Command-line interface¶

The racerts CLI mirrors the core functionality of the Python API. The command is always:

$ racerts filename.xyz [options]

where the filename.xyz is the path to an .xyz file containing a single TS conformer.

General inputs¶

Command	Options	Explanation
-c --charge	<INT> [0]	Overall molecular charge
-smiles --input_smiles	<STR...>	One (or multiple) SMILES for either product or starting material to define topology
-atoms --reacting_atoms	<INT...>	List of (0-based) indices of reacting atoms
-frozen --frozen_atoms	<INT...>	Optional: overwrite of atoms to freeze; if omitted, neighbors of reacting atoms are inferred

Ensemble size¶

Command	Options	Explanation
-cf --conf_factor	<INT> [80]	Number of initially generated conformers: NumRotatableBonds × conf_factor + 30
-n --number_of_conformers	<INT> [-1]	Specify number of initially generated conformers (and overwrite conf_factor)

Conformer Generation Configuration¶

Command	Options	Explanation
-m --mol	<smiles|bonds|connect>	Method to infer molecular graph from .xyz: smiles use MolGetterSMILES; bonds use MolGetterBonds; connect use MolGetterConnectivity
-e --embed	<dm|cmap>	Embedding method: dm = bounds-matrix; uses BoundsMatrixEmbedder; cmap = coordinate map; uses CmapEmbedder
-ff --ff	<mmff|uff> [mmff]	Force-field refinement: ; mmff uses MMFFOptimizer; uff uses UFFOptimizer

Output¶

Command	Options	Explanation
-o --output	<STR> [conformer_ensemble.xyz]	Output .xyz filename
--out_energies	-	Write energies in Eh in the comment line; conformer property remains in kcal/mol
-v --verbose	-	Verbose output

Performance and reproducibility¶

Command	Options	Explanation
--num_threads	<INT> [1]	Threads for embedding/optimization
--seed	<INT> [12]	Random seed
--no_fallback	-	Disable automatic fallback (see below)

molgetter options¶

Command	Explanation
--no_assignbonds	For bonds getter: don’t assign bonds [default: True]
--disallow-charged	For bonds getter: disallow charged fragments [default: True]

embedder options¶

Command	Explanation
--no-random_coords	Disable random coordinates

optimizer options¶

Command	Explanation
--force_constant	<FLOAT> [1e6]

RMSDPruner options¶

Command	Options	Explanation
-rmsd --rmsd_thres	<FLOAT> [0.125]	RMSD threshold in Å
-rmsd_hs --rmsd_include_hs	-	Include hydrogens when computing RMSDs [default: False]
--no_filter_energies	-	Disable energy-based dissimilarity prefilter [default: True]
--no_filter_rotations	-	Disable rotational-profile prefilter [default: True]
--rmsd_energy	<FLOAT> [0.1]	Energy difference threshold (kcal/mol) for the prefilter
--rmsd_rot_fraction	<FLOAT> [0.03]	Rotational-difference fraction threshold
-rmsd_match --rmsd_max_matches	<INT> [10000]	Max substructure matches for RMSD calculation

EnergyPruner options¶

Command	Options	Explanation
-energy --energy_thres	<FLOAT> [20.0]	Energy window for pruning (kcal/mol)

Common recipes¶

Basic run

$ racerts example.xyz --charge 0 --reacting_atoms 2 3 4

Use SMILES-defined topology and coordinate-map embedding

$ racerts example.xyz --charge 0 \
  --reacting_atoms 2 3 4 \
  --input_smiles "C1=CC=CC=C1" "O" \
  --mol smiles --embed cmap --ff mmff --out_energies

Increase diversity by allowing more initial conformers

$ racerts example.xyz --charge 0 --reacting_atoms 2 3 4 --conf_factor 120

Faster refinement on many conformers with threads (if using multithreaded optimizers)

$ racerts example.xyz --charge 0 --reacting_atoms 2 3 4 --num_threads 4