.FullTensorProduct(self.sh_irreps, "2e")
self.tor_bond_conv = TensorProductConvLayer(
in_irreps=self.conv_layers[-1].out_irreps,
sh_irreps=self.final_tp_tor.irreps_out,
out_irreps=f'{ns}x0o + {ns}x0e',
n_edge_features=3 * ns,
residual=False,
dropout=dropout,
batch_norm=batch_norm
)
self.tor_final_layer = nn.Sequential(
nn.Linear(2 * ns if not self.odd_parity else ns, ns, bias=False),
nn.Tanh(),
nn.Dropout(dropout),
nn.Linear(ns, 1, bias=False)
)
def forward(self, data):
if not self.confidence_mode:
tr_sigma, rot_sigma, tor_sigma = self.t_to_sigma(*[data.complex_t[noise_type] for noise_type in ['tr', 'rot', 'tor']])
else:
tr_sigma, rot_sigma, tor_sigma = [data.complex_t[noise_type] for noise_type in ['tr', 'rot', 'tor']]
# build ligand graph
lig_node_attr, lig_edge_index, lig_edge_attr, lig_edge_sh = self.build_lig_conv_graph(data)
lig_node_attr = self.lig_node_embedding(lig_node_attr)
lig_edge_attr = self.lig_edge_embedding(lig_edge_attr)
# build receptor graph
rec_node_attr, rec_edge_index, rec_edge_attr, rec_edge_sh = self.build_rec_conv_graph(data)
rec_node_attr = self.rec_node_embedding(rec_node_attr)
rec_edge_attr = self.rec_edge_embedding(rec_edge_attr)
# build atom graph
atom_node_attr, atom_edge_index, atom_edge_attr, atom_edge_sh = self.build_atom_conv_graph(data)
atom_node_attr = self.atom_node_embedding(atom_node_attr)
atom_edge_attr = self.atom_edge_embedding(atom_edge_attr)
# build cross graph
cross_cutoff = (tr_sigma * 3 + 20).unsqueeze(1) if self.dynamic_max_cross else self.cross_max_distance
lr_edge_index, lr_edge_attr, lr_edge_sh, la_edge_index, la_edge_attr, \
la_edge_sh, ar_edge_index, ar_edge_attr, ar_edge_sh = self.build_cross_conv_graph(data, cross_cutoff)
lr_edge_attr= self.lr_edge_embedding(lr_edge_attr)
la_edge_attr = self.la_edge_embedding(la_edge_attr)
ar_edge_attr = self.ar_edge_embedding(ar_edge_attr)
for l in range(self.num_conv_layers):
# LIGAND updates
lig_edge_attr_ = torch.cat([lig_edge_attr, lig_node_attr[lig_edge_index[0], :self.ns], lig_node_attr[lig_edge_index[1], :self.ns]], -1)
lig_update = self.conv_layers[9*l](lig_node_attr, lig_edge_index, lig_edge_attr_, lig_edge_sh)
lr_edge_attr_ = torch.cat([lr_edge_attr, lig_node_attr[lr_edge_index[0], :self.ns], rec_node_attr[lr_edge_index[1], :self.ns]], -1)
lr_update = self.conv_layers[9*l+1](rec_node_attr, lr_edge_index, lr_edge_attr_, lr_edge_sh,
out_nodes=lig_node_attr.shape[0])
la_edge_attr_ = torch.cat([la_edge_attr, lig_node_attr[la_edge_index[0], :self.ns], atom_node_attr[la_edge_index[1], :self.ns]], -1)
la_update = self.conv_layers[9*l+2](atom_node_attr, la_edge_index, la_edge_attr_, la_edge_sh,
out_nodes=lig_node_attr.shape[0])
if l != self.num_conv_layers-1: # last layer optimisation
# ATOM UPDATES
atom_edge_attr_ = torch.cat([atom_edge_attr, atom_node_attr[atom_edge_index[0], :self.ns], atom_node_attr[atom_edge_index[1], :self.ns]], -1)
atom_update = self.conv_layers[9*l+3](atom_node_attr, atom_edge_index, atom_edge_attr_, atom_edge_sh)
al_edge_attr_ = torch.cat([la_edge_attr, atom_node_attr[la_edge_index[1], :self.ns], lig_node_attr[la_edge_index[0], :self.ns]], -1)
al_update = self.conv_layers[9*l+4](lig_node_attr, torch.flip(la_edge_index, dims=[0]), al_edge_attr_,
la_edge_sh, out_nodes=atom_node_attr.shape[0])
ar_edge_attr_ = torch.cat([ar_edge_attr, atom_node_attr[ar_edge_index[0], :self.ns], rec_node_attr[ar_edge_index[1], :self.ns]],-1)
ar_update = self.conv_layers[9*l+5](rec_node_attr, ar_edge_index, ar_edge_attr_, ar_edge_sh, out_nodes=atom_node_attr.shape[0])
# RECEPTOR updates
rec_edge_attr_ = torch.cat([rec_edge_attr, rec_node_attr[rec_edge_index[0], :self.ns], rec_node_attr[rec_edge_index[1], :self.ns]], -1)
