AuToGraFS 3.2.0

Automatic Topological Generator for Framework Structures

AuToGraFS

AuToGraFS — the Automatic Topological Generator for Framework Structures — generates Metal-Organic Frameworks (MOFs), Covalent Organic Frameworks (COFs) and other periodic framework materials by mapping molecular building blocks (SBUs) onto topological blueprints (nets). It also runs the pipeline in reverse: deconstruct an experimental structure back into building blocks and identify its net.

from autografs import Autografs

mofgen = Autografs()
pcu = mofgen.topologies["pcu"]
mof = mofgen.build(pcu, mappings={
    slot: "Zn_mof5_octahedral" if len(slot.atoms.indices_from_symbol("X")) == 6
    else "Benzene_linear"
    for slot in pcu.mappings
})
mof.write_cif("mof5.cif")   # cubic, a = 12.89 A (experiment: 12.9)

Original publication: "Automatic Topological Generator for Framework Structures", Addicoat, Coupry & Heine, J. Phys. Chem. A 2014, 118 (40), 9607.

Why AuToGraFS?

Several excellent framework assemblers exist — notably PORMAKE (Lee et al., whose MIT-licensed building-block library AuToGraFS gratefully bundles) and ToBaCCo (Colón / Gómez-Gualdrón groups). AuToGraFS was one of the first tools in this space (2014) and version 3 is a ground-up rewrite around a small set of design choices:

• Works out of the box. pip install AuToGraFS ships 2686 RCSR topologies and 930 building blocks (63 curated SBUs + the 867-block PORMAKE library, 2- to 24-connected). No database generation step, no external binaries for building. 96.5 % of the shipped topologies are buildable immediately (see library coverage).
• 2D nets are first-class. The 200 RCSR layer nets (hcb, sql, kgm, ...) that COF chemistry builds on are stored as plane-group topologies; a build produces a flat layer, and Framework.stack() turns it into a bulk crystal with AA / AB / serrated / staggered stacking at a chosen interlayer spacing.
• Geometry, not symmetry tables. SBUs are matched to slots by optimally rotating their connection vectors onto the slot's (Hungarian assignment + Kabsch, proper rotations only — chiral building blocks are never silently mirrored). Point-group labels are metadata, not gates, so low-symmetry (C1) vertices stay usable.
• Physically meaningful cells. The cell is optimized so that every inter-SBU bond sits at its covalent (Cordero) bond length, with the crystal system's constraints enforced (a cubic net optimizes a single length). MOF-5 comes out cubic at 12.89 Å against the experimental 12.9 — before any force-field relaxation. For lower-symmetry nets, whose idealized blueprint fixes proportions no cell parameter can repair, build(..., relax_embedding=True) additionally frees the slot positions within their site symmetry: measured over CoRE MOF, that cuts the built-versus-experimental density error about 3.3× (see embedding relaxation).
• Fails loudly, never silently. Optional hard gates (max_rmsd, min_distance) raise typed exceptions instead of returning distorted or interpenetrating structures. Identical inputs give identical outputs.
• Runs in reverse. Deconstruct a CIF (MOF or COF) into library-ready SBUs and identify its net; harvest a whole SBU library from a folder of structures.
• Rod MOFs, both directions. The MOF-74 family and other rod MOFs are built around an infinite 1-periodic metal-oxo chain — no finite building block. AuToGraFS deconstructs them, gives each rod a screw-aware canonical identity (helicity is chiral and preserved), and builds them forward again — for straight and helical rods, including general (non-180°) screws. See Rod MOFs.
• Post-processing built in. UFF4MOF assignment on every output, GULP input generation, EQeq partial charges, and one-call relaxation — in-process LAMMPS/UFF4MOF or any ASE calculator (GFN-FF, GFN1-xTB, DFTB+) — plus elastic constants via finite differences (pip install "autografs[relax]").
• Safe, versioned data formats. Topology libraries are plain JSON (diffable, shareable, survives pymatgen upgrades) — not pickles.
• A guided CLI. The autografs wizard walks through topology → SBUs → build → stack → export without writing a script.
• MIT licensed, pure-Python installation on Linux / macOS / Windows.

