### Example DP5 Analysis Run

Source: https://github.com/aelashkin/dp5/blob/master/readme.md

Navigates to a specific directory and runs DP5 analysis with example files.

```bash
cd reassignments/S11
pydp4 -s S11a_.sdf S11b_.sdf -n S11_NMR -w w
```

--------------------------------

### Install DP5 with uv

Source: https://github.com/aelashkin/dp5/blob/master/readme.md

Installs the DP5 package in editable mode using uv.

```bash
uv pip install -e .
```

--------------------------------

### Run README Example

Source: https://github.com/aelashkin/dp5/blob/master/AGENTS.md

Execute the example provided in the README file from the 'reassignments/S11' directory. This command runs the DP4 analysis and writes outputs to the current directory.

```bash
pydp4 -s S11a_.sdf S11b_.sdf -n S11_NMR -w w
```

--------------------------------

### Install DP5 Package

Source: https://github.com/aelashkin/dp5/blob/master/docs/source/usage.md

Install the DP5 package in editable mode after cloning the repository.

```bash
pip install -e .
```

--------------------------------

### Install DP5 with Development Dependencies

Source: https://github.com/aelashkin/dp5/blob/master/readme.md

Installs DP5 and its development dependencies in editable mode using uv.

```bash
uv pip install -e ".[dev]"
```

--------------------------------

### Install DP5 with Development Dependencies

Source: https://github.com/aelashkin/dp5/blob/master/docs/source/usage.md

Install DP5 along with development dependencies like Sphinx for documentation building.

```bash
pip install -e ".[dev]"
```

--------------------------------

### Install uv on macOS

Source: https://github.com/aelashkin/dp5/blob/master/readme.md

Installs the uv package manager on macOS using Homebrew.

```bash
brew install uv
```

--------------------------------

### Install uv on Linux

Source: https://github.com/aelashkin/dp5/blob/master/readme.md

Installs the uv package manager on Linux using a curl script.

```bash
curl -LsSf https://astral.sh/uv/install.sh | sh
```

--------------------------------

### Build Sphinx Documentation

Source: https://github.com/aelashkin/dp5/blob/master/AGENTS.md

Build the project's documentation in HTML format using Sphinx after installing the 'dev' dependencies. The output will be placed in the 'docs/build/' directory.

```bash
sphinx-build -M html docs/source/ docs/build/
```

--------------------------------

### Load NMR Dataset

Source: https://github.com/aelashkin/dp5/blob/master/nmrdb-dataset/README.md

Loads a compressed pickled Pandas DataFrame containing NMR shift data. Ensure you have pandas and rdkit installed. Replace 'your filename' with the actual path to the dataset file.

```python
import numpy as np
import pandas as pd

from rdkit import Chem # useful for further manipulations

filename = 'your filename'
data = pd.read_pickle(filename, compression='gzip')
```

--------------------------------

### Create and Activate Python Environment with uv

Source: https://github.com/aelashkin/dp5/blob/master/readme.md

Creates a Python 3.10 virtual environment using uv and activates it.

```bash
uv venv --python 3.10 .venv && source .venv/bin/activate
```

--------------------------------

### Activate uv Environment

Source: https://github.com/aelashkin/dp5/blob/master/AGENTS.md

Activate the created virtual environment to begin using the project's tools and dependencies.

```bash
source .venv/bin/activate
```

--------------------------------

### Create Temporary Output Folder

Source: https://github.com/aelashkin/dp5/blob/master/AGENTS.md

Create a temporary directory using mkdir to specify an explicit output location for DP5 analysis results.

```bash
mkdir -p /tmp/dp5-check
```

--------------------------------

### Show DP4 CLI Help

Source: https://github.com/aelashkin/dp5/blob/master/AGENTS.md

Display the help message for the DP4 command-line interface, showing available commands, options, and arguments.

```bash
pydp4 --help
```