rec_update = self.conv_layers[9*l+6](rec_node_attr, rec_edge_index, rec_edge_attr_, rec_edge_sh)
rl_edge_attr_ = torch.cat([lr_edge_attr, rec_node_attr[lr_edge_index[1], :self.ns], lig_node_attr[lr_edge_index[0], :self.ns]], -1)
rl_update = self.conv_layers[9*l+7](lig_node_attr, torch.flip(lr_edge_index, dims=[0]), rl_edge_attr_,
lr_edge_sh, out_nodes=rec_node_attr.shape[0])
ra_edge_attr_ = torch.cat([ar_edge_attr, rec_node_attr[ar_edge_index[1], :self.ns], atom_node_attr[ar_edge_index[0], :self.ns]], -1)
ra_update = self.conv_layers[9*l+8](atom_node_attr, torch.flip(ar_edge_index, dims=[0]), ra_edge_attr_,
ar_edge_sh, out_nodes=rec_node_attr.shape[0])
# padding original features and update features with residual updates
lig_node_attr = F.pad(lig_node_attr, (0, lig_update.shape[-1] - lig_node_attr.shape[-1]))
lig_node_attr = lig_node_attr + lig_update + la_update + lr_update
if l != self.num_conv_layers - 1: # last layer optimisation
atom_node_attr = F.pad(atom_node_attr, (0, atom_update.shape[-1] - rec_node_attr.shape[-1]))
atom_node_attr = atom_node_attr + atom_update + al_update + ar_update
rec_node_attr = F.pad(rec_node_attr, (0, rec_update.shape[-1] - rec_node_attr.shape[-1]))
rec_node_attr = rec_node_attr + rec_update + ra_update + rl_update
# confidence and affinity prediction
if self.confidence_mode:
scalar_lig_attr = torch.cat([lig_node_attr[:,:self.ns],lig_node_attr[:,-self.ns:]], dim=1) if self.num_conv_layers >= 3 else lig_node_attr[:,:self.ns]
confidence = self.confidence_predictor(scatter_mean(scalar_lig_attr, data['ligand'].batch, dim=0)).squeeze(dim=-1)
return confidence
# compute translational and rotational score vectors
center_edge_index, center_edge_attr, center_edge_sh = self.build_center_conv_graph(data)
center_edge_attr = self.center_edge_embedding(center_edge_attr)
center_edge_attr = torch.cat([center_edge_attr, lig_node_attr[center_edge_index[0], :self.ns]], -1)
global_pred = self.final_conv(lig_node_attr, center_edge_index, center_edge_attr, center_edge_sh, out_nodes=data.num_graphs)
tr_pred = global_pred[:, :3] + global_pred[:, 6:9]
rot_pred = global_pred[:, 3:6] + global_pred[:, 9:]
data.graph_sigma_emb = self.timestep_emb_func(data.complex_t['tr'])
# adjust the magniture of the score vectors
tr_norm = torch.linalg.vector_norm(tr_pred, dim=1).unsqueeze(1)
tr_pred = tr_pred / tr_norm * self.tr_final_layer(torch.cat([tr_norm, data.graph_sigma_emb], dim=1))
rot_norm = torch.linalg.vector_norm(rot_pred, dim=1).unsqueeze(1)
rot_pred = rot_pred / rot_norm * self.rot_final_layer(torch.cat([rot_norm, data.graph_sigma_emb], dim=1))
if self.scale_by_sigma:
tr_pred = tr_pred / tr_sigma.unsqueeze(1)
rot_pred = rot_pred * so3.score_norm(rot_sigma.cpu()).unsqueeze(1).to(data['ligand'].x.device)
if self.no_torsion or data['ligand'].edge_mask.sum() == 0: return tr_pred, rot_pred, torch.empty(0,device=self.device)
# torsional components
tor_bonds, tor_edge_index, tor_edge_attr, tor_edge_sh = self.build_bond_conv_graph(data)
tor_bond_vec = data['ligand'].pos[tor_bonds[1]] - data['ligand'].pos[tor_bonds[0]]
tor_bond_attr = lig_node_attr[tor_bonds[0]] + lig_node_attr[tor_bonds[1]]
tor_bonds_sh = o3.spherical_harmonics("2e", tor_bond_vec, normalize=True, normalization='component')
tor_edge_sh = self.final_tp_tor(tor_edge_sh, tor_bonds_sh[tor_edge_index[0]])
tor_edge_attr = torch.cat([tor_edge_attr, lig_node_attr[tor_edge_index[1], :self.ns],
tor_bond_attr[tor_edge_index[0], :self.ns]], -1)
tor_pred = self.tor_bond_conv(lig_node_attr, tor_edge_index, tor_edge_attr, tor_edge_sh,
out_nodes=data['ligand'].edge_mask.sum(), reduce='mean')
