aiida.tools.dbimporters package¶
-
class
aiida.tools.dbimporters.
DbImporter
[source]¶ Bases:
object
Base class for database importers.
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__dict__
= mappingproxy({'__module__': 'aiida.tools.dbimporters.baseclasses', '__doc__': '\n Base class for database importers.\n ', 'query': <function DbImporter.query>, 'setup_db': <function DbImporter.setup_db>, 'get_supported_keywords': <function DbImporter.get_supported_keywords>, '__dict__': <attribute '__dict__' of 'DbImporter' objects>, '__weakref__': <attribute '__weakref__' of 'DbImporter' objects>})¶
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__module__
= 'aiida.tools.dbimporters.baseclasses'¶
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__weakref__
¶ list of weak references to the object (if defined)
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get_supported_keywords
()[source]¶ Returns the list of all supported query keywords.
- Returns
list of strings
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query
(**kwargs)[source]¶ 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.
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Subpackages¶
Submodules¶
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class
aiida.tools.dbimporters.baseclasses.
CifEntry
(db_name=None, db_uri=None, id=None, version=None, extras={}, uri=None)[source]¶ Bases:
aiida.tools.dbimporters.baseclasses.DbEntry
Represents an entry from the structure database (COD, ICSD, …).
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__module__
= 'aiida.tools.dbimporters.baseclasses'¶
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property
cif
¶ Returns raw contents of a CIF file as string.
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get_aiida_structure
(converter='pymatgen', store=False, **kwargs)[source]¶ - Returns
AiiDA structure corresponding to the CIF file.
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get_ase_structure
()[source]¶ Returns ASE representation of the CIF.
Note
To be removed, as it is duplicated in
aiida.orm.nodes.data.cif.CifData
.
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get_cif_node
(store=False, parse_policy='lazy')[source]¶ Creates a CIF node, that can be used in AiiDA workflow.
- Returns
-
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class
aiida.tools.dbimporters.baseclasses.
DbEntry
(db_name=None, db_uri=None, id=None, version=None, extras={}, uri=None)[source]¶ Bases:
object
Represents an entry from external database.
-
__dict__
= mappingproxy({'__module__': 'aiida.tools.dbimporters.baseclasses', '__doc__': '\n Represents an entry from external database.\n ', '_license': None, '__init__': <function DbEntry.__init__>, '__repr__': <function DbEntry.__repr__>, 'contents': <property object>, '__dict__': <attribute '__dict__' of 'DbEntry' objects>, '__weakref__': <attribute '__weakref__' of 'DbEntry' objects>})¶
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__init__
(db_name=None, db_uri=None, id=None, version=None, extras={}, uri=None)[source]¶ 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)
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__module__
= 'aiida.tools.dbimporters.baseclasses'¶
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__weakref__
¶ list of weak references to the object (if defined)
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_license
= None¶
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property
contents
¶ Returns raw contents of a file as string.
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class
aiida.tools.dbimporters.baseclasses.
DbImporter
[source]¶ Bases:
object
Base class for database importers.
-
__dict__
= mappingproxy({'__module__': 'aiida.tools.dbimporters.baseclasses', '__doc__': '\n Base class for database importers.\n ', 'query': <function DbImporter.query>, 'setup_db': <function DbImporter.setup_db>, 'get_supported_keywords': <function DbImporter.get_supported_keywords>, '__dict__': <attribute '__dict__' of 'DbImporter' objects>, '__weakref__': <attribute '__weakref__' of 'DbImporter' objects>})¶
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__module__
= 'aiida.tools.dbimporters.baseclasses'¶
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__weakref__
¶ list of weak references to the object (if defined)
-
get_supported_keywords
()[source]¶ Returns the list of all supported query keywords.
- Returns
list of strings
-
query
(**kwargs)[source]¶ 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.
-
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class
aiida.tools.dbimporters.baseclasses.
DbSearchResults
(results)[source]¶ 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)[source]¶ Bases:
object
Iterator for search results
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__dict__
= mappingproxy({'__module__': 'aiida.tools.dbimporters.baseclasses', '__doc__': '\n Iterator for search results\n ', '__init__': <function DbSearchResults.DbSearchResultsIterator.__init__>, '__next__': <function DbSearchResults.DbSearchResultsIterator.__next__>, 'next': <function DbSearchResults.DbSearchResultsIterator.next>, '__dict__': <attribute '__dict__' of 'DbSearchResultsIterator' objects>, '__weakref__': <attribute '__weakref__' of 'DbSearchResultsIterator' objects>})¶
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__init__
(results, increment=1)[source]¶ Initialize self. See help(type(self)) for accurate signature.
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__module__
= 'aiida.tools.dbimporters.baseclasses'¶
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__weakref__
¶ list of weak references to the object (if defined)
-
-
__dict__
= mappingproxy({'__module__': 'aiida.tools.dbimporters.baseclasses', '__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 DbSearchResults.__init__>, 'DbSearchResultsIterator': <class 'aiida.tools.dbimporters.baseclasses.DbSearchResults.DbSearchResultsIterator'>, '__iter__': <function DbSearchResults.__iter__>, '__len__': <function DbSearchResults.__len__>, '__getitem__': <function DbSearchResults.__getitem__>, 'fetch_all': <function DbSearchResults.fetch_all>, 'next': <function DbSearchResults.next>, 'at': <function DbSearchResults.at>, '_get_source_dict': <function DbSearchResults._get_source_dict>, '_get_url': <function DbSearchResults._get_url>, '__dict__': <attribute '__dict__' of 'DbSearchResults' objects>, '__weakref__': <attribute '__weakref__' of 'DbSearchResults' objects>})¶
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__iter__
()[source]¶ Instances of
aiida.tools.dbimporters.baseclasses.DbSearchResults
can be used as iterators.
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__module__
= 'aiida.tools.dbimporters.baseclasses'¶
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__weakref__
¶ list of weak references to the object (if defined)
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_get_source_dict
(result_dict)[source]¶ 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.
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_get_url
(result_dict)[source]¶ Returns an URL of an entry CIF file.
- Parameters
result_dict – dictionary, describing an entry in the results.
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at
(position)[source]¶ Returns
position
-th result asaiida.tools.dbimporters.baseclasses.DbEntry
.- Parameters
position – zero-based index of a result.
- Raises
IndexError – if
position
is out of bounds.
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fetch_all
()[source]¶ Returns all query results as an array of
aiida.tools.dbimporters.baseclasses.DbEntry
.
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next
()[source]¶ Returns the next result of the query (instance of
aiida.tools.dbimporters.baseclasses.DbEntry
).- Raises
StopIteration – when the end of result array is reached.
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class
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class
aiida.tools.dbimporters.baseclasses.
UpfEntry
(db_name=None, db_uri=None, id=None, version=None, extras={}, uri=None)[source]¶ Bases:
aiida.tools.dbimporters.baseclasses.DbEntry
Represents an entry from the pseudopotential database.
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__module__
= 'aiida.tools.dbimporters.baseclasses'¶
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