aiida.tools.dbimporters package

aiida.tools.dbimporters.DbImporterFactory(pluginname)

This function loads the correct DbImporter plugin class

Subpackages

• aiida.tools.dbimporters.plugins package
  • Submodules

Submodules

class aiida.tools.dbimporters.baseclasses.CifEntry(db_name=None, db_uri=None, id=None, version=None, extras={}, uri=None)

Bases: aiida.tools.dbimporters.baseclasses.DbEntry

Represents an entry from the structure database (COD, ICSD, …).

__module__ = 'aiida.tools.dbimporters.baseclasses'

cif

Returns raw contents of a CIF file as string.

get_aiida_structure()

Returns:AiiDA structure corresponding to the CIF file.

get_ase_structure()

Returns ASE representation of the CIF.

Note

To be removed, as it is duplicated in aiida.orm.data.cif.CifData.

get_cif_node(store=False)

Creates a CIF node, that can be used in AiiDA workflow.

Returns:aiida.orm.data.cif.CifData object

get_parsed_cif()

Returns data structure, representing the CIF file. Can be created using PyCIFRW or any other open-source parser.

Returns:list of lists

get_raw_cif()

Returns raw contents of a CIF file as string.

Returns:contents of a file as string

class aiida.tools.dbimporters.baseclasses.DbEntry(db_name=None, db_uri=None, id=None, version=None, extras={}, uri=None)

Bases: object

Represents an entry from external database.

__dict__ = dict_proxy({'__module__': 'aiida.tools.dbimporters.baseclasses', 'contents': <property object>, '__dict__': <attribute '__dict__' of 'DbEntry' objects>, '__weakref__': <attribute '__weakref__' of 'DbEntry' objects>, '_license': None, '__doc__': '\n Represents an entry from external database.\n ', '__init__': <function __init__>, '__repr__': <function __repr__>})

__init__(db_name=None, db_uri=None, id=None, version=None, extras={}, uri=None)

Sets the basic parameters for the database entry:

Parameters:

• db_name – name of the source database
• db_uri – URI of the source database
• id – structure identifyer in the database
• version – version of the database
• extras – a dictionary with some extra parameters (e.g. database ID number)
• uri – URI of the structure (should be permanent)

__module__ = 'aiida.tools.dbimporters.baseclasses'

__repr__() <==> repr(x)

__weakref__

list of weak references to the object (if defined)

_license = None

contents

Returns raw contents of a file as string.

class aiida.tools.dbimporters.baseclasses.DbImporter

Bases: object

Base class for database importers.

__dict__ = dict_proxy({'get_supported_keywords': <function get_supported_keywords>, '__module__': 'aiida.tools.dbimporters.baseclasses', '__weakref__': <attribute '__weakref__' of 'DbImporter' objects>, '__dict__': <attribute '__dict__' of 'DbImporter' objects>, 'query': <function query>, 'setup_db': <function setup_db>, '__doc__': '\n Base class for database importers.\n '})

__module__ = 'aiida.tools.dbimporters.baseclasses'

__weakref__

list of weak references to the object (if defined)

get_supported_keywords()

Returns the list of all supported query keywords.

Returns:list of strings

query(**kwargs)

Method to query the database.

Parameters:

• id – database-specific entry identificator
• element – element name from periodic table of elements
• number_of_elements – number of different elements
• mineral_name – name of mineral
• chemical_name – chemical name of substance
• formula – chemical formula
• volume – volume of the unit cell in cubic angstroms
• spacegroup – symmetry space group symbol in Hermann-Mauguin notation
• spacegroup_hall – symmetry space group symbol in Hall notation
• a – length of lattice vector in angstroms
• b – length of lattice vector in angstroms
• c – length of lattice vector in angstroms
• alpha – angles between lattice vectors in degrees
• beta – angles between lattice vectors in degrees
• gamma – angles between lattice vectors in degrees
• z – number of the formula units in the unit cell
• measurement_temp – temperature in kelvins at which the unit-cell parameters were measured
• measurement_pressure – pressure in kPa at which the unit-cell parameters were measured
• diffraction_temp – mean temperature in kelvins at which the intensities were measured
• diffraction_pressure – mean pressure in kPa at which the intensities were measured
• authors – authors of the publication
• journal – name of the journal
• title – title of the publication
• year – year of the publication
• journal_volume – journal volume of the publication
• journal_issue – journal issue of the publication
• first_page – first page of the publication
• last_page – last page of the publication
• doi – digital object identifyer (DOI), refering to the publication

