chem-db-mof

chem-db-mof

Goal

Provide a unified interface for retrieving Metal-Organic Framework (MOF) crystal structures from multiple curated databases. Currently supported:

Prerequisites

• Environment: base-agent
• Packages: mpcontribs-client, requests, pandas, pymatgen
• Credentials: MP_API_KEY environment variable (required for qmof only)

Instructions

Step 1: Choose a database and set filters

Decide which database to query and which element/identifier filters to apply.

For QMOF — best for DFT-validated, experimentally-derived MOFs:

• Use --formula for element filtering (e.g., Zn or Cu,N,O)
• Use --identifier for a specific CSD refcode (e.g., KAXQIL)

For ARC-MOF DB7 (Majumdar et al.) — best for diverse hypothetical MOFs with underrepresented inorganic SBUs:

• Use --elements for element filtering (e.g., Zn,O,C)
• Use --identifier for a specific structure ID (e.g., DB7_00042)
• First run: downloads geometric_properties.csv (~110 MB) to ~/.cache/arcmof/ — one-time only; subsequent runs are fast

Step 2: Run the query

# Env: base-agent
# QMOF — 10 Zn-containing MOFs
MP_API_KEY=<your_key> python .agents/skills/chem-db-mof/scripts/query_mof_db.py \
    --database qmof \
    --formula Zn \
    --max-results 10 \
    --output-dir ./research/<date>_<task>/structures/qmof

# Env: base-agent
# ARC-MOF DB7 (Majumdar) — 20 Zn,O,C hypothetical MOFs
python .agents/skills/chem-db-mof/scripts/query_mof_db.py \
    --database arcmof-majumdar \
    --elements Zn,O,C \
    --max-results 20 \
    --output-dir ./research/<date>_<task>/structures/arcmof_db7

# Env: base-agent
# ARC-MOF DB7 — retrieve a specific structure by identifier
python .agents/skills/chem-db-mof/scripts/query_mof_db.py \
    --database arcmof-majumdar \
    --identifier DB7_00042 \
    --output-dir ./research/<date>_<task>/structures/arcmof_db7

Available Arguments

Step 3: Inspect outputs

The script saves:

• Individual .cif files named by structure identifier
• arcmof_db7_metadata.csv (ARC-MOF only) — geometric properties for the downloaded subset

Verify the download:

ls -lh <output-dir>/*.cif | head -20

Download Behavior: ARC-MOF DB7

The first call with --database arcmof-majumdar performs:

1. Metadata download (~110 MB, one-time): geometric_properties.csv cached at ~/.cache/arcmof/
2. DB7 filtering: identifies the 12,316 Majumdar structures from the full 288k-entry CSV
3. CIF streaming: streams the ARC-MOF tarball (ARCMOF_20241004.tar.gz, ~670 MB) and extracts only the requested CIFs — the stream is read once but only matching files are written to disk

Subsequent runs with the same --output-dir skip already-downloaded CIFs.

Examples

Example 1: Query Zn MOFs from QMOF for CO₂ screening pre-processing

# Env: base-agent
MP_API_KEY=<your_mp_api_key> \
python .agents/skills/chem-db-mof/scripts/query_mof_db.py \
    --database qmof \
    --formula Zn \
    --max-results 10 \
    --output-dir ./research/2026-03-27_test/qmof_zn

Example 2: Query Zn, Ni, or Mg hypothetical MOFs from ARC-MOF DB7

# Env: base-agent
# Zn-based
python .agents/skills/chem-db-mof/scripts/query_mof_db.py \
    --database arcmof-majumdar \
    --elements Zn,O,C \
    --max-results 50 \
    --output-dir ./research/2026-03-27_arcmof_zn

# Ni-based
python .agents/skills/chem-db-mof/scripts/query_mof_db.py \
    --database arcmof-majumdar \
    --elements Ni,O,C \
    --max-results 50 \
    --output-dir ./research/2026-03-27_arcmof_ni

# Mg-based
python .agents/skills/chem-db-mof/scripts/query_mof_db.py \
    --database arcmof-majumdar \
    --elements Mg,O,C \
    --max-results 50 \
    --output-dir ./research/2026-03-27_arcmof_mg

Tip: You can expand diversity by adding more elements to --elements (e.g., Zn,Ni,O,C,N to retrieve MOFs containing all of those elements simultaneously), or run separate queries per metal node and combine the resulting CIF directories for a broader screening campaign.

Constraints

• API limits: QMOF via MPContribs has rate limits; keep --max-results ≤ 100 per call.
• ARC-MOF first-run time: Downloading the metadata CSV (~110 MB) takes ~1–2 min; streaming the tarball for CIF extraction adds ~5–15 min depending on how many structures are requested and network speed.
• ARC-MOF CIF fallback: If some DB7 structures are not found in ARCMOF_20241004.tar.gz, they may reside in all_structures_1.tar.gz or all_structures_2.tar.gz. Update ARCMOF_STRUCTURES_NAME in the script if needed.
• Element filtering (ARC-MOF): Requires a formula or chemical_formula column in geometric_properties.csv. If the column is absent, all DB7 entries are returned without element filtering.
• Post-download: Structures from ARC-MOF DB7 include REPEAT partial charges embedded in the CIF. These can be used directly for classical force-field simulations but should be relaxed with an MLIP before running Widom insertion (see chem-sorption-relax).

References

• Raza, A. et al., "ARC–MOF: A Diverse Database of Metal-Organic Frameworks with DFT-Derived Partial Atomic Charges and Descriptors for Machine Learning", Chem. Mater., 2022. DOI: 10.1021/acs.chemmater.2c02485
• Majumdar, S., Moosavi, S.M., Jablonka, K.M., Ongari, D., Smit, B., "Diversifying Databases of Metal Organic Frameworks for High-Throughput Computational Screening", ACS Appl. Mater. Interfaces, 2021. DOI: 10.1021/acsami.1c16220; dataset: Materials Cloud Archive 2021.126, DOI: 10.24435/materialscloud:yn-de
• Chung, Y.G. et al., "Computation-Ready, Experimental Metal-Organic Frameworks: A Tool To Enable High-Throughput Screening of Nanoporous Crystals", Chem. Mater., 2014 (QMOF precursor). DOI: 10.1021/cm502594j
• Rosen, A.S. et al., "Machine learning the quantum-chemical properties of metal-organic frameworks for accelerated materials discovery", Matter, 2021 (QMOF). DOI: 10.1016/j.matt.2021.02.015

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Author: Sauradeep Majumdar Contact: GitHub @sauradeep93