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ARCReaction instance creation error from RMGDB #625

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kfir4444 opened this issue Mar 26, 2023 · 0 comments
Open

ARCReaction instance creation error from RMGDB #625

kfir4444 opened this issue Mar 26, 2023 · 0 comments

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@kfir4444
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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.
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