oniom-import

Overview

Summary: Import a Gaussian/ORCA ONIOM input file and reconstruct an XYZ plus a B-factor layered PDB.

Minimal example

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

Output checklist

  • <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.

Common examples

# 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

Usage

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

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. Write <out_prefix>.xyz.

  2. 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.

CLI options

Option

Description

Default

-i, --input FILE

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

Required

`–mode [g16

orca]`

Import mode. If omitted, inferred from input suffix.

-o, --out-prefix PATH

Output prefix.

Input stem in current directory

--ref-pdb FILE

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

None

Outputs

<out_prefix>.xyz
<out_prefix>_layered.pdb

See Also