make it possible to explicitly forbid molecules and groups in the inp…

…ut file

rmgpy/constraints.py

@@ -83,6 +83,16 @@ def fails_species_constraints(species):
         if struct.is_isomorphic(molecule):
             return False
 
+    explicitly_forbidden_molecules = species_constraints.get('explicitlyForbiddenMolecules', [])
+    for molecule in explicitly_forbidden_molecules:
+        if struct.is_isomorphic(molecule):
+            return True
+
+    explicitly_forbidden_groups = species_constraints.get('explicitlyForbiddenGroups', [])
+    for group in explicitly_forbidden_groups:
+        if struct.is_subgraph_isomorphic(group):
+            return True
+
     max_carbon_atoms = species_constraints.get('maximumCarbonAtoms', -1)
     if max_carbon_atoms != -1:
         if struct.get_num_atoms('C') > max_carbon_atoms:

rmgpy/rmg/input.py

@@ -36,8 +36,7 @@
 from rmgpy import settings
 from rmgpy.data.base import Entry
 from rmgpy.exceptions import DatabaseError, InputError
-from rmgpy.molecule import Molecule
-from rmgpy.molecule.group import Group
+from rmgpy.molecule import Molecule, Group
 from rmgpy.quantity import Quantity, Energy, RateCoefficient, SurfaceConcentration
 from rmgpy.rmg.model import CoreEdgeReactionModel
 from rmgpy.rmg.settings import ModelSettings, SimulatorSettings
@@ -238,7 +237,7 @@ def inchi(string):
 def adjacency_list(string):
     return Molecule().from_adjacency_list(string)
 
-def adjacency_list_group(string):
+def group_adjacency_list(string):
     return Group().from_adjacency_list(string)
 
 def react(tups):
@@ -1381,6 +1380,8 @@ def generated_species_constraints(**kwargs):
         'maximumCarbeneRadicals',
         'allowSingletO2',
         'speciesCuttingThreshold',
+        'explicitlyForbiddenMolecules',
+        'explicitlyForbiddenGroups',
     ]
 
     for key, value in kwargs.items():
@@ -1528,6 +1529,7 @@ def read_input_file(path, rmg0):
         'InChI': inchi,
         'adjacencyList': adjacency_list,
         'adjacencyListGroup': adjacency_list_group,
+        'groupAdjacencyList': group_adjacency_list,
         'react': react,
         'simpleReactor': simple_reactor,
         'constantVIdealGasReactor' : constant_V_ideal_gas_reactor,

rmgpy/rmg/main.py

@@ -65,7 +65,7 @@
 from rmgpy.kinetics.diffusionLimited import diffusion_limiter
 from rmgpy.data.vaporLiquidMassTransfer import vapor_liquid_mass_transfer
 from rmgpy.kinetics import ThirdBody
-from rmgpy.molecule import Molecule
+from rmgpy.molecule import Molecule, Group
 from rmgpy.qm.main import QMDatabaseWriter
 from rmgpy.reaction import Reaction
 from rmgpy.rmg.listener import SimulationProfileWriter, SimulationProfilePlotter