2nd release (#9)

- Improved the way splitting works
- Added SLURM scripts to simplify generating releases in the future
- Modified a bunch of scripts to simplify making new releases
- Moved the mmCIF generation code to rna3db/parser.py
- Added pre-commits
- Modified CITATION.cff to reflect JMB article
- Add READMEs for scripts
- Fix setup.py

.gitignore

@@ -13,4 +13,4 @@ data/
 [._]ss[a-gi-z]
 [._]sw[a-p]
 
-**/.DS_Store
+**/.DS_Store

.pre-commit-config.yaml

@@ -0,0 +1,19 @@
+repos:
+  - repo: local
+    hooks:
+      - id: unittests
+        name: run unit tests
+        entry: python -m unittest
+        language: system
+        pass_filenames: false
+        args: ["discover"]
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v2.3.0
+    hooks:
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+  - repo: https://github.com/psf/black
+    rev: 24.3.0
+    hooks:
+      - id: black

CITATION.cff

@@ -1,6 +1,7 @@
 cff-version: 1.2.0
 message: "If you use this software, please cite it as below."
 title: "RNA3DB: A dataset for training and benchmarking deep learning models for RNA structure prediction"
+version: 1.1
 authors:
   - given-names: "Marcell"
     family-names: "Szikszai"
@@ -15,3 +16,24 @@ authors:
   - given-names: "Elena
     family-names: Rivas"
 url: "https://github.com/marcellszi/rna3db"
+doi: "10.1016/j.jmb.2024.168552"
+date-released: 2024-04-26
+preferred-citation:
+  type: article
+  authors:
+  - given-names: "Marcell"
+    family-names: "Szikszai"
+  - given-names: "Marcin"
+    family-names: Magnus
+  - given-names: "Siddhant"
+    family-names: "Sanghi"
+  - given-names: "Sachin"
+    family-names: "Kadyan"
+  - given-names: "Nazim"
+    family-names: "Bouatta"
+  - given-names: "Elena"
+    family-names: Rivas"
+  doi: "10.1016/j.jmb.2024.168552"
+  journal: "Journal of Molecular Biology"
+  title: "RNA3DB: A structurally-dissimilar dataset split for training and benchmarking deep learning models for RNA structure prediction"
+  year: 2024

rna3db/__main__.py

@@ -132,7 +132,16 @@ def main(args):
                 args.input, args.output, args.tbl_dir, args.structural_e_value_cutoff
             )
     elif args.command == "split":
-        split(args.input, args.output, args.train_percentage, args.force_zero_test)
+        split(
+            args.input,
+            args.output,
+            splits=[
+                args.train_ratio,
+                args.valid_ratio,
+                1 - args.train_ratio - args.valid_ratio,
+            ],
+            force_zero_last=args.force_zero_test,
+        )
     else:
         raise ValueError
 
@@ -246,10 +255,16 @@ def main(args):
     split_parser.add_argument("input", type=Path, help="Input JSON file")
     split_parser.add_argument("output", type=Path, help="Output JSON file")
     split_parser.add_argument(
-        "--train_percentage",
+        "--train_ratio",
         type=float,
-        default=0.3,
-        help="Percentage of data for the train set",
+        default=0.7,
+        help="Ratio of data to use for the training set",
+    )
+    split_parser.add_argument(
+        "--valid_ratio",
+        type=float,
+        default=0.0,
+        help="Ratio of the data to use for the validation set",
     )
     split_parser.add_argument(
         "--force_zero_test",

rna3db/parser.py

@@ -135,6 +135,10 @@ def __getitem__(self, idx):
     def __len__(self):
         return len(self.residues)
 
+    @property
+    def has_atoms(self):
+        return any([not res.is_missing for res in self])
+
     def add_residue(self, res: Residue):
         """Add a residue to the chain.
 
