Delete configs

configs/geom_difflinker.yml

@@ -1,38 +0,0 @@
-exp_name: 'geom_difflinker'
-data: datasets
-train_data_prefix: geom_multifrag_train
-val_data_prefix: geom_multifrag_val
-checkpoints: models
-logs: logs
-device: gpu
-log_iterations: null
-wandb_entity: null
-enable_progress_bar: False
-
-model: egnn_dynamics
-lr: 2.0e-4
-batch_size: 64
-n_layers: 6
-n_epochs: 1500
-test_epochs: 20
-n_stability_samples: 10
-nf: 128
-activation: silu
-attention: False
-condition_time: True
-tanh: False
-norm_constant: 0.000001
-inv_sublayers: 2
-include_charges: False
-diffusion_loss_type: l2
-data_augmentation: False
-center_of_mass: fragments
-remove_anchors_context: True
-
-sin_embedding: False
-normalization_factor: 100
-normalize_factors: [1, 4, 10]
-aggregation_method: 'sum'
-normalization: batch_norm
-
-resume:

configs/geom_difflinker_given_anchors.yml

@@ -1,37 +0,0 @@
-exp_name: 'geom_difflinker_given_anchors'
-data: datasets
-train_data_prefix: geom_multifrag_train
-val_data_prefix: geom_multifrag_val
-checkpoints: models
-logs: logs
-device: gpu
-log_iterations: null
-wandb_entity: null
-enable_progress_bar: False
-
-model: egnn_dynamics
-lr: 2.0e-4
-batch_size: 128
-n_layers: 6
-n_epochs: 1500
-test_epochs: 20
-n_stability_samples: 10
-nf: 128
-activation: silu
-attention: False
-condition_time: True
-tanh: False
-norm_constant: 0.000001
-inv_sublayers: 2
-include_charges: False
-diffusion_loss_type: l2
-data_augmentation: False
-center_of_mass: anchors
-
-sin_embedding: False
-normalization_factor: 100
-normalize_factors: [1, 4, 10]
-aggregation_method: 'sum'
-normalization: batch_norm
-
-resume:

configs/pockets_difflinker_backbone.yml

@@ -1,38 +0,0 @@
-exp_name: 'pockets_difflinker_backbone'
-data: datasets
-train_data_prefix: MOAD_train.bb
-val_data_prefix: MOAD_val.bb
-checkpoints: models
-logs: logs
-device: gpu
-log_iterations: null
-wandb_entity: null
-enable_progress_bar: False
-
-model: egnn_dynamics
-lr: 2.0e-4
-batch_size: 32
-n_layers: 6
-n_epochs: 1000
-test_epochs: 20
-n_stability_samples: 5
-nf: 128
-activation: silu
-attention: False
-condition_time: True
-tanh: False
-norm_constant: 0.000001
-inv_sublayers: 2
-include_charges: False
-diffusion_loss_type: l2
-data_augmentation: False
-center_of_mass: anchors
-graph_type: 4A
-
-sin_embedding: False
-normalization_factor: 100
-normalize_factors: [1, 4, 10]
-aggregation_method: 'sum'
-normalization: batch_norm
-
-resume:

configs/pockets_difflinker_full.yml

@@ -1,38 +0,0 @@
-exp_name: 'pockets_difflinker_full'
-data: datasets
-train_data_prefix: MOAD_train.full
-val_data_prefix: MOAD_val.full
-checkpoints: models
-logs: logs
-device: gpu
-log_iterations: null
-wandb_entity: null
-enable_progress_bar: False
-
-model: egnn_dynamics
-lr: 2.0e-4
-batch_size: 32
-n_layers: 6
-n_epochs: 1000
-test_epochs: 20
-n_stability_samples: 5
-nf: 128
-activation: silu
-attention: False
-condition_time: True
-tanh: False
-norm_constant: 0.000001
-inv_sublayers: 2
-include_charges: False
-diffusion_loss_type: l2
-data_augmentation: False
-center_of_mass: anchors
-graph_type: 4A
-
-sin_embedding: False
-normalization_factor: 100
-normalize_factors: [1, 4, 10]
-aggregation_method: 'sum'
-normalization: batch_norm
-
-resume:

configs/pockets_difflinker_full_no_anchors.yml

@@ -1,39 +0,0 @@
-exp_name: 'pockets_difflinker_full'
-data: datasets
-train_data_prefix: MOAD_train.full
-val_data_prefix: MOAD_val.full
-checkpoints: models
-logs: logs
-device: gpu
-log_iterations: null
-wandb_entity: null
-enable_progress_bar: False
-
-model: egnn_dynamics
-lr: 2.0e-4
-batch_size: 32
-n_layers: 6
-n_epochs: 1000
-test_epochs: 20
-n_stability_samples: 5
-nf: 128
-activation: silu
-attention: False
-condition_time: True
-tanh: False
-norm_constant: 0.000001
-inv_sublayers: 2
-include_charges: False
-diffusion_loss_type: l2
-data_augmentation: False
-center_of_mass: fragments
-remove_anchors_context: True
-graph_type: 4A
-
-sin_embedding: False
-normalization_factor: 100
-normalize_factors: [1, 4, 10]
-aggregation_method: 'sum'
-normalization: batch_norm
-
-resume:

