def finalize_sdf_items(self):
# ontological axioms
for prop, dtype in self._props.items():
self._g.add((prop, RDF.term('type'), OWL.term('DatatypeProperty')))
self._g.add((prop, RDFS.term('domain'), self.cls_molecule))
self._g.add((prop, RDFS.term('range'), dtype))
# the actual data
for prop, data in self._props_data.items():
dtype = self._props[prop]
for subj, val in data:
self._g.add((subj, prop, Literal(val, None, dtype)))
def data_make_address(self, address):
addressTermsMap = {
"addr": RDFS.term("label"),
"city": vcard.locality,
"country": vcard.term("country-name"),
"county": vcard.term("country-name"),
"email": vcard.term("hasEmail"),
"name": vcard.term("hasFN"),
"postcode": vcard.term("postal-code"),
"street": vcard.term("street-address"),
"tel": vcard.term("hasTelephone"),
}
addressObject = BNode()
# Address has either type Home or Work
if address.has_key("addr") and address["addr"] is not None:
self.g.add((addressObject, RDF.type, vcard.term("Work")))
else:
self.g.add((addressObject, RDF.type, vcard.term("Home")))
# Add the address values
for key, val in address.iteritems():
if addressTermsMap.has_key(key):
self.g.add((addressObject, addressTermsMap[key], Literal(val)))
return (vcard.hasAddress, addressObject)
def data_make_address(self, address):
addressTermsMap = {
"addr": RDFS.term("label"),
"city": vcard.locality,
"country": vcard.term("country-name"),
"county": vcard.term("country-name"),
"email": vcard.term("hasEmail"),
"name": vcard.term("hasFN"),
"postcode": vcard.term("postal-code"),
"street": vcard.term("street-address"),
"tel": vcard.term("hasTelephone")
}
addressObject = BNode()
# Address has either type Home or Work
if address.has_key('addr') and address['addr'] is not None:
self.g.add((addressObject, RDF.type, vcard.term("Work")))
else:
self.g.add((addressObject, RDF.type, vcard.term("Home")))
# Add the address values
for key, val in address.iteritems():
if addressTermsMap.has_key(key):
self.g.add((addressObject, addressTermsMap[key], Literal(val)))
return (vcard.hasAddress, addressObject)
def get_jsonld_context() -> List[dict]:
"""
Get JSON-LD context for the whole namespace. Ignores namespaces in _internal.
English language only.
Returns:
List[dict]. Example below.
```
context = [
{"@foaf": "http://xmlns.com/foaf/0.1/", "@language": "en"},
{"@sdo": "https://schema.org/", "@language": "en"},
{"@owl": "http://www.w3.org/2002/07/owl#", "@language": "en"},
{"@xsd": "http://www.w3.org/2001/XMLSchema#", "@language": "en"},
{"@wd": "http://www.wikidata.org/entity/", "@language": "en"},
{"@wdt": "http://www.wikidata.org/prop/direct/", "@language": "en"},
{"@prov": "http://www.w3.org/ns/prov#", "@language": "en"},
{"@rdfs": "http://www.w3.org/2000/01/rdf-schema#", "@language": "en"},
{"@skos": "http://www.w3.org/2004/02/skos/core#", "@language": "en"},
]
```
"""
context = [
{
"@xsd": XSD.__str__(),
"@language": "en"
},
{
"@foaf": FOAF.__str__(),
"@language": "en"
},
{
"@owl": OWL.__str__(),
"@language": "en"
},
{
"@rdf": RDF.__str__(),
"@language": "en"
},
{
"@rdfs": RDFS.__str__(),
"@language": "en"
},
{
"@prov": PROV.__str__(),
"@language": "en"
},
{
"@sdo": SDO.__str__(),
"@language": "en"
},
{
"@skos": SKOS.__str__(),
"@language": "en"
},
{
"@wd": WD.__str__(),
"@language": "en"
},
{
"@wdt": WDT.__str__(),
"@language": "en"
},
{
"@hc": HC.__str__(),
"@language": "en"
},
]
return context
class ClosedConstraintComponent(ConstraintComponent):
"""
The RDF data model offers a huge amount of flexibility. Any node can in principle have values for any property. However, in some cases it makes sense to specify conditions on which properties can be applied to nodes. The SHACL Core language includes a property called sh:closed that can be used to specify the condition that each value node has values only for those properties that have been explicitly enumerated via the property shapes specified for the shape via sh:property.