@@ -341,6 +345,182 @@ def __repr__(self):
             f"resolution={self.resolution}, release_date={self.release_date}, structure_method={self.structure_method})"
         )
 
+    @staticmethod
+    def _gen_mmcif_loop_str(name: str, headers: Sequence[str], values: Sequence[tuple]):
+        s = "#\nloop_\n"
+        for header in headers:
+            s += f"_{name}.{header}\n"
+
+        max_widths = {k: 0 for k in headers}
+        for V in values:
+            for k, v in zip(headers, V):
+                max_widths[k] = max(max_widths[k], len(str(v)))
+
+        for V in values:
+            row = ""
+            for k, v in zip(headers, V):
+                row += f"{str(v):<{max_widths[k]}} "
+            s += row + "\n"
+
+        return s
+
+    def write_mmcif_chain(self, output_path, author_id):
+        if not self[author_id].has_atoms:
+            raise ValueError(
+                f"Did not find any atoms for chain {author_id}. Did you set `include_atoms=True`?"
+            )
+        # extract needed info
+        entity_poly_seq_data = []
+        atom_site_data = []
+        for i, res in enumerate(self[author_id]):
+            entity_poly_seq_data.append((1, res.index + 1, res.code, "n"))
+            for idx, (atom_name, atom_coords) in enumerate(res.atoms.items()):
+                x, y, z = atom_coords
+                atom_site_data.append(
+                    (
+                        "ATOM",
+                        idx + 1,
+                        atom_name[0],
+                        atom_name,
+                        ".",
+                        res.code,
+                        author_id,
+                        "?",
+                        i + 1,
+                        "?",
+                        x,
+                        y,
+                        z,
+                        1.0,
+                        0.0,
+                        "?",
+                        i + 1,
+                        res.code,
+                        author_id,
+                        atom_name,
+                        1,
+                    )
+                )
+
+        # build required strings
+        header_str = (
+            f"# generated by rna3db\n"
+            f"#\n"
+            f"data_{self.pdb_id}_{author_id}\n"
+            f"_entry.id {self.pdb_id}_{author_id}\n"
+            f"_pdbx_database_status.recvd_initial_deposition_date {self.release_date}\n"
+            f"_exptl.method '{self.structure_method.upper()}'\n"
+            f"_reflns.d_resolution_high {self.resolution}\n"
+            f"_entity_poly.pdbx_seq_one_letter_code_can {self[author_id].sequence}\n"
+        )
+        struct_asym_str = StructureFile._gen_mmcif_loop_str(
+            "_struct_asym",
+            [
+                "id",
+                "pdbx_blank_PDB_chainid_flag",
+                "pdbx_modified",
+                "entity_id",
+                "details",
+            ],
+            [("A", "N", "N", 1, "?")],
+        )
+        chem_comp_str = StructureFile._gen_mmcif_loop_str(
+            "_chem_comp",
+            [
+                "id",
+                "type",
+                "mon_nstd_flag",
+                "pdbx_synonyms",
+                "formula",
+                "formula_weight",
+            ],
+            [
+                (
+                    "A",
+                    "'RNA linking'",
+                    "y",
+                    '"ADENOSINE-5\'-MONOPHOSPHATE"',
+                    "?",
+                    "'C10 H14 N5 O7 P'",
+                    347.221,
+                ),
+                (
+                    "C",
+                    "'RNA linking'",
+                    "y",
+                    '"CYTIDINE-5\'-MONOPHOSPHATE"',
+                    "?",
+                    "'C9 H14 N3 O8 P'",
+                    323.197,
+                ),
+                (
+                    "G",
+                    "'RNA linking'",
+                    "y",
+                    '"GUANOSINE-5\'-MONOPHOSPHATE"',
+                    "?",
+                    "'C9 H13 N2 O9 P'",
+                    363.221,
+                ),
+                (
+                    "U",
+                    "'RNA linking'",
+                    "y",
+                    '"URIDINE-5\'-MONOPHOSPHATE"',
+                    "?",
+                    "'C9 H13 N2 O9 P'",
+                    324.181,
+                ),
+                ("T", "'RNA linking'", "y", '"T"', "?", "''", 0),
+                ("N", "'RNA linking'", "y", '"N"', "?", "''", 0),
+            ],
+        )
+        entity_poly_seq_str = StructureFile._gen_mmcif_loop_str(
+            "entity_poly_seq",
+            [
+                "entity_id",
+                "num",
+                "mon_id",
+                "heter",
+            ],
+            entity_poly_seq_data,
+        )
+        atom_site_str = StructureFile._gen_mmcif_loop_str(
+            "atom_site",
+            [
+                "group_PDB",
+                "id",
+                "type_symbol",
+                "label_atom_id",
+                "label_alt_id",
+                "label_comp_id",
+                "label_asym_id",
+                "label_entity_id",
+                "label_seq_id",
+                "pdbx_PDB_ins_code",
+                "Cartn_x",
+                "Cartn_y",
+                "Cartn_z",
+                "occupancy",
+                "B_iso_or_equiv",
+                "pdbx_formal_charge",
+                "auth_seq_id",
+                "auth_comp_id",
+                "auth_asym_id",
+                "auth_atom_id",
+                "pdbx_PDB_model_num",
+            ],
+            atom_site_data,
+        )
+
+        # write to file
+        with open(output_path, "w") as f:
+            f.write(header_str)
+            f.write(struct_asym_str)
+            f.write(chem_comp_str)
+            f.write(entity_poly_seq_str)
+            f.write(atom_site_str)
+
 
