pymatgen.util.provenance module

Classes and methods related to the Structure Notation Language (SNL)

class Author(name, email)

Bases: Author

An Author contains two fields:

name

Name of author (String)

email

Email of author (String)

Create new instance of Author(name, email)

as_dict()

Returns: MSONable dict.

static from_dict(d)

Parameters:

d (dict) – Dict representation

Returns:

Author

static parse_author(author)

Parses an Author object from either a String, dict, or tuple

Parameters:

author – A String formatted as “NAME <email@domain.com>”, (name, email) tuple, or a dict with name and email keys.

Returns:

An Author object.

class HistoryNode(name, url, description)

Bases: HistoryNode

A HistoryNode represents a step in the chain of events that lead to a Structure. HistoryNodes leave ‘breadcrumbs’ so that you can trace back how a Structure was created. For example, a HistoryNode might represent pulling a Structure from an external database such as the ICSD or CSD. Or, it might represent the application of a code (e.g. pymatgen) to the Structure, with a custom description of how that code was applied (e.g. a site removal Transformation was applied).

A HistoryNode contains three fields:

name

The name of a code or resource that this Structure encountered in its history (String)

url

The URL of that code/resource (String)

description

A free-form description of how the code/resource is related to the Structure (dict).

Create new instance of HistoryNode(name, url, description)

as_dict() → dict[str, str]

Returns: Dict

static from_dict(h_node: dict[str, str]) → HistoryNode

Parameters:

d (dict) – Dict representation

Returns:

HistoryNode

static parse_history_node(h_node)

Parses a History Node object from either a dict or a tuple.

Parameters:

h_node – A dict with name/url/description fields or a 3-element tuple.

Returns:

History node.

class StructureNL(struct_or_mol, authors, projects=None, references='', remarks=None, data=None, history=None, created_at=None)

Bases: object

The Structure Notation Language (SNL, pronounced ‘snail’) is a container for a pymatgen Structure/Molecule object with some additional fields for enhanced provenance. It is meant to be imported/exported in a JSON file format with the following structure:

• about

  • created_at

  • authors

  • projects

  • references

  • remarks

  • data

  • history

• lattice (optional)

• sites

Parameters:

• struct_or_mol – A pymatgen.core.structure Structure/Molecule object

• authors – List of {“name”:’’, “email”:’’} dicts, list of Strings as ‘John Doe <johndoe@gmail.com>’, or a single String with commas separating authors

• projects – List of Strings [‘Project A’, ‘Project B’]

• references – A String in BibTeX format

• remarks – List of Strings [‘Remark A’, ‘Remark B’]

• data – A free form dict. Namespaced at the root level with an underscore, e.g. {“_materialsproject”: <custom data>}

• history – List of dicts - [{‘name’:’’, ‘url’:’’, ‘description’:{}}]

• created_at – A datetime object

as_dict()

Returns: MSONable dict

classmethod from_dict(d)

Parameters:

d (dict) – Dict representation

Returns:

Class

classmethod from_structures(structures: Sequence[Structure], authors: Sequence[dict[str, str]], projects=None, references='', remarks=None, data=None, histories=None, created_at=None)

A convenience method for getting a list of StructureNL objects by specifying structures and metadata separately. Some of the metadata is applied to all of the structures for ease of use.

Parameters:

• structures – A list of Structure objects

• authors – List of {“name”:’’, “email”:’’} dicts, list of Strings as ‘John Doe <johndoe@gmail.com>’, or a single String with commas separating authors

• projects – List of Strings [‘Project A’, ‘Project B’]. This applies to all structures.

• references – A String in BibTeX format. Again, this applies to all structures.

• remarks – List of Strings [‘Remark A’, ‘Remark B’]

• data – A list of free form dict. Namespaced at the root level with an underscore, e.g. {“_materialsproject”:<custom data>} . The length of data should be the same as the list of structures if not None.

• histories – List of list of dicts - [[{‘name’:’’, ‘url’:’’, ‘description’:{}}], …] The length of histories should be the same as the list of structures if not None.

• created_at – A datetime object

is_valid_bibtex(reference: str) → bool

Use pybtex to validate that a reference is in proper BibTeX format

Parameters:

reference – A String reference in BibTeX format.

Returns:

Boolean indicating if reference is valid bibtex.