tor_pred = self.tor_final_layer(tor_pred).squeeze(1)
edge_sigma = tor_sigma[data['ligand'].batch][data['ligand', 'ligand'].edge_index[0]][data['ligand'].edge_mask]
if self.scale_by_sigma:
tor_pred = tor_pred * torch.sqrt(torch.tensor(torus.score_norm(edge_sigma.cpu().numpy())).float()
.to(data['ligand'].x.device))
return tr_pred, rot_pred, tor_pred
def build_lig_conv_graph(self, data):
# build the graph between ligand atoms
data['ligand'].node_sigma_emb = self.timestep_emb_func(data['ligand'].node_t['tr'])
radius_edges = radius_graph(data['ligand'].pos, self.lig_max_radius, data['ligand'].batch)
edge_index = torch.cat([data['ligand', 'ligand'].edge_index, radius_edges], 1).long()
edge_attr = torch.cat([
data['ligand', 'ligand'].edge_attr,
torch.zeros(radius_edges.shape[-1], self.in_lig_edge_features, device=data['ligand'].x.device)
], 0)
edge_sigma_emb = data['ligand'].node_sigma_emb[edge_index[0].long()]
edge_attr = torch.cat([edge_attr, edge_sigma_emb], 1)
node_attr = torch.cat([data['ligand'].x, data['ligand'].node_sigma_emb], 1)
src, dst = edge_index
edge_vec = data['ligand'].pos[dst.long()] - data['ligand'].pos[src.long()]
edge_length_emb = self.lig_distance_expansion(edge_vec.norm(dim=-1))
edge_attr = torch.cat([edge_attr, edge_length_emb], 1)
edge_sh = o3.spherical_harmonics(self.sh_irreps, edge_vec, normalize=True, normalization='component')
return node_attr, edge_index, edge_attr, edge_sh
def build_rec_conv_graph(self, data):
# build the graph between receptor residues
data['receptor'].node_sigma_emb = self.timestep_emb_func(data['receptor'].node_t['tr'])
node_attr = torch.cat([data['receptor'].x, data['receptor'].node_sigma_emb], 1)
# this assumes the edges were already created in preprocessing since protein's structure is fixed
edge_index = data['receptor', 'receptor'].edge_index
src, dst = edge_index
edge_vec = data['receptor'].pos[dst.long()] - data['receptor'].pos[src.long()]
edge_length_emb = self.rec_distance_expansion(edge_vec.norm(dim=-1))
edge_sigma_emb = data['receptor'].node_sigma_emb[edge_index[0].long()]
edge_attr = torch.cat([edge_sigma_emb, edge_length_emb], 1)
edge_sh = o3.spherical_harmonics(self.sh_irreps, edge_vec, normalize=True, normalization='component')
return node_attr, edge_index, edge_attr, edge_sh
def build_atom_conv_graph(self, data):
# build the graph between receptor atoms
data['atom'].node_sigma_emb = self.timestep_emb_func(data['atom'].node_t['tr'])
node_attr = torch.cat([data['atom'].x, data['atom'].node_sigma_emb], 1)
# this assumes the edges were already created in preprocessing since protein's structure is fixed
edge_index = data['atom', 'atom'].edge_index
src, dst = edge_index
edge_vec = data['atom'].pos[dst.long()] - data['atom'].pos[src.long()]
edge_length_emb = self.lig_distance_expansion(edge_vec.norm(dim=-1))
edge_sigma_emb = data['atom'].node_sigma_emb[edge_index[0].long()]
edge_attr = torch.cat([edge_sigma_emb, edge_length_emb], 1)
edge_sh = o3.spherical_harmonics(self.sh_irreps, edge_vec, normalize=True, normalization='component')
return node_attr, edge_index, edge_attr, edge_sh
def build_cross_conv_graph(self, data, lr_cross_distance_cutoff):
# build the cross edges between ligan atoms, receptor residues and receptor atoms
# LIGAND to RECEPTOR
if torch.is_tensor(lr_cross_distance_cutoff):
# different cutoff for every graph
lr_edge_index = radius(data['receptor'].pos / lr_cross_distance_cutoff[data['receptor'].batch],
data['ligand'].pos / lr_cross_distance_cutoff[data['ligand'].batch], 1,
data['receptor'].batch, data['ligand'].batch, max_num_neighbors=10000)
else:
lr_edge_index = radius(data['receptor'].pos, data['ligand'].pos, lr_cross_distance_cutoff,
