changed PointEnum to an is_lattice boolean

cadnano/document.py

@@ -745,7 +745,7 @@ def setViewNames(self, view_name_list: List[str], do_clear: bool = False):
     def createNucleicAcidPart(  self,
                                 use_undostack: bool = True,
                                 grid_type: EnumType = GridEnum.NONE,
-                                point_type: EnumType = PointEnum.Z_ONLY
+                                is_lattice: bool = True
                             ) -> NucleicAcidPart:
         """Create and store a new DnaPart and instance, and return the instance.
 
@@ -756,7 +756,7 @@ def createNucleicAcidPart(  self,
         Returns
             new :obj:`NucleicAcidPart`
         """
-        dna_part = NucleicAcidPart(document=self, grid_type=grid_type, point_type=point_type)
+        dna_part = NucleicAcidPart(document=self, grid_type=grid_type, is_lattice=is_lattice)
         self._addPart(dna_part, use_undostack=use_undostack)
         return dna_part
     # end def

cadnano/fileio/c25decode.py

@@ -62,12 +62,16 @@ def decode(document: DocT, obj: dict, emit_signals: bool = True):
     if lattice_type == LatticeEnum.HONEYCOMB:
         doLattice = HoneycombDnaPart.latticeCoordToModelXY
         isEven = HoneycombDnaPart.isEvenParity
+        grid_type = GridEnum.HONEYCOMB
     elif lattice_type == LatticeEnum.SQUARE:
         doLattice = SquareDnaPart.latticeCoordToModelXY
         isEven = SquareDnaPart.isEvenParity
+        grid_type = GridEnum.SQUARE
     else:
         raise TypeError("Lattice type not recognized")
-    part = document.createNucleicAcidPart(use_undostack=False)
+    part = document.createNucleicAcidPart(  use_undostack=False,
+                                            is_lattice=True,
+                                            grid_type=grid_type)
     part.setActive(True)
     setBatch(True)
     # POPULATE VIRTUAL HELICES

cadnano/fileio/v2decode.py

@@ -59,7 +59,9 @@ def decode(document: DocT, obj: dict, emit_signals: bool = True):
         isEven = SquareDnaPart.isEvenParity
     else:
         raise TypeError("Lattice type not recognized")
-    part = document.createNucleicAcidPart(grid_type=grid_type, use_undostack=False)
+    part = document.createNucleicAcidPart(  grid_type=grid_type,
+                                            is_lattice=True,
+                                            use_undostack=False)
     part.setActive(True)
     document.setGridType(grid_type)
     # document.setSliceOrGridViewVisible(OrthoViewEnum.SLICE)

cadnano/fileio/v3decode.py

@@ -143,15 +143,23 @@ def decodePart( document: DocT,
         grid_type:
         emit_signals:
     """
-    part = document.createNucleicAcidPart(use_undostack=False, grid_type=grid_type)
+    if ( part_dict.get('point_type') == PointEnum.ARBITRARY or
+        not part_dict.get('is_lattice', True) ):
+        is_lattice = False
+    else:
+        is_lattice = True
+
+    part = document.createNucleicAcidPart(  use_undostack=False,
+                                            is_lattice=is_lattice,
+                                            grid_type=grid_type)
     part.setActive(True)
 
     vh_id_list = part_dict.get('vh_list')
     vh_props = part_dict.get('virtual_helices')
     origins = part_dict.get('origins')
     keys = list(vh_props.keys())
 
-    if part_dict.get('point_type') == PointEnum.ARBITRARY:
+    if not is_lattice:
         # TODO add code to deserialize parts
         pass
     else:

cadnano/fileio/v3encode.py

@@ -46,7 +46,7 @@ def encodePart(part: PartT) -> dict:
     # iterate through virtualhelix list
     group_props = part.getModelProperties().copy()
 
-    if group_props.get('point_type') == PointEnum.ARBITRARY:
+    if not group_props.get('is_lattice', True):
         # TODO add code to encode Parts with ARBITRARY point configurations
         pass
     else:
@@ -96,7 +96,7 @@ def reEmitPart(part: PartT):
     # iterate through virtualhelix list
     group_props = part.getModelProperties().copy()
 
-    if group_props.get('point_type') == PointEnum.ARBITRARY:
+    if not group_props.get('is_lattice', True):
         # TODO add code to encode Parts with ARBITRARY point configurations
         pass
     else:
@@ -175,7 +175,7 @@ def encodePartList(part_instance: ObjectInstance, vh_group_list: List[int]) -> d
     group_props = part.getModelProperties().copy()
     assert('grid_type' in group_props)
 
