import datasets import csv import random class ppb_affinity(datasets.GeneratorBasedBuilder): VERSION = datasets.Version("1.0.0") BUILDER_CONFIGS = [ datasets.BuilderConfig(name="raw", description="Raw parsed PDBs dataset with critical filtrations only."), datasets.BuilderConfig(name="raw_rec", description="Raw parsed PDBs dataset with critical filtrations and missing residues recovered."), datasets.BuilderConfig(name="filtered", description="Raw dataset with additional cleaning and train/val/test splits."), datasets.BuilderConfig(name="filtered_random", description="Filtered dataset with random 80-10-10 splits."), ] def _info(self): return datasets.DatasetInfo() def _split_generators(self, dl_manager): if self.config.name == "raw": filepath = dl_manager.download_and_extract("raw.csv") return [datasets.SplitGenerator( name=datasets.Split.TRAIN, gen_kwargs={"filepath": filepath} )] elif self.config.name == "raw_rec": filepath = dl_manager.download_and_extract("raw_recover_missing_res.csv") return [datasets.SplitGenerator( name=datasets.Split.TRAIN, gen_kwargs={"filepath": filepath} )] elif self.config.name == "filtered": filepath = dl_manager.download_and_extract("filtered.csv") return [ datasets.SplitGenerator( name=datasets.Split.TRAIN, gen_kwargs={"filepath": filepath, "split": "train"}, ), datasets.SplitGenerator( name=datasets.Split.VALIDATION, gen_kwargs={"filepath": filepath, "split": "val"}, ), datasets.SplitGenerator( name=datasets.Split.TEST, gen_kwargs={"filepath": filepath, "split": "test"}, ), ] elif self.config.name == "filtered_random": filepath = dl_manager.download_and_extract("filtered.csv") with open(filepath, encoding="utf-8") as f: reader = csv.DictReader(f) rows = list(reader) n_total = len(rows) indices = list(range(n_total)) rng = random.Random(42) rng.shuffle(indices) n_train = int(0.8 * n_total) n_val = int(0.1 * n_total) n_test = n_total - n_train - n_val return [ datasets.SplitGenerator( name=datasets.Split.TRAIN, gen_kwargs={ "filepath": filepath, "shuffled_indices": indices, "split_start": 0, "split_end": n_train, }, ), datasets.SplitGenerator( name=datasets.Split.VALIDATION, gen_kwargs={ "filepath": filepath, "shuffled_indices": indices, "split_start": n_train, "split_end": n_train + n_val, }, ), datasets.SplitGenerator( name=datasets.Split.TEST, gen_kwargs={ "filepath": filepath, "shuffled_indices": indices, "split_start": n_train + n_val, "split_end": n_total, }, ), ] def _generate_examples(self, filepath, split=None, shuffled_indices=None, split_start=None, split_end=None): with open(filepath, encoding="utf-8") as f: reader = csv.DictReader(f) rows = list(reader) if self.config.name in ["raw", "raw_rec"]: for idx, row in enumerate(rows): yield idx, row elif self.config.name == "filtered": for idx, row in enumerate(rows): if row["split"] == split: del row["split"] yield idx, row elif self.config.name == "filtered_random": for global_idx in range(split_start, split_end): original_idx = shuffled_indices[global_idx] row = rows[original_idx] del row["split"] yield global_idx, row