Claude Opus 4.7 (1M context)

AlloGen public release: Q_theta scorer + PXDesign guidance + Colab demo

ad9572d 5 months ago

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"""
PXDesign + SMC Reranking.
Post-hoc Sequential Monte Carlo: generate multiple batches of vanilla PXDesign
binders, score with Q_theta, and rank by selectivity margin. No modification
to the PXDesign diffusion process — pure generate-score-rank pipeline.
This is the simplest Q_theta integration strategy: generate a large pool of
candidates and select the best ones by selectivity score.
Usage:
    python code/scripts/pxdesign_guidance/smc_pxdesign.py \
        --input experiments/pxdesign_cam/output/cam_binder.json \
        --qtheta_checkpoint results/checkpoints_cam_v3/best_phase2.pt \
        --ref_holo data/pdbs/cam_holo/3CLN.pdb \
        --ref_apo data/pdbs/cam_apo/1CFD.pdb \
        --n_particles 16 --n_rounds 4 \
        --gpu 0
"""

import os
import sys
import argparse
import json
import logging
import shutil
import subprocess
from glob import glob

import numpy as np
import torch

logging.basicConfig(level=logging.INFO, format='%(asctime)s %(levelname)s %(message)s')
logger = logging.getLogger(__name__)

_SCRIPT_DIR = os.path.dirname(os.path.abspath(__file__))
_ALLO_CODE_DIR = os.path.abspath(os.path.join(_SCRIPT_DIR, '..', '..'))
_ALLO_ROOT = os.path.abspath(os.path.join(_ALLO_CODE_DIR, '..'))

if _ALLO_CODE_DIR not in sys.path:
    sys.path.insert(0, _ALLO_CODE_DIR)


def run_pxdesign_batch(input_json, outdir, n_sample, n_step, gpu):
    """Run vanilla PXDesign via CLI subprocess."""
    pxdesign_python = 'python'

    # Use pxdesign CLI
    cmd = [
        pxdesign_python, '-m', 'pxdesign.runner.cli', 'infer',
        '-o', outdir,
        '-i', input_json,
        '--dtype', 'bf16',
        '--N_sample', str(n_sample),
        '--N_step', str(n_step),
    ]

    env = os.environ.copy()
    # Inherit CUDA_VISIBLE_DEVICES from parent

    logger.info(f"Running PXDesign: {n_sample} samples -> {outdir}")
    result = subprocess.run(cmd, capture_output=True, text=True, env=env,
                            timeout=7200)

    if result.returncode != 0:
        # Try alternative invocation via module
        cmd_alt = [
            pxdesign_python, '-m', 'pxdesign.runner.inference',
            '--dump_dir', outdir,
            '--input', input_json,
            '--dtype', 'bf16',
            '--N_sample', str(n_sample),
            '--N_step', str(n_step),
        ]
        result = subprocess.run(cmd_alt, capture_output=True, text=True, env=env,
                                timeout=7200)
        if result.returncode != 0:
            logger.error(f"PXDesign failed:\nstdout: {result.stdout[-1000:]}\nstderr: {result.stderr[-1000:]}")
            return False
    return True


def collect_pdbs(outdir):
    """Collect PDB/CIF files from PXDesign output."""
    pdbs = []
    for ext in ('*.pdb', '*.cif'):
        pdbs.extend(glob(os.path.join(outdir, '**/' + ext), recursive=True))
    pdbs = sorted(pdbs)
    filtered = [p for p in pdbs if 'sample' in os.path.basename(p).lower()
                or 'design' in os.path.basename(p).lower()
                or 'rank' in os.path.basename(p).lower()]
    return filtered if filtered else pdbs


def smc_particle_filter(args):
    """Run SMC reranking with PXDesign."""
    os.chdir(_ALLO_ROOT)

    from qtheta_pxdesign import QThetaPXDesignGuidance

    outdir = args.outdir
    os.makedirs(outdir, exist_ok=True)

    # Initialize scorer
    guidance = QThetaPXDesignGuidance(
        checkpoint=args.qtheta_checkpoint,
        ref_holo=args.ref_holo,
        ref_apo=args.ref_apo,
        ref_chain=args.ref_chain,
        device=f'cuda:{args.gpu}',
    )
    guidance._lazy_init()

    all_designs = []
    round_summaries = []

    for round_idx in range(args.n_rounds):
        round_dir = os.path.join(outdir, f'round_{round_idx}')
        os.makedirs(round_dir, exist_ok=True)

        logger.info(f"\n{'='*60}")
        logger.info(f"SMC Round {round_idx + 1}/{args.n_rounds}")
        logger.info(f"{'='*60}")

        # Generate particles via vanilla PXDesign
        gen_dir = os.path.join(round_dir, 'generated')
        success = run_pxdesign_batch(
            input_json=args.input,
            outdir=gen_dir,
            n_sample=args.n_particles,
            n_step=args.N_step,
            gpu=args.gpu,
        )

        if not success:
            # If subprocess fails, try using existing PXDesign outputs
            logger.warning(f"Round {round_idx} generation failed. "
                           f"Checking for existing outputs...")
            pdbs = collect_pdbs(args.designs_dir) if hasattr(args, 'designs_dir') else []
            if not pdbs:
                continue
        else:
            pdbs = collect_pdbs(gen_dir)

        if not pdbs:
            logger.warning(f"No PDBs found in round {round_idx}")
            continue

        # Score all particles
        logger.info(f"Scoring {len(pdbs)} particles...")
        round_results = []
        for pdb_path in pdbs:
            result = guidance.score_design(pdb_path)
            if result is not None:
                result['pdb_path'] = pdb_path
                result['design_id'] = os.path.basename(pdb_path).replace('.pdb', '').replace('.cif', '')
                result['round'] = round_idx
                round_results.append(result)

        if not round_results:
            continue

        margins = np.array([r['margin'] for r in round_results])

        round_summary = {
            'round': round_idx,
            'n_particles': len(round_results),
            'margin_mean': float(margins.mean()),
            'margin_std': float(margins.std()),
            'margin_max': float(margins.max()),
            'frac_positive': float((margins > 0).mean()),
        }
        round_summaries.append(round_summary)

        logger.info(f"Round {round_idx}: margin={margins.mean():.3f}±{margins.std():.3f}, "
                     f"max={margins.max():.3f}, S>0={round_summary['frac_positive']:.1%}")

        all_designs.extend(round_results)

    # Final ranking and summary
    if all_designs:
        all_designs.sort(key=lambda x: x['margin'], reverse=True)
        all_margins = np.array([d['margin'] for d in all_designs])
        holo_scores = np.array([d['q_holo'] for d in all_designs])

        # Best-of-K
        bok = {}
        for K in [1, 2, 5, 10]:
            n_trials = 2000
            n_avail = len(all_margins)
            successes = sum(
                1 for _ in range(n_trials)
                if all_margins[np.random.choice(n_avail, min(K, n_avail), replace=False)].max() > 0
            )
            bok[K] = successes / n_trials

        summary = {
            'method': 'PXDesign + SMC',
            'n_rounds': args.n_rounds,
            'n_particles_per_round': args.n_particles,
            'total_designs': len(all_designs),
            'margin_mean': float(all_margins.mean()),
            'margin_std': float(all_margins.std()),
            'margin_max': float(all_margins.max()),
            'frac_positive': float((all_margins > 0).mean()),
            'q_holo_mean': float(holo_scores.mean()),
            'q_apo_mean': float(np.mean([d['q_apo'] for d in all_designs])),
            'best_of_k': {str(k): v for k, v in bok.items()},
            'round_summaries': round_summaries,
            'top5': all_designs[:5],
        }

        with open(os.path.join(outdir, 'smc_scores.json'), 'w') as f:
            json.dump(all_designs, f, indent=2)
        with open(os.path.join(outdir, 'smc_summary.json'), 'w') as f:
            json.dump(summary, f, indent=2)

        # Copy best designs
        best_dir = os.path.join(outdir, 'best_designs')
        os.makedirs(best_dir, exist_ok=True)
        for i, d in enumerate(all_designs[:20]):
            if os.path.exists(d['pdb_path']):
                dest = os.path.join(best_dir, f'rank_{i:02d}_{d["design_id"]}.pdb')
                shutil.copy2(d['pdb_path'], dest)

        logger.info(f"\n{'='*60}")
        logger.info(f"PXDesign + SMC Results ({len(all_designs)} total designs)")
        logger.info(f"  Margin: {all_margins.mean():.3f} ± {all_margins.std():.3f}")
        logger.info(f"  Max margin: {all_margins.max():.3f}")
        logger.info(f"  Fraction S > 0: {(all_margins > 0).mean():.1%}")
        logger.info(f"  Q(holo) mean: {holo_scores.mean():.3f}")
        logger.info(f"  Best-of-K:")
        for k, v in sorted(bok.items()):
            logger.info(f"    K={k:3d}: {v:.3f}")
        logger.info(f"{'='*60}")


def main():
    parser = argparse.ArgumentParser(description='PXDesign + SMC Reranking')
    parser.add_argument('--input', default='experiments/pxdesign_cam/output/cam_binder.json',
                        help='PXDesign input JSON')
    parser.add_argument('--designs_dir', default='experiments/pxdesign_cam/output/',
                        help='Existing PXDesign outputs (fallback if generation fails)')
    parser.add_argument('--qtheta_checkpoint',
                        default='results/checkpoints_cam_v3/best_phase2.pt')
    parser.add_argument('--ref_holo', default='data/pdbs/cam_holo/3CLN.pdb')
    parser.add_argument('--ref_apo', default='data/pdbs/cam_apo/1CFD.pdb')
    parser.add_argument('--ref_chain', default='A')
    parser.add_argument('--n_particles', type=int, default=16,
                        help='Particles per round')
    parser.add_argument('--n_rounds', type=int, default=4,
                        help='Number of SMC rounds')
    parser.add_argument('--N_step', type=int, default=400)
    parser.add_argument('--gpu', type=int, default=0)
    parser.add_argument('--outdir', default='results/pxdesign_smc')
    args = parser.parse_args()

    smc_particle_filter(args)


if __name__ == '__main__':
    main()

	"""
	PXDesign + SMC Reranking.

	Post-hoc Sequential Monte Carlo: generate multiple batches of vanilla PXDesign
	binders, score with Q_theta, and rank by selectivity margin. No modification
	to the PXDesign diffusion process — pure generate-score-rank pipeline.

	This is the simplest Q_theta integration strategy: generate a large pool of
	candidates and select the best ones by selectivity score.

	Usage:
	python code/scripts/pxdesign_guidance/smc_pxdesign.py \
	--input experiments/pxdesign_cam/output/cam_binder.json \
	--qtheta_checkpoint results/checkpoints_cam_v3/best_phase2.pt \
	--ref_holo data/pdbs/cam_holo/3CLN.pdb \
	--ref_apo data/pdbs/cam_apo/1CFD.pdb \
	--n_particles 16 --n_rounds 4 \
	--gpu 0
	"""

	import os
	import sys
	import argparse
	import json
	import logging
	import shutil
	import subprocess
	from glob import glob

	import numpy as np
	import torch

	logging.basicConfig(level=logging.INFO, format='%(asctime)s %(levelname)s %(message)s')
	logger = logging.getLogger(__name__)

	_SCRIPT_DIR = os.path.dirname(os.path.abspath(__file__))
	_ALLO_CODE_DIR = os.path.abspath(os.path.join(_SCRIPT_DIR, '..', '..'))
	_ALLO_ROOT = os.path.abspath(os.path.join(_ALLO_CODE_DIR, '..'))

	if _ALLO_CODE_DIR not in sys.path:
	sys.path.insert(0, _ALLO_CODE_DIR)


	def run_pxdesign_batch(input_json, outdir, n_sample, n_step, gpu):
	"""Run vanilla PXDesign via CLI subprocess."""
	pxdesign_python = 'python'

	# Use pxdesign CLI
	cmd = [
	pxdesign_python, '-m', 'pxdesign.runner.cli', 'infer',
	'-o', outdir,
	'-i', input_json,
	'--dtype', 'bf16',
	'--N_sample', str(n_sample),
	'--N_step', str(n_step),
	]

	env = os.environ.copy()
	# Inherit CUDA_VISIBLE_DEVICES from parent

	logger.info(f"Running PXDesign: {n_sample} samples -> {outdir}")
	result = subprocess.run(cmd, capture_output=True, text=True, env=env,
	timeout=7200)

	if result.returncode != 0:
	# Try alternative invocation via module
	cmd_alt = [
	pxdesign_python, '-m', 'pxdesign.runner.inference',
	'--dump_dir', outdir,
	'--input', input_json,
	'--dtype', 'bf16',
	'--N_sample', str(n_sample),
	'--N_step', str(n_step),
	]
	result = subprocess.run(cmd_alt, capture_output=True, text=True, env=env,
	timeout=7200)
	if result.returncode != 0:
	logger.error(f"PXDesign failed:\nstdout: {result.stdout[-1000:]}\nstderr: {result.stderr[-1000:]}")
	return False
	return True


	def collect_pdbs(outdir):
	"""Collect PDB/CIF files from PXDesign output."""
	pdbs = []
	for ext in ('.pdb', '.cif'):
	pdbs.extend(glob(os.path.join(outdir, '**/' + ext), recursive=True))
	pdbs = sorted(pdbs)
	filtered = [p for p in pdbs if 'sample' in os.path.basename(p).lower()
	or 'design' in os.path.basename(p).lower()
	or 'rank' in os.path.basename(p).lower()]
	return filtered if filtered else pdbs


	def smc_particle_filter(args):
	"""Run SMC reranking with PXDesign."""
	os.chdir(_ALLO_ROOT)

	from qtheta_pxdesign import QThetaPXDesignGuidance

	outdir = args.outdir
	os.makedirs(outdir, exist_ok=True)

	# Initialize scorer
	guidance = QThetaPXDesignGuidance(
	checkpoint=args.qtheta_checkpoint,
	ref_holo=args.ref_holo,
	ref_apo=args.ref_apo,
	ref_chain=args.ref_chain,
	device=f'cuda:{args.gpu}',
	)
	guidance._lazy_init()

	all_designs = []
	round_summaries = []

	for round_idx in range(args.n_rounds):
	round_dir = os.path.join(outdir, f'round_{round_idx}')
	os.makedirs(round_dir, exist_ok=True)

	logger.info(f"\n{'='*60}")
	logger.info(f"SMC Round {round_idx + 1}/{args.n_rounds}")
	logger.info(f"{'='*60}")

	# Generate particles via vanilla PXDesign
	gen_dir = os.path.join(round_dir, 'generated')
	success = run_pxdesign_batch(
	input_json=args.input,
	outdir=gen_dir,
	n_sample=args.n_particles,
	n_step=args.N_step,
	gpu=args.gpu,
	)

	if not success:
	# If subprocess fails, try using existing PXDesign outputs
	logger.warning(f"Round {round_idx} generation failed. "
	f"Checking for existing outputs...")
	pdbs = collect_pdbs(args.designs_dir) if hasattr(args, 'designs_dir') else []
	if not pdbs:
	continue
	else:
	pdbs = collect_pdbs(gen_dir)

	if not pdbs:
	logger.warning(f"No PDBs found in round {round_idx}")
	continue

	# Score all particles
	logger.info(f"Scoring {len(pdbs)} particles...")
	round_results = []
	for pdb_path in pdbs:
	result = guidance.score_design(pdb_path)
	if result is not None:
	result['pdb_path'] = pdb_path
	result['design_id'] = os.path.basename(pdb_path).replace('.pdb', '').replace('.cif', '')
	result['round'] = round_idx
	round_results.append(result)

	if not round_results:
	continue

	margins = np.array([r['margin'] for r in round_results])

	round_summary = {
	'round': round_idx,
	'n_particles': len(round_results),
	'margin_mean': float(margins.mean()),
	'margin_std': float(margins.std()),
	'margin_max': float(margins.max()),
	'frac_positive': float((margins > 0).mean()),
	}
	round_summaries.append(round_summary)

	logger.info(f"Round {round_idx}: margin={margins.mean():.3f}±{margins.std():.3f}, "
	f"max={margins.max():.3f}, S>0={round_summary['frac_positive']:.1%}")

	all_designs.extend(round_results)

	# Final ranking and summary
	if all_designs:
	all_designs.sort(key=lambda x: x['margin'], reverse=True)
	all_margins = np.array([d['margin'] for d in all_designs])
	holo_scores = np.array([d['q_holo'] for d in all_designs])

	# Best-of-K
	bok = {}
	for K in [1, 2, 5, 10]:
	n_trials = 2000
	n_avail = len(all_margins)
	successes = sum(
	1 for _ in range(n_trials)
	if all_margins[np.random.choice(n_avail, min(K, n_avail), replace=False)].max() > 0
	)
	bok[K] = successes / n_trials

	summary = {
	'method': 'PXDesign + SMC',
	'n_rounds': args.n_rounds,
	'n_particles_per_round': args.n_particles,
	'total_designs': len(all_designs),
	'margin_mean': float(all_margins.mean()),
	'margin_std': float(all_margins.std()),
	'margin_max': float(all_margins.max()),
	'frac_positive': float((all_margins > 0).mean()),
	'q_holo_mean': float(holo_scores.mean()),
	'q_apo_mean': float(np.mean([d['q_apo'] for d in all_designs])),
	'best_of_k': {str(k): v for k, v in bok.items()},
	'round_summaries': round_summaries,
	'top5': all_designs[:5],
	}

	with open(os.path.join(outdir, 'smc_scores.json'), 'w') as f:
	json.dump(all_designs, f, indent=2)
	with open(os.path.join(outdir, 'smc_summary.json'), 'w') as f:
	json.dump(summary, f, indent=2)

	# Copy best designs
	best_dir = os.path.join(outdir, 'best_designs')
	os.makedirs(best_dir, exist_ok=True)
	for i, d in enumerate(all_designs[:20]):
	if os.path.exists(d['pdb_path']):
	dest = os.path.join(best_dir, f'rank_{i:02d}_{d["design_id"]}.pdb')
	shutil.copy2(d['pdb_path'], dest)

	logger.info(f"\n{'='*60}")
	logger.info(f"PXDesign + SMC Results ({len(all_designs)} total designs)")
	logger.info(f" Margin: {all_margins.mean():.3f} ± {all_margins.std():.3f}")
	logger.info(f" Max margin: {all_margins.max():.3f}")
	logger.info(f" Fraction S > 0: {(all_margins > 0).mean():.1%}")
	logger.info(f" Q(holo) mean: {holo_scores.mean():.3f}")
	logger.info(f" Best-of-K:")
	for k, v in sorted(bok.items()):
	logger.info(f" K={k:3d}: {v:.3f}")
	logger.info(f"{'='*60}")


	def main():
	parser = argparse.ArgumentParser(description='PXDesign + SMC Reranking')
	parser.add_argument('--input', default='experiments/pxdesign_cam/output/cam_binder.json',
	help='PXDesign input JSON')
	parser.add_argument('--designs_dir', default='experiments/pxdesign_cam/output/',
	help='Existing PXDesign outputs (fallback if generation fails)')
	parser.add_argument('--qtheta_checkpoint',
	default='results/checkpoints_cam_v3/best_phase2.pt')
	parser.add_argument('--ref_holo', default='data/pdbs/cam_holo/3CLN.pdb')
	parser.add_argument('--ref_apo', default='data/pdbs/cam_apo/1CFD.pdb')
	parser.add_argument('--ref_chain', default='A')
	parser.add_argument('--n_particles', type=int, default=16,
	help='Particles per round')
	parser.add_argument('--n_rounds', type=int, default=4,
	help='Number of SMC rounds')
	parser.add_argument('--N_step', type=int, default=400)
	parser.add_argument('--gpu', type=int, default=0)
	parser.add_argument('--outdir', default='results/pxdesign_smc')
	args = parser.parse_args()

	smc_particle_filter(args)


	if __name__ == '__main__':
	main()