Link:
https://www.w3.org/TR/shacl/#InConstraintComponent
Textual Definition:
If $closed is true then there is a validation result for each triple that has a value node as its subject and a predicate that is not explicitly enumerated as a value of sh:path in any of the property shapes declared via sh:property at the current shape. If $ignoredProperties has a value then the properties enumerated as members of this SHACL list are also permitted for the value node. The validation result MUST have the predicate of the triple as its sh:resultPath, and the object of the triple as its sh:value.
"""
ALWAYS_IGNORE = {(RDF_type, RDFS.term('Resource'))}
def __init__(self, shape):
super(ClosedConstraintComponent, self).__init__(shape)
sg = self.shape.sg.graph
closed_vals = list(self.shape.objects(SH_closed))
if len(closed_vals) < 1:
raise ConstraintLoadError(
"ClosedConstraintComponent must have at least one sh:closed predicate.",
"https://www.w3.org/TR/shacl/#ClosedConstraintComponent")
elif len(closed_vals) > 1:
raise ConstraintLoadError(
"ClosedConstraintComponent must have at most one sh:closed predicate.",
"https://www.w3.org/TR/shacl/#ClosedConstraintComponent")
assert isinstance(
closed_vals[0],
rdflib.Literal), "sh:closed must take a xsd:boolean literal."
self.is_closed = bool(closed_vals[0].value)
ignored_vals = list(self.shape.objects(SH_ignoredProperties))
self.ignored_props = set()
for i in ignored_vals:
try:
items = set(sg.items(i))
for list_item in items:
self.ignored_props.add(list_item)
except ValueError:
continue
self.property_shapes = list(self.shape.objects(SH_property))
@classmethod
def constraint_parameters(cls):
return [SH_closed, SH_ignoredProperties]
@classmethod
def constraint_name(cls):
return "ClosedConstraintComponent"
@classmethod
def shacl_constraint_class(cls):
return SH_ClosedConstraintComponent
def evaluate(self, target_graph, focus_value_nodes):
"""
:type focus_value_nodes: dict
:type target_graph: rdflib.Graph
"""
reports = []
non_conformant = False
if not self.is_closed:
return True, []
working_shapes = set()
for p_shape in self.property_shapes:
property_shape = self.shape.get_other_shape(p_shape)
if not property_shape or not property_shape.is_property_shape:
raise ReportableRuntimeError(
"The shape pointed to by sh:property does "
"not exist, or is not a well defined SHACL PropertyShape.")
