Upload MofasaDB

.gitattributes

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 # Video files - compressed
 *.mp4 filter=lfs diff=lfs merge=lfs -text
 *.webm filter=lfs diff=lfs merge=lfs -text
+relaxed.db filter=lfs diff=lfs merge=lfs -text
+samples.db filter=lfs diff=lfs merge=lfs -text

README.md

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----
-license: cc-by-4.0
----
+# MofasaDB
+
+---
+
+## Table of Contents
+
+1. [Database Overview](#database-overview)
+2. [Quick Start](#quick-start)
+3. [Property Reference](#property-reference)
+4. [Structural Properties](#structural-properties)
+5. [MOFID Properties](#mofid-properties)
+6. [Zeo++ Geometric Properties](#zeo-geometric-properties)
+7. [ORB Properties](#orb-properties)
+8. [MOFChecker Properties](#mofchecker-properties)
+9. [MOF Fragment Properties](#mof-fragment-properties)
+10. [Linker Properties](#linker-properties)
+11. [Validation Metrics](#validation-metrics)
+
+---
+
+## Database Overview
+
+The database contains unconditionally generated MOF (Metal-Organic Framework) structures from Mofasa, along with their geometry-relaxed counterparts.
+
+### Files
+
+| File | Description |
+|------|-------------|
+| `samples.db` | Original generated MOF structures |
+| `relaxed.db` | Geometry-relaxed versions of the samples |
+| `sample_latents/` | ORB latent embeddings for samples |
+| `relaxed_latents/` | ORB latent embeddings for relaxed structures |
+
+### Data Alignment
+
+The databases are **row-aligned**: row *i* in `samples.db` corresponds to row *i* in `relaxed.db`.
+
+**Indexing:**
+- ASE databases are **1-indexed**: first row is `db.get(1)`
+- NumPy arrays are **0-indexed**: first element is `array[0]`
+- Therefore: `latent[i]` corresponds to `db.get(i + 1)`
+
+---
+
+## Quick Start
+
+### Load a Structure
+
+```python
+from ase.db import connect
+
+db = connect("samples.db")
+row_id = 1
+row = db.get(row_id)                    # Get first structure (1-indexed)
+atoms = row.toatoms()              # Convert to ASE Atoms object
+print(atoms.get_chemical_formula())
+```
+
+### Access Properties
+
+```python
+# Get energy per atom
+energy = row.data['properties']['orb_properties']['orb_energy_per_atom']
+
+# Get pore diameter
+lcd = row.data['properties']['pyzeo_geometric_properties']['lcd']
+
+# Get topology (top-level property)
+topology = row.data['topology']
+```
+
+### Load Orb Latent Embeddings
+
+```python
+import numpy as np
+
+latents = np.load("sample_latents/orb_latent_4_graph.npy")
+latent = latents[row_id - 1]  # Convert 1-indexed row to 0-indexed array
+```
+
+### Compare Sample and Relaxed
+
+```python
+sample_db = connect("samples.db")
+relaxed_db = connect("relaxed.db")
+
+# Row i in both databases correspond to the same structure
+row_id = 100
+sample_atoms = sample_db.get(row_id).toatoms()
+relaxed_atoms = relaxed_db.get(row_id).toatoms()
+
+print(f"Sample formula:  {sample_atoms.get_chemical_formula()}")
+print(f"Relaxed formula: {relaxed_atoms.get_chemical_formula()}")
+```
+
+---
+
+## Property Reference
+
+Properties are stored in `row.data` with nested paths:
+
+```python
+PROPERTY_PATHS = {
+    # ORB model properties
+    'orb_energy_per_atom': 'properties.orb_properties.orb_energy_per_atom',
+    'orb_max_force': 'properties.orb_properties.orb_max_force',
+    # Pyzeo geometric properties
+    'lcd': 'properties.pyzeo_geometric_properties.lcd',
+    'pld': 'properties.pyzeo_geometric_properties.pld',
+    'dif': 'properties.pyzeo_geometric_properties.dif',
+    'av_volume_fraction': 'properties.pyzeo_geometric_properties.av_volume_fraction',
+    'av_cm3_per_g': 'properties.pyzeo_geometric_properties.av_cm3_per_g',
+    'number_of_channels': 'properties.pyzeo_geometric_properties.number_of_channels',
+    # Crystal symmetry
+    'spacegroup_number': 'properties.crystal_symmetry.spacegroup_number',
+    # Top-level properties
+    'max_force': 'max_force',
+    'geo_converged': 'geo_converged',
+    'mofid': 'mofid',
+    'topology': 'topology',
+}
+```
+
+---
+
+## Structural Properties
+
+### Lattice Parameters
+
+| Key | Type | Description |
+|-----|------|-------------|
+| `lattice_a` | float | Unit cell length along the *a*-axis (Å) |
+| `lattice_b` | float | Unit cell length along the *b*-axis (Å) |
+| `lattice_c` | float | Unit cell length along the *c*-axis (Å) |
+| `lattice_alpha` | float | Angle between *b* and *c* axes (degrees) |
+| `lattice_beta` | float | Angle between *a* and *c* axes (degrees) |
+| `lattice_gamma` | float | Angle between *a* and *b* axes (degrees) |
+
+### Chemical Composition
+
+| Key | Type | Description |
+|-----|------|-------------|
+| `reduced_formula` | str | Empirical (reduced) chemical formula of the structure |
+
+---
+
+## MOFID Properties
+
+MOFID is a standardized identifier for MOF structures that encodes topology, nodes, linkers, and catenation information.
