Print warning when a property is guessed

[kain88-de]

See: https://twitter.com/sperezconesa/status/1106556146427543552

@MDAnalysis I think it would be nice if MDAnalysis gave a warning message if masses are being guessed and not read from files (this is general for any guess property). It can give problems to guess stuff and not warn the user. Keep up the good work!! 😀

[sperezconesa]

Hello,
In addition to what I said in the tweet. I saw the other day a video of prof. Woods about some principles he is using in his latest software project. I thought many of them were good in general for software. One of them was something like: never guess anything unless the user specifically asks it.

https://www.youtube.com/watch?v=w1d1xtbGhHc&t=1434s

[jbarnoud]

It just did bite me. The PDB writer guess the atom elements. Not only did it get one of them wrong, but there is no way of provided the right elements.

[orbeckst]

Where do we guess automatically?

• PDB masses
• PDB bonds

Anywhere else? It would be good to have such a list. We can then open issues for specific cases.

In general I agree that I'd rather fail than work with dubious data. What I then like in those cases is a suggestion how to fix the failure or how to explicitly take the risk.

[jbarnoud]

On 7/19/19 12:53 AM, Oliver Beckstein wrote: Where do we guess automatically? * PDB masses * PDB bonds Anywhere else? It would be good to have such a list. We can then open issues for specific cases. In general I agree that I'd rather fail than work with dubious data. What I then like in those cases is a suggestion how to fix the failure or how to explicitly take the risk. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#2222?email_source=notifications&email_token=AAKRNOXWA6HKREEJMVYXRWTQAD66DA5CNFSM4G67I6YKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD2KFBRA#issuecomment-513036484>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAKRNOXLKC2BG3HDAV63PBDQAD66DANCNFSM4G67I6YA>.

We also guess the element, at least when we write a PDB file.

[orbeckst]

@aya9aladdin does your PR #3753 address this issue?

[aya9aladdin]

@aya9aladdin does your PR #3753 address this issue?

yes any successfully guessed attribute is tracked in a log message