working_shapes.add(property_shape)
working_paths = set()
for w in working_shapes:
p = w.path()
if p:
working_paths.add(p)
for f, value_nodes in focus_value_nodes.items():
for v in value_nodes:
pred_obs = target_graph.predicate_objects(v)
for p, o in pred_obs:
if (p, o) in self.ALWAYS_IGNORE:
continue
elif p in self.ignored_props:
continue
elif p in working_paths:
continue
non_conformant = True
rept = self.make_v_result(target_graph,
f,
value_node=o,
result_path=p)
reports.append(rept)
return (not non_conformant), reports
def main():
# Parse Swift book to retrieve concepts and related resources
start = "https://docs.swift.org/swift-book/"
nextURL = start
urls = [nextURL]
concepts = {}
while nextURL:
url = nextURL
page = urlopen(url)
soup = BeautifulSoup(page, 'html.parser')
#title = soup.find('title').string
article = soup.select_one('article.page')
headings = article.find_all(re.compile('^h[1-6]$'))
for heading in headings:
heading_text = str(heading.contents[0]).lower()
permalink = url + heading.contents[1].get('href')
doc = nlp(heading_text)
noun_phrases = [chunk for chunk in doc.noun_chunks]
if len(noun_phrases) > 0:
new_concepts = [lemmatize(lstrip_stopwords(chunk)).strip() for chunk in noun_phrases]
else:
# if no noun-phrases, take as verbatim (e.g. break, continue)
new_concepts = [heading_text]
for c in new_concepts:
if c not in concepts:
concepts[c] = []
if permalink not in concepts[c]:
# optionally: don't add if permalink (apart from fragment) is already contained (to avoid reindexing the same page multiple times, as a concept like "Function" might appear many times on its dedicated page in different headers)
if not page_included(permalink, concepts[c]):
concepts[c].append(permalink)
# continue to next page (if any)
nextLink = soup.select_one("p.next a")
if nextLink:
parts = urlsplit(nextURL)
base_path, _ = split(parts.path)
base_url = urlunsplit((parts.scheme, parts.netloc, join(base_path, ""), parts.query, parts.fragment))
nextURL = urljoin(base_url, nextLink.get('href'))
urls.append(nextURL)
else:
nextURL = None
# RDF Graph creation
g = Graph()
# Namespace bindings
NS = Namespace(ALMA_NS + SCHEME_NAME + "#")
DBPEDIA = Namespace('http://dbpedia.org/page/')
g.namespace_manager.bind('owl', OWL)
g.namespace_manager.bind('skos', SKOS)
g.namespace_manager.bind('dct', DCTERMS)
g.namespace_manager.bind('foaf', FOAF)
g.namespace_manager.bind('dbr', DBPEDIA)
g.namespace_manager.bind(SCHEME_NAME, NS)
# Ontology Metadata
ontology = URIRef(ALMA_NS + SCHEME_NAME)
g.add((ontology, RDF.type, OWL.term("Ontology")))
g.add((ontology, DCTERMS.term("title"), Literal("{} Ontology".format(SCHEME_NAME.title()))))
g.add((ontology, DCTERMS.term("description"), Literal("This is an SKOS-based lightweight ontology about the Swift programming language.")))
g.add((ontology, DCTERMS.term("subject"), URIRef(quote("http://dbpedia.org/page/Swift_(programming_language)"))))
g.add((ontology, DCTERMS.term("license"), URIRef("https://creativecommons.org/licenses/by-sa/4.0/")))
g.add((ontology, DCTERMS.term("created"), Literal(DATE_CREATED)))
g.add((ontology, DCTERMS.term("modified"), Literal(DATE_MODIFIED)))
