Describe the bug
ARCReaction could not be generated for a reaction from the RMGDB.
How to reproduce
db = make_rmg_database_object()
load_families_only(db, "all")
reaction_families = ["Birad_R_Recombination"]
rxn = [ARCReaction(rmg_reaction=rxn.item) for rxn in list(db.kinetics.families[""].depositories[0].entries.values())][2]
Expected behavior
Create the object correctly.
Additional context
The error is:
WARNING:arc:The requested ARC reaction ARCReaction(label="NO2_p <=> NO + O", rmg_reaction="NO2_p <=> NO + O", multiplicity=2, charge=0) could not be atom mapped using ARC. Trying again with the flipped reaction.
WARNING:arc:Scissors were requested to remove a non-single bond in s1s2.
ERROR:root:Could not update atomtypes for this molecule:
1 O u0 p2 c+2
ERROR:root:The following molecule has at least one atom with an undefined atomtype:
1 O u0 p2 c+2
If this structure was entered in SMILES, try using the adjacencyList format for an unambiguous definition.
ERROR:root:Could not update atomtypes for this molecule:
1 O u0 p2 c+2
ERROR:root:The following molecule has at least one atom with an undefined atomtype:
1 O u0 p2 c+2
If this structure was entered in SMILES, try using the adjacencyList format for an unambiguous definition.
ERROR:root:Could not update atomtypes for this molecule:
1 0 O u0 p2 c+2
ERROR:root:The following molecule has at least one atom with an undefined atomtype:
1 0 O u0 p2 c+2
If this structure was entered in SMILES, try using the adjacencyList format for an unambiguous definition.
ERROR:root:Could not update atomtypes for this molecule:
multiplicity 2
1 1 O u1 p2 c0 {2,S}
2 2 N u0 p1 c+2 {1,S}
ERROR:root:The following molecule has at least one atom with an undefined atomtype:
multiplicity 2
1 1 O u1 p2 c0 {2,S}
2 2 N u0 p1 c+2 {1,S}
If this structure was entered in SMILES, try using the adjacencyList format for an unambiguous definition.
ERROR:root:Could not update atomtypes for this molecule:
1 0 O u0 p2 c+2
ERROR:root:The following molecule has at least one atom with an undefined atomtype:
1 0 O u0 p2 c+2
If this structure was entered in SMILES, try using the adjacencyList format for an unambiguous definition.
ERROR:root:Could not update atomtypes for this molecule:
multiplicity 2
1 1 O u1 p2 c0 {2,S}
2 2 N u0 p1 c+2 {1,S}
ERROR:root:The following molecule has at least one atom with an undefined atomtype:
multiplicity 2
1 1 O u1 p2 c0 {2,S}
2 2 N u0 p1 c+2 {1,S}
If this structure was entered in SMILES, try using the adjacencyList format for an unambiguous definition.
Describe the bug ARCReaction could not be generated for a reaction from the RMGDB.
How to reproduce
Expected behavior Create the object correctly.
Additional context The error is: