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This commit is contained in:
Tony Shen
2025-05-21 11:11:01 -04:00
parent 32614490eb
commit bf2e63c40f
8 changed files with 30 additions and 40 deletions
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3
README.md
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@@ -83,7 +83,7 @@ python scripts/b_create_env.py -b building_blocks/enamine_catalog.smi -o envs/ca
#### Option B: Download Prepared Files
```bash
cd experiments/data
cd experiments/data/envs
gdown https://drive.google.com/uc?id=192RuXBzM51Mk__-kSKcCs4kthnKHWAgm
tar -xzvf stock.tar.gz
```
@@ -122,6 +122,7 @@ wandb agent <sweep-id>
1. Get `crossdocked.tar.gz` from [here](https://drive.google.com/file/d/1BKYx_H1m-TzG_75Gk-7sjPkt5ow-Acdw/view?usp=sharing)
2. Extract dataset:
```bash
cd experiments/data/
gdown 1BKYx_H1m-TzG_75Gk-7sjPkt5ow-Acdw
tar -xzvf crossdocked.tar.gz
```

4
experiments/scripts/exp3A_sbdd_proxy.py
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@@ -21,8 +21,8 @@ if __name__ == "__main__":
config.cgflow.use_predicted_pose = True
config.cgflow.num_inference_steps = 100
config.task.pocket_conditional.pocket_dir = "./data/experiments/CrossDocked2020/crossdocked_pocket10/"
config.task.pocket_conditional.train_key = "./data/experiments/CrossDocked2020/train_keys.csv"
config.task.pocket_conditional.pocket_dir = "./data/CrossDocked2020/"
config.task.pocket_conditional.train_key = "./data/CrossDocked2020/train_keys.csv"
trainer = Proxy_MultiPocket_Trainer(config)
trainer.run()

4
experiments/scripts/exp3B_sbdd_unidock.py
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@@ -21,8 +21,8 @@ if __name__ == "__main__":
config.cgflow.use_predicted_pose = True
config.cgflow.num_inference_steps = 100
config.task.pocket_conditional.pocket_dir = "./data/experiments/CrossDocked2020/crossdocked_pocket10/"
config.task.pocket_conditional.train_key = "./data/experiments/CrossDocked2020/train_keys.csv"
config.task.pocket_conditional.pocket_dir = "./data/CrossDocked2020/"
config.task.pocket_conditional.train_key = "./data/CrossDocked2020/train_keys.csv"
trainer = UniDock_MultiPocket_Trainer(config)
trainer.run()

4
experiments/scripts/exp3C_sbdd_localopt.py
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@@ -21,8 +21,8 @@ if __name__ == "__main__":
config.cgflow.use_predicted_pose = True
config.cgflow.num_inference_steps = 100
config.task.pocket_conditional.pocket_dir = "./data/experiments/CrossDocked2020/crossdocked_pocket10/"
config.task.pocket_conditional.train_key = "./data/experiments/CrossDocked2020/train_keys.csv"
config.task.pocket_conditional.pocket_dir = "./data/CrossDocked2020/"
config.task.pocket_conditional.train_key = "./data/CrossDocked2020/train_keys.csv"
trainer = AutoDock_MultiPocket_Trainer(config)
trainer.run()

2
experiments/scripts/exp3Z_sampling.py
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@@ -11,7 +11,7 @@ from tqdm import tqdm
from synthflow.config import Config, init_empty
from synthflow.pocket_conditional.sampler import PocketConditionalSampler
POCKET_DIR = Path("./data/experiments/CrossDocked2020/crossdocked_pocket10/")
POCKET_DIR = Path("./data/CrossDocked2020/")
TEST_KEY_PATH = Path("./data/experiments/CrossDocked2020/test_keys.csv")

23
scripts/A_semlaflow_train_ar_plinder.sh
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@@ -1,26 +1,33 @@
DATA_DIR="/projects/jlab/to.shen/CGFlow/data/complex/plinder/smol"
DATA_DIR="experiments/data/complex/plinder_15A"
python scripts/_a1_cgflow_train.py \
python scripts/_a1_semlaflow_train.py \
--data_path ${DATA_DIR} \
--dataset plinder \
--categorical_strategy auto-regressive \
--ordering_strategy connected \
--decomposition_strategy reaction \
--pocket_n_layers 4 \
--n_coord_sets 64 \
--d_message 64 \
--d_message_hidden 96 \
--time_alpha 1.0 \
--t_per_ar_action 0.3 \
--max_interp_time 0.4 \
--max_action_t 0.6 \
--t_per_ar_action 0.33 \
--max_interp_time 1.0 \
--max_action_t 0.66 \
--max_num_cuts 2 \
--dist_loss_weight 0. \
--type_loss_weight 0. \
--bond_loss_weight 0. \
--charge_loss_weight 0. \
--optimal_transport None \
--monitor val-strain \
--monitor val-conformer-no-align-rmsd \
--monitor_mode min \
--val_check_epochs 1 \
--batch_cost 600 \
--num_gpus 8
--acc_batches 2 \
--batch_cost 6 \
--num_workers 8 \
--ligand_local_connections 30 \
--pocket_local_connections 30 \
--pocket_ligand_local_connections 30 \
--max_atoms 800 \
--num_gpus 1

20
src/cgflow/models/fm.py
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@@ -536,26 +536,6 @@ class MolecularCFM(L.LightningModule):
self.builder = builder
self.ema_gen = ema_gen if use_ema else None
# Anything else passed into kwargs will also be saved
# hparams = {
# "lr": lr,
# "coord_scale": coord_scale,
# "dist_loss_weight": dist_loss_weight,
# "type_loss_weight": type_loss_weight,
# "bond_loss_weight": bond_loss_weight,
# "type_strategy": type_strategy,
# "bond_strategy": bond_strategy,
# "self_condition": self_condition,
# "distill": distill,
# "lr_schedule": lr_schedule,
# "sampling_strategy": sampling_strategy,
# "use_ema": use_ema,
# "compile_model": compile_model,
# "warm_up_steps": warm_up_steps,
# **gen.hparams,
# **integrator.hparams,
# **kwargs,
# }
self.save_hyperparameters(vars(args))
stability_metrics = {

10
src/synthflow/tasks/config.py
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@@ -74,9 +74,10 @@ class PocketConditionalConfig:
Proxy Key from PharmacoNet
"""
proxy: tuple[str, str, str] = ("TacoGFN_Reward", "QVina", "CrossDocked2020")
pocket_dir: str = "./data/experiments/CrossDocked2020/crossdocked_pocket10/"
train_key: str = "./data/experiments/CrossDocked2020/train_keys.csv"
proxy: tuple[str, str,
str] = ("TacoGFN_Reward", "QVina", "CrossDocked2020")
pocket_dir: str = "./data/CrossDocked2020/"
train_key: str = "./data/CrossDocked2020/train_keys.csv"
@dataclass
@@ -84,4 +85,5 @@ class TasksConfig:
moo: MOOTaskConfig = field(default_factory=MOOTaskConfig)
constraint: ConstraintConfig = field(default_factory=ConstraintConfig)
docking: DockingTaskConfig = field(default_factory=DockingTaskConfig)
pocket_conditional: PocketConditionalConfig = field(default_factory=PocketConditionalConfig)
pocket_conditional: PocketConditionalConfig = field(
default_factory=PocketConditionalConfig)