g.add((ontology, RDFS.term("seeAlso"), URIRef("https://coast.uni.lu/alma/")))
g.add((ontology, OWL.term("versionIRI"), URIRef("http://purl.org/lu/uni/alma/{}/{}".format(SCHEME_NAME, LANGUAGE_VERSION))))
g.add((ontology, OWL.term("versionInfo"), Literal("{}/{}".format(LANGUAGE_VERSION, ONTOLOGY_VERSION))))
g.add((ontology, OWL.term("imports"), URIRef("http://www.w3.org/2004/02/skos/core")))
creator = BNode()
g.add((ontology, DCTERMS.term("creator"), creator))
g.add((creator, RDF.type, FOAF.term("Person")))
g.add((creator, FOAF.term("name"), Literal(AUTHOR_NAME)))
g.add((creator, FOAF.term("mbox"), URIRef(AUTHOR_EMAIL)))
# Concept Scheme
schemeURI = NS.term("Scheme")
g.add((schemeURI, RDF.type, SKOS.term("ConceptScheme")))
g.add((schemeURI, DCTERMS.term("title"), Literal(SCHEME_NAME.title())))
# Concepts
for (concept, urls) in concepts.items():
conceptURI = NS.term(cleanse(concept))
prefLabel = concept.title()
g.add((conceptURI, RDF.type, SKOS.term("Concept")))
g.add((conceptURI, RDF.type, OWL.term("NamedIndividual")))
g.add((conceptURI, SKOS.term("inScheme"), schemeURI))
g.add((conceptURI, SKOS.term("prefLabel"), Literal(prefLabel, lang='en')))
# Resources from Swift book
for url in urls:
g.add((conceptURI, SKOS.term("definition"), URIRef(url)))
# Serialization
for (format, file_extension) in SERIALIZATION_FORMATS.items():
file_name = "{}_{}_{}.{}".format(SCHEME_NAME, LANGUAGE_VERSION, ONTOLOGY_VERSION, file_extension)
g.serialize(format=format, destination=file_name)
print("Saved under {}".format(file_name))
print("# triples:", len(g))
def _init_ontology(self):
# ---------------------- basic vocabulary elements --------------------
self.xsd_nnint = XSD.term('nonNegativeInteger')
self.xsd_int = XSD.term('integer')
self.xsd_bool = XSD.term('boolean')
self.xsd_double = XSD.term('double')
a = RDF.term('type')
rdfs_dom = RDFS.term('domain')
rdfs_rnge = RDFS.term('range')
rdfs_subcls_of = RDFS.term('subClassOf')
owl_class = OWL.term('Class')
owl_dtype_prop = OWL.term('DatatypeProperty')
owl_obj_prop = OWL.term('ObjectProperty')
# --------------------------- basic classes ---------------------------
# dllont:Molecule
self.cls_molecule = URIRef(self._ont_uri_prefix + 'Molecule')
self._g.add((self.cls_molecule, a, owl_class))
# dllont:Atom
self.cls_atom = URIRef(self._ont_uri_prefix + 'Atom')
self._g.add((self.cls_atom, a, owl_class))
# dllont:AtomSymbol
self.cls_atom_symbol = URIRef(self._ont_uri_prefix + 'AtomSymbol')
self._g.add((self.cls_atom_symbol, a, owl_class))
# ----------------- atom stereo parity class hierarchy ----------------
# dllont:AtomParity
cls_atom_parity = URIRef(self._ont_uri_prefix + 'AtomParity')
self._g.add((cls_atom_parity, a, owl_class))
# dllont:AtomParityNotStereo, dllont:AtomParityOdd,
# dllont:AtomParityEven, dllont:AtomParityEitherOrUnmarkedStereoCenter
for val in atom_stereo_parity_mapping.values():
cls = self._get_cls_uri(
self._atom_stereo_parity_type_to_cls_local_part, val)
self._g.add((cls, a, owl_class))
self._g.add((cls, rdfs_subcls_of, cls_atom_parity))
# ----------------- hydrogen count resources and class ----------------
# dllont:HydrogenCount
self.cls_hydrogen_count = \
URIRef(self._ont_uri_prefix + 'HydrogenCount')
