Update README for renamed molecular data repository

README.md

@@ -1,5 +1,5 @@
 ---
-pretty_name: MolWeaver Ligands 100M
+pretty_name: MolWeaver Molecular Data
 task_categories:
   - text-generation
   - feature-extraction
@@ -9,15 +9,47 @@ tags:
   - selfies
   - conformers
   - rdkit
+  - protein-ligand
 ---
 
-# MolWeaver Ligands 100M
+# MolWeaver Molecular Data
 
-This dataset contains 100,000,000 globally unique heavy-atom molecular
-records split across five LMDB shards. Each shard contains 20,000,000
-records and all records are assigned to the training split.
+This repository contains the molecular data used by MolWeaver: a
+100-million-record ligand corpus, preprocessed CrossDocked protein-ligand
+examples, and protein-pocket train/validation data in a centered Cartesian
+frame. The dataset repository ID is `shaipranesh/mol_data`.
 
-## Record schema
+## Dataset layout
+
+```text
+ligands/
+  shard_1.lmdb
+  shard_1_metadata.json
+  ...
+  shard_5.lmdb
+  shard_5_metadata.json
+crossdock/
+  crossdocked_v1.0_rmsd_1_to_2_all_heavy_pocket_train.lmdb
+  crossdocked_v1.0_rmsd_1_to_2_all_heavy_pocket_train.lmdb.{keys.pkl,meta.json,split.json}
+  crossdocked_v1.0_rmsd_1_to_2_all_heavy_pocket_valid_3000.lmdb
+  crossdocked_v1.0_rmsd_1_to_2_all_heavy_pocket_valid_3000.lmdb.{keys.pkl,meta.json,split.json}
+pockets_center_frame_cartesian/
+  train.lmdb
+  train.lmdb.{keys.pkl,meta.json}
+  valid.lmdb
+  valid.lmdb.{keys.pkl,meta.json}
+```
+
+The sidecar files record key indexes, preprocessing metadata, and split
+information where applicable.
+
+## Ligand corpus
+
+The `ligands/` directory contains 100,000,000 globally unique heavy-atom
+molecular records split across five LMDB shards. Each shard contains
+20,000,000 records, and all records are assigned to the training split.
+
+### Ligand record schema
 
 Each numeric LMDB key contains a pickled Python dictionary with:
 
@@ -34,17 +66,7 @@ Each numeric LMDB key contains a pickled Python dictionary with:
 Explicit hydrogen atoms and hydrogen coordinates are not included. Standard
 implicit hydrogens are used by RDKit when calculating molecular properties.
 
-## Files
-
-```text
-shard_1/train.lmdb
-shard_1/metadata.json
-...
-shard_5/train.lmdb
-shard_5/metadata.json
-```
-
-Every `train.lmdb` stores numeric keys `b"0"` through `b"19999999"` and a
+Every ligand shard stores numeric keys `b"0"` through `b"19999999"` and a
 pickled `b"length"` value equal to `20_000_000`.
 
 The local deduplication registries used during generation are not uploaded;
@@ -57,7 +79,7 @@ import lmdb
 import pickle
 
 env = lmdb.open(
-    "shard_1/train.lmdb",
+    "ligands/shard_1.lmdb",
     readonly=True,
     subdir=False,
     lock=False,