data['receptor'].batch, data['ligand'].batch, max_num_neighbors=10000)
lr_edge_vec = data['receptor'].pos[lr_edge_index[1].long()] - data['ligand'].pos[lr_edge_index[0].long()]
lr_edge_length_emb = self.cross_distance_expansion(lr_edge_vec.norm(dim=-1))
lr_edge_sigma_emb = data['ligand'].node_sigma_emb[lr_edge_index[0].long()]
lr_edge_attr = torch.cat([lr_edge_sigma_emb, lr_edge_length_emb], 1)
lr_edge_sh = o3.spherical_harmonics(self.sh_irreps, lr_edge_vec, normalize=True, normalization='component')
cutoff_d = lr_cross_distance_cutoff[data['ligand'].batch[lr_edge_index[0]]].squeeze() \
if torch.is_tensor(lr_cross_distance_cutoff) else lr_cross_distance_cutoff
# LIGAND to ATOM
la_edge_index = radius(data['atom'].pos, data['ligand'].pos, self.lig_max_radius,
data['atom'].batch, data['ligand'].batch, max_num_neighbors=10000)
la_edge_vec = data['atom'].pos[la_edge_index[1].long()] - data['ligand'].pos[la_edge_index[0].long()]
la_edge_length_emb = self.cross_distance_expansion(la_edge_vec.norm(dim=-1))
la_edge_sigma_emb = data['ligand'].node_sigma_emb[la_edge_index[0].long()]
la_edge_attr = torch.cat([la_edge_sigma_emb, la_edge_length_emb], 1)
la_edge_sh = o3.spherical_harmonics(self.sh_irreps, la_edge_vec, normalize=True, normalization='component')
# ATOM to RECEPTOR
ar_edge_index = data['atom', 'receptor'].edge_index
ar_edge_vec = data['receptor'].pos[ar_edge_index[1].long()] - data['atom'].pos[ar_edge_index[0].long()]
ar_edge_length_emb = self.rec_distance_expansion(ar_edge_vec.norm(dim=-1))
ar_edge_sigma_emb = data['atom'].node_sigma_emb[ar_edge_index[0].long()]
ar_edge_attr = torch.cat([ar_edge_sigma_emb, ar_edge_length_emb], 1)
ar_edge_sh = o3.spherical_harmonics(self.sh_irreps, ar_edge_vec, normalize=True, normalization='component')
return lr_edge_index, lr_edge_attr, lr_edge_sh, la_edge_index, la_edge_attr, \
la_edge_sh, ar_edge_index, ar_edge_attr, ar_edge_sh
def build_center_conv_graph(self, data):
# build the filter for the convolution of the center with the ligand atoms
# for translational and rotational score
edge_index = torch.cat([data['ligand'].batch.unsqueeze(0), torch.arange(len(data['ligand'].batch)).to(data['ligand'].x.device).unsqueeze(0)], dim=0)
center_pos, count = torch.zeros((data.num_graphs, 3)).to(data['ligand'].x.device), torch.zeros((data.num_graphs, 3)).to(data['ligand'].x.device)
center_pos.index_add_(0, index=data['ligand'].batch, source=data['ligand'].pos)
center_pos = center_pos / torch.bincount(data['ligand'].batch).unsqueeze(1)
edge_vec = data['ligand'].pos[edge_index[1]] - center_pos[edge_index[0]]
edge_attr = self.center_distance_expansion(edge_vec.norm(dim=-1))
edge_sigma_emb = data['ligand'].node_sigma_emb[edge_index[1].long()]
edge_attr = torch.cat([edge_attr, edge_sigma_emb], 1)
edge_sh = o3.spherical_harmonics(self.sh_irreps, edge_vec, normalize=True, normalization='component')
return edge_index, edge_attr, edge_sh
def build_bond_conv_graph(self, data):
# build graph for the pseudotorque layer
bonds = data['ligand', 'ligand'].edge_index[:, data['ligand'].edge_mask].long()
bond_pos = (data['ligand'].pos[bonds[0]] + data['ligand'].pos[bonds[1]]) / 2
bond_batch = data['ligand'].batch[bonds[0]]
edge_index = radius(data['ligand'].pos, bond_pos, self.lig_max_radius, batch_x=data['ligand'].batch, batch_y=bond_batch)
edge_vec = data['ligand'].pos[edge_index[1]] - bond_pos[edge_index[0]]
edge_attr = self.lig_distance_expansion(edge_vec.norm(dim=-1))
edge_attr = self.final_edge_embedding(edge_attr)
edge_sh = o3.spherical_harmonics(self.sh_irreps, edge_vec, normalize=True, normalization='component')
return bonds, edge_index, edge_attr, edge_sh