self._g.add((self.cls_hydrogen_count, a, owl_class))
for val in hydrogen_count_mapping.values():
if val is not None:
hc_res = URIRef(self._resource_uri_prefix + val.lower())
self._g.add((hc_res, a, self.cls_hydrogen_count))
# ------------------------ bond class hierarchy -----------------------
# dllont:Bond
self.cls_bond = URIRef(self._ont_uri_prefix + 'Bond')
self._g.add((self.cls_bond, a, owl_class))
# dllont:SingleBond, dllont:DoubleBond, dllont:TripleBond,
# dllont:AromaticBond, dllont:SingleOrDoubleBond,
# dllont:SingleOrAromaticBond, dllont:DoubleOrAromaticBond
for val in bond_type_mapping.values():
bond_cls = self._get_bond_cls_uri(val)
self._g.add((bond_cls, a, owl_class))
for sdf_type in self._bond_type_to_cls_local_part[val][1]:
super_cls = self._get_bond_cls_uri(sdf_type)
self._g.add((bond_cls, rdfs_subcls_of, super_cls))
# ------------------- bond isomerism class hierarchy ------------------
# dllont:NonStereoBond
non_st_bond_cls = self._get_cls_uri(
self._bond_stereo_to_cls_local_part, 'Not stereo')
self._g.add((non_st_bond_cls, a, owl_class))
self._g.add((non_st_bond_cls, rdfs_subcls_of, self.cls_bond))
# dllont:SingleBondEitherUpOrDownStereochemistry
either_up_or_down_cls = self._get_cls_uri(
self._bond_stereo_to_cls_local_part, 'Either')
self._g.add((either_up_or_down_cls, a, owl_class))
self._g.add((
either_up_or_down_cls,
rdfs_subcls_of,
self._get_bond_cls_uri('Single')
))
# dllont:SingleBondUpStereochemistry
up_stereo_cls = self._get_cls_uri(
self._bond_stereo_to_cls_local_part, 'Up')
self._g.add((up_stereo_cls, a, owl_class))
self._g.add((up_stereo_cls, rdfs_subcls_of, either_up_or_down_cls))
# dllont:SingleBondDownStereochemistry
down_stereo_cls = self._get_cls_uri(
self._bond_stereo_to_cls_local_part, 'Down')
self._g.add((down_stereo_cls, a, owl_class))
self._g.add((down_stereo_cls, rdfs_subcls_of, either_up_or_down_cls))
cls_double_bond = self._get_bond_cls_uri('Double')
# dllont:DoubleBondDeriveCisOrTransIsomerismFromXYZCoords
derive_iso_cls = self._get_cls_uri(
self._bond_stereo_to_cls_local_part,
'Use x-, y-, z-coords from atom block to determine cis or trans')
self._g.add((derive_iso_cls, a, owl_class))
self._g.add((derive_iso_cls, rdfs_subcls_of, cls_double_bond))
# dllont:DoubleBondEitherCisOrTransIsomerism
cis_or_trans_cls = self._get_cls_uri(
self._bond_stereo_to_cls_local_part,
'Either cis or trans double bond')
self._g.add((cis_or_trans_cls, a, owl_class))
self._g.add((cis_or_trans_cls, rdfs_subcls_of, cls_double_bond))
# -------------------------- topology classes -------------------------
# dllont:BondTopology
topology_cls = URIRef(self._ont_uri_prefix + 'BondTopology')
self._g.add((topology_cls, a, owl_class))
# dllont:EitherRingOrChainTopology
either_topo_cls = self._get_cls_uri(
self._bond_topology_to_cls_local_part, 'Either')
self._g.add((either_topo_cls, a, owl_class))
self._g.add((either_topo_cls, rdfs_subcls_of, topology_cls))
# dllont:RingTopology
ring_topo_cls = self._get_cls_uri(
self._bond_topology_to_cls_local_part, 'Ring')
self._g.add((ring_topo_cls, a, owl_class))
self._g.add((ring_topo_cls, rdfs_subcls_of, either_topo_cls))
# dllont:ChainTopology
chain_topo_cls = self._get_cls_uri(
