pyscal_rdf package

Submodules

pyscal_rdf.structure module

StructureGraph is the central object in pyscal_rdf which combines all the functionality of pyscal_rdf.graph.RDFGraph along with easy structural creation routines.

class pyscal_rdf.structure.StructureGraph(graph_file=None, store='Memory', store_file=None, identifier='http://default_graph')

Bases: RDFGraph

__init__(graph_file=None, store='Memory', store_file=None, identifier='http://default_graph')

read_structure(filename, format='lammps-dump', add_to_graph=True, names=True)

Read an input file and return it as a System object.

Parameters:

• filename (string) – name of the input file

• format (string) – format of the input file

• add_to_graph (bool, optinal) – If False, the created structure will not be added to the graph

• names (bool, optional) – If True, names will be used as IDs

Returns:

• System (pyscal System)

• system will be populated with given atoms and simulation box

pyscal_rdf.graph module

Graph module contains the basic RDFGraph object in pyscal_rdf. This object gets a structure as an input and annotates it with the CMSO ontology (PLDO and PODO too as needed). The annotated object is stored in triplets.

class pyscal_rdf.graph.RDFGraph(graph_file=None, store='Memory', store_file=None, identifier='http://default_graph', ontology=None)

Bases: object

__init__(graph_file=None, store='Memory', store_file=None, identifier='http://default_graph', ontology=None)

add(triple)

add_atoms(name=None)

Add Atoms including their species and positions

Parameters:

name – if provided, the name will be used instead of random identifier

add_calculated_quantity(propertyname, value, unit=None, sample=None)

add_chemical_composition(name=None)

Add chemical composition

Parameters:

name – if provided, the name will be used instead of random identifier

add_crystal_structure(name=None)

Add a CMSO Crystal Structure

Parameters:

name – if provided, the name will be used instead of random identifier

add_gb(gb_dict, name=None)

Add GB details which will be annotated using PLDO

Parameters:

• gb_dict (dict) – dict containing details about the grain boundary

• name – if provided, the name will be used instead of random identifier

add_lattice_properties(name=None)

Add CMSO lattice properties such as Lattice Parameter, and its lengths and angles.

Parameters:

name – if provided, the name will be used instead of random identifier

add_material(name=None)

Add a CMSO Material object

Parameters:

name – if provided, the name will be used instead of random identifier

add_sample(name=None)

Add a CMSO Sample object

Parameters:

name – if provided, the name will be used instead of random identifier

add_simulation_cell(name=None)

Add a CMSO SimulationCell

Parameters:

name – if provided, the name will be used instead of random identifier

add_simulation_cell_properties(name=None)

Add a CMSO SimulationCell properties such as SimulationCellLength, and Vectors.

Parameters:

name – if provided, the name will be used instead of random identifier

add_space_group(name=None)

Add a CMSO Space Group

Parameters:

name – if provided, the name will be used instead of random identifier

add_structure_to_graph(structure, names=True, name_index=None, format=None)

Add a given pyscal.core.System to the Graph object

Parameters:

• structure (pyscal.core.System) – input structure

• names (bool) – if True, alphanumeric names will be used instead of random BNodes

Return type:

None

add_unit_cell(name=None)

Add a CMSO Unit Cell

Parameters:

name – if provided, the name will be used instead of random identifier

add_vacancy(concentration, number=None, name=None)

Add Vacancy details which will be annotated by PODO

Parameters:

• concentration (float) – vacancy concentration, value should be between 0-1

• name – if provided, the name will be used instead of random identifier

auto_query(source, destination, condition=None, return_query=False, enforce_types=True)

create_graph(names=False, name_index='1')

Create the RDF Graph from the data stored

Parameters:

• names (bool) – if True, alphanumeric names will be used instead of random BNodes

• name_index (string) – Prefix to be added to identifiers, default 01

Return type:

None

data(key)

get_sample(sample, no_atoms=False)

Get the Sample as an RDFGraph

Parameters:

• sample (string) – sample id

• no_atoms (bool, optional) – if True, returns the number of atoms in the sample

Returns:

sgraph – the RDFGraph of the queried sample

Return type:

RDFGraph

get_system_from_sample(sample)

Get a pyscal pyscal.core.System from the selected sample

Parameters:

sample (string) – sample id

Returns:

system – corresponding system

Return type:

pyscal.core.System

inspect_sample(sample=None)

iterate_graph(item, create_new_graph=False)

property n_samples

Number of samples in the Graph

process_structure(structure, format=None)

Convert a given pyscal.core.System to a data dictionary which can be used for annotation and storing the data in the RDF Graph.

