Merge branch 'main' of hf.co:spaces/libokj/GenFBDD

app/main.py

@@ -1,3 +1,4 @@
+import os
 import uuid
 import zipfile
 from datetime import datetime
@@ -22,6 +23,7 @@ from app import static, fn, db
 
 gr.set_static_paths(paths=["data/", "results/", "app/"])
 job_db = db.init_job_db()
+os.chmod('./fpocket', 0o755)
 
 FRAG_LIBS = {'': None} | {
     lib_path.stem.replace('_', ' '): str(lib_path) for lib_path in Path('data/fragment_libraries').glob('*')

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:

fpocket

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:7754e5992549d29ae2e31ca88c14ba49d8d5dccab234444859f932e231a49641
+size 1772592

resources/checkpoints/DiffDock/confidence_model/model_parameters.yml

@@ -1,117 +1,117 @@
-affinity_prediction: false
-all_atoms: true
-asyncronous_noise_schedule: false
-atom_max_neighbors: 8
-atom_radius: 5
-balance: false
-batch_size: 16
-best_model_save_frequency: 5
-c_alpha_max_neighbors: 24
-cache_creation_id: 1
-cache_ids_to_combine:
-- '1'
-- '2'
-- '3'
-- '4'
-cache_path: data/cacheNew
-chain_cutoff: 10
-ckpt: best_model.pt
-confidence_dropout: 0.0
-confidence_loss_weigth: 1
-confidence_no_batchnorm: false
-confidence_weight: 0.33
-config: null
-correct_torsion_sigmas: true
-cross_distance_embed_dim: 32
-cross_max_distance: 80
-data_dir: data/PDBBind_processed/
-dataloader_drop_last: false
-different_schedules: false
-distance_embed_dim: 32
-dropout: 0.1
-dynamic_max_cross: true
-embedding_scale: 10000
-embedding_type: sinusoidal
-esm_embeddings_path: data/esm2_3billion_embeddings.pt
-high_confidence_threshold: 5.0
-include_confidence_prediction: false
-inf_sched_alpha: 1.0
-inf_sched_beta: 1.0
-inference_steps: 20
-limit_complexes: 0
-lm_embeddings_path: null
-log_dir: workdir
-lr: 0.0003
-main_metric: loss
-main_metric_goal: min
-matching_maxiter: 20
-matching_popsize: 20
-max_lig_size: null
-max_radius: 5.0
-model_save_frequency: 0
-multiplicity: 1
-n_epochs: 100
-no_batch_norm: false
-no_torsion: false
-norm_by_sigma: false
-not_full_dataset: false
-ns: 24
-num_conformers: 1
-num_conv_layers: 5
-num_workers: 1
-nv: 6
-odd_parity: false
-original_model_dir: workdir/temp_restart_ema_ESM2emb_tr34
-parallel: 1
-parallel_aggregators: mean max min std
-project: ligbind_filtering
-receptor_radius: 15.0
-remove_hs: true
-restart_dir: null
-rmsd_classification_cutoff:
-- 2.0
-rmsd_prediction: false
-rot_alpha: 1
-rot_beta: 1
-rot_inf_sched_alpha: 1
-rot_inf_sched_beta: 1
-rot_sigma_max: 1.55
-rot_sigma_min: 0.03
-rot_sigma_schedule: expbeta
-rot_sigmoid_schedule: false
-rot_weight: 0.33
-run_name: fixedSamples28_id1_FILTERFROM_temp_restart_ema_ESM2emb_tr34
-samples_per_complex: 7
-sampling_alpha: 1
-sampling_beta: 1
-scale_by_sigma: true
-schedule_k: 10
-schedule_m: 0.4
-scheduler: plateau
-scheduler_patience: 50
-separate_noise_schedule: false
-sigma_embed_dim: 32
-sigma_schedule: expbeta
-smooth_edges: false
-split_test: data/splits/timesplit_test
-split_train: data/splits/timesplit_no_lig_overlap_train
-split_val: data/splits/timesplit_no_lig_overlap_val
-tor_alpha: 1
-tor_beta: 1