self._bond_topology_to_cls_local_part, 'Chain')
self._g.add((chain_topo_cls, a, owl_class))
self._g.add((chain_topo_cls, rdfs_subcls_of, either_topo_cls))
# --------------- reacting center status class hierarchy --------------
# dllont:ReactingCenterStatus
react_center_status_cls = URIRef(
self._ont_uri_prefix + 'ReactingCenterStatus')
self._g.add((react_center_status_cls, a, owl_class))
# dllont:Unmarked
react_unmarked_cls = self._get_cls_uri(
self._reacting_center_status_to_cls_local_part, 'unmarked')
self._g.add((react_unmarked_cls, a, owl_class))
self._g.add(
(react_unmarked_cls, rdfs_subcls_of, react_center_status_cls))
# dllont:ACenter
react_a_center_cls = self._get_cls_uri(
self._reacting_center_status_to_cls_local_part, 'a center')
self._g.add((react_a_center_cls, a, owl_class))
self._g.add(
(react_a_center_cls, rdfs_subcls_of, react_center_status_cls))
# dllont:NotACenter
react_not_a_center_cls = self._get_cls_uri(
self._reacting_center_status_to_cls_local_part, 'not a center')
self._g.add((react_not_a_center_cls, a, owl_class))
self._g.add(
(react_not_a_center_cls, rdfs_subcls_of, react_center_status_cls))
self._g.add((
react_a_center_cls,
OWL.term('disjointWith'),
react_not_a_center_cls
))
# dllont:NoChange
react_no_change_cls = self._get_cls_uri(
self._reacting_center_status_to_cls_local_part, 'no change')
self._g.add((react_no_change_cls, a, owl_class))
self._g.add(
(react_no_change_cls, rdfs_subcls_of, react_center_status_cls))
# FIXME: add class intersections
# dllont:BondMadeOrBroken
react_bond_made_or_broken_cls = self._get_cls_uri(
self._reacting_center_status_to_cls_local_part, 'bond made/broken')
self._g.add((react_bond_made_or_broken_cls, a, owl_class))
self._g.add((
react_bond_made_or_broken_cls,
rdfs_subcls_of,
react_center_status_cls
))
# dllont:BondOrderChanges
react_bond_order_change_cls = self._get_cls_uri(
self._reacting_center_status_to_cls_local_part,
'bond order changes')
self._g.add((react_bond_order_change_cls, a, owl_class))
self._g.add((
react_bond_order_change_cls,
rdfs_subcls_of,
react_center_status_cls
))
# dllont:BondMadeOrBrokenAndBondOrderChanges
react_bmob_and_boc_cls = self._get_cls_uri(
self._reacting_center_status_to_cls_local_part,
'bond made/broken + bond order changes')
self._g.add((react_bmob_and_boc_cls, a, owl_class))
self._g.add((
react_bmob_and_boc_cls,
rdfs_subcls_of,
react_bond_made_or_broken_cls
))
self._g.add((
react_bmob_and_boc_cls,
rdfs_subcls_of,
react_bond_order_change_cls
))
# dllont:BondMadeOrBrokenAndACenter
react_bmob_and_a_center_cls = self._get_cls_uri(
self._reacting_center_status_to_cls_local_part,
'bond made/broken + a center')
self._g.add((react_bmob_and_a_center_cls, a, owl_class))
self._g.add((
react_bmob_and_a_center_cls,
rdfs_subcls_of,
react_bond_made_or_broken_cls
))
self._g.add((
react_bmob_and_a_center_cls,
rdfs_subcls_of,
react_a_center_cls
))
# dllont:BondMadeOrBrokenAndBondOrderChangesAndACenter
react_bmob_and_boc_and_a_center_cls = self._get_cls_uri(
self._reacting_center_status_to_cls_local_part,
'bond made/broken + bond order changes + a center')
self._g.add((react_bmob_and_boc_and_a_center_cls, a, owl_class))
self._g.add((
