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sample_diffusion.py
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sample_diffusion.py
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import argparse
import os
import shutil
import time
import sys
sys.path.append(os.path.abspath('./'))
import numpy as np
import torch
from torch_geometric.data import Batch
from torch_geometric.transforms import Compose
from torch_scatter import scatter_sum, scatter_mean
from tqdm.auto import tqdm
import utils.misc as misc
import utils.transforms as trans
from datasets import get_dataset
from datasets.pl_data import FOLLOW_BATCH
from models.molopt_score_model import ScorePosNet3D, log_sample_categorical
from utils.evaluation import atom_num
def unbatch_v_traj(ligand_v_traj, n_data, ligand_cum_atoms):
all_step_v = [[] for _ in range(n_data)]
for v in ligand_v_traj: # step_i
v_array = v.cpu().numpy()
for k in range(n_data):
all_step_v[k].append(v_array[ligand_cum_atoms[k]:ligand_cum_atoms[k + 1]])
all_step_v = [np.stack(step_v) for step_v in all_step_v] # num_samples * [num_steps, num_atoms_i]
return all_step_v
def sample_diffusion_ligand(model, data, num_samples, batch_size=16, device='cuda',
num_steps=None, center_pos_mode='protein',
sample_num_atoms='prior',guide_mode='joint',
value_model=None,
type_grad_weight=1.,pos_grad_weight=1.):
all_pred_pos, all_pred_v, all_pred_exp = [], [], []
all_pred_pos_traj, all_pred_v_traj, all_pred_exp_traj, all_pred_exp_atom_traj = [], [], [], []
all_pred_v0_traj, all_pred_vt_traj = [], []
time_list = []
num_batch = int(np.ceil(num_samples / batch_size))
current_i = 0
for i in tqdm(range(num_batch)):
n_data = batch_size if i < num_batch - 1 else num_samples - batch_size * (num_batch - 1)
batch = Batch.from_data_list([data.clone() for _ in range(n_data)], follow_batch=FOLLOW_BATCH).to(device)
t1 = time.time()
with torch.no_grad():
batch_protein = batch.protein_element_batch
if sample_num_atoms == 'prior':
pocket_size = atom_num.get_space_size(batch.protein_pos.detach().cpu().numpy())
ligand_num_atoms = [atom_num.sample_atom_num(pocket_size).astype(int) for _ in range(n_data)]
batch_ligand = torch.repeat_interleave(torch.arange(n_data), torch.tensor(ligand_num_atoms)).to(device)
elif sample_num_atoms == 'range':
ligand_num_atoms = list(range(current_i + 1, current_i + n_data + 1))
batch_ligand = torch.repeat_interleave(torch.arange(n_data), torch.tensor(ligand_num_atoms)).to(device)
elif sample_num_atoms == 'ref':
batch_ligand = batch.ligand_element_batch
ligand_num_atoms = scatter_sum(torch.ones_like(batch_ligand), batch_ligand, dim=0).tolist()
else:
raise ValueError
# init ligand pos
center_pos = scatter_mean(batch.protein_pos, batch_protein, dim=0)
batch_center_pos = center_pos[batch_ligand]
init_ligand_pos = batch_center_pos + torch.randn_like(batch_center_pos)
# init ligand v
uniform_logits = torch.zeros(len(batch_ligand), model.num_classes).to(device)
init_ligand_v_prob = log_sample_categorical(uniform_logits)
init_ligand_v = init_ligand_v_prob.argmax(dim=-1)
r = model.sample_diffusion(
guide_mode=guide_mode,
value_model=value_model,
type_grad_weight=type_grad_weight,
pos_grad_weight=pos_grad_weight,
protein_pos=batch.protein_pos,
protein_v=batch.protein_atom_feature.float(),
batch_protein=batch_protein,
init_ligand_pos=init_ligand_pos,
init_ligand_v=init_ligand_v,
batch_ligand=batch_ligand,
num_steps=num_steps,
center_pos_mode=center_pos_mode
)
ligand_pos, ligand_v, ligand_pos_traj, ligand_v_traj = r['pos'], r['v'], r['pos_traj'], r['v_traj']
ligand_v0_traj, ligand_vt_traj = r['v0_traj'], r['vt_traj']
exp_traj = r['exp_traj']
exp_atom_traj = r['exp_atom_traj']
# unbatch exp
if guide_mode == 'joint' or guide_mode == 'pdbbind_random' or guide_mode == 'valuenet' or guide_mode == 'wo':
all_pred_exp += exp_traj[-1]
all_pred_exp_traj += exp_traj
# unbatch pos
ligand_cum_atoms = np.cumsum([0] + ligand_num_atoms)
ligand_pos_array = ligand_pos.cpu().numpy().astype(np.float64)
all_pred_pos += [ligand_pos_array[ligand_cum_atoms[k]:ligand_cum_atoms[k + 1]] for k in
range(n_data)] # num_samples * [num_atoms_i, 3]
all_step_pos = [[] for _ in range(n_data)]
for p in ligand_pos_traj: # step_i
p_array = p.cpu().numpy().astype(np.float64)
for k in range(n_data):
all_step_pos[k].append(p_array[ligand_cum_atoms[k]:ligand_cum_atoms[k + 1]])
all_step_pos = [np.stack(step_pos) for step_pos in
all_step_pos] # num_samples * [num_steps, num_atoms_i, 3]
all_pred_pos_traj += [p for p in all_step_pos]
# unbatch v
ligand_v_array = ligand_v.cpu().numpy()
all_pred_v += [ligand_v_array[ligand_cum_atoms[k]:ligand_cum_atoms[k + 1]] for k in range(n_data)]