If you need features AuToGraFS doesn't have yet (see Roadmap), PORMAKE and ToBaCCo are actively maintained and may fit better — comparisons age quickly, so evaluate against their current versions.

Installation

pip install AuToGraFS

Requires Python ≥ 3.11. Core dependencies: pymatgen, ASE, numpy, scipy, networkx.

Optional extras:

pip install "autografs[relax]"   # UFF4MOF relaxation via LAMMPS

On Windows, the LAMMPS wheel additionally needs the Microsoft MPI runtime (winget install Microsoft.MSMPI).

Development install:

git clone https://github.com/DCoupry/autografs.git
cd autografs
pip install -e ".[dev]"

Quickstart: MOF-5

from autografs import Autografs

mofgen = Autografs()

# what fits the pcu net?
available = mofgen.list_building_units(sieve="pcu")
for slot_type, sbu_names in available.items():
    print(slot_type, len(sbu_names), "candidates")
# Oh 6 : ... candidates      (the octahedral node)
# D*h 2 : ... candidates     (the linear edge)

# pick one SBU per slot type
topology = mofgen.topologies["pcu"]
mappings = {}
for slot_type in topology.mappings:
    n_connections = len(slot_type.atoms.indices_from_symbol("X"))
    if n_connections == 6:
        mappings[slot_type] = "Zn_mof5_octahedral"
    else:
        mappings[slot_type] = "Benzene_linear"

mof = mofgen.build(topology, mappings=mappings)
print(mof)
# Framework('pcu', 'Zn4 H12 C24 O13', abc=(12.89, 12.89, 12.89))

mof.write_cif("mof5.cif")

Then keep going: build options and batch enumeration, 2D COFs, editing, or deconstruction.

Command line

No script needed — the autografs wizard covers build, deconstruct, stack, and export interactively, and autografs-topologies (re)builds a topology library:

autografs                                    # bundled libraries; guided session
autografs --xyz my_sbus.xyz                  # add custom building blocks
autografs-topologies --use_rcsr -o topologies.json.gz   # regenerate the library

Full walkthrough of both commands: Command line.

Documentation

The README is the overview; the depth lives in docs/:

• Building frameworks — the Python API: exploring the libraries, build, build_all, working with the Framework result (porosity, save/load, exports), relaxation (LAMMPS or any ASE calculator), partial charges, elastic constants, error handling.
• 2D COFs and stacking — layer nets, turning a layer into a bulk crystal (AA / AB / serrated / staggered), and commensurate twisted (moiré) bilayers.
• Rod MOFs — 1-periodic building units (MOF-74 & friends): deconstructing, screw-aware canonical identity, and forward building of straight and helical rods.
• Editing — editing SBUs before a build, and post-build supercells, statistical defects, and functionalization.
• Deconstruction — CIF → SBUs + net, net identification, interpenetration, COFs, batch harvesting, and assembly fingerprints.
• Command line — the autografs wizard and autografs-topologies in full.
• Extending the libraries — custom SBUs (XYZ) and custom topologies (CGD → JSON).
• How it works & architecture — the 2014 idea, the build pipeline, and a module map of the codebase.
• Library coverage — what fraction of RCSR is buildable today, and the nets that aren't.

FAQ

Does it build COFs? Yes — 2D layer nets are first-class. Build a flat layer on a layer net (hcb, sql, ...), then Framework.stack() turns it into a bulk crystal. See 2D COFs and stacking.

Do I need LAMMPS? Only for Framework.relax(). Building, export, deconstruction, and everything else are pure-Python. Install the relaxation backend with pip install "autografs[relax]".

My SBU is rejected / I get AlignmentError — why? Usually the geometric gate: the SBU's connection-vector shape doesn't match the slot's within max_rmsd. Raise max_rmsd, pick a net whose vertex figure fits, or edit the SBU. Point-group symmetry is diagnostic metadata, not the gate. If you passed bond_tolerance, the same exception also means the build did not close — correctly shaped units that no cell can bring to bonding distance.