-tor_inf_sched_alpha: 1
-tor_inf_sched_beta: 1
-tor_sigma_max: 3.14
-tor_sigma_min: 0.0314
-tor_sigma_schedule: expbeta
-tor_weight: 0.33
-tp_attention: false
-tr_only_confidence: true
-tr_sigma_max: 34.0
-tr_sigma_min: 0.1
-tr_weight: 0.33
-train_sampling: linear
-transfer_weights: false
-use_original_model_cache: false
-use_second_order_repr: false
-w_decay: 0.0
-wandb: true
+affinity_prediction: false
+all_atoms: true
+asyncronous_noise_schedule: false
+atom_max_neighbors: 8
+atom_radius: 5
+balance: false
+batch_size: 16
+best_model_save_frequency: 5
+c_alpha_max_neighbors: 24
+cache_creation_id: 1
+cache_ids_to_combine:
+- '1'
+- '2'
+- '3'
+- '4'
+cache_path: data/cacheNew
+chain_cutoff: 10
+ckpt: best_model.pt
+confidence_dropout: 0.0
+confidence_loss_weigth: 1
+confidence_no_batchnorm: false
+confidence_weight: 0.33
+config: null
+correct_torsion_sigmas: true
+cross_distance_embed_dim: 32
+cross_max_distance: 80
+data_dir: data/PDBBind_processed/
+dataloader_drop_last: false
+different_schedules: false
+distance_embed_dim: 32
+dropout: 0.1
+dynamic_max_cross: true
+embedding_scale: 10000
+embedding_type: sinusoidal
+esm_embeddings_path: data/esm2_3billion_embeddings.pt
+high_confidence_threshold: 5.0
+include_confidence_prediction: false
+inf_sched_alpha: 1.0
+inf_sched_beta: 1.0
+inference_steps: 20
+limit_complexes: 0
+lm_embeddings_path: null
+log_dir: workdir
+lr: 0.0003
+main_metric: loss
+main_metric_goal: min
+matching_maxiter: 20
+matching_popsize: 20
+max_lig_size: null
+max_radius: 5.0
+model_save_frequency: 0
+multiplicity: 1
+n_epochs: 100
+no_batch_norm: false
+no_torsion: false
+norm_by_sigma: false
+not_full_dataset: false
+ns: 24
+num_conformers: 1
+num_conv_layers: 5
+num_workers: 1
+nv: 6
+odd_parity: false
+original_model_dir: workdir/temp_restart_ema_ESM2emb_tr34
+parallel: 1
+parallel_aggregators: mean max min std
+project: ligbind_filtering
+receptor_radius: 15.0
+remove_hs: true
+restart_dir: null
+rmsd_classification_cutoff:
+- 2.0
+rmsd_prediction: false
+rot_alpha: 1
+rot_beta: 1
+rot_inf_sched_alpha: 1
+rot_inf_sched_beta: 1
+rot_sigma_max: 1.55
+rot_sigma_min: 0.03
+rot_sigma_schedule: expbeta
+rot_sigmoid_schedule: false
+rot_weight: 0.33
+run_name: fixedSamples28_id1_FILTERFROM_temp_restart_ema_ESM2emb_tr34
+samples_per_complex: 7
+sampling_alpha: 1
+sampling_beta: 1
+scale_by_sigma: true
+schedule_k: 10
+schedule_m: 0.4
+scheduler: plateau
+scheduler_patience: 50
+separate_noise_schedule: false
+sigma_embed_dim: 32
+sigma_schedule: expbeta
+smooth_edges: false
+split_test: data/splits/timesplit_test
+split_train: data/splits/timesplit_no_lig_overlap_train
+split_val: data/splits/timesplit_no_lig_overlap_val
+tor_alpha: 1
+tor_beta: 1
+tor_inf_sched_alpha: 1
+tor_inf_sched_beta: 1
+tor_sigma_max: 3.14
+tor_sigma_min: 0.0314
+tor_sigma_schedule: expbeta
+tor_weight: 0.33
+tp_attention: false
+tr_only_confidence: true
+tr_sigma_max: 34.0
+tr_sigma_min: 0.1
+tr_weight: 0.33
+train_sampling: linear
+transfer_weights: false
+use_original_model_cache: false
+use_second_order_repr: false
+w_decay: 0.0
+wandb: true

