add pdb element column to pdb2sqlAlchemy

Author: CunliangGeng

pdb2sql/pdb2sqlAlchemy.py

@@ -18,17 +18,18 @@ class ATOM(Base):
     __tablename__ = 'ATOM'
     rowID = Column(Integer, primary_key=True)
     serial = Column(Integer, nullable=False)
-    name = Column(String(5), nullable=False)
-    altLoc = Column(String(5), nullable=False)
-    resName = Column(String(5), nullable=False)
-    chainID = Column(String(5), nullable=False)
+    name = Column(String(6), nullable=False)
+    altLoc = Column(String(1), nullable=False)
+    resName = Column(String(3), nullable=False)
+    chainID = Column(String(1), nullable=False)
     resSeq = Column(Integer, nullable=False)
-    iCode = Column(String(5), nullable=False)
+    iCode = Column(String(1), nullable=False)
     x = Column(Float, nullable=False)
     y = Column(Float, nullable=False)
     z = Column(Float, nullable=False)
     occ = Column(Float, nullable=False)
     temp = Column(Float, nullable=False)
+    element = Column(String(2), nullable=False)
     model = Column(Integer, nullable=False)
 
 
@@ -115,6 +116,7 @@ def _create_sql(self):
                 z=at['z'],
                 occ=at['occ'],
                 temp=at['temp'],
+                element=at['element'],
                 model=self.nModel)
 
             # add the atom to the data base