Usage

Installation

To use DP5, clone this repository:

git clone https://github.com/ruslankotl/DP5.git

Then change to the top-level directory of the repository and install the repository using

pip install -e .

To also install documentation build dependencies (sphinx and sphinx-rtd-theme), use the dev extra:

pip install -e ".[dev]"

Note

The repository works best on x86 Linux machines. For Apple Silicon, additional library Tensorflow-metal will be installed automatically.

Configuration

This version adds human-editable configuration files. They can be supplied in .json and .toml formats. The basic elements of former command-line interface are retained for experienced user convenience.

Command line arguments

Attention

Arguments from command line override arguments from configuration file!

Command Line Flags	What they mean
`-s`, `--structure_files`	Paths to structure files.
`-n`, `--nmr_file`	Paths to NMR spectra or their description.
`-c`, `--config`	Path to configuration file for the run. Defaults to `dp5/config/default_config.toml`.
`-o`, `--output`	Path to output directory. Defaults to current working folder.
`-i`, `--input_type`	Input file type. Can be `sdf`, `smiles`, `smarts`, or `inchi`. Default is `sdf`.
`-w`, `--workflow <flags>`	Workflow type. Must be followed by workflow flags without spaces.
`--stereocentres`	When generating diastereomers, limit generation to specified stereocentres.
`-l`, `--log_filename`	Log file name.
`--log_level`	Logging levels. Can be `warning`, `info`, or `debug`. Default level is `info`.

Workflow arguments

Specifies workflow actions. Will load the values from the configuration file if left unset.

Workflow Flags	Config file equivalents	What they mean
`c`	`cleanup`	generate 3D structure, optimise using MMFF
`g`	`generate`	generate diastereomers
`m`	`conf_search`	perform conformational search
`o`	`dft_opt`	optimise geometries using DFT
`e`	`dft_energies`	calculate single point energies using DFT
`n`	`dft_nmr`	calculate NMR spectra using DFT-GIAO method
`a`	`assign_only`	assignment only (currently not supported)
`s`	`dp4`	perform DP4 analysis
`w`	`dp5`	perform DP5 analysis

Default DP4 workflow for establishing stereochemistry would be specified as -w gnms, the best results would be produced using -w gnomes.

In general, conformational search should provide representative geometries, DFT optimisation would provide accurate geometries, and single-point energies would increase precision by re-weighting the conformers.