Merge branch 'ReactionMechanismGenerator:main' into feature/yaml-input-support

Author: vincthnngyn

documentation/source/users/rmg/installation/anacondaDeveloper.rst

@@ -81,6 +81,19 @@ Installation by Source Using Anaconda Environment for Unix-based Systems: Linux
 
     source ~/.zshrc
 
+   NOTE: You may wish to forbid ``conda`` from installing from the Anaconda channels due to licensing restrictions.
+   The ``environment.yml`` file already forbids using default channels, but you may further add the file ``.condarc`` to your RMG-Py directory (or modify the ``.condarc`` in your home directory) with the following contents before running the ``conda env create`` command: ::
+
+     channels:
+       - conda-forge
+       - nodefaults
+     channel_priority: strict
+     custom_channels:
+       main: null
+       r: null
+       anaconda: null
+       msys2: null
+
 #. Activate conda environment ::
 
     conda activate rmg_env

environment.yml

@@ -26,6 +26,7 @@ name: rmg_env
 channels:
   - conda-forge
   - rmg
+  - nodefaults
 dependencies:
 # System-level dependencies - we could install these at the OS level
 # but by installing them in the conda environment we get better control

rmgpy/molecule/atomtype.py

@@ -374,7 +374,7 @@ def get_features(self):
 
 ATOMTYPES['Li'] = AtomType('Li', generic=['R', 'R!H', 'R!H!Val7'], specific=['Li0','Li+'],
                             single=[0,1], all_double=[0], r_double=[0], o_double=[0], s_double=[0], triple=[0], quadruple=[0], benzene=[0], lone_pairs=[0], charge=[0,1])
-ATOMTYPES['Li0'] = AtomType('Li', generic=['Li','R', 'R!H', 'R!H!Val7'], specific=[],
+ATOMTYPES['Li0'] = AtomType('Li0', generic=['Li','R', 'R!H', 'R!H!Val7'], specific=[],
                             single=[0,1], all_double=[0], r_double=[0], o_double=[0], s_double=[0], triple=[0], quadruple=[0], benzene=[0], lone_pairs=[0], charge=[0])
 ATOMTYPES['Li+'] = AtomType('Li+', generic=['Li','R', 'R!H', 'R!H!Val7'], specific=[],
                             single=[0], all_double=[0], r_double=[0], o_double=[0], s_double=[0], triple=[0], quadruple=[0], benzene=[0], lone_pairs=[0], charge=[1])
@@ -720,7 +720,7 @@ def get_features(self):
 ATOMTYPES['H+'].set_actions(increment_bond=[], decrement_bond=[], form_bond=[], break_bond=[], increment_radical=[], decrement_radical=[], increment_lone_pair=[], decrement_lone_pair=[], increment_charge=[], decrement_charge=['H0'])
 
 ATOMTYPES['Li'].set_actions(increment_bond=[], decrement_bond=[], form_bond=['Li'], break_bond=['Li'], increment_radical=['Li'], decrement_radical=['Li'], increment_lone_pair=[], decrement_lone_pair=[], increment_charge=['Li'], decrement_charge=['Li'])
-ATOMTYPES['Li0'].set_actions(increment_bond=[], decrement_bond=[], form_bond=['Li0'], break_bond=['Li0'], increment_radical=['Li0'], decrement_radical=['H0'], increment_lone_pair=[], decrement_lone_pair=[], increment_charge=['Li+'], decrement_charge=[])
+ATOMTYPES['Li0'].set_actions(increment_bond=[], decrement_bond=[], form_bond=['Li0'], break_bond=['Li0'], increment_radical=['Li0'], decrement_radical=['Li0'], increment_lone_pair=[], decrement_lone_pair=[], increment_charge=['Li+'], decrement_charge=[])
 ATOMTYPES['Li+'].set_actions(increment_bond=[], decrement_bond=[], form_bond=[], break_bond=[], increment_radical=[], decrement_radical=[], increment_lone_pair=[], decrement_lone_pair=[], increment_charge=[], decrement_charge=['Li0'])
 
 ATOMTYPES['He'].set_actions(increment_bond=[], decrement_bond=[], form_bond=[], break_bond=[], increment_radical=['He'], decrement_radical=['He'], increment_lone_pair=[], decrement_lone_pair=[], increment_charge=[], decrement_charge=[])
@@ -911,7 +911,7 @@ def get_atomtype(atom, bonds):
 
     # Use element and counts to determine proper atom type
     atom_symbol = atom.symbol
-    # These elements do not do not have a more specific atomtype
+    # These elements do not have a more specific atomtype
     if atom_symbol in nonSpecifics:
         return ATOMTYPES[atom_symbol]
 

test/rmgpy/molecule/atomtypeTest.py

@@ -824,7 +824,10 @@ def setup_class(self):
             """1 C u0 p0 c+1 {2,T}
                                                        2 C u0 p1 c-1 {1,T}"""
         )
-        
+
+        self.mol96 = Molecule().from_adjacency_list('''1 Li u0 p0 c+1''')
+        self.mol97 = Molecule().from_adjacency_list('''1 Li u1 p0 c0''')
+
         self.electron = Molecule().from_adjacency_list('''1 e u1 p0 c-1''')
         self.proton = Molecule().from_adjacency_list('''1 H u0 p0 c+1''')
 
@@ -992,6 +995,13 @@ def test_fluorine_types(self):
         """
         assert self.atom_type(self.mol75, 1) == "F1s"
 
+    def test_lithium_types(self):
+        """
+        Test that get_atomtype() returns appropriate lithium atom types.
+        """
+        assert self.atom_type(self.mol96, 0) == "Li+"
+        assert self.atom_type(self.mol97, 0) == "Li0"
+
     def test_other_types(self):
         """
         Test that get_atomtype() returns appropriate types for other misc inerts.