AutoCG

AutoCG generates well-aligned reactant/product structures for transition state (TS) searches from reaction SMILES (with optional atom mapping) or 3D geometries.

Requirements

• Python ≥ 3.10
• numpy, scipy ≥ 1.11
• cclib ≥ 1.7.1
• ORCA or Gaussian available on PATH (select with -ca orca|gaussian)
• Optional: CREST 6.2.3 for TS conformer sampling (https://github.com/crest-lab/crest)

Installation

conda create -n autocg python=3.10
conda activate autocg
git clone https://github.com/Romarin87/autoCG
cd autoCG
pip install .
# or editable
pip install -e .

Quick start

• From mapped SMILES:

  autocg "[H:1][H:2].[C-:3]#[O+:4]>>[O:4]=[C:3]([H:1])[H:2]" \
    -sd /path/to/save -wd /path/to/work

• From unmapped SMILES (AutoCG will infer bond changes):

  autocg "[H][H].[C-]#[O+]>>C=O" -sd /path/to/save -wd /path/to/work

• From geometry + bond changes (input.com):

  autocg "/path/to/input.com" -sd /path/to/save -wd /path/to/work

  Minimal input.com example:

  0 1  # charge multiplicity
  H 0.35400009037695684 0.0 0.0
  H -0.35400009037695684 0.0 0.0
  C 0.5640604828962581 0.0 4.0
  O -0.5640604828962581 0.0 4.0
  # Must give empty line
  1 2 B  # Bond change: B -> break
  1 3 F  # Bond change: F -> form
  2 3 F
  

Important options:

• -nc (#conformers), -ts/-fs/-bs (bond scaling), -p (UFF preopt), -se (stereo enumeration), -uc (CREST), -ca (calculator).
• -cc 0 disables connectivity checks (useful for special bridged rings/strained structures where long bonds may be flagged as disconnected).
• -cs 0 disables stereochemical checks.

Calculator setup: ensure g09/g16 or orca is on PATH; pick with -ca gaussian|orca. CREST is optional but needed for -uc 1.

Inputs

• SMILES:
  • If atom mapping is present, it is used directly to infer bond changes; otherwise AutoCG infers minimal bond form/break automatically.
  • Quote the SMILES in the shell to avoid expansion.
  • Example (mapped): [C:1](=[O:2])[O:3][H:4]>>[C:1](=[O:2])[O-:3].[H+:4]
  • Example (unmapped): [C](=O)O>>CO
• Geometry: input.com style must include charge/multiplicity on the first line, coordinates, a blank line, then bond-change lines (B for break, F for form).
• Charge/multiplicity should be provided; missing values are inferred when possible but may be ambiguous.

Outputs

Each generated conformer is saved under result_<idx>/ in the save directory:

• initial_ts.xyz: starting pseudo-TS geometry
• TS_to_R.xyz, TS_to_P.xyz: constrained scans toward reactant/product
• UFF_R.xyz, UFF_P.xyz (if preopt): UFF preoptimization trajectories
• opt_R.xyz, opt_P.xyz: QC relaxation trajectories
• R.xyz, P.xyz (+ .com): final relaxed reactant/product structures
• guess.log: summary of generation and matching results

Notes

• If reaction SMILES carries atom mapping, AutoCG uses it directly to infer bond changes; otherwise, bond changes are inferred automatically.
• Geometry input must include charge/multiplicity and bond-change info; initial alignment is not required.
• Spectator molecules that do not participate in bond breaking/formation are ignored and not modeled.
• Algorithm details on bond-change inference and generation follow Chem. Sci. 2018 / J. Chem. Inf. Model. 2012 (see: https://pubs.acs.org/doi/full/10.1021/ci3002217).
• Original extended instructions and calculator implementation notes are kept in subpage/details.md.

License

BSD 3-Clause License.