oniom-import

Import a Gaussian/ORCA ONIOM input file and reconstruct an XYZ and a B-factor layered PDB, bringing an externally prepared ONIOM input back into the ML/MM toolchain. The XYZ comment line carries the QM-region charge and multiplicity (q=<charge> m=<multiplicity>), and the layered PDB encodes ML/Movable-MM/Frozen-MM layers in its B-factor column. Import mode is taken from --mode or inferred from the input suffix. Pass --ref-pdb to recover atom/residue metadata from a reference PDB when reconstructing a layered structure.

Examples

mlmm oniom-import -i ts_guess.inp -o ts_guess_imported

Let mode be inferred from suffix (.gjf/.com -> g16, .inp -> orca):

mlmm oniom-import -i model.gjf -o model_imported

Force mode explicitly:

mlmm oniom-import -i model.inp --mode orca -o model_imported

Keep atom/residue metadata from a reference PDB (atom count must match):

mlmm oniom-import -i model.inp --ref-pdb complex_layered.pdb -o model_imported

Workflow

  1. Resolve import mode from --mode or input suffix.

  2. Parse coordinates and layer-related atom sets:

  • Gaussian mode: ONIOM coordinate rows (H/L layer markers).

  • ORCA mode: %qmmm (QMAtoms/ActiveAtoms) + * xyz block.

  1. Parse the QM-region charge and multiplicity (Gaussian: the ONIOM charge/multiplicity line — the six-integer line; ORCA: the * xyz <charge> <mult> header) and emit them as q=<charge> m=<multiplicity> in the XYZ comment line.

  2. Write <out_prefix>.xyz.

  3. Write <out_prefix>_layered.pdb:

  • Without --ref-pdb: generic atom/residue labels are generated.

  • With --ref-pdb: original naming/residue metadata is preserved while coordinates/B-factors are updated.

Outputs

<out_prefix>.xyz
<out_prefix>_layered.pdb

  • <out_prefix>.xyz exists and atom count matches the source ONIOM input.

  • <out_prefix>_layered.pdb exists and B-factor values encode layers (0/10/20).

  • Log lines report parsed mode, atom count, and QM/movable/frozen counts.

CLI options

Command form:

mlmm oniom-import -i INPUT.[gjf|com|inp] [--mode g16|orca] \
  [-o OUT_PREFIX] [--ref-pdb REF.pdb]

Input

Required

Notes

-i, --input

yes

Input ONIOM file (.gjf/.com for g16, .inp for ORCA).

--mode

no

Import mode (g16/orca). If omitted, inferred from input suffix.

-o, --out-prefix

no

Output prefix. Defaults to the input stem in the current directory.

--ref-pdb

no

Reference PDB to preserve atom naming/residue metadata (atom count must match).

The full flag list (including advanced options) is in the generated command reference.

See Also