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. :download:`Click to download an example <../../dp5/config/default_config.toml>` 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 :py:func:`~dp5.run.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: stereocentres -------------- List of atom indices where stereochemistry is changed. Empty by default. Useful when :ref:`generating stereoisomers `. .. _solvent: 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.* .. _cfg_workflowflags: workflow -------- Set of the boolean workflow flags. .. _cleanup: cleanup ^^^^^^^ .. tip:: Setting ``c`` in the workflow flags (e.g., ``pydp4 ... -w c``) 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: generate ^^^^^^^^ .. tip:: Setting ``g`` in the workflow flags (e.g., ``pydp4 ... -w g``) 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 :ref:`stereocentres ` option. .. _conf_search: conf_search ^^^^^^^^^^^^ .. tip:: Setting ``m`` in the workflow flags (e.g., ``pydp4 ... -w m``) 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: dft_energies ^^^^^^^^^^^^ .. tip:: Setting ``e`` in the workflow flags (e.g., ``pydp4 ... -w e``) 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``) 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``) 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``) 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``) 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: 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 :py:mod:`dp5.conformer_search.macromodel`. Force field to use. Currently supports ``mmff`` or ``opls``. Default is ``mmff``. step_count ^^^^^^^^^^^ .. note:: Only has an effect on :py:mod:`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 :py:mod:`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 :py:mod:`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 :py:mod:`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 :ref:`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.