all_step_v = unbatch_v_traj(ligand_v_traj, n_data, ligand_cum_atoms)
all_pred_v_traj += [v for v in all_step_v]
all_step_v0 = unbatch_v_traj(ligand_v0_traj, n_data, ligand_cum_atoms)
all_pred_v0_traj += [v for v in all_step_v0]
all_step_vt = unbatch_v_traj(ligand_vt_traj, n_data, ligand_cum_atoms)
all_pred_vt_traj += [v for v in all_step_vt]
all_step_exp_atom = unbatch_v_traj(exp_atom_traj, n_data, ligand_cum_atoms)
all_pred_exp_atom_traj += [v for v in all_step_exp_atom]
t2 = time.time()
time_list.append(t2 - t1)
current_i += n_data
all_pred_exp = torch.stack(all_pred_exp,dim=0).numpy()
all_pred_exp_traj = torch.stack(all_pred_exp_traj,dim=0).numpy()
return all_pred_pos, all_pred_v, all_pred_exp, all_pred_pos_traj, all_pred_v_traj, all_pred_exp_traj, all_pred_v0_traj, all_pred_vt_traj, all_pred_exp_atom_traj, time_list
def main():
parser = argparse.ArgumentParser()
parser.add_argument('--config', type=str, default='./configs/sampling.yml')
parser.add_argument('-i', '--data_id', type=int, default=81)
parser.add_argument('--device', type=str, default='cuda')
parser.add_argument('--batch_size', type=int, default=4)
parser.add_argument('--guide_mode', type=str, default='joint', choices=['joint', 'pdbbind_random', 'vina', 'valuenet', 'wo'])
parser.add_argument('--type_grad_weight', type=float, default=0)
parser.add_argument('--pos_grad_weight', type=float, default=0)
parser.add_argument('--result_path', type=str, default='./test_package')
if len(sys.argv[1:]) == 0:
parser.print_help()
exit()
args = parser.parse_args()
result_path = args.result_path
os.makedirs(result_path, exist_ok=True)
shutil.copyfile(args.config, os.path.join(result_path, 'sample.yml'))
logger = misc.get_logger('sampling', log_dir=result_path)
# Load config
config = misc.load_config(args.config)
logger.info(config)
misc.seed_all(config.sample.seed)
# Load checkpoint
if args.guide_mode == 'joint':
ckpt = torch.load(config.model['joint_ckpt'], map_location=args.device)
value_ckpt = None
elif args.guide_mode == 'pdbbind_random':
ckpt = torch.load(config.model['pdbbind_random'], map_location=args.device)
value_ckpt = None
elif args.guide_mode == 'vina':
ckpt = torch.load(config.model['policy_ckpt'], map_location=args.device)
value_ckpt = None
elif args.guide_mode == 'valuenet':
ckpt = torch.load(config.model['policy_ckpt'], map_location=args.device)
value_ckpt = torch.load(config.model['value_ckpt'], map_location=args.device)
elif args.guide_mode == 'wo':
ckpt = torch.load(config.model['policy_ckpt'], map_location=args.device)
value_ckpt = None
else:
raise NotImplementedError
logger.info(f"Training Config: {ckpt['config']}")
logger.info(f"args: {args}")
# Transforms
protein_featurizer = trans.FeaturizeProteinAtom()
ligand_atom_mode = ckpt['config'].data.transform.ligand_atom_mode
ligand_featurizer = trans.FeaturizeLigandAtom(ligand_atom_mode)
transform = Compose([
protein_featurizer,
ligand_featurizer,
trans.FeaturizeLigandBond(),
])
# Load dataset
dataset, subsets = get_dataset(
config=ckpt['config'].data,
transform=transform
)
if ckpt['config'].data.name == 'pl':
test_set = subsets['test']
elif ckpt['config'].data.name == 'pdbbind':
test_set = subsets['test']
else:
raise ValueError
logger.info(f'Test: {len(test_set)}')
# Load model
model = ScorePosNet3D(
ckpt['config'].model,
protein_atom_feature_dim=protein_featurizer.feature_dim,
ligand_atom_feature_dim=ligand_featurizer.feature_dim
).to(args.device)
model.load_state_dict(ckpt['model'])
if value_ckpt is not None:
# value model
value_model = ScorePosNet3D(
value_ckpt['config'].model,
protein_atom_feature_dim=protein_featurizer.feature_dim,
ligand_atom_feature_dim=ligand_featurizer.feature_dim
).to(args.device)
value_model.load_state_dict(value_ckpt['model'])
else:
value_model = None
data = test_set[args.data_id]
pred_pos, pred_v, pred_exp, pred_pos_traj, pred_v_traj, pred_exp_traj, pred_v0_traj, pred_vt_traj, pred_exp_atom_traj, time_list = sample_diffusion_ligand(
model, data, config.sample.num_samples,
batch_size=args.batch_size, device=args.device,
num_steps=config.sample.num_steps,
center_pos_mode=config.sample.center_pos_mode,
sample_num_atoms=config.sample.sample_num_atoms,
guide_mode=args.guide_mode,
value_model=value_model,
type_grad_weight=args.type_grad_weight,
pos_grad_weight=args.pos_grad_weight
)
result = {
'data': data,
'pred_ligand_pos': pred_pos,
'pred_ligand_v': pred_v,
'pred_exp': pred_exp,
'pred_ligand_pos_traj': pred_pos_traj,
'pred_ligand_v_traj': pred_v_traj,
'pred_exp_traj': pred_exp_traj,
'pred_exp_atom_traj': pred_exp_atom_traj,
'time': time_list
}
logger.info('Sample done!')
torch.save(result, os.path.join(result_path, f'result_{args.data_id}.pt'))
if __name__ == '__main__':
main()