react_bmob_and_boc_and_a_center_cls,
rdfs_subcls_of,
react_bmob_and_boc_cls
))
self._g.add((
react_bmob_and_boc_and_a_center_cls,
rdfs_subcls_of,
react_bmob_and_a_center_cls
))
self._g.add((
react_bmob_and_boc_and_a_center_cls,
rdfs_subcls_of,
react_a_center_cls
))
# ------------------------ property definitions -----------------------
# dllont:number_of_atoms
self.prop_num_atoms = \
URIRef(self._ont_uri_prefix + 'number_of_atoms')
self._g.add((self.prop_num_atoms, a, owl_dtype_prop))
self._g.add((self.prop_num_atoms, rdfs_dom, self.cls_molecule))
self._g.add((self.prop_num_atoms, rdfs_rnge, self.xsd_nnint))
# dllont:number_of_bounds
self.prop_num_bounds = \
URIRef(self._ont_uri_prefix + 'number_of_bounds')
self._g.add((self.prop_num_bounds, a, owl_dtype_prop))
self._g.add((self.prop_num_bounds, rdfs_dom, self.cls_molecule))
self._g.add((self.prop_num_bounds, rdfs_rnge, self.xsd_nnint))
# dllont:number_of_atom_lists
self.prop_num_atom_lists = URIRef(
self._ont_uri_prefix + 'number_of_atom_lists')
self._g.add((self.prop_num_atom_lists, a, owl_dtype_prop))
self._g.add((self.prop_num_atom_lists, rdfs_dom, self.cls_molecule))
self._g.add((self.prop_num_atom_lists, rdfs_rnge, self.xsd_nnint))
# dllont:molecule_is_chiral
self.prop_molec_is_chiral = URIRef(
self._ont_uri_prefix + 'molecule_is_chiral')
self._g.add((self.prop_molec_is_chiral, a, owl_dtype_prop))
self._g.add((self.prop_molec_is_chiral, rdfs_dom, self.cls_molecule))
self._g.add((self.prop_molec_is_chiral, rdfs_rnge, self.xsd_bool))
# dllont:atom
self.prop_atom = URIRef(self._ont_uri_prefix + 'atom')
self._g.add((self.prop_atom, a, owl_obj_prop))
self._g.add((self.prop_atom, rdfs_dom, self.cls_molecule))
self._g.add((self.prop_atom, rdfs_rnge, self.cls_atom))
# dllont:atom_number
self.prop_atom_number = URIRef(self._ont_uri_prefix + 'atom_number')
self._g.add((self.prop_atom_number, a, owl_dtype_prop))
self._g.add((self.prop_atom_number, rdfs_dom, self.cls_atom))
self._g.add((self.prop_atom_number, rdfs_rnge, self.xsd_nnint))
# dllont:atom_coordinate_x
self.prop_coord_x = URIRef(self._ont_uri_prefix + 'atom_coordinate_x')
self._g.add((self.prop_coord_x, a, owl_dtype_prop))
self._g.add((self.prop_coord_x, rdfs_dom, self.cls_atom))
self._g.add((self.prop_coord_x, rdfs_rnge, self.xsd_double))
# dllont:atom_coordinate_y
self.prop_coord_y = URIRef(self._ont_uri_prefix + 'atom_coordinate_y')
self._g.add((self.prop_coord_y, a, owl_dtype_prop))
self._g.add((self.prop_coord_y, rdfs_dom, self.cls_atom))
self._g.add((self.prop_coord_y, rdfs_rnge, self.xsd_double))
# dllont:atom_coordinate_z
self.prop_coord_z = URIRef(self._ont_uri_prefix + 'atom_coordinate_z')
self._g.add((self.prop_coord_z, a, owl_dtype_prop))
self._g.add((self.prop_coord_z, rdfs_dom, self.cls_atom))
self._g.add((self.prop_coord_z, rdfs_rnge, self.xsd_double))
# dllont:atom_symbol
self.prop_atom_symbol = URIRef(self._ont_uri_prefix + 'atom_symbol')
self._g.add((self.prop_atom_symbol, a, owl_obj_prop))
self._g.add((self.prop_atom_symbol, rdfs_dom, self.cls_atom))
self._g.add((self.prop_atom_symbol, rdfs_rnge, self.cls_atom_symbol))
# dllont:mass_difference
self.prop_mass_difference = URIRef(