configs/pockets_difflinker_full_no_anchors_fc.yml

@@ -1,39 +0,0 @@
-exp_name: 'pockets_full_no_anchors_fc'
-data: /home/igashov/work/diffusion_linker_data/e3_ddpm_linker_design/bindingmoad
-train_data_prefix: MOAD_train.full
-val_data_prefix: MOAD_val.full
-checkpoints: /home/igashov/work/diffusion_linker_data/e3_ddpm_linker_design/checkpoints
-logs: /home/igashov/work/diffusion_linker_data/e3_ddpm_linker_design/logs
-device: gpu
-log_iterations: null
-wandb_entity: geometric
-enable_progress_bar: False
-
-model: egnn_dynamics
-lr: 2.0e-4
-batch_size: 16
-n_layers: 6
-n_epochs: 1000
-test_epochs: 20
-n_stability_samples: 5
-nf: 128
-activation: silu
-attention: False
-condition_time: True
-tanh: False
-norm_constant: 0.000001
-inv_sublayers: 2
-include_charges: False
-diffusion_loss_type: l2
-data_augmentation: False
-center_of_mass: fragments
-remove_anchors_context: True
-graph_type: FC-10A-4A
-
-sin_embedding: False
-normalization_factor: 100
-normalize_factors: [1, 4, 10]
-aggregation_method: 'sum'
-normalization: batch_norm
-
-resume:

configs/pockets_difflinker_unconditioned.yml

@@ -1,38 +0,0 @@
-exp_name: 'pockets_difflinker_unconditioned'
-data: datasets
-train_data_prefix: MOAD_train
-val_data_prefix: MOAD_val
-checkpoints: models
-logs: logs
-device: gpu
-log_iterations: null
-wandb_entity: null
-enable_progress_bar: False
-
-model: egnn_dynamics
-lr: 2.0e-4
-batch_size: 32
-n_layers: 6
-n_epochs: 1000
-test_epochs: 20
-n_stability_samples: 5
-nf: 128
-activation: silu
-attention: False
-condition_time: True
-tanh: False
-norm_constant: 0.000001
-inv_sublayers: 2
-include_charges: False
-diffusion_loss_type: l2
-data_augmentation: False
-center_of_mass: anchors
-graph_type: 4A
-
-sin_embedding: False
-normalization_factor: 100
-normalize_factors: [1, 4, 10]
-aggregation_method: 'sum'
-normalization: batch_norm
-
-resume:

configs/zinc_difflinker.yml

@@ -1,38 +0,0 @@
-exp_name: 'zinc_difflinker'
-data: datasets
-train_data_prefix: zinc_final_train
-val_data_prefix: zinc_final_val
-checkpoints: models
-logs: logs
-device: gpu
-log_iterations: null
-wandb_entity: null
-enable_progress_bar: True
-
-model: egnn_dynamics
-lr: 2.0e-4
-batch_size: 128
-n_layers: 8
-n_epochs: 1000
-test_epochs: 20
-n_stability_samples: 10
-nf: 128
-activation: silu
-attention: False
-condition_time: True
-tanh: False
-norm_constant: 0.000001
-inv_sublayers: 2
-include_charges: False
-diffusion_loss_type: l2
-data_augmentation: False
-center_of_mass: fragments
-remove_anchors_context: True
-
-sin_embedding: False
-normalization_factor: 100
-normalize_factors: [1, 4, 10]
-aggregation_method: 'sum'
-normalization: batch_norm
-
-resume:

configs/zinc_difflinker_given_anchors.yml

@@ -1,37 +0,0 @@
-exp_name: 'zinc_difflinker_given_anchors'
-data: datasets
-train_data_prefix: zinc_final_train
-val_data_prefix: zinc_final_val
-checkpoints: models
-logs: logs
-device: gpu
-log_iterations: null
-wandb_entity: null
-enable_progress_bar: False
-
-model: egnn_dynamics
-lr: 2.0e-4
-batch_size: 128
-n_layers: 8
-n_epochs: 1000
-test_epochs: 20
-n_stability_samples: 10
-nf: 128
-activation: silu
-attention: False
-condition_time: True
-tanh: False
-norm_constant: 0.000001
-inv_sublayers: 2
-include_charges: False
-diffusion_loss_type: l2
-data_augmentation: False
-center_of_mass: anchors
-
-sin_embedding: False
-normalization_factor: 100
-normalize_factors: [1, 4, 10]
-aggregation_method: 'sum'
-normalization: batch_norm
-
-resume: