Anatomy of a config file

New config file is available in .toml and .json formats. Keywords are now grouped together for the ease of handling. This page outlines the configurable parameters. Click to download an example

structure

List of paths to the structure files used in the workflow. If structure cleanup or diastereomer genereation is requested, the new molecules are saved to the config file instead.

input_type

Input type of the structure file as text. Default value is sdf.Handled by mol_file_preparation().

nmr_file

List of paths to NMR data. Can be a folder containing FID data in (Bruker or JCAMP-DX format) or NMR description file.

stereocentres

List of atom indices where stereochemistry is changed. Empty by default. Useful when generating stereoisomers.

solvent

Name of the solvent (as in Gaussian) used in subsequent calculations.

log_level

Logging level in the run. Can be set to info, debug, and other options specified in Python documentation

output_folder

Path to the output folder.

gui_running

Boolean flag (true or false). Currently not in use.

workflow

Set of the boolean workflow flags.

cleanup

Tip

Setting c in the workflow flags (e.g., pydp4 ... -w c<other flags>) will override the configuration file value.

Performs MMFF optimisation of the structure candidates. Default is false If both dft_opt and conf_search are set to false, automatically set to true.

generate

Tip

Setting g in the workflow flags (e.g., pydp4 ... -w g<other flags>) will override the configuration file value.

Generates diastereomers of the input molecule. Default is false. Works on all stereocentres by default, but can be limited to selected atoms by stereocentres option.

conf_search

Tip

Setting m in the workflow flags (e.g., pydp4 ... -w m<other flags>) will override the configuration file value.

Runs conformational search using method provided. Default is true. Recommended for accurate estimation of spectra, especially for flexible molecules.

dft_energies

Tip

Setting e in the workflow flags (e.g., pydp4 ... -w e<other flags>) will override the configuration file value.

Runs single-point energy DFT calculations. Default value is false, but we recommend setting it to true for more accurate results. The re-ranked ensemble of conformers should lead to more precise NMR spectrum estimation.

dft_opt

Tip

Setting o in the workflow flags (e.g., pydp4 ... -w o<other flags>) will override the configuration file value.

Runs geometry optimisation using DFT. Default value is false, but we recommend setting it to true. DFT-optimised geometries tend to produce better match to experimental NMR spectra at the increased computational cost.

dft_nmr

Tip

Setting n in the workflow flags (e.g., pydp4 ... -w n<other flags>) will override the configuration file value.

Default value is false. If set to true, calculates NMR shifts by DFT-GIAO method. Otherwise, if set to false, uses a neural net to predict the shifts.

Warning

Neural network is implemented for carbon NMR only

dp4

Tip

Setting s in the workflow flags (e.g., pydp4 ... -w s<other flags>) will override the configuration file value.

Performs DP4 analysis of structure candidates. Default is true.

dp5

Tip

Setting w in the workflow flags (e.g., pydp4 ... -w w<other flags>) will override the configuration file value.

Performs DP5 analysis of structure candidates. Default is false.

Warning

DP5 analysis is implemented for carbon NMR only

assign_only

Error

The method is not implemented.

Assigns the structures to the provided spectra and nothing else. Default is false.

calculations_complete

Assumes the calculations are complete. Default is false.

optimisation_converged

Assumes all optimisations have converged. Default is false.

restart_dft

Use when conformational search has completed, but the DFT calculations must be restarted. Default is false.

mm_complete

Does nothing. Default is false.

dft_complete

Does nothing. Default is false.

conformer_search

Configuration of conformational search.

method

Currently supports macromodel, etkdg. Default is macromodel. tinker is not tested on the current version. It is possible to add support for the new methods (will be shown in the appropriate section).

force_field

Note

Only has an effect on dp5.conformer_search.macromodel.

Force field to use. Currently supports mmff or opls. Default is mmff.

step_count

Note

Only has an effect on dp5.conformer_search.macromodel.

Maximum number of steps to use in the conformational search. Default is 10000.

steps_per_rotatable_bond

Note

Only has an effect on dp5.conformer_search.macromodel.

Maximum number of steps per bond to use in the conformational search. Default is 2500.

manual_five_membered_rings

Use special method dp5.conformer_search.five_conf to generate conformers for five-membred rings. Default is false.

five_membered_ring_atoms

List of 1-based indices for atoms in five-membred rings to be handled by dp5.conformer_search.five_conf. Default is an empty list.

conf_prune

Warning

This method is not aware of molecular symmetry

If number of conformers per molecule exceeds conf_per_structure, remove redundant conformers if their RMSD is below rmsd_cutoff Ångström. Default value is true.

conf_limit

Note

This method does nothing.

Total limit of conformers across all candidates. Default is 1000.

rmsd_cutoff

Cutoff threshold (in Ångström) to use when conf_prune is set to true.

energy_cutoff

Energy cutoff (in kJ/mol). Default is 10.

executable

Path to your favourite executable. Add your new methods as appropriate.

schrodinger

Path to root folder for Schrodinger Suite (Maestro, MacroModel).

tinker

Path to root folder for tinker.

dft

Configuration of DFT workflows.

Note

Uses Gaussian keywords as default.

method

Accepts gaussian, nwchem, orca. Default is gaussian. It is possible to add support for the new methods (will be shown in the appropriate section).

charge

Leave as nan if charges are computed from structure input, set manually otherwise.

solvent

Solvent to use in implicit solvation DFT calculations. Automatically takes the value specified previously.

n_basis_set

Basis set for DFT NMR calculations. Default is "6-311g(d)".

n_functional

Functional for DFT NMR calculations. Default is "mPW1PW91".

o_basis_set

Basis set for DFT geometry optimisation. Default is "6-31g(d,p)""

o_functional

Functional for DFT geometry optimisation. Default is "b3lyp".

e_basis_set

Basis set for DFT single-point energy calculation. Default is "def2tzvp".

e_functional

Functional for DFT single-point energy calculation. Default is "m062x".

optimisation_converged

Use to skip optimisation convergence check. Default is false.

dft_complete

Use if DFT calculations are complete and new calculations are not required. Default is false.

max_opt_cycles

Number of optimisation cycles allowed. Default is 50.

calc_force_constants

Use to include Hessian calculations in DFT optimisation. Default is false. Speeds up optimisation convergence.

opt_step_size

Optimisation step size (in Bohr or radians). Default value is 0.3.

num_processors

Number of processors for each DFT calculation. Default is 1.

memory

Allocated memory in megabytes. Default is 2000.

c13_tms

Total isotropic shielding tensor for carbon in tetramethylsilane. Default value 191.69255 is calculated using B3LYP/6-31G** in gas phase.

h1_tms

Total isotropic shielding tensor for proton in tetramethylsilane. Default value 31.7518583 is calculated using B3LYP/6-31G** in gas phase.

executable

Path to your favourite executable. Add your new methods as appropriate.

gaussian

Path to Gaussian executable.

nwchem

Path to NWChem executable.

orca

Path to ORCA executable.

cluster

Support for running DFT jobs on the remote cluster yet to be implemented.

dp4

Parameters for DP4 analysis.

stats_model

Accepts g for single gaussian, m for multuple gaussian. Type of statictical model to use.

param_file

Path to DP4 parameters file. If left as none, uses default parameters.