--------------------------------

### Create Compatible uv Environment

Source: https://github.com/aelashkin/dp5/blob/master/AGENTS.md

Use this command to create a Python virtual environment compatible with the project's requirements, specifically Python 3.10.

```bash
uv venv --python 3.10 .venv
```

--------------------------------

### DP5 Command Line Arguments

Source: https://github.com/aelashkin/dp5/blob/master/docs/source/usage.md

Overview of command-line flags for DP5, including input files, output directory, and workflow specifications. Arguments from the command line override those in configuration files.

```bash
# Example usage of command line flags:
# -s: Paths to structure files.
# -n: Paths to NMR spectra or their description.
# -c: Path to configuration file for the run. Defaults to dp5/config/default_config.toml.
# -o: Path to output directory. Defaults to current working folder.
# -i: Input file type. Can be sdf, smiles, smarts, or inchi. Default is sdf.
# -w: Workflow type. Must be followed by workflow flags without spaces.
# --stereocentres: Limit generation to specified stereocentres when generating diastereomers.
# --nmr-assignment-mode: Manual NMR assignment mode: strict (default) or legacy.
# --allow-extra-peaks: In strict manual mode, report extra experimental carbon shifts instead of aborting.
# --allow-missing-peaks: In strict manual mode, report missing required carbon groups instead of aborting.
# -l: Log file name.
# --log_level: Logging levels. Can be warning, info, or debug. Default level is info.
```

--------------------------------

### DFTMethod.prepare_command

Source: https://github.com/aelashkin/dp5/blob/master/docs/source/dft_architecture.md

Builds a shell command to run a single calculation. Subclasses can override this for engine-specific syntax.

```APIDOC
## DFTMethod.prepare_command

### Description
Build a shell command to run one calculation.
Concrete subclasses can override this to handle engine-specific command
syntax.

### Parameters
* **file** (pathlib.Path) – File stem without extension.

### Returns
Shell command string.

### Return type
str
```

--------------------------------

### dp5.dft.base_dft_method.BaseDFTMethod.prepare_command

Source: https://github.com/aelashkin/dp5/blob/master/docs/source/dft_api.md

Builds a shell command to run a single DFT calculation. Concrete subclasses can override this method to handle engine-specific command syntax.

```APIDOC
## dp5.dft.base_dft_method.BaseDFTMethod.prepare_command(file)

### Description
Build a shell command to run one calculation. Concrete subclasses can override this to handle engine-specific command syntax.

### Parameters
* **file** (*pathlib.Path*) – File stem without extension.

### Returns
Shell command string.

### Return type
str
```

--------------------------------

### Run DP5 with Explicit Output Folder

Source: https://github.com/aelashkin/dp5/blob/master/AGENTS.md

Run the DP5 analysis specifying an existing output folder using the -o flag. Replace placeholders with actual file paths and workflow flags.

```bash
pydp4 -s <SD_FILE> -n <NMR_FILE> -w <workflow_flags> -o /tmp/dp5-check
```

--------------------------------

### NWChem DFT Methods

Source: https://github.com/aelashkin/dp5/blob/master/docs/source/dft_api.md

Methods for configuring and interacting with NWChem DFT calculations.

```APIDOC
## e_options()

### Description
Build NWChem task block for single-point energy.

### Returns
NWChem task block.

### Return type
str
```

```APIDOC
## nmr_options()

### Description
Build NWChem task block for NMR shielding calculation.

### Returns
NWChem task block.

### Return type
str
```

```APIDOC
## opt_options()

### Description
Build NWChem task block for geometry optimisation.

### Returns
NWChem task block.

### Return type
str
```

```APIDOC
## prepare_command(file)

### Description
Build a shell command to run one calculation.

Concrete subclasses can override this to handle engine-specific command
syntax.

### Parameters
#### Path Parameters
- **file** (pathlib.Path) - Required - File stem without extension.

### Returns
Shell command string.

### Return type
str
```

```APIDOC
## read_file(file)

### Description
Parse NWChem output into DP5-standard result fields.

### Parameters
#### Path Parameters
- **file** (pathlib.Path) - Required - NWChem output path.

### Returns
`(atoms, coordinates, energy, shieldings, shielding_labels,
  completed, opt_converged)`.

### Return type
tuple
```

```APIDOC
## write_file(filename, coordinates, atoms, charge, calc_type)

### Description
Write an NWChem `.nw` input file for one conformer.

### Parameters
#### Path Parameters
- **filename** (pathlib.Path) - Required - Output file stem.
- **coordinates** (list) - Required - Cartesian coordinates.
- **atoms** (list[str]) - Required - Element symbols.
- **charge** (int | float) - Required - Molecular charge.
- **calc_type** (str) - Required - Calculation type.
```

--------------------------------

### Run DP5 Analysis

Source: https://github.com/aelashkin/dp5/blob/master/readme.md

Executes the DP5 analysis tool with specified SDF and NMR files.

```bash
pydp4 -s <SD_FILE> -n <NMR_FILE> -w w
```

--------------------------------

### DFTMethod.get_files

Source: https://github.com/aelashkin/dp5/blob/master/docs/source/dft_architecture.md

Retrieves completed calculation files, loading from disk if DFT_complete is set, otherwise preparing and executing new calculations.

```APIDOC
## DFTMethod.get_files

### Description
Return completed calculation files for the requested calculation.
If `self.dft_complete` is set, pre-existing files are loaded from
disk. Otherwise new calculations are prepared and executed.

### Parameters
* **mols** (list) – Molecules with conformer geometries.
* **calc_type** (str) – Calculation type label.

### Returns
Output file stems grouped per molecule.

### Return type
list[list[pathlib.Path]]
```

--------------------------------

### dp5.dft.gaussian.DFTMethod.e_options

Source: https://github.com/aelashkin/dp5/blob/master/docs/source/dft_api.md

Builds the Gaussian route section specifically for single-point energy jobs.

```APIDOC
## dp5.dft.gaussian.DFTMethod.e_options()

### Description
Build Gaussian route section for single-point energy jobs.

### Returns
Gaussian route section.

### Return type
str
```

--------------------------------

### Gaussian DFT Methods

Source: https://github.com/aelashkin/dp5/blob/master/docs/source/dft_api.md

Methods for configuring and interacting with Gaussian DFT calculations.

```APIDOC
## nmr_options()

### Description
Build Gaussian route section for NMR shielding jobs.

### Returns
Gaussian route section.

### Return type
str
```

```APIDOC
## opt_options()

### Description
Build Gaussian route section for geometry optimisation jobs.

### Returns
Gaussian route section.

### Return type
str
```

```APIDOC
## prepare_command(file)

### Description
Prepare Gaussian execution command using input redirection.

### Parameters
#### Path Parameters
- **file** (pathlib.Path) - Required - Input/output file stem.

### Returns
Shell command string.

### Return type
str
```

```APIDOC
## read_file(file)

### Description
Parse Gaussian output into DP5-standard result fields.

### Parameters
#### Path Parameters
- **file** (pathlib.Path) - Required - Gaussian output path.

### Returns
`(atoms, coordinates, energy, shieldings, shielding_labels,
  completed, opt_converged)`.

### Return type
tuple
```

```APIDOC
## write_file(filename, coordinates, atoms, charge, type)

### Description
Write a Gaussian `.com` input file for one conformer.

### Parameters
#### Path Parameters
- **filename** (pathlib.Path) - Required - Output file stem.
- **coordinates** (list) - Required - Cartesian coordinates.
- **atoms** (list[str]) - Required - Element symbols.
- **charge** (int | float) - Required - Molecular charge.
- **type** (str) - Required - Calculation type (`"opt"`, `"e"`, `"nmr"`).
```