-    if group_props.get('point_type') == PointEnum.ARBITRARY:
+    if not group_props.get('is_lattice', True):
         # TODO add code to encode Parts with ARBITRARY point configurations
         pass
     else:

cadnano/part/nucleicacidpart.py

@@ -164,12 +164,12 @@ def __init__(self, *args, **kwargs):
             uuid: str
             do_copy
             grid_type
-            point_type
+            is_lattice
         '''
         super(NucleicAcidPart, self).__init__(*args, **kwargs)
         do_copy: bool = kwargs.get('do_copy', False)
         grid_type: EnumType = kwargs.get('grid_type', GridEnum.NONE)
-        point_type: EnumType = kwargs.get('point_type', PointEnum.Z_ONLY)
+        is_lattice: EnumType = kwargs.get('is_lattice', True)
 
         if do_copy:
             return
@@ -216,7 +216,7 @@ def __init__(self, *args, **kwargs):
         gps['neighbor_active_angle'] = ''
         gps['grid_type'] = grid_type
         gps['virtual_helix_order'] = []
-        gps['point_type'] = point_type
+        gps['is_lattice'] = is_lattice
 
         ############################
         # Begin low level attributes
@@ -2394,7 +2394,7 @@ def isZEditable(self) -> bool:
         Returns:
             ``True`` or ``False``
         """
-        return self._group_properties['point_type'] == PointEnum.Z_ONLY
+        return self._group_properties['is_lattice'] == True
     # end def
 
     def getVirtualHelicesInArea(self, rect: RectT) -> Set[int]:

cadnano/proxies/cnenum.py

@@ -57,6 +57,9 @@ class PartEnum(IntEnum):
 class PointEnum(IntEnum):
     """For serializing virtual helices as only pointing in the Z direction
     or pointing in arbitrary directions.
+
+    NOTE: This exists for legacy part importing of lattice designs when moving
+    towards the v3 file convention
     """
     Z_ONLY = 0
     ARBITRARY = 1

cadnano/tests/nucleicacidparttest.py

@@ -8,7 +8,7 @@
 
 
 def create3Helix(doc, direction, length):
-    part = doc.createNucleicAcidPart()
+    part = doc.createNucleicAcidPart(is_lattice=True)
     assert len(part.getidNums()) == 0
     radius = part.radius()
     origin_pt00 = (0, 0, 0)

cadnano/views/cnmainwindow.py

@@ -961,20 +961,27 @@ def actionCreateNucleicAcidPartHoneycomb(self) -> NucleicAcidPartT:
         # TODO[NF]:  Docstring
         return self.actionCreateNucleicAcidPart(
             grid_type=GridEnum.HONEYCOMB,
-            point_type=PointEnum.Z_ONLY
+            is_lattice=True
         )
 
     def actionCreateNucleicAcidPartSquare(self) -> NucleicAcidPartT:
         # TODO[NF]:  Docstring
         return self.actionCreateNucleicAcidPart(
             grid_type=GridEnum.SQUARE,
-            point_type=PointEnum.Z_ONLY
+            is_lattice=True
         )
 
     def actionCreateNucleicAcidPart(self,
             grid_type: EnumType,
-            point_type: EnumType = PointEnum.ARBITRARY) -> NucleicAcidPartT:
-        # TODO[NF]:  Docstring
+            is_lattice: bool = False) -> NucleicAcidPartT:
+        '''
+        Args:
+            grid_type:
+            is_lattice: defaults to False, aka freeform
+
+        Returns:
+            the part created
+        '''
         if ONLY_ONE:
             if len(self._document.children()) is not 0:
                 if self.promptSaveDialog() is SAVE_DIALOG_OPTIONS['CANCEL']:
@@ -983,7 +990,7 @@ def actionCreateNucleicAcidPart(self,
         doc = self._document
         part = doc.createNucleicAcidPart(   use_undostack=True,
                                             grid_type=grid_type,
-                                            point_type=point_type)
+                                            is_lattice=is_lattice)
         active_part = doc.activePart()
         if active_part is not None:
             active_part.setActive(False)

misc/examples/04_threejs/vhelixpythree.ipynb

@@ -65,7 +65,7 @@
    ],
    "source": [
     "doc = Document()\n",
-    "part = doc.createNucleicAcidPart()\n",
+    "part = doc.createNucleicAcidPart(is_lattice=False)\n",
     "vh_points = [\n",
     "            (2, 0, 0, (0, 0, 1.)),\n",
     "            (-2, 0, 0, (0, 0, 1.)),\n",