mobley_352111 and mobley_4689084 are the same molecule about freesolv HOT 9 CLOSED

Yes. I'm surprised this wasn't caught by my scripts as I've checked for
duplicates numerous occasions.

Normally the procedure when there are duplicates is to check if the two
experimental values are consistent within uncertainty, and if so, merge
them, taking the more recent calculated value and the experimental value
which either (a) has the smaller uncertainty estimate or (b) goes back to
original literature rather than a compilation. (b) is usually preferable.
Then I update the notes field in the database, as well as the revisions
log, with an explanation of what was done.

Do you want to make that change or shall I?

Thanks.

On Fri, Oct 10, 2014 at 8:37 AM, Lee-Ping [email protected] wrote:

These two molecules have the same IUPAC name, SMILES string, identical
experimental values and nearly identical calculated values. I think these
are the only two entries in the set where the molecules are the same by the
above criteria.

A few things are different such as the uncertainty estimate and the
citation. I'm wondering if we should remove one of the entries?

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#6.

David Mobley
Associate Professor
Department of Pharmaceutical Sciences
Department of Chemistry
3134B Natural Sciences I
University of California, Irvine
Irvine, CA 92697
[email protected]
work (949) 824-6383
cell (949) 385-2436

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Would it be okay if you changed it? You could probably do it much faster. :)

from freesolv.

I'm happy to help once you guys decide on the outcome.

@leeping note that this is @mobley's first introduction to GitHub, so he's
probably eager to have pointers (e