--------------------------------

### dp5.dft.run_dft.dft_calculations

Source: https://github.com/aelashkin/dp5/blob/master/docs/source/dft_api.md

Runs DFT stages (optimization, single-point energy, NMR) based on workflow flags. It dynamically loads the configured backend, instantiates its DFTMethod class, and executes the requested calculations.

```APIDOC
## dp5.dft.run_dft.dft_calculations(mols, workflow, config)

### Description
Run DFT stages requested by the workflow and update molecule objects. This function dynamically imports the configured backend module, instantiates its `DFTMethod` class, and then executes optimisation, single-point energy, and/or NMR stages depending on workflow flags.

### Parameters
* **mols** (*list*) – Molecule objects handled by the molecules container.
* **workflow** (*dict*) – Workflow control flags (for example `dft_opt`, `dft_energies`, `dft_nmr`).
* **config** (*dict*) – DFT configuration subsection.

### Returns
Updated molecule list.

### Return type
list
```

--------------------------------

### Clone DP5 Repository

Source: https://github.com/aelashkin/dp5/blob/master/readme.md

Clones the DP5 repository from GitHub to your local machine.

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

--------------------------------

### ORCA DFT Methods

Source: https://github.com/aelashkin/dp5/blob/master/docs/source/dft_api.md

Methods for configuring and interacting with ORCA DFT calculations.

```APIDOC
## prepare_command(file)

### Description
Build a shell command to run one calculation.

Concrete subclasses can override this to handle engine-specific command
syntax.

### Parameters
#### Path Parameters
- **file** (pathlib.Path) - Required - File stem without extension.

### Returns
Shell command string.

### Return type
str
```

```APIDOC
## read_file(file)

### Description
Parse ORCA output into DP5-standard result fields.

### Parameters
#### Path Parameters
- **file** (pathlib.Path) - Required - ORCA output path.

### Returns
`(atoms, coordinates, energy, shieldings, shielding_labels,
  completed, converged)`.

### Return type
tuple
```

```APIDOC
## write_file(filename, coordinates, atoms, charge, calc_type)

### Description
Write an ORCA `.inp` input file for one conformer.

### Parameters
#### Path Parameters
- **filename** (pathlib.Path) - Required - Output file stem.
- **coordinates** (list) - Required - Cartesian coordinates.
- **atoms** (list[str]) - Required - Element symbols.
- **charge** (int | float) - Required - Molecular charge.
- **calc_type** (str) - Required - Calculation type.
```

--------------------------------

### dp5.dft.base_dft_method.BaseDFTMethod.get_files

Source: https://github.com/aelashkin/dp5/blob/master/docs/source/dft_api.md

Retrieves calculation files for a specified calculation type. If the DFT calculation is already complete, it loads existing files from disk; otherwise, it prepares and executes new calculations.

```APIDOC
## dp5.dft.base_dft_method.BaseDFTMethod.get_files(mols, calc_type)

### Description
Return completed calculation files for the requested calculation. If `self.dft_complete` is set, pre-existing files are loaded from disk. Otherwise new calculations are prepared and executed.

### Parameters
* **mols** (*list*) – Molecules with conformer geometries.
* **calc_type** (*str*) – Calculation type label.

### Returns
Output file stems grouped per molecule.

### Return type
list[list[pathlib.Path]]
```

--------------------------------

### dp5.dft.base_dft_method.BaseDFTMethod.write_file

Source: https://github.com/aelashkin/dp5/blob/master/docs/source/dft_api.md

Writes an engine-specific input file for a single conformer. This method is intended to be overridden by concrete subclasses to handle the specific input file format of different DFT engines.

```APIDOC
## dp5.dft.base_dft_method.BaseDFTMethod.write_file(filename, coordinates, atoms, charge, calc_type)

### Description
Write an engine-specific input file for one conformer.

### Parameters
* **filename** (*pathlib.Path*) – File stem without extension.
* **coordinates** (*list*) – Cartesian coordinates for one conformer.
* **atoms** (*list* *[**str* *]*) – Element symbols matching `coordinates`.
* **charge** (*int* *|* *float*) – Molecular charge to use for the job.
* **calc_type** (*str*) – Calculation type label.
```

