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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.
The text was updated successfully, but these errors were encountered:
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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:
The text was updated successfully, but these errors were encountered: