Refactor into modular molecular workloads
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Emil
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"""Exact sparse molecular similarity graph workload."""
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from __future__ import annotations
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import argparse
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import csv
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import sys
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import time
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from dataclasses import dataclass
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from pathlib import Path
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from typing import Any
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from rdkit import DataStructs
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from scimesh.chemistry.dataset import DatasetStats, MoleculeRecord, iter_valid_molecules
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from scimesh.chemistry.fingerprints import fingerprint
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@dataclass(frozen=True)
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class GraphMolecule:
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"""A valid record and its fingerprint, built once for graph construction."""
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molecule_id: str
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fingerprint: Any
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@dataclass(frozen=True)
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class SimilarityEdge:
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"""A thresholded, undirected similarity edge represented once as i < j."""
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source_id: str
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target_id: str
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similarity: float
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@dataclass
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class GraphResult:
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"""Edges, dataset statistics, and pair-comparison statistics."""
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edges: list[SimilarityEdge]
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stats: DatasetStats
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checked_pairs: int
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elapsed_seconds: float
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def _fingerprinted_molecules(
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tsv_path: Path, max_rows: int | None
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) -> tuple[list[GraphMolecule], DatasetStats]:
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stats = DatasetStats()
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molecules = [
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GraphMolecule(record.molecule_id, fingerprint(record.molecule))
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for record in iter_valid_molecules(tsv_path, stats, max_rows=max_rows)
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]
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return molecules, stats
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def build_similarity_graph(
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tsv_path: Path,
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threshold: float,
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block_size: int,
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max_rows: int | None = None,
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progress_every: int = 0,
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) -> GraphResult:
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"""Build an exact sparse graph without creating a dense similarity matrix."""
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if not 0.0 <= threshold <= 1.0:
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raise ValueError("--threshold must be between 0 and 1")
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if block_size < 1:
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raise ValueError("--block-size must be a positive integer")
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molecules, stats = _fingerprinted_molecules(tsv_path, max_rows)
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edges: list[SimilarityEdge] = []
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checked_pairs = 0
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started_at = time.perf_counter()
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next_report = progress_every
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for left_block_start in range(0, len(molecules), block_size):
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left_block_end = min(left_block_start + block_size, len(molecules))
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for right_block_start in range(left_block_start, len(molecules), block_size):
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right_block_end = min(right_block_start + block_size, len(molecules))
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same_block = left_block_start == right_block_start
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for left_index in range(left_block_start, left_block_end):
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right_start = left_index + 1 if same_block else right_block_start
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for right_index in range(right_start, right_block_end):
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checked_pairs += 1
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similarity = DataStructs.TanimotoSimilarity(
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molecules[left_index].fingerprint,
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molecules[right_index].fingerprint,
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)
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if similarity >= threshold:
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edges.append(
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SimilarityEdge(
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molecules[left_index].molecule_id,
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molecules[right_index].molecule_id,
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similarity,
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)
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)
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if progress_every and checked_pairs >= next_report:
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elapsed = time.perf_counter() - started_at
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rate = checked_pairs / elapsed if elapsed else 0.0
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print(
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f"Checked {checked_pairs:,} pairs | {len(edges):,} edges | "
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f"{rate:,.0f} pairs/s | {elapsed:.1f}s elapsed",
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file=sys.stderr,
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)
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next_report += progress_every
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elapsed_seconds = time.perf_counter() - started_at
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edges.sort(key=lambda edge: (edge.source_id, edge.target_id, -edge.similarity))
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return GraphResult(edges, stats, checked_pairs, elapsed_seconds)
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def write_graph_edges(output_path: Path, edges: list[SimilarityEdge]) -> None:
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"""Write a deterministic sparse edge list CSV."""
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with output_path.open("w", encoding="utf-8", newline="") as destination:
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writer = csv.DictWriter(destination, fieldnames=["source_id", "target_id", "similarity"])
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writer.writeheader()
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for edge in edges:
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writer.writerow(
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{
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"source_id": edge.source_id,
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"target_id": edge.target_id,
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"similarity": f"{edge.similarity:.6f}",
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}
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)
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class SimilarityGraphWorkload:
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"""CLI adapter for exact block-wise sparse similarity graph construction."""
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name = "similarity-graph"
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help = "Build an exact sparse graph of thresholded molecular similarities."
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def configure_parser(self, parser: argparse.ArgumentParser) -> None:
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parser.add_argument("input", type=Path, help="Path to ChEMBL TSV file")
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parser.add_argument(
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"--threshold", type=float, required=True,
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help="Create edges at or above this Tanimoto similarity",
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)
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parser.add_argument(
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"--block-size", type=int, default=1_000,
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help="Number of molecules per comparison block (default: 1000)",
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)
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parser.add_argument(
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"--max-rows", type=int,
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help="Read only the first N dataset rows",
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)
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parser.add_argument(
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"--progress-every", type=int, default=100_000,
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help="Print progress after this many pairs; 0 disables it",
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)
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parser.add_argument(
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"-o", "--output", type=Path, default=Path("similarity_graph.csv"),
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help="Output edge-list CSV path",
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)
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def run(self, args: argparse.Namespace) -> int:
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if args.max_rows is not None and args.max_rows < 1:
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raise ValueError("--max-rows must be a positive integer")
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if args.progress_every < 0:
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raise ValueError("--progress-every cannot be negative")
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result = build_similarity_graph(
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args.input,
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args.threshold,
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args.block_size,
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args.max_rows,
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args.progress_every,
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)
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write_graph_edges(args.output, result.edges)
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rate = (
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result.checked_pairs / result.elapsed_seconds
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if result.elapsed_seconds
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else 0.0
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)
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print(
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f"Valid molecules: {result.stats.valid:,} | invalid SMILES: "
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f"{result.stats.invalid:,} | scanned rows: {result.stats.scanned:,}"
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)
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print(
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f"Checked pairs: {result.checked_pairs:,} | edges: {len(result.edges):,} | "
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f"{rate:,.0f} pairs/s | {result.elapsed_seconds:.1f}s elapsed"
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)
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if result.stats.stopped_early:
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print("Stopped early because of --max-rows; graph covers only that subset.")
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print(f"Saved {len(result.edges)} edges to {args.output}")
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return 0
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