 class mmCIFParser:
     def __init__(

rna3db/split.py

@@ -1,11 +1,32 @@
+import random
+
+from typing import Sequence
+
 from rna3db.utils import PathLike, read_json, write_json
 
 
+def find_optimal_components(lengths_dict, capacity):
+    component_name = list(lengths_dict.keys())
+    lengths = list(lengths_dict.values())
+
+    dp = [0] * (capacity + 1)
+    trace = [[] for i in range(capacity + 1)]
+    for i in range(len(lengths)):
+        for j in range(capacity, lengths[i] - 1, -1):
+            if dp[j] < dp[j - lengths[i]] + lengths[i]:
+                dp[j] = dp[j - lengths[i]] + lengths[i]
+                trace[j] = trace[j - lengths[i]] + [component_name[i]]
+
+    return set(trace[capacity])
+
+
 def split(
     input_path: PathLike,
     output_path: PathLike,
-    train_size: float = 0.7,
-    force_zero_test: bool = True,
+    splits: Sequence[float] = [0.7, 0.0, 0.3],
+    split_names: Sequence[str] = ["train_set", "valid_set", "test_set"],
+    shuffle: bool = False,
+    force_zero_last: bool = False,
 ):
     """A function that splits a JSON of components into a train/test set.
 
@@ -16,35 +37,37 @@ def split(
     Args:
         input_path (PathLike): path to JSON containing components
         output_path (PathLike): path to output JSON
-        train_size (float): percentage of data to use as training set
-        force_zero_test (bool): whether to force component_0 into the test set
     """
+    if sum(splits) != 1.0:
+        raise ValueError("Sum of splits must equal 1.0.")
+
     # read json
     cluster_json = read_json(input_path)
+
     # count number of repr sequences
-    total_repr_clusters = sum(len(v) for v in cluster_json.values())
-
-    # figure out which components need to go into training set
-    train_components = set()
-    train_set_length = 0
-    i = 1 if force_zero_test else 0
-    while train_set_length / total_repr_clusters < train_size:
-        # skip if it's not a real component (should only happen with 0)
-        if f"component_{i}" not in cluster_json:
-            i += 1
-            continue
-        train_components.add(f"component_{i}")
-        train_set_length += len(cluster_json[f"component_{i}"].keys())
-        i += 1
-
-    # test_components are just total-train_components
-    test_components = set(cluster_json.keys()) - train_components
-
-    # actually build JSON
-    output = {"train_set": {}, "test_set": {}}
-    for k in sorted(train_components):
-        output["train_set"][k] = cluster_json[k]
-    for k in sorted(test_components):
-        output["test_set"][k] = cluster_json[k]
+    lengths = {k: len(v) for k, v in cluster_json.items()}
+    total_repr_clusters = sum(lengths.values())
+
+    # shuffle if we want to add randomness
+    if shuffle:
+        L = list(zip(component_name, lengths))
+        random.shuffle(L)
+        component_name, lengths = zip(*L)
+        component_name, lengths = list(component_name), list(lengths)
+
+    output = {k: {} for k in split_names}
+
+    if force_zero_last:
+        output[split_names[-1]]["component_0"] = cluster_json["component_0"]
+        lengths.pop("component_0")
+
+    capacities = [round(total_repr_clusters * ratio) for ratio in splits]
+    for name, capacity in zip(split_names, capacities):
+        components = find_optimal_components(lengths, capacity)
+        for k in sorted(components):
+            lengths.pop(k)
+            output[name][k] = cluster_json[k]
+
+    assert len(lengths) == 0
 
     write_json(output, output_path)