self._ont_uri_prefix + 'mass_difference')
self._g.add((self.prop_mass_difference, a, owl_dtype_prop))
self._g.add((self.prop_mass_difference, rdfs_dom, self.cls_atom))
self._g.add((self.prop_mass_difference, rdfs_rnge, self.xsd_double))
# dllont:charge
self.prop_charge = URIRef(self._ont_uri_prefix + 'charge')
self._g.add((self.prop_charge, a, owl_dtype_prop))
self._g.add((self.prop_charge, rdfs_dom, self.cls_atom))
self._g.add((self.prop_charge, rdfs_rnge, self.xsd_int))
# dllont:hydrogen_count
self.prop_hydrogen_count = URIRef(
self._ont_uri_prefix + 'hydrogen_count')
self._g.add((self.prop_hydrogen_count, a, owl_obj_prop))
self._g.add((self.prop_hydrogen_count, rdfs_dom, self.cls_atom))
self._g.add(
(self.prop_hydrogen_count, rdfs_rnge, self.cls_hydrogen_count))
# dllont:valence
self.prop_valence = URIRef(self._ont_uri_prefix + 'valence')
self._g.add((self.prop_valence, a, owl_dtype_prop))
self._g.add((self.prop_valence, rdfs_dom, self.cls_atom))
self._g.add((self.prop_valence, rdfs_rnge, self.xsd_nnint))
# dllont:h_atoms_allowed
self.prop_h_atoms_allowed = URIRef(
self._ont_uri_prefix + 'h_atoms_allowed')
self._g.add((self.prop_h_atoms_allowed, a, owl_dtype_prop))
self._g.add((self.prop_h_atoms_allowed, rdfs_dom, self.cls_atom))
self._g.add((self.prop_h_atoms_allowed, rdfs_rnge, self.xsd_bool))
# dllont:atom-atom_mapping_number
self.prop_atom_atom_mapping_nr = URIRef(
self._ont_uri_prefix + 'atom-atom_mapping_number')
self._g.add((self.prop_atom_atom_mapping_nr, a, owl_dtype_prop))
self._g.add((self.prop_atom_atom_mapping_nr, rdfs_dom, self.cls_atom))
self._g.add(
(self.prop_atom_atom_mapping_nr, rdfs_rnge, self.xsd_nnint))
# dllont:has_binding_with
self.prop_has_binding_with = URIRef(
self._ont_uri_prefix + 'has_binding_with')
self._g.add((
self.prop_has_binding_with,
a,
URIRef(OWL.term('SymmetricProperty'))
))
self._g.add((self.prop_has_binding_with, rdfs_dom, self.cls_atom))
self._g.add((self.prop_has_binding_with, rdfs_rnge, self.cls_atom))
# dllont:first_bound_atom
self.prop_first_bound_atom = URIRef(
self._ont_uri_prefix + 'first_bound_atom')
self._g.add((self.prop_first_bound_atom, a, owl_obj_prop))
self._g.add((self.prop_first_bound_atom, rdfs_dom, self.cls_bond))
self._g.add((self.prop_first_bound_atom, rdfs_rnge, self.cls_atom))
# dllont:second_bound_atom
self.prop_second_bound_atom = URIRef(
self._ont_uri_prefix + 'second_bound_atom')
self._g.add((self.prop_second_bound_atom, a, owl_obj_prop))
self._g.add((self.prop_second_bound_atom, rdfs_dom, self.cls_bond))
self._g.add((self.prop_second_bound_atom, rdfs_rnge, self.cls_atom))
# dllont:has_topology
self.prop_has_topology = URIRef(self._ont_uri_prefix + 'has_topology')
self._g.add((self.prop_has_topology, a, owl_obj_prop))
self._g.add((self.prop_has_topology, rdfs_dom, self.cls_bond))
self._g.add((self.prop_has_topology, rdfs_rnge, topology_cls))
# dllont:has_reacting_center_status
self.prop_has_rc_status = URIRef(
self._ont_uri_prefix + 'has_reacting_center_status')
self._g.add((self.prop_has_rc_status, a, owl_obj_prop))
self._g.add((self.prop_has_rc_status, rdfs_dom, self.cls_bond))
self._g.add(
(self.prop_has_rc_status, rdfs_rnge, react_center_status_cls))
