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inference.yaml
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inference.yaml
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test_set:
class: SideChainDataset
path: null
atom_feature: residue_symbol
bond_feature: null
residue_feature: null
mol_feature: null
sanitize: true
removeHs: true
transform:
class: Compose
transforms: []
task:
class: TorsionalDiffusion
train_chi_id: null
schedule_1pi_periodic:
class: SO2VESchedule
pi_periodic: true
annealed_temp: 3
cache_folder: ~/scratch/output/diffpack
mode: ode
schedule_2pi_periodic:
class: SO2VESchedule
pi_periodic: false
annealed_temp: 3
cache_folder: ~/scratch/output/diffpack
mode: ode
sigma_embedding:
class: SigmaEmbeddingLayer
input_dim: 39
hidden_dims: [ 64, 128 ]
sigma_dim: 64
model:
class: GearNet
input_dim: 128
hidden_dims: [128, 128, 128, 128, 128, 128]
batch_norm: True
concat_hidden: True
short_cut: True
readout: 'sum'
num_relation: 6
edge_input_dim: 58
num_angle_bin: 8
torsion_mlp_hidden_dims: [ 64, 128 ]
graph_construction_model:
class: GraphConstruction
edge_layers:
- class: BondEdge
- class: SpatialEdge
radius: 4.5
min_distance: 2
- class: KNNEdge
k: 10
min_distance: 0
edge_feature: gearnet
optimizer:
class: Adam
lr: 1.0e-4
engine:
gpus: [0] #, 1, 2, 3]
batch_size: 32
log_interval: 1000
model_checkpoint: ~/scratch/trained_model/diffpack/gearnet_edge_confidence_converted.pth
train:
num_epoch: 0