--------------------------------

### DFTMethod.read_file

Source: https://github.com/aelashkin/dp5/blob/master/docs/source/dft_architecture.md

Parses ORCA output files into DP5-standard result fields.

```APIDOC
## DFTMethod.read_file

### Description
Parse ORCA output into DP5-standard result fields.

### Parameters
* **file** (pathlib.Path) – ORCA output path.

### Returns
`(atoms, coordinates, energy, shieldings, shielding_labels,
completed, converged)`.

### Return type
tuple
```

--------------------------------

### Manual NMR Description Format

Source: https://github.com/aelashkin/dp5/blob/master/readme.md

Illustrates the format for manual NMR descriptions, including carbon shifts, proton shifts, and atom assignments.

```text
140.1(any),129.7(any),126.7(C10),20.3(C14,C23)

0.0(any)

C1,C3
C4,C5
C14,C23
OMIT C19,H51
```

--------------------------------

### DFTMethod.opt

Source: https://github.com/aelashkin/dp5/blob/master/docs/source/dft_architecture.md

Runs or reads geometry optimization results for a list of molecules.

```APIDOC
## DFTMethod.opt

### Description
Run/read geometry optimisation results.

### Parameters
* **mols** (list) – Molecules to optimise.

### Returns
Tuple of `(atoms, conformers, energies)` grouped by
molecule, where conformers and energies correspond to converged
optimisation outputs.

### Return type
tuple[list, list, list]
```

--------------------------------

### Legacy NMR Assignment Mode

Source: https://github.com/aelashkin/dp5/blob/master/readme.md

Enables the previous loose assignment behavior for NMR descriptions.

```bash
--nmr-assignment-mode legacy
```

--------------------------------

### DP5 Workflow Flags

Source: https://github.com/aelashkin/dp5/blob/master/docs/source/usage.md

Specifies workflow actions for DP5. These flags correspond to configuration file settings and control tasks like structure generation, conformational search, and analysis.

```bash
# Workflow flags and their meanings:
# 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

# Example: Default DP4 workflow for establishing stereochemistry
# -w gnms

# Example: Best results using DP5 workflow
# -w gnomes
```

--------------------------------

### dp5.dft.base_dft_method.BaseDFTMethod.opt

Source: https://github.com/aelashkin/dp5/blob/master/docs/source/dft_api.md

Runs or reads geometry optimization results for a list of molecules. Returns conformers and energies corresponding to converged optimization outputs.

```APIDOC
## dp5.dft.base_dft_method.BaseDFTMethod.opt(mols)

### Description
Run/read geometry optimisation results.

### Parameters
* **mols** (*list*) – Molecules to optimise.

### Returns
Tuple of `(atoms, conformers, energies)` grouped by molecule, where conformers and energies correspond to converged optimisation outputs.

### Return type
tuple[list, list, list]
```

--------------------------------

### dp5.dft.base_dft_method.BaseDFTMethod.read_file

Source: https://github.com/aelashkin/dp5/blob/master/docs/source/dft_api.md

Reads the output file of a DFT calculation, inspired by the cclib parser. It extracts atoms, coordinates, energies, shieldings, shielding labels, and flags for calculation termination and optimization convergence.

```APIDOC
## dp5.dft.base_dft_method.BaseDFTMethod.read_file(file)

### Description
Reads output file. Inspired by cclib parser

### Returns
- atoms
- coordinates
- energies
- shieldings
- shielding labels
- if calculation terminated normally
- if optimisation has converged
```