+
+| Key | Type | Description |
+|-----|------|-------------|
+| `mofid` | str | Full MOFID identifier string. Format: `{nodes}.{linkers} MOFid-v1.{topology}.cat{n}`. Value is `"UNKNOWN"` if MOFID could not be computed. |
+| `mofkey` | str | MOFKey identifier (a hash-based representation of the MOF structure). Format: `{hash}.{topology}.MOFkey-v1.{short_code}`. Value is `"UNKNOWN"` if MOFKey could not be computed. |
+| `nodes` | str | Concatenated SMILES strings of all distinct metal nodes (`.`-separated). Value is `"UNKNOWN"` if not available. |
+| `linkers` | str | Concatenated SMILES strings of all distinct organic linkers (`.`-separated). Value is `"UNKNOWN"` if not available. |
+| `num_distinct_nodes` | int | Number of chemically distinct metal node types in the MOF |
+| `num_distinct_linkers` | int | Number of chemically distinct organic linker types in the MOF |
+| `topology` | str | Three-letter RCSR topology code (e.g., `"pcu"`, `"dia"`, `"fcu"`). Value is `"UNKNOWN"` if topology could not be determined. |
+| `topology_v2` | str | Alternative topology assignment (may differ from primary if ambiguous) |
+| `catenation` | int | Catenation number (degree of interpenetration). 0 = non-catenated, n = n-fold catenated |
+| `mofid_comment` | str | Additional comments from MOFID analysis (may contain warnings or processing notes) |
+
+---
+
+## Crystal Symmetry
+
+Computed using [pymatgen](https://pymatgen.org/)'s `SpacegroupAnalyzer`.
+
+| Key | Type | Description |
+|-----|------|-------------|
+| `spacegroup` | str | Crystal system from space group analysis at `symprec=0.01` (e.g., `"cubic"`, `"triclinic"`) |
+| `spacegroup_v2` | str | Crystal system from space group analysis at `symprec=0.1` (more tolerant symmetry detection) |
+
+### Detailed Crystal Symmetry (nested under `properties.crystal_symmetry`)
+
+| Key | Type | Description |
+|-----|------|-------------|
+| `symprec_0.01/pointgroup` | str | Point group symbol (Hermann-Mauguin notation) |
+| `symprec_0.01/spacegroup` | str | Space group symbol (Hermann-Mauguin notation) |
+| `symprec_0.01/spacegroup_number` | int | International Tables space group number (1-230) |
+| `symprec_0.01/spacegroup_crystal` | str | Crystal system name |
+| `symprec_0.1/pointgroup` | str | Point group symbol (at looser tolerance) |
+| `symprec_0.1/spacegroup` | str | Space group symbol (at looser tolerance) |
+| `symprec_0.1/spacegroup_number` | int | Space group number (at looser tolerance) |
+| `symprec_0.1/spacegroup_crystal` | str | Crystal system name (at looser tolerance) |
+
+---
+
+## Zeo++ Geometric Properties
+
+Computed using [Zeo++](http://www.zeoplusplus.org/) via the pyzeo wrapper. These properties characterize the pore geometry and accessibility using a spherical probe (default: N₂ probe radius of 1.86 Å).
