Update graph.py

pyscal · Jun 27, 2023 · 4c67d53 · 4c67d53
1 parent a785461
commit 4c67d53
Showing 1 changed file with 9 additions and 6 deletions.
diff --git a/pyscal_rdf/graph.py b/pyscal_rdf/graph.py
@@ -534,7 +534,10 @@ def add_atoms(self, name=None):
  """
  self._atom_ids = []
 
- for x in range(len(self.data("Positions"))):
+ positions = self.data("Positions")
+ elements = self.data("Element")
+ coordination = self.data("Coordination")
+ for x in range(len(positions)):
  uname = None
  if name is not None:
  uname = f'{name}_{x}' 
@@ -550,11 +553,11 @@ def add_atoms(self, name=None):
  position = BNode(uname)
  self.add((atom, CMSO.hasPositionVector, position))
  self.add((position, RDF.type, CMSO.PositionVector))
- self.add((position, CMSO.hasComponent_x, Literal(self.data("Positions")[x][0],
+ self.add((position, CMSO.hasComponent_x, Literal(positions[x][0],
  datatype=XSD.float)))
- self.add((position, CMSO.hasComponent_y, Literal(self.data("Positions")[x][1],
+ self.add((position, CMSO.hasComponent_y, Literal(positions[x][1],
  datatype=XSD.float)))
- self.add((position, CMSO.hasComponent_z, Literal(self.data("Positions")[x][2],
+ self.add((position, CMSO.hasComponent_z, Literal(positions[x][2],
  datatype=XSD.float)))
  #now add coordination
  uname = None
@@ -563,10 +566,10 @@ def add_atoms(self, name=None):
  element = BNode(uname)
  self.add((atom, CMSO.hasElement, element))
  self.add((element, RDF.type, CMSO.Element))
- self.add((element, CMSO.hasSymbol, Literal(str(self.data("Element")[x]),
+ self.add((element, CMSO.hasSymbol, Literal(str(elements[x]),
  datatype=XSD.string)))
  #finally occupancy
- self.add((atom, CMSO.hasCoordinationNumber, Literal(self.data("Coordination")[x],
+ self.add((atom, CMSO.hasCoordinationNumber, Literal(coordination[x],
  datatype=XSD.integer)))