Refactor into modular molecular workloads
This commit is contained in:
Emil
@@ -0,0 +1,13 @@
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"""Built-in SciMesh workloads."""
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from __future__ import annotations
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from scimesh.core.registry import WorkloadRegistry
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from scimesh.workloads.similarity_graph import SimilarityGraphWorkload
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from scimesh.workloads.similarity_search import SimilaritySearchWorkload
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def register_workloads(registry: WorkloadRegistry) -> None:
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"""Register built-in workloads in one place, outside the main CLI."""
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registry.register(SimilaritySearchWorkload())
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registry.register(SimilarityGraphWorkload())
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@@ -0,0 +1,185 @@
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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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@@ -0,0 +1,225 @@
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"""Top-k molecular similarity search 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 heapq
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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 rdkit import Chem, DataStructs
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from rdkit.Chem import Draw
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from scimesh.chemistry.dataset import (
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DatasetStats,
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MoleculeRecord,
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find_molecule_by_id,
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iter_valid_molecules,
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parse_smiles,
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)
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from scimesh.chemistry.fingerprints import fingerprint
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@dataclass(frozen=True)
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class SimilarityMatch:
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"""A candidate ranked by descending similarity and stable tie-breakers."""
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similarity: float
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molecule_id: str
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smiles: str
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def sort_key(self) -> tuple[float, str, str]:
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return (-self.similarity, self.molecule_id, self.smiles)
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@dataclass
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class _HeapEntry:
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"""Heap item whose minimum is the worst retained match."""
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match: SimilarityMatch
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def __lt__(self, other: object) -> bool:
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if not isinstance(other, _HeapEntry):
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return NotImplemented
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return self.match.sort_key() > other.match.sort_key()
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@dataclass
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class SearchResult:
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"""Results and scan statistics for a similarity search."""
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matches: list[SimilarityMatch]
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stats: DatasetStats
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def search_similar(
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tsv_path: Path,
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query: MoleculeRecord,
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top_k: int,
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max_rows: int | None = None,
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progress_every: int = 0,
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) -> SearchResult:
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"""Stream top-k matches, retaining only a bounded heap in memory."""
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if top_k < 1:
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raise ValueError("--top-k must be a positive integer")
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query_fingerprint = fingerprint(query.molecule)
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query_canonical_smiles = Chem.MolToSmiles(query.molecule, canonical=True)
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stats = DatasetStats()
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heap: list[_HeapEntry] = []
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started_at = time.perf_counter()
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last_report_at = started_at
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last_report_rows = 0
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for record in iter_valid_molecules(tsv_path, stats, max_rows=max_rows):
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candidate_canonical_smiles = Chem.MolToSmiles(record.molecule, canonical=True)
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if (
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record.molecule_id == query.molecule_id
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or candidate_canonical_smiles == query_canonical_smiles
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):
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continue
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match = SimilarityMatch(
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DataStructs.TanimotoSimilarity(query_fingerprint, fingerprint(record.molecule)),
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record.molecule_id,
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record.smiles,
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)
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entry = _HeapEntry(match)
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if len(heap) < top_k:
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heapq.heappush(heap, entry)
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elif match.sort_key() < heap[0].match.sort_key():
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heapq.heapreplace(heap, entry)
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if progress_every and stats.scanned % progress_every == 0:
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now = time.perf_counter()
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interval = now - last_report_at
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total = now - started_at
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current_rate = (stats.scanned - last_report_rows) / interval if interval else 0.0
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average_rate = stats.scanned / total if total else 0.0
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print(
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f"Processed {stats.scanned:,} rows | {current_rate:,.0f} rows/s current | "
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f"{average_rate:,.0f} rows/s average | {total:.1f}s elapsed | "
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f"{stats.valid:,} valid | {stats.invalid:,} invalid | top {len(heap)}",
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file=sys.stderr,
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)
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last_report_at = now
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last_report_rows = stats.scanned
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return SearchResult(sorted((entry.match for entry in heap), key=SimilarityMatch.sort_key), stats)
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def write_search_results(output_path: Path, matches: list[SimilarityMatch]) -> None:
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"""Write ranked matches to a deterministic CSV file."""
