shaipranesh commited on
Commit
4f25fbc
·
verified ·
1 Parent(s): 3d3a727

Add dataset card

Browse files
Files changed (1) hide show
  1. README.md +78 -0
README.md ADDED
@@ -0,0 +1,78 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ ---
2
+ pretty_name: MolWeaver Ligands 100M
3
+ task_categories:
4
+ - text-generation
5
+ - feature-extraction
6
+ tags:
7
+ - chemistry
8
+ - molecules
9
+ - selfies
10
+ - conformers
11
+ - rdkit
12
+ ---
13
+
14
+ # MolWeaver Ligands 100M
15
+
16
+ This dataset contains 100,000,000 globally unique heavy-atom molecular
17
+ records split across five LMDB shards. Each shard contains 20,000,000
18
+ records and all records are assigned to the training split.
19
+
20
+ ## Record schema
21
+
22
+ Each numeric LMDB key contains a pickled Python dictionary with:
23
+
24
+ - `smi`: canonical heavy-atom molecule encoded as SELFIES.
25
+ - `atoms`: heavy-atom symbols in decoded SELFIES atom order.
26
+ - `coordinates`: `float32` NumPy array shaped `(10, n_heavy, 3)` containing
27
+ ten original Cartesian conformers. Coordinate atom `i` matches `atoms[i]`.
28
+ - `qed`: RDKit QED.
29
+ - `sa_score`: RDKit Contrib synthetic accessibility score.
30
+ - `molecular_weight`: RDKit average molecular weight.
31
+ - `mol_log_p`: RDKit MolLogP.
32
+ - `tpsa`: RDKit topological polar surface area.
33
+
34
+ Explicit hydrogen atoms and hydrogen coordinates are not included. Standard
35
+ implicit hydrogens are used by RDKit when calculating molecular properties.
36
+
37
+ ## Files
38
+
39
+ ```text
40
+ shard_1/train.lmdb
41
+ shard_1/metadata.json
42
+ ...
43
+ shard_5/train.lmdb
44
+ shard_5/metadata.json
45
+ ```
46
+
47
+ Every `train.lmdb` stores numeric keys `b"0"` through `b"19999999"` and a
48
+ pickled `b"length"` value equal to `20_000_000`.
49
+
50
+ The local deduplication registries used during generation are not uploaded;
51
+ they are not needed to train from the finalized records.
52
+
53
+ ## Loading
54
+
55
+ ```python
56
+ import lmdb
57
+ import pickle
58
+
59
+ env = lmdb.open(
60
+ "shard_1/train.lmdb",
61
+ readonly=True,
62
+ subdir=False,
63
+ lock=False,
64
+ readahead=False,
65
+ )
66
+ with env.begin() as txn:
67
+ length = pickle.loads(txn.get(b"length"))
68
+ record = pickle.loads(txn.get(b"0"))
69
+ ```
70
+
71
+ Pickle should only be loaded from a trusted dataset source.
72
+
73
+ ## Uniqueness
74
+
75
+ SELFIES were deduplicated exactly within each shard and separated across
76
+ shards by SHA-256 hash ownership. All five finalized registries contained
77
+ exactly 20,000,000 entries with no registry-only extras, establishing
78
+ 100,000,000 unique SELFIES records in total.