--------------------------------

### Allow Extra or Missing Peaks

Source: https://github.com/aelashkin/dp5/blob/master/readme.md

Flags to report partial coverage instead of aborting when extra or missing peaks are detected in NMR assignments.

```bash
--allow-extra-peaks
```

```bash
--allow-missing-peaks
```

--------------------------------

### dp5.dft.base_dft_method.BaseDFTMethod.energy

Source: https://github.com/aelashkin/dp5/blob/master/docs/source/dft_api.md

Runs or reads single-point energy calculations for a list of molecules.

```APIDOC
## dp5.dft.base_dft_method.BaseDFTMethod.energy(mols)

### Description
Run/read single-point energy calculations.

### Parameters
* **mols** (*list*) – Molecules to evaluate.

### Returns
Tuple of `(atoms, conformers, energies)` grouped by molecule.

### Return type
tuple[list, list, list]
```

--------------------------------

### DFTMethod.energy

Source: https://github.com/aelashkin/dp5/blob/master/docs/source/dft_architecture.md

Runs or reads single-point energy calculations for a list of molecules.

```APIDOC
## DFTMethod.energy

### Description
Run/read single-point energy calculations.

### Parameters
* **mols** (list) – Molecules to evaluate.

### Returns
Tuple of `(atoms, conformers, energies)` grouped by molecule.

### Return type
tuple[list, list, list]
```

--------------------------------

### dp5.nmr_processing.proton.bic_minimisation.BIC_minimisation_region_full

Source: https://github.com/aelashkin/dp5/blob/master/docs/source/nmr_processing_api.md

Fits and prunes a Pearson-VII model for a single proton region. It constructs an initial multi-peak model, relaxes parameters using lmfit, and iteratively removes peaks based on the Bayesian Information Criterion.

```APIDOC
## dp5.nmr_processing.proton.bic_minimisation.BIC_minimisation_region_full(ind1, uc, peak_regions, grouped_peaks, total_spectral_ydata, corr_distance, std)

### Description
Fit and prune a Pearson-VII model for a single proton region. The routine constructs an initial multi-peak model from the candidate peaks in one region, relaxes the Pearson-VII parameters with `lmfit`, and then removes peaks one at a time whenever doing so lowers the Bayesian Information Criterion by more than a fixed threshold.

### Parameters
#### Path Parameters
- **ind1** (int) - Required - Region index within `peak_regions`.
- **uc** (object) - Required - `nmrglue` unit-conversion object.
- **peak_regions** (sequence) - Required - Regions of the spectrum identified as containing proton signal.
- **grouped_peaks** (sequence) - Required - Candidate peak indices grouped by region.
- **total_spectral_ydata** (numpy.ndarray) - Required - Processed proton spectrum intensities.
- **corr_distance** (int) - Required - Correlation distance used to constrain peak widths and movement during fitting.
- **std** (float) - Required - Estimated noise level.

### Returns
Surviving fitted peaks, fitted parameters, and the simulated line shape for the region.

### Return type
tuple[list, lmfit.Parameters, numpy.ndarray]
```

--------------------------------

### dp5.nmr_processing.proton.bic_minimisation.multiproc_BIC_minimisation

Source: https://github.com/aelashkin/dp5/blob/master/docs/source/nmr_processing_api.md

