Update to version 1.1

README.md

@@ -25,10 +25,10 @@ dataset_info:
     list: float32
   splits:
   - name: train
-    num_bytes: 4494736359
-    num_examples: 9323426
-  download_size: 5223426623
-  dataset_size: 4494736359
+    num_bytes: 4561229719
+    num_examples: 9418152
+  download_size: 3631622198
+  dataset_size: 4561229719
 - config_name: metadata
   features:
   - name: OMol25_data_id
@@ -49,18 +49,30 @@ dataset_info:
     dtype: bool
   - name: OpenFF_spin=1
     dtype: bool
+  - name: lowdin_charges
+    list: float64
   - name: smiles
     dtype: string
-  - name: source
+  - name: smiles_n_fragments
+    dtype: int64
+  - name: smiles_n_orphaned_h
+    dtype: int64
+  - name: smiles_sanitizes
+    dtype: bool
+  - name: smiles_sanitize_error
     dtype: string
-  - name: lowdin_charges
-    list: float64
+  - name: smiles_radical
+    dtype: bool
+  - name: smiles_formal_charge
+    dtype: int64
+  - name: smiles_charge_matches
+    dtype: bool
   splits:
   - name: train
-    num_bytes: 3018911478
-    num_examples: 9323426
-  download_size: 1632616300
-  dataset_size: 3018911478
+    num_bytes: 2934223690
+    num_examples: 9418152
+  download_size: 1384927303
+  dataset_size: 2934223690
 configs:
 - config_name: descent_data
   data_files:
@@ -73,7 +85,7 @@ configs:
 ---
 
 
-# Dataset Card for Meta-OMol25 Descent Formatted ANI2X v1.0
+# Dataset Card for Meta-OMol25 Descent Formatted ANI2X v1.1
 
 ## Dataset Details
 
@@ -90,6 +102,7 @@ Meta-OMol25 provides molecular structures, coordinates, energies, and forces, an
 ### Dataset Sources
 
 - Repository: https://huggingface.co/facebook/OMol25
+- Hugging Face dataset repository: {{HF_REPO_URL}}
 
 ## Uses
 
@@ -104,24 +117,24 @@ Meta-OMol25 provides molecular structures, coordinates, energies, and forces, an
 ### Overall Statistics
 
 - Meta-OMol25 rows: 9641964
-- Metadata rows: 9323426
-- Smee rows: 9323426
-- Failed rows: 318538
-- Failed unique indices: 318538
+- Metadata rows: 9418152
+- Smee rows: 9418152
+- Failed rows: 223812
+- Failed unique indices: 223812
 - Accounted total (metadata + failed - overlap): 9641964
 - All Meta-OMol25 structures accounted for: True
 - Uncovered Meta-OMol25 rows: 0
 
 ### Metadata Split and Chemistry Summary
 
-- Sample size used for summary: 9323426
+- Sample size used for summary: 9418152
 - Sample split counts: {
-  "val": 2861,
-  "train": 9320565
+  "val": 2932,
+  "train": 9415220
 }
 - Sample charge range: [0, 0]
-- Sample molecular weight (g/mol, min / max / mean): 16.043000 / 408.458000 / 122.197604
-- Molecular weight sample count: 9323426
+- Sample molecular weight (g/mol, min / max / mean): 16.043000 / 408.458000 / 122.161221
+- Molecular weight sample count: 9418152
 
 ### Metadata Schema
 
@@ -134,9 +147,15 @@ Meta-OMol25 provides molecular structures, coordinates, energies, and forces, an
 - OpenFF_Elements: Value('bool')
 - OpenFF_abs(q)<=1: Value('bool')
 - OpenFF_spin=1: Value('bool')
-- smiles: Value('string')
-- source: Value('string')
 - lowdin_charges: List(Value('float64'))
+- smiles: Value('string')
+- smiles_n_fragments: Value('int64')
+- smiles_n_orphaned_h: Value('int64')
+- smiles_sanitizes: Value('bool')
+- smiles_sanitize_error: Value('string')
+- smiles_radical: Value('bool')
+- smiles_formal_charge: Value('int64')
+- smiles_charge_matches: Value('bool')
 
 ### Smee Schema
 
@@ -148,7 +167,7 @@ Meta-OMol25 provides molecular structures, coordinates, energies, and forces, an
 Sample energy stats (kcal/mol):
 - Min: -2065007.125000
 - Max: -25377.093750
-- Mean: -367128.856687
+- Mean: -366824.406342
 