+
+### Pore Descriptors
+
+| Key | Type | Unit | Description |
+|-----|------|------|-------------|
+| `lcd` | float | Å | **Largest Cavity Diameter** – Diameter of the largest sphere that can fit in the pore without overlapping framework atoms |
+| `pld` | float | Å | **Pore Limiting Diameter** – Diameter of the largest sphere that can percolate through the framework (i.e., the narrowest point along the largest channel) |
+| `dif` | float | Å | **Diameter of Included sphere along Free path** – Diameter of the largest sphere that can diffuse along the accessible path |
+| `number_of_channels` | int | — | Number of distinct connected channel systems in the framework |
+| `number_of_pockets` | int | — | Number of isolated pores (inaccessible to the probe molecule) |
+
+### Volume Properties
+
+| Key | Type | Unit | Description |
+|-----|------|------|-------------|
+| `av_volume_fraction` | float | — | Fraction of unit cell volume that is accessible to the probe |
+| `av_cm3_per_g` | float | cm³/g | Accessible pore volume per gram of framework |
+| `nav_volume_fraction` | float | — | Fraction of unit cell volume that is non-accessible (pocket volume) |
+| `nav_cm3_per_g` | float | cm³/g | Non-accessible volume per gram of framework |
+| `channel_volume_fraction` | float | — | Fraction of total void volume that belongs to channels |
+| `pocket_volume_fraction` | float | — | Fraction of total void volume that belongs to pockets |
+
+### Surface Area Properties
+
+| Key | Type | Unit | Description |
+|-----|------|------|-------------|
+| `asa_m2_per_cm3` | float | m²/cm³ | Accessible surface area per unit volume |
+| `asa_m2_per_g` | float | m²/g | **Accessible Surface Area** per gram (comparable to BET surface area) |
+| `nasa_m2_per_cm3` | float | m²/cm³ | Non-accessible surface area per unit volume |
+| `nasa_m2_per_g` | float | m²/g | Non-accessible surface area per gram |
+| `channel_surface_area_fraction` | float | — | Fraction of total surface area belonging to channels |
+| `pocket_surface_area_fraction` | float | — | Fraction of total surface area belonging to pockets |
+
+---
+
+## ORB Properties
+
+Properties computed using the [ORB](https://github.com/orbital-materials/orb-models) machine learning force field.
+
+### Energy and Forces
+
+| Key | Type | Unit | Description |
+|-----|------|------|-------------|
+| `orb_energy_per_atom` | float | eV/atom | Total predicted energy divided by number of atoms |
+| `orb_max_force` | float | eV/Å | Maximum force magnitude on any atom in the structure |
+
+### ORB Latent Embeddings
+
+ORB latent embeddings are stored as NumPy files in the `sample_latents/` and `relaxed_latents/` directories.
+
+**File naming:** `orb_latent_{layer}_{component}.npy`
+
+| File Pattern | Shape | Description |
+|--------------|-------|-------------|
+| `orb_latent_{0-4}_graph` | (N, 256) | Graph-level pooled latent |
+| `orb_latent_{0-4}_nodes_and_bridges` | (N, 256) | Mean-pooled over metal nodes |
+| `orb_latent_{0-4}_linkers` | (N, 256) | Mean-pooled over organic linkers |
+| `orb_latent_{0-4}_bound_solvent` | (N, 256) | Mean-pooled over bound solvents |
+| `orb_latent_{0-4}_free_solvent` | (N, 256) | Mean-pooled over free solvents |
+
+- Layers 0-4 correspond to different depths in the ORB GNN (layer 4 = final layer)
+- **Zero vectors** indicate missing data (e.g., structures without solvents)
+
+---
+
+## MOFChecker Properties
+
+Computed using [MOFChecker](https://github.com/kjappelbaum/mofchecker), a tool for validating MOF structures. All keys are prefixed with `mofchecker_`.
+
+### Validity Checks (Binary)
+
+These descriptors are used to determine overall MOF validity. **True indicates a problem** (except where noted).