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with output_path.open("w", encoding="utf-8", newline="") as destination:
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writer = csv.DictWriter(
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destination,
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fieldnames=["rank", "chembl_id", "canonical_smiles", "similarity"],
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)
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writer.writeheader()
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for rank, match in enumerate(matches, start=1):
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writer.writerow(
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{
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"rank": rank,
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"chembl_id": match.molecule_id,
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"canonical_smiles": match.smiles,
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"similarity": f"{match.similarity:.6f}",
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}
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)
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def write_search_images(
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output_dir: Path, query: MoleculeRecord, matches: list[SimilarityMatch], columns: int
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) -> tuple[Path, Path]:
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"""Create PNG depictions for the query molecule and retained matches."""
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output_dir.mkdir(parents=True, exist_ok=True)
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query_path = output_dir / "query.png"
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Draw.MolToImage(
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query.molecule, size=(600, 400), legend=f"Query: {query.molecule_id}"
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).save(query_path)
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candidates_path = output_dir / "top_candidates.png"
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molecules = [parse_smiles(match.smiles) for match in matches]
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legends = [
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f"#{rank} {match.molecule_id}\nTanimoto: {match.similarity:.4f}"
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for rank, match in enumerate(matches, start=1)
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]
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Draw.MolsToGridImage(
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molecules, molsPerRow=columns, subImgSize=(350, 250), legends=legends
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).save(candidates_path)
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return query_path, candidates_path
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class SimilaritySearchWorkload:
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"""CLI adapter for streaming top-k molecular similarity search."""
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name = "similarity-search"
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help = "Find top-k molecules similar to a query molecule."
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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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query_group = parser.add_mutually_exclusive_group(required=True)
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query_group.add_argument("--query-id", help="ChEMBL ID of the query molecule")
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query_group.add_argument("--query-smiles", help="SMILES of the query molecule")
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parser.add_argument(
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"--top-k", "--top", dest="top_k", type=int, default=20,
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help="Number of matches to retain (default: 20)",
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)
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parser.add_argument(
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"-o", "--output", type=Path, default=Path("similarity_results.csv"),
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help="Output CSV path",
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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 rows; 0 disables it",
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)
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parser.add_argument(
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"--max-rows", type=int,
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help="Scan only the first N rows after resolving the query",
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)
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parser.add_argument(
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"--images-dir", type=Path,
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help="Directory for query and top-candidate PNG images",
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)
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parser.add_argument(
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"--image-columns", type=int, default=4,
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help="Number of molecules per row in the candidate image",
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)
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def run(self, args: argparse.Namespace) -> int:
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if args.progress_every < 0:
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raise ValueError("--progress-every cannot be negative")
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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.image_columns < 1:
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raise ValueError("--image-columns must be a positive integer")
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if args.query_id:
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query = find_molecule_by_id(args.input, args.query_id)
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else:
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molecule = parse_smiles(args.query_smiles)
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if molecule is None:
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raise ValueError("--query-smiles is invalid")
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query = MoleculeRecord("query", args.query_smiles, molecule)
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result = search_similar(
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args.input, query, args.top_k, args.max_rows, args.progress_every
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)
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write_search_results(args.output, result.matches)
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image_paths: tuple[Path, Path] | None = None
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if args.images_dir:
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image_paths = write_search_images(
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args.images_dir, query, result.matches, args.image_columns
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)
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print(f"Query {query.molecule_id}: {query.smiles}")
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print(
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f"Scanned {result.stats.scanned:,} rows: {result.stats.valid:,} valid, "
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f"{result.stats.invalid:,} invalid SMILES."
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)
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if result.stats.stopped_early:
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print("Stopped early because of --max-rows; results cover only that subset.")
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print(f"Saved {len(result.matches)} matches to {args.output}")
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if image_paths:
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print(f"Saved query image to {image_paths[0]}")
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print(f"Saved candidate image to {image_paths[1]}")
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return 0
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