 ### Cross-Table Consistency
 
@@ -171,22 +190,69 @@ Sample energy stats (kcal/mol):
 ### Quality and Validation
 
 - smee importable: True
-- descent importable: True
-- descent create_dataset on sample succeeded: True
-- Validation sample size: 256
-- Validation error (if any): 
-
-Top failure modes:
-- InconsistentStereochemistryError('Programming error: OpenEye atom stereochemistry assumptions failed. The atom in the oemol has stereochemistry None and the atom in the offmol has stereochemistry R.'): 47184
-- InconsistentStereochemistryError('Programming error: OpenEye atom stereochemistry assumptions failed. The atom in the oemol has stereochemistry None and the atom in the offmol has stereochemistry S.'): 43965
-- ValueError('Inconsistent charge with target!'): 5567
-- RadicalsNotSupportedError('The OpenFF Toolkit does not currently support parsing molecules with S- and P-block radicals. Found 2 radical electrons on molecule [H][O+].[O-].[O]Cl.'): 278
-- RadicalsNotSupportedError('The OpenFF Toolkit does not currently support parsing molecules with S- and P-block radicals. Found 1 radical electrons on molecule [H].[H].[H]C([H])([H])C([N-])=[O+].'): 256
-- RadicalsNotSupportedError('The OpenFF Toolkit does not currently support parsing molecules with S- and P-block radicals. Found 2 radical electrons on molecule [H][C][C@@]12N3[C@@]([H])(C1([H])[H])[C@@]3([H])C([H])([H])C2([H])[H].'): 231
-- RadicalsNotSupportedError('The OpenFF Toolkit does not currently support parsing molecules with S- and P-block radicals. Found 2 radical electrons on molecule [H+].[H+].[H+].[H]N([H])C([H])([H])[C][C][C-3].'): 228
-- InconsistentStereochemistryError('Programming error: OpenEye bond stereochemistry assumptions failed. The bond in the oemol has stereochemistry None and the bond in the offmol has stereochemistry Z.'): 219
-- InconsistentStereochemistryError('Programming error: OpenEye bond stereochemistry assumptions failed. The bond in the oemol has stereochemistry None and the bond in the offmol has stereochemistry E.'): 209
-- RadicalsNotSupportedError('The OpenFF Toolkit does not currently support parsing molecules with S- and P-block radicals. Found 1 radical electrons on molecule [H].[H].[H]C([H])=C([H])C([N-])=[O+].'): 173
+- descent importable: False
+- descent create_dataset on sample succeeded: False
+- Validation sample size: 0
+- Validation error (if any): descent import failed: AttributeError("module 'smee' has no attribute 'TensorForceField'")
+
+#### SMILES Column Statistics (smiles_*)
+
+Rows analyzed: 9418152
+
+Number of fragments (smiles_n_fragments):
+- 1: 7423400
+- 2: 1438136
+- 3: 214689
+- 4: 79503
+- 5: 29967
+- 6: 24006
+- 7: 28574
+- 8: 22551
+- 9: 24798
+- 10: 26116
+- 11: 25511
+- 12: 26082
+- 13: 26676
+- 14: 13904
+- 15: 14238
+- 16: 1
+
+Orphaned hydrogens per molecule (smiles_n_orphaned_h; total 1639904):
+- 0: 8146250
+- 1: 1000758
+- 2: 190524
+- 3: 67246
+- 4: 11398
+- 5: 1206
+- 6: 668
+- 7: 90
+- 8: 8
+- 9: 4
+
+RDKit sanitization (smiles_sanitizes):
+- True: 9418152
+
+Sanitization errors (smiles_sanitize_error; top 10):
+N/A
+
+Radicals among sanitized molecules (smiles_radical):
+- False: 9418152
+
+SMILES formal charge (smiles_formal_charge):
+- 0: 9418152
+
+SMILES formal charge matches record charge (smiles_charge_matches):
+- True: 9418152
+
+#### Conversion Failures
+
+Failure classes (instance details such as atom indices and SMILES are collapsed):
+- 169,487: RadicalsNotSupportedError(… Found 1 radical electrons on molecule <SMILES>.)
+- 45,739: RadicalsNotSupportedError(… Found 2 radical electrons on molecule <SMILES>.)
+- 5,379: ValueError('Inconsistent charge with target!')
+- 3,107: RadicalsNotSupportedError(… Found 3 radical electrons on molecule <SMILES>.)
+- 62: AssertionError('E/Z stereo could not be converted to local stereo')
+- 38: AtomValenceException('Explicit valence for atom # <idx> N, 4, is greater than permitted')
 
 ## Dataset Card Authors
 

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