+
+| Key | Type | Description |
+|-----|------|-------------|
+| `mofchecker_valid` | bool | Overall validity flag. `True` if structure passes all validity checks. |
+| `mofchecker_no_carbon` | bool | `True` if structure contains no carbon atoms (invalid for organic-based MOFs) |
+| `mofchecker_no_hydrogen` | bool | `True` if structure contains no hydrogen atoms |
+| `mofchecker_no_metal` | bool | `True` if structure contains no metal atoms |
+| `mofchecker_has_atomic_overlaps` | bool | `True` if any atoms are too close together |
+| `mofchecker_has_lone_molecule` | bool | `True` if structure contains disconnected molecular fragments |
+| `mofchecker_has_overcoordinated_c` | bool | `True` if any carbon has too many bonds |
+| `mofchecker_has_overcoordinated_n` | bool | `True` if any nitrogen has too many bonds |
+| `mofchecker_has_overcoordinated_h` | bool | `True` if any hydrogen has too many bonds |
+| `mofchecker_has_undercoordinated_c` | bool | `True` if any carbon has too few bonds |
+| `mofchecker_has_undercoordinated_n` | bool | `True` if any nitrogen has too few bonds |
+| `mofchecker_has_undercoordinated_rare_earth` | bool | `True` if any rare earth metal is undercoordinated |
+| `mofchecker_has_undercoordinated_alkali_alkaline` | bool | `True` if any alkali/alkaline earth metal is undercoordinated |
+| `mofchecker_has_suspicious_terminal_oxo` | bool | `True` if structure has potentially incorrect terminal oxo groups on metals |
+| `mofchecker_has_geometrically_exposed_metal` | bool | `True` if any metal has unusual coordination geometry |
+| `mofchecker_has_high_charges` | bool | `True` if computed partial charges are unusually high |
+
+### Informative Checks (Binary, not used for validity)
+
+| Key | Type | Description |
+|-----|------|-------------|
+| `mofchecker_has_oms` | bool | `True` if structure has Open Metal Sites (coordinatively unsaturated metals) |
+| `mofchecker_has_3d_connected_graph` | bool | `True` if the framework is 3D-connected (expected for MOFs) |
+
+### Structure Hashes
+
+| Key | Type | Description |
+|-----|------|-------------|
+| `mofchecker_graph_hash` | str | Hash of the full structure graph (atoms + bonds) |
+| `mofchecker_undecorated_graph_hash` | str | Hash of graph with hydrogen atoms removed |
+| `mofchecker_decorated_scaffold_hash` | str | Hash of framework scaffold with decorations |
+| `mofchecker_undecorated_scaffold_hash` | str | Hash of bare framework scaffold |
+| `mofchecker_symmetry_hash` | str | Hash encoding symmetry information |
+
+---
+
+## MOF Fragment Properties
+
+Properties of the decomposed MOF components (nodes, linkers, solvents). Stored under `properties.mof_fragments`.
+
+### Component Types
+
+MOF structures are decomposed into four component types:
+- **nodes_and_bridges**: Metal nodes and bridging groups
+- **linkers**: Organic linker molecules
+- **bound_solvent**: Solvent molecules coordinated to metal centers
+- **free_solvent**: Unbound solvent molecules in pores
+
+### Fragment Formulas
+
+| Key | Type | Description |
+|-----|------|-------------|
+| `{component}_formulas` | List[str] | Chemical formulas of each fragment of this component type |
+
+*Example: `nodes_and_bridges_formulas = ["Zn4O", "Zn4O"]` for a structure with two identical zinc nodes*
+
+### Linker SMILES
+
+| Key | Type | Description |
+|-----|------|-------------|
+| `linkers_smiles` | List[str] | Full SMILES strings for each linker fragment, including stereochemistry and charges where applicable |
+| `linkers_simple_smiles` | List[str] | Simplified SMILES (scaffold only, no stereochemistry). More robust for parsing but less chemically accurate |
+
+---
+
+## Linker Properties
+
+Molecular descriptors and fingerprints for organic linker molecules. Stored under `properties.linker_properties`.
+
+### Morgan Fingerprints
+
+Morgan (circular) fingerprints are stored as NumPy files. For similarity search, use the standardized versions.
