bugs fixed.

tutorial updated.

Author: stsouko

CGRdb/database/molecule.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 #
-#  Copyright 2017-2019 Ramil Nugmanov <[email protected]>
+#  Copyright 2017-2020 Ramil Nugmanov <[email protected]>
 #  Copyright 2019 Adelia Fatykhova <[email protected]>
 #  This file is part of CGRdb.
 #
@@ -272,9 +272,11 @@ def unite_molecule(self, molecule, mapping: Dict[int, int]):
         Unite molecules into single.
         Don't use this in parallel mode!
 
-        :param molecule: molecule id with will be moved into self.
+        :param molecule: Molecule object or id which will be moved into self.
         :param mapping: atom-to-atom mapping of molecule into self
         """
+        if not isinstance(molecule, int):
+            molecule = molecule.id
         mapping = [list(x) for x in mapping.items()]
         self._database_.execute(f"SELECT test.cgrdb_merge_molecules({molecule}, {self.id}, '{mapping}')")
 

CGRdb/sql/after_insert_molecule.sql

@@ -43,7 +43,7 @@ WHERE x.reaction IN (
     FROM "{schema}"."MoleculeReaction" y
     WHERE y.molecule = {molecule}
 )
-GROUP BY x.reaction'''
+GROUP BY x.reaction ORDER BY x.reaction'''
 
 get_ms = f'''SELECT array_agg(x.molecule) m, array_agg(x.id) s, array_agg(x.structure) d
 FROM "{schema}"."MoleculeStructure" x JOIN (
@@ -55,7 +55,7 @@ FROM "{schema}"."MoleculeStructure" x JOIN (
         WHERE z.molecule = {molecule}
     )
 ) mr ON x.molecule = mr.molecule
-GROUP BY mr.reaction'''
+GROUP BY mr.reaction ORDER BY mr.reaction'''
 
 cache = lru_cache(cache_size)(lambda x: loads(s, compression='gzip'))
 for ms_row, mp_row in zip(plpy.cursor(get_ms), plpy.cursor(get_mp)):

CGRdb/sql/merge_molecules.sql

@@ -90,7 +90,7 @@ for molecule, update_s, update_si in ((source, t_structures, t_ids), (target, s_
         FROM "{schema}"."MoleculeReaction" y
         WHERE y.molecule = {molecule}
     )
-    GROUP BY x.reaction'''
+    GROUP BY x.reaction ORDER BY x.reaction'''
 
     get_ms = f'''SELECT array_agg(x.molecule) m, array_agg(x.id) s, array_agg(x.structure) d
     FROM "{schema}"."MoleculeStructure" x JOIN (
@@ -102,7 +102,7 @@ for molecule, update_s, update_si in ((source, t_structures, t_ids), (target, s_
             WHERE z.molecule = {molecule}
         )
     ) mr ON x.molecule = mr.molecule
-    GROUP BY mr.reaction'''
+    GROUP BY mr.reaction ORDER BY mr.reaction'''
 
     update = list(zip(update_si, update_s))
     for ms_row, mp_row in zip(plpy.cursor(get_ms), plpy.cursor(get_mp)):