updating for organizing obj_model extra_attributes into bio, chem, an…

…d math modules
KarrLab · Dec 19, 2018 · 0ef6231 · 0ef6231
1 parent 94537f8
commit 0ef6231
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Showing 2 changed files with 6 additions and 4 deletions.
diff --git a/wc_rules/attributes.py b/wc_rules/attributes.py
@@ -1,4 +1,5 @@
-from obj_model import core, extra_attributes
+from obj_model import core
+from obj_model import bio
 
 # scalar attributes
 class IdAttribute(core.StringAttribute):
@@ -41,6 +42,6 @@ class OneToManyAttribute(core.OneToManyAttribute):pass
 class ManyToManyAttribute(core.ManyToManyAttribute):pass
 
 # extra_attributes
-class BioSeqAttribute(extra_attributes.BioSeqAttribute):
+class BioSeqAttribute(bio.BioSeqAttribute):
     def __init__(self):
         super().__init__(default=None)
diff --git a/wc_rules/seq.py b/wc_rules/seq.py
@@ -6,15 +6,16 @@
 """
 from . import rete_nodes as rn
 from . import chem, utils
-from obj_model import core,extra_attributes
+from obj_model import core
 import Bio.Seq
 import Bio.Alphabet
+import obj_model.bio
 
 
 class SequenceMolecule(chem.Molecule):
     """ Generic SequenceMolecule (template for DNA, RNA, protein sequence objects) """
 
-    sequence = extra_attributes.BioSeqAttribute()
+    sequence = obj_model.bio.BioSeqAttribute()
     alphabet_dict = { 'strict': None, 'permissive': None }
     use_permissive_alphabet = True
     alphabet = None