Fits all proton regions in parallel and rebuilds the final multiplets. This function dispatches `BIC_minimisation_region_full` across regions, collects models, and reconstructs boundaries.

```APIDOC
## dp5.nmr_processing.proton.bic_minimisation.multiproc_BIC_minimisation(peak_regions, grouped_peaks, total_spectral_ydata, corr_distance, uc, std)

### Description
Fit all proton regions in parallel and rebuild the final multiplets. This wrapper dispatches [`BIC_minimisation_region_full()`](#dp5.nmr_processing.proton.bic_minimisation.BIC_minimisation_region_full) over all preliminary proton regions, collects the per-region peak models, and then rebuilds the final region boundaries after splitting fitted groups that are more than 20 Hz apart.

### Parameters
#### Path Parameters
- **peak_regions** (sequence) - Required - Preliminary proton signal regions.
- **grouped_peaks** (sequence) - Required - Candidate peak indices grouped by preliminary region.
- **total_spectral_ydata** (numpy.ndarray) - Required - Processed proton spectrum intensities.
- **corr_distance** (int) - Required - Correlation distance estimated during spectral processing.
- **uc** (object) - Required - `nmrglue` unit-conversion object.
- **std** (float) - Required - Estimated noise level.

### Returns
Final picked peaks, grouped peaks, region boundaries, simulated global fit, and the combined fitted parameters.

### Return type
tuple
```

--------------------------------

### DFTMethod.is_completed

Source: https://github.com/aelashkin/dp5/blob/master/docs/source/dft_architecture.md

Checks if a calculation terminated normally by looking for a completion flag.

```APIDOC
## DFTMethod.is_completed

### Description
Check whether a calculation terminated normally.

### Parameters
* **file** (pathlib.Path) – Output file path.

### Returns
`True` if calculation completion flag is found.

### Return type
bool
```

--------------------------------

### DFTMethod.is_converged

Source: https://github.com/aelashkin/dp5/blob/master/docs/source/dft_architecture.md

Checks if an optimization is marked as converged.

```APIDOC
## DFTMethod.is_converged

### Description
Check whether an optimisation is marked as converged.

### Parameters
* **file** (pathlib.Path) – Output file path.

### Returns
`True` if optimisation converged.

### Return type
bool
```

--------------------------------

### dp5.dft.base_dft_method.BaseDFTMethod.nmr

Source: https://github.com/aelashkin/dp5/blob/master/docs/source/dft_api.md

Runs or reads NMR shielding calculations for a list of molecules.

```APIDOC
## dp5.dft.base_dft_method.BaseDFTMethod.nmr(mols)

### Description
Run/read NMR shielding calculations.

### Parameters
* **mols** (*list*) – Molecules to evaluate.

### Returns
Tuple of `(atoms, conformers, energies, shieldings, shielding_labels)` grouped by molecule.

### Return type
tuple[list, list, list, list, list]
```

--------------------------------

### dp5.dft.base_dft_method.BaseDFTMethod.is_completed

Source: https://github.com/aelashkin/dp5/blob/master/docs/source/dft_api.md

Checks if a calculation terminated normally by looking for a completion flag in the output file.

```APIDOC
## dp5.dft.base_dft_method.BaseDFTMethod.is_completed(file)

### Description
Check whether a calculation terminated normally.

### Parameters
* **file** (*pathlib.Path*) – Output file path.

### Returns
`True` if calculation completion flag is found.

### Return type
bool
```

--------------------------------

### dp5.dft.base_dft_method.BaseDFTMethod.is_converged

Source: https://github.com/aelashkin/dp5/blob/master/docs/source/dft_api.md

Checks if an optimization calculation is marked as converged in the output file.

```APIDOC
## dp5.dft.base_dft_method.BaseDFTMethod.is_converged(file)

### Description
Check whether an optimisation is marked as converged.

### Parameters
* **file** (*pathlib.Path*) – Output file path.

### Returns
`True` if optimisation converged.

### Return type
bool
```

--------------------------------

### DFTMethod.atom_num_to_symbol

Source: https://github.com/aelashkin/dp5/blob/master/docs/source/dft_architecture.md

Converts an atomic number to its corresponding element symbol.

```APIDOC
## DFTMethod.atom_num_to_symbol

### Description
Convert atomic number to element symbol.

### Parameters
* **anum** (int) – Atomic number (1-indexed).

### Returns
Element symbol.

### Return type
str
```

--------------------------------

### DFTMethod.nmr

Source: https://github.com/aelashkin/dp5/blob/master/docs/source/dft_architecture.md