resources/checkpoints/DiffDock/score_model/model_parameters.yml

@@ -1,171 +1,171 @@
-add_bootstrapping_dataset: false
-all_atoms: false
-asyncronous_noise_schedule: false
-atom_max_neighbors: 8
-atom_radius: 5
-backbone_loss_weight: 0
-batch_size: 12
-bootstrap_alpha: 1
-bootstrap_beta: 1
-bootstrap_tmin: 0
-bootstrapping_dataset_confidence_cutoff: 0
-bootstrapping_dataset_iterations: 1
-bootstrapping_dataset_max_per_complex: 1000
-bootstrapping_fixed_length: null
-bootstrapping_temperature: 0
-c_alpha_max_neighbors: 24
-cache_creation_id: null
-cache_ids_to_combine: null
-cache_path: cache
-chain_cutoff: 10.0
-combined_training: true
-confidence_dropout: 0.0
-confidence_model_ckpt: best_model.pt
-confidence_model_dir: workdir/masked_confidence_model
-confidence_no_batchnorm: false
-confidence_weight: 0.33
-config: null
-crop_beyond: 20
-cross_distance_embed_dim: 64
-cross_max_distance: 80
-cudnn_benchmark: true
-dataloader_drop_last: false
-dataset: generalisation
-depthwise_convolution: false
-different_schedules: false
-distance_embed_dim: 64
-double_val: true
-dropout: 0.1
-dynamic_max_cross: true
-ema_rate: 0.999
-embed_also_ligand: true
-embedding_scale: 1000
-embedding_type: sinusoidal
-enforce_timesplit: true
-esm_embeddings_model: null
-freeze_params: 0
-high_confidence_threshold: 5.0
-include_confidence_prediction: false
-include_miscellaneous_atoms: false
-inf_pocket_cutoff: 5
-inf_pocket_knowledge: false
-inf_sched_alpha: 1
-inf_sched_beta: 1
-inference_earlystop_goal: max
-inference_earlystop_metric: valinf2_rmsds_lt2
-inference_samples: 5
-inference_secondary_metric: valinf_min_rmsds_lt2
-inference_steps: 20
-limit_complexes: 0
-log_dir: workdir
-lr: 0.001
-lr_start_factor: 0.001
-matching_maxiter: 20
-matching_popsize: 20
-matching_tries: 1
-max_lig_size: null
-max_radius: 5.0
-max_receptor_size: null
-merge_clusters: 3
-min_ligand_size: 2
-moad_dir: data/BindingMOAD_2020_ab_processed_biounit/
-moad_esm_embeddings_path: data/BindingMOAD_2020_ab_processed_biounit/moad_sequences_new.pt
-moad_esm_embeddings_sequences_path: data/BindingMOAD_2020_ab_processed_biounit/sequences_to_id.fasta
-n_epochs: 1000
-no_aminoacid_identities: false
-no_batch_norm: false
-no_differentiate_convolutions: false
-no_torsion: false
-norm_by_sigma: false
-not_fixed_center_conv: false
-not_fixed_knn_radius_graph: false
-not_full_dataset: false
-not_knn_only_graph: false
-ns: 48
-num_conformers: 1
-num_conv_layers: 11
-num_dataloader_workers: 1
-num_inference_complexes: 500
-num_prot_emb_layers: 3
-num_workers: 1
-nv: 10
-odd_parity: false
-original_model_ckpt: best_model.pt
-original_model_dir: workdir
-pdbbind_dir: data/PDBBind_processed/
-pdbbind_esm_embeddings_path: data/esm2_3billion_embeddings.pt
-pdbsidechain_dir: data/pdb_2021aug02
-pdbsidechain_esm_embeddings_path: data/pdb_2021aug02/pdb_sequences_esm_20k.pt
-pdbsidechain_esm_embeddings_sequences_path: pdb_2021aug02/sequences_to_id.fasta
