moved properties to structures table

saezlab · Nov 22, 2024 · 7894e03 · 7894e03
1 parent 9184864
commit 7894e03
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Showing 2 changed files with 10 additions and 12 deletions.
diff --git a/omnipath_metabo/schema/_main.py b/omnipath_metabo/schema/_main.py
@@ -18,7 +18,7 @@ def create(con):
     Base.metadata.create_all(con.engine)
 
 
-TABLES = {'structures', 'identifiers', 'resources'}
+TABLES = {'structures', 'identifiers', 'resources', 'properties'}
 
 
 class Database:
@@ -90,14 +90,12 @@ def load_all(self):
     def chem_properties_populate(self):
         _log('Querying mol structures', level=-1)
         query = text(r"""
-            UPDATE identifiers
+            UPDATE structures
             SET
-                is_polymer = (structures.inchi ~ '.*\\p.*'),
-                has_conformation = (structures.smiles ~ '.*[\\/]=.*'),
-                has_stereo = (structures.smiles ~ '.*@.*'),
-                complete_formula = NOT (structures.smiles ~ '.*\*.*')
-            FROM structures
-            WHERE identifiers.structure_id = structures.id;
+                is_polymer = (inchi ~ '.*\\p.*'),
+                has_conformation = (smiles ~ '.*[\\/]=.*'),
+                has_stereo = (smiles ~ '.*@.*'),
+                complete_formula = NOT (smiles ~ '.*\*.*')
         """)
         self.con.session.execute(query)
         self.con.session.commit()

diff --git a/omnipath_metabo/schema/_structure.py b/omnipath_metabo/schema/_structure.py
@@ -30,6 +30,10 @@ class Structure(Base):
     smiles = Column(String, unique= True)
     inchi = Column(String(4096))
     mol = Column(MolType)
+    is_polymer = Column(Boolean)
+    has_stereo = Column(Boolean)
+    has_conformation = Column(Boolean)
+    complete_formula = Column(Boolean)
     identifier = relationship(
         'Identifier',
         backref='structure',
@@ -55,10 +59,6 @@ class Identifier(Base):
         Integer,
         ForeignKey('resources.id'),
         nullable = False)
-    is_polymer = Column(Boolean)
-    has_stereo = Column(Boolean)
-    has_conformation = Column(Boolean)
-    complete_formula = Column(Boolean)
     __table_args__ = (
         Index(
             'identifers_unique',