Merge pull request #131 from pyscal/add_angle_to_ldo

Add angle to ldo

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.9.0
+current_version = 0.9.1
 commit = True
 tag = False
 

CITATION.cff

@@ -19,4 +19,4 @@ url: 'https://atomrdf.pyscal.org'
 license: "MIT"
 repository-code: https://github.com/pyscal/atomRDF
 type: software
-version: 0.9.0
+version: 0.9.1

atomrdf/data/ldo.owl

@@ -253,6 +253,15 @@
 
 
 
+    <!-- http://purls.helmholtz-metadaten.de/cdos/ldo/hasCharacterAngle -->
+
+    <owl:DatatypeProperty rdf:about="http://purls.helmholtz-metadaten.de/cdos/ldo/hasCharacterAngle">
+        <rdfs:domain rdf:resource="http://purls.helmholtz-metadaten.de/cdos/ldo/MixedDislocation"/>
+        <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#float"/>
+    </owl:DatatypeProperty>
+
+
+
     <!-- http://purls.helmholtz-metadaten.de/cdos/ldo/hasDislocationDensity -->
 
     <owl:DatatypeProperty rdf:about="http://purls.helmholtz-metadaten.de/cdos/ldo/hasDislocationDensity">
@@ -308,6 +317,7 @@
     <!-- http://purls.helmholtz-metadaten.de/cdos/ldo/AngularVector -->
 
     <owl:Class rdf:about="http://purls.helmholtz-metadaten.de/cdos/ldo/AngularVector">
+        <rdfs:subClassOf rdf:resource="http://purls.helmholtz-metadaten.de/cmso/Vector"/>
         <rdfs:label>Angular Vector</rdfs:label>
         <skos:altLabel>Frank Vector</skos:altLabel>
     </owl:Class>
@@ -324,6 +334,14 @@
 
 
 
+    <!-- http://purls.helmholtz-metadaten.de/cdos/ldo/CharacterAngle -->
+
+    <owl:Class rdf:about="http://purls.helmholtz-metadaten.de/cdos/ldo/CharacterAngle">
+        <rdfs:label>Character Angle</rdfs:label>
+    </owl:Class>
+
+
+
     <!-- http://purls.helmholtz-metadaten.de/cdos/ldo/Disclination -->
 
     <owl:Class rdf:about="http://purls.helmholtz-metadaten.de/cdos/ldo/Disclination">
@@ -467,6 +485,15 @@
 
 
 
+    <!-- http://purls.helmholtz-metadaten.de/cmso/Angle -->
+
+    <owl:Class rdf:about="http://purls.helmholtz-metadaten.de/cmso/Angle">
+        <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An angle is a measure of the the space (usually in degrees) between two intersecting lines at the point where they meet or vertex.</obo:IAO_0000115>
+        <rdfs:label>Angle</rdfs:label>
+    </owl:Class>
+
+
+
     <!-- http://purls.helmholtz-metadaten.de/cmso/Vector -->
 
     <owl:Class rdf:about="http://purls.helmholtz-metadaten.de/cmso/Vector">

atomrdf/network/ontology.py

@@ -38,7 +38,7 @@ def read_ontology():
     pldo = OntologyNetwork(os.path.join(file_location, "data/pldo.owl")) #d15d27712e3f64b405d75c70ad970c9d54ff0b51
     podo = OntologyNetwork(os.path.join(file_location, "data/podo.owl")) #6a74d511c5b78042e1cb7a6e76e948fa56de598e
     asmo = OntologyNetwork(os.path.join(file_location, "data/asmo.owl")) #c7e2da99b9126844f19f225c6a10cdb01aeb55e6
-    ldo = OntologyNetwork(os.path.join(file_location, "data/ldo.owl")) #52fc756d2e2f9baedfce478e7f8b790365648cea
+    ldo = OntologyNetwork(os.path.join(file_location, "data/ldo.owl")) #e23fa9930351787e701347878a3e1a0e3924d084
 
     # combine them
     combo = cmso + pldo + podo + asmo + ldo

atomrdf/structure.py

@@ -1973,10 +1973,13 @@ def add_dislocation(self, disl_dict):
         angle_deg = disl_dict['DislocationCharacter']
         if (np.abs(angle_deg-0) < 1E-3) or (np.abs(angle_deg-180) < 1E-3) or (np.abs(angle_deg-360) < 1E-3):
             disl_type = LDO.ScrewDislocation
+            disl_name = "ScrewDislocation"
         elif (np.abs(angle_deg-90) < 1E-3) or (np.abs(angle_deg-270) < 1E-3):
             disl_type = LDO.EdgeDislocation
+            disl_name = "EdgeDislocation"
         else:
             disl_type = LDO.MixedDislocation
+            disl_name = "MixedDislocation"
 
         line_defect = self.graph.create_node(f"{self._name}_Dislocation", disl_type)
         self.graph.add((self.material, CMSO.hasDefect, line_defect))
@@ -1993,6 +1996,8 @@ def add_dislocation(self, disl_dict):
         self.graph.add((burgers_vector, CMSO.hasComponent_z, Literal(disl_dict['BurgersVector'][2], datatype=XSD.float)))
         self.graph.add((line_defect, LDO.hasBurgersVector, burgers_vector))
 
+        self.graph.add((line_defect, LDO.hasCharacterAngle, Literal(angle_deg, datatype=XSD.float)))
+
         slip_direction = self.graph.create_node(f"{self._name}_DislocationSlipDirection", LDO.SlipDirection)
         self.graph.add((slip_direction, CMSO.hasComponent_x, Literal(disl_dict['SlipDirection'][0], datatype=XSD.float)))
         self.graph.add((slip_direction, CMSO.hasComponent_y, Literal(disl_dict['SlipDirection'][1], datatype=XSD.float)))

setup.py

@@ -6,7 +6,7 @@
 
 setup(
     name='atomrdf',
-    version='0.9.0',
+    version='0.9.1',
     author='Abril Azocar Guzman, Sarath Menon',
     author_email='sarath.menon@pyscal.org',
     description='Ontology based structural manipulation and quering',