+
+| File | Description |
+|------|-------------|
+| `linkers_morgan_ecfp4.npy` | ECFP4 (radius=2), 2048-bit |
+| `linkers_morgan_ecfp6.npy` | ECFP6 (radius=3), 2048-bit |
+| `linkers_morgan_ecfp4_standardized.npy` | ECFP4 from standardized molecules |
+| `linkers_morgan_ecfp6_standardized.npy` | ECFP6 from standardized molecules |
+
+**Scalar metadata:**
+
+| Key | Type | Description |
+|-----|------|-------------|
+| `linkers_smiles_used` | List[str] | Which SMILES string was successfully parsed for each linker (original, fixed, or simple) |
+| `linkers_smiles_standardized` | List[str] | Chemically standardized SMILES (neutralized, canonical tautomer) |
+| `linkers_morgan_count_sum` | List[int] | Sum of Morgan fingerprint bit counts (molecular complexity proxy) |
+| `linkers_morgan_count_sum_max` | List[int] | Maximum count in Morgan fingerprint (indicates highly represented substructures) |
+| `linkers_morgan_count_sum_standardized` | List[int] | Sum of counts for standardized fingerprints |
+| `linkers_morgan_count_sum_max_standardized` | List[int] | Maximum count for standardized fingerprints |
+
+### Molecular Descriptors
+
+Computed on standardized molecules using RDKit.
+
+| Key | Type | Description |
+|-----|------|-------------|
+| `linkers_rotatable_bonds` | List[int] | Number of rotatable bonds per linker (flexibility metric) |
+| `linkers_ring_count` | List[int] | Number of rings per linker |
+
+### Coordination Site Descriptors
+
+Counts of metal-coordinating functional groups (computed on as-parsed molecules).
+
+| Key | Type | Description |
+|-----|------|-------------|
+| `linkers_coordination_site_count` | List[int] | Total number of potential metal coordination sites per linker |
+| `linkers_coordination_site_breakdown` | List[Dict] | Breakdown by coordination site type |
+| `linkers_carboxylate_count` | List[int] | Number of carboxylate groups (-COO⁻/-COOH) |
+| `linkers_pyridine_count` | List[int] | Number of aromatic nitrogen sites |
+| `linkers_imidazole_n_count` | List[int] | Number of imidazole/triazole NH groups |
+| `linkers_primary_amine_count` | List[int] | Number of primary amine groups (-NH₂) |
+| `linkers_secondary_amine_count` | List[int] | Number of secondary amine groups (-NH-) |
+| `linkers_tertiary_amine_count` | List[int] | Number of tertiary amine groups (-N<) |
+| `linkers_phosphonate_count` | List[int] | Number of phosphonate groups |
+| `linkers_sulfonate_count` | List[int] | Number of sulfonate groups |
+| `linkers_phenolic_oh_count` | List[int] | Number of phenolic hydroxyl groups |
+| `linkers_alcoholic_oh_count` | List[int] | Number of alcoholic hydroxyl groups |
+| `linkers_thiol_count` | List[int] | Number of thiol groups (-SH) |
+| `linkers_nitrile_count` | List[int] | Number of nitrile groups (-C≡N) |
+
+---
+
+## Validation Metrics
+
+Binary metrics used to assess structure quality.
+
+| Key | Type | Description |
+|-----|------|-------------|
+| `no_atom_too_close` | bool | `True` if all interatomic distances are physically reasonable |
+| `smact_valid` | bool | `True` if composition passes SMACT electronegativity/charge balance checks |
+| `reconstruction_failed` | bool | `True` if structure reconstruction from latent space failed |
+
+---
+## License
+
+cc-by-4.0
+
+## References
+
+- **MOFID**: Bucior, B. J., et al. (2019). [Identification Schemes for Metal-Organic Frameworks...](https://doi.org/10.1021/acs.cgd.9b00050)
+- **Zeo++**: Willems, T. F., et al. (2012). [Algorithms and tools for high-throughput geometry-based analysis...](https://doi.org/10.1016/j.micromeso.2011.08.020)
+- **MOFChecker**: Ongari, D., et al. (2019). [Building a Consistent and Reproducible Database for Adsorption Evaluation...](https://doi.org/10.1021/acscentsci.9b00619)
+- **ORB**: [Orbital ORB v3 Force Field](https://github.com/orbital-materials/orb-models)
+- **RDKit Morgan Fingerprints**: [RDKit Documentation](https://www.rdkit.org/docs/GettingStartedInPython.html#morgan-fingerprints-circular-fingerprints)

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