Parameters:

structure (pyscal.core.System) – input structure

Return type:

None

query(inquery)

Query the graph using SPARQL

Parameters:

inquery (string) – SPARQL query to be executed

Returns:

res – pandas dataframe results

Return type:

pandas DataFrame

query_sample(destination, condition=None, return_query=False, enforce_types=True)

property samples

Returns a list of all Samples in the graph

to_file(sample, filename=None, format='lammps-dump')

Save a given sample to a file

Parameters:

• sample – ID of the sample

• filename (string) – name of output file

• format (string, {"lammps-dump","lammps-data", "poscar"}) –

Return type:

None

visualise(backend='ipycytoscape', edge_color='#37474F', styledict=None, graph_attr={'rankdir': 'BT'}, layoutname='cola')

Vosualise the RDF tree of the Graph

Parameters:

• backend (string, {'ipycytoscape', 'graphviz'}) – Chooses the backend with which the graph will be plotted. ipycytoscape provides an interactive, but slow visualisation, whereas graphviz provides a non-interactive fast visualisation.

• edge_color (string) – Edge color of the boxes

• styledict (dict) – If provided, allows customisation of color and other properties.

• graph_attr (dict) – further attributes that allow customisation of graphs

• layoutname (string) – name of the layout for graph

Notes

styledict has the following options. Refer to graphviz and ipycytoscape documentation for more details BNode:

color: shape: style:

URIRef:

color: shape: style:

Literal:

color: shape: style:

visualize(*args, **kwargs)

Vosualise the RDF tree of the Graph

Parameters:

• backend (string, {'ipycytoscape', 'graphviz'}) – Chooses the backend with which the graph will be plotted. ipycytoscape provides an interactive, but slow visualisation, whereas graphviz provides a non-interactive fast visualisation.

• edge_color (string) – Edge color of the boxes

• styledict (dict) – If provided, allows customisation of color and other properties.

• graph_attr (dict) – further attributes that allow customisation of graphs

• layoutname (string) – name of the layout for graph

Notes

styledict has the following options. Refer to graphviz and ipycytoscape documentation for more details BNode:

color: shape: style:

URIRef:

color: shape: style:

Literal:

color: shape: style:

write(filename, format='json-ld')

Write the serialised version of the graph to a file

Parameters:

• filename (string) – name of output file

• format (string, {'turtle', 'xml', 'json-ld', 'ntriples', 'n3'}) – output format to be written to

Return type:

None

pyscal_rdf.network module

pyscal_rdf.properties module

pyscal_rdf.properties.get_angle(vec1, vec2)

Get angle between two vectors in degrees

Parameters:

• vec1 (list) – first vector

• vec2 (list) – second vector

Returns:

angle – angle in degrees

Return type:

float

Notes

Angle is rounded to two decimal points

pyscal_rdf.properties.get_basis(sys)

pyscal_rdf.properties.get_bravais_lattice(sys)

pyscal_rdf.properties.get_coordination(sys)

pyscal_rdf.properties.get_lattice_vector(sys, cartesian=False)

pyscal_rdf.properties.get_space_group(sys)

pyscal_rdf.queries module

pyscal_rdf.rdfutils module

pyscal_rdf.visualize module

pyscal_rdf.visualize.get_string_from_URI(x)

pyscal_rdf.visualize.get_title_from_BNode(x)

pyscal_rdf.visualize.parse_object(x)

pyscal_rdf.visualize.visualize_graph(g, backend='ipycytoscape', edge_color='#37474F', styledict={'BNode': {'color': '#ffe6ff', 'shape': 'box', 'style': 'filled'}, 'Literal': {'color': '#e6ffcc', 'shape': 'ellipse', 'style': 'filled'}, 'URIRef': {'color': '#ffffcc', 'shape': 'box', 'style': 'filled'}}, graph_attr={'rankdir': 'LR'}, layoutname='cola')

Module contents