-pin_memory: false
-pocket_mode_graph: false
-pretrain_ckpt: null
-pretrain_dir: null
-project: gen_train
-protein_file: protein_processed
-receptor_radius: 15.0
-reduce_pseudoscalars: true
-remove_hs: true
-remove_promiscuous_targets: null
-remove_second_segment: false
-restart_ckpt: last_model
-restart_dir: null
-restart_lr: null
-rot_alpha: 1.0
-rot_beta: 1.0
-rot_inf_sched_alpha: 1
-rot_inf_sched_beta: 1
-rot_sigma_max: 1.55
-rot_sigma_min: 0.03
-rot_sigma_schedule: expbeta
-rot_weight: 0.33
-run_name: diffdockL
-samples_per_complex: 3
-sampling_alpha: 1.0
-sampling_beta: 1.0
-save_model_freq: null
-scale_by_sigma: true
-scheduler: plateau
-scheduler_patience: 30
-separate_noise_schedule: false
-sh_lmax: 2
-sidechain_loss_weight: 0
-sigma_embed_dim: 64
-sigma_schedule: expbeta
-smooth_edges: false
-split_test: data/splits/timesplit_test
-split_train: data/splits/timesplit_no_lig_overlap_train
-split_val: data/splits/timesplit_no_lig_overlap_val
-test_sigma_intervals: true
-tor_alpha: 1.0
-tor_beta: 1.0
-tor_inf_sched_alpha: 1
-tor_inf_sched_beta: 1
-tor_sigma_max: 3.14
-tor_sigma_min: 0.0314
-tor_sigma_schedule: expbeta
-tor_weight: 0.33
-torsional_data_dir: data/QM9/qm9/
-torsional_split_path: data/QM9/splits/split0.npy
-tp_weights_layers: 2
-tr_only_confidence: true
-tr_sigma_max: 19.0
-tr_sigma_min: 0.1
-tr_weight: 0.33
-train_inference_freq: null
-train_multiplicity: 1
-triple_training: true
-unroll_clusters: true
-use_ema: true
-use_full_size_protein_file: false
-use_old_atom_encoder: false
-use_old_wrong_embedding_order: false
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+max_radius: 5.0
+max_receptor_size: null
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+moad_esm_embeddings_sequences_path: data/BindingMOAD_2020_ab_processed_biounit/sequences_to_id.fasta
+n_epochs: 1000
+no_aminoacid_identities: false
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+original_model_ckpt: best_model.pt
+original_model_dir: workdir
+pdbbind_dir: data/PDBBind_processed/
+pdbbind_esm_embeddings_path: data/esm2_3billion_embeddings.pt
+pdbsidechain_dir: data/pdb_2021aug02
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+pdbsidechain_esm_embeddings_sequences_path: pdb_2021aug02/sequences_to_id.fasta
+pin_memory: false
+pocket_mode_graph: false
+pretrain_ckpt: null
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+project: gen_train
+protein_file: protein_processed
+receptor_radius: 15.0
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+split_test: data/splits/timesplit_test
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+split_val: data/splits/timesplit_no_lig_overlap_val
+test_sigma_intervals: true
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+torsional_data_dir: data/QM9/qm9/
+torsional_split_path: data/QM9/splits/split0.npy
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