find_tss wrong about autode

[small-bamboo]

I Have read it, Thank you for your efforts, this is a good software, looking forward to its improvement

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------------------ Original ------------------ From: Tom Young ***@***.***> Date: Wed,May 12,2021 10:54 PM To: duartegroup/autodE ***@***.***> Cc: small-bamboo ***@***.***>, Author ***@***.***> Subject: Re: [duartegroup/autodE] find_tss wrong (#45) Have you checked out the online documentation? There's a reasonably comprehensive selection of examples and walkthrough of some Python there. Almost all examples in the paper were generated just by reaction.calculate_reaction_profile() with different SMILES. The multistep reactions will be added to the examples set when I've removed the redundancy in the conformer generation... I'll be working on this project full time for 6-months in September so most of the todo list is for then! — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

[t-young31]

autode.transition_states.locate_tss.find_tss requires a reaction with reaction.product and reaction.reactant set. A more helpful exceptions should definitely be thrown – thanks! However, you can find transition states for your reaction just by:

from autode import Reactant, Product, Reaction

p = Product('2.xyz')
r = Reactant('1.xyz')
reaction = Reaction(r, p, name='cope')
reaction.locate_transition_state()

# reaction.tss should now be a list of all the located transition states
print(reaction.tss)

[small-bamboo]

Thanks，but I still find an error，when the reaction mult and product  mult is different, it also gives an error

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------------------ Original ------------------ From: Tom Young ***@***.***> Date: Wed,May 12,2021 9:21 PM To: duartegroup/autodE ***@***.***> Cc: small-bamboo ***@***.***>, Author ***@***.***> Subject: Re: [duartegroup/autodE] find_tss wrong (#45) autode.transition_states.locate_tss.find_tss requires a reaction with reaction.product and reaction.reactant set. A more helpful exceptions should definitely be thrown – thanks! However, you can find transition states for your reaction just by: from autode import Reactant, Product, Reaction p = Product('2.xyz') r = Reactant('1.xyz') reaction = Reaction(r, p, name='cope') reaction.locate_transition_state() # reaction.tss should now be a list of all the located transition states print(reaction.tss) — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

[t-young31]

Unfortunately that type of reaction is not yet supported. I assume a NotImplementedError was thrown? This is because there is currently no way to find minimum energy crossing points in the code – hopefully at some point they will be, but it's not my top priority at the moment I'm afraid.

[small-bamboo]

Thanks，I have a small request. There are not many examples now, and my programming language ability is not good. Could you please send me some more examples of your previous tests, such as those in the article

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------------------ Original ------------------ From: Tom Young ***@***.***> Date: Wed,May 12,2021 10:26 PM To: duartegroup/autodE ***@***.***> Cc: small-bamboo ***@***.***>, Author ***@***.***> Subject: Re: [duartegroup/autodE] find_tss wrong (#45) Unfortunately that type of reaction is not yet supported. I assume a NotImplementedError was thrown? This is because there is currently no way to find minimum energy crossing points in the code – hopefully at some point they will be, but it's not my top priority at the moment I'm afraid. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

[t-young31]

Have you checked out the online documentation? There's a reasonably comprehensive selection of examples and walkthrough of some Python there. Almost all examples in the paper were generated just by reaction.calculate_reaction_profile() with different SMILES. The multistep reactions will be added to the examples set when I've removed the redundancy in the conformer generation... I'll be working on this project full time for 6-months in September so most of the todo list is for then!