Runs or reads NMR shielding calculations for a list of molecules.

```APIDOC
## DFTMethod.nmr

### Description
Run/read NMR shielding calculations.

### Parameters
* **mols** (list) – Molecules to evaluate.

### Returns
Tuple of `(atoms, conformers, energies, shieldings,
shielding_labels)` grouped by molecule.

### Return type
tuple[list, list, list, list, list]
```

--------------------------------

### dp5.nmr_processing.proton.process.proton_processing

Source: https://github.com/aelashkin/dp5/blob/master/docs/source/nmr_processing_api.md

Processes a proton FID into assignment-ready multiplets. This function implements the full DP4-AI processing path, including spectral correction, peak picking, pruning, solvent removal, and region simulation.

```APIDOC
## dp5.nmr_processing.proton.process.proton_processing(total_spectral_ydata, uc, solvent)

### Description
Process a proton FID into assignment-ready multiplets. The proton pipeline implements the most complete DP4-AI processing path: spectral correction, derivative-based peak picking, BIC-guided peak-model pruning, solvent removal, and region simulation for later integration.

### Parameters
#### Path Parameters
- **total_spectral_ydata** (numpy.ndarray) - Required - Complex frequency-domain proton spectrum.
- **uc** (object) - Required - `nmrglue` unit-conversion object for converting point indices into ppm and Hz.
- **solvent** (str) - Required - Solvent identifier used for solvent detection and referencing.

### Returns
PPM axis, processed spectrum, final peak regions, grouped peaks, fitted peak indices, combined fit parameters, and simulated regions for downstream integration.

### Return type
tuple
```

--------------------------------

### dp5.dft.base_dft_method.BaseDFTMethod.atom_num_to_symbol

Source: https://github.com/aelashkin/dp5/blob/master/docs/source/dft_api.md

Converts an atomic number to its corresponding element symbol.

```APIDOC
## dp5.dft.base_dft_method.BaseDFTMethod.atom_num_to_symbol(anum: int) → str

### Description
Convert atomic number to element symbol.

### Parameters
* **anum** (*int*) – Atomic number (1-indexed).

### Returns
Element symbol.

### Return type
str
```

--------------------------------

### dp5.nmr_processing.proton.assign.iterative_assignment

Source: https://github.com/aelashkin/dp5/blob/master/docs/source/nmr_processing_api.md

Assigns calculated proton shifts to processed multiplet centres using a strategy similar to DP4-AI. It involves initial scaling, integral-constrained methyl group assignment, Hungarian optimization, and iterative refinement.

```APIDOC
## dp5.nmr_processing.proton.assign.iterative_assignment(mol, exp_peaks, calculated_shifts, H_labels, rounded_integrals)

### Description
Assign calculated proton shifts to processed multiplet centres. The implementation mirrors the DP4-AI proton assignment strategy described in the paper and ESI. A first pass uses external scaling, methyl groups are assigned as integral-constrained bundles, the remaining protons are matched with a Hungarian optimisation over a probability matrix, and the assignment is repeated after internal scaling until it converges.

### Parameters
#### Path Parameters
- **mol** (object) - Required - RDKit molecule used to identify methyl groups from connectivity.
- **exp_peaks** (numpy.ndarray) - Required - Experimental multiplet centres in ppm, expanded according to the rounded integrals so that peaks can be assigned multiple times.
- **calculated_shifts** (numpy.ndarray) - Required - Calculated proton shifts from DFT or a surrogate model.
- **H_labels** (numpy.ndarray) - Required - Proton labels corresponding to `calculated_shifts`.
- **rounded_integrals** (numpy.ndarray) - Required - Integer-like multiplet integrals derived from the deconvolved proton spectrum.

### Returns
Assigned calculated shifts, assigned experimental peaks, assigned labels, and the final scaled shifts used internally.

### Return type
tuple[list, list, list, numpy.ndarray]
```

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