My built structure is too open / its density looks wrong. Most likely the blueprint's proportions rather than your SBUs. A build places every unit at its idealized slot centre and only varies the cell, and the idealized (maximum-symmetry, near-equal-edge) embedding is systematically more open than real chemistry — no single cell scale can fix a fractional coordinate. Try build(..., relax_embedding=True), which frees the slot positions within their site symmetry; on nets that have any such freedom it cuts the density error about 3.3× over a CoRE MOF corpus. High-symmetry nets (pcu, dia, fcu) have nothing to free and are unaffected. Details and the measured trade-offs are in embedding relaxation.

Is my net in the library? 2686 RCSR nets ship; list them with mofgen.list_topologies(). 96.5 % are buildable out of the box — the rest, and how to enable them, are in library coverage.

Does it handle rod MOFs (MOF-74, metal carboxylates)? Yes — rod MOFs, whose building unit is an infinite 1-periodic chain, are a first-class case in both directions: deconstruct them, harvest rod families with a screw-aware canonical identity, and build them forward (straight and helical rods, including general non-180° screws). See Rod MOFs.

deconstruct() raised DeconstructionError — why? It refuses disordered structures, molecular crystals (no periodic framework to analyze), bare 1-periodic polymers with no framework connections, and 2-periodic (layer) building units. Rod MOFs and metal-free COFs are supported. See Deconstruction.

CIF or JSON — which should I save? CIF for downstream tools, but it loses the bond graph and per-atom provenance that post-build editing needs. Use Framework.save() / Framework.load() (versioned JSON) to keep a framework editable across sessions.

Can I still load my old .pkl topology library? Yes, with a warning. Convert it once with autografs.topology_io.save_topologies to the JSON format and keep that.

Development

pip install -e ".[dev]"

pytest                    # slow tests auto-skipped
pytest -m slow            # only the slow tests
ruff check src tests      # lint
ruff format src tests     # format
mypy src/autografs        # type check

Tests live in tests/; scripts/ holds the coverage audit (sbu_coverage.py), the PORMAKE import (import_pormake_bbs.py), and fixture generators. Architecture and module map: How it works.

Roadmap

The 3.x line has reached feature parity with 2.x and gone well beyond it: the inverse pipeline (deconstruction, net identification, SBU harvesting for MOFs and COFs), rod-MOF support in both directions (helical, cross-linked multi-rod etb/MOF-74, woven multi-axis and lattice-diagonal channels), IZA zeolite import (autografs-topologies --use_iza), partial charges, ASE-driven relaxation, elastic constants, commensurate twisted bilayers, and embedding relaxation for low-symmetry nets have all landed. Remaining directions — EPINET import and curated high-connectivity SBU packs for the last uncovered nets — are tracked in the issue tracker.

Citing

If you use AuToGraFS, please cite:

@article{autografs2014,
  title   = {AuToGraFS: Automatic Topological Generator for Framework Structures},
  author  = {Addicoat, Matthew A. and Coupry, Damien E. and Heine, Thomas},
  journal = {The Journal of Physical Chemistry A},
  volume  = {118},
  number  = {40},
  pages   = {9607--9614},
  year    = {2014},
  doi     = {10.1021/jp507643v}
}

Related work you may also want to cite:

• UFF4MOF (the force field used for typing and relaxation): Addicoat, Vankova, Akter & Heine, J. Chem. Theory Comput. 2014, 10, 880; Coupry, Addicoat & Heine, J. Chem. Theory Comput. 2016, 12, 5215.
• PORMAKE (if you use the bundled pormake.xyz building blocks): S. Lee et al., ACS Appl. Mater. Interfaces 2021, 13, 23647.
• RCSR (the source of the bundled topologies): O'Keeffe, Peskov, Ramsden & Yaghi, Acc. Chem. Res. 2008, 41, 1782.

License

MIT License — see LICENSE.txt.

The bundled building-block library pormake.xyz is converted from PORMAKE (MIT License, Copyright (c) 2022 Sangwon Lee; see PORMAKE_LICENSE.md).