Raises:

NotImplementedError – if search using given keyword is not implemented.

setup_db(**kwargs)

Sets the database parameters. The method should reconnect to the database using updated parameters, if already connected.

class aiida.tools.dbimporters.baseclasses.DbSearchResults(results)

Bases: object

Base class for database results.

All classes, inheriting this one and overriding at(), are able to benefit from having functions __iter__, __len__ and __getitem__.

class DbSearchResultsIterator(results, increment=1)

Bases: object

Iterator for search results

__dict__ = dict_proxy({'__module__': 'aiida.tools.dbimporters.baseclasses', 'next': <function next>, '__dict__': <attribute '__dict__' of 'DbSearchResultsIterator' objects>, '__weakref__': <attribute '__weakref__' of 'DbSearchResultsIterator' objects>, '__doc__': '\n Iterator for search results\n ', '__init__': <function __init__>})

__init__(results, increment=1)

x.__init__(…) initializes x; see help(type(x)) for signature

__module__ = 'aiida.tools.dbimporters.baseclasses'

__weakref__

list of weak references to the object (if defined)

next()

__dict__ = dict_proxy({'__module__': 'aiida.tools.dbimporters.baseclasses', '_get_url': <function _get_url>, 'fetch_all': <function fetch_all>, '__getitem__': <function __getitem__>, 'next': <function next>, 'DbSearchResultsIterator': <class 'aiida.tools.dbimporters.baseclasses.DbSearchResultsIterator'>, '__iter__': <function __iter__>, '__len__': <function __len__>, '_get_source_dict': <function _get_source_dict>, '__dict__': <attribute '__dict__' of 'DbSearchResults' objects>, '__weakref__': <attribute '__weakref__' of 'DbSearchResults' objects>, '__doc__': '\n Base class for database results.\n\n All classes, inheriting this one and overriding ``at()``, are able to\n benefit from having functions ``__iter__``, ``__len__`` and\n ``__getitem__``.\n ', '__init__': <function __init__>, 'at': <function at>})

__getitem__(key)

__init__(results)

x.__init__(…) initializes x; see help(type(x)) for signature

__iter__()

Instances of aiida.tools.dbimporters.baseclasses.DbSearchResults can be used as iterators.

__len__()

__module__ = 'aiida.tools.dbimporters.baseclasses'

__weakref__

list of weak references to the object (if defined)

_get_source_dict(result_dict)

Returns a dictionary, which is passed as kwargs to the created DbEntry instance, describing the source of the entry.

Parameters:result_dict – dictionary, describing an entry in the results.

_get_url(result_dict)

Returns an URL of an entry CIF file.

Parameters:result_dict – dictionary, describing an entry in the results.

at(position)

Returns position-th result as aiida.tools.dbimporters.baseclasses.DbEntry.

Parameters:position – zero-based index of a result. Raises:IndexError – if position is out of bounds.

fetch_all()

Returns all query results as an array of aiida.tools.dbimporters.baseclasses.DbEntry.

next()

Returns the next result of the query (instance of aiida.tools.dbimporters.baseclasses.DbEntry).

Raises:StopIteration – when the end of result array is reached.

class aiida.tools.dbimporters.baseclasses.UpfEntry(db_name=None, db_uri=None, id=None, version=None, extras={}, uri=None)

Bases: aiida.tools.dbimporters.baseclasses.DbEntry

Represents an entry from the pseudopotential database.

__module__ = 'aiida.tools.dbimporters.baseclasses'

get_upf_node(store=False)

Creates an UPF node, that can be used in AiiDA workflow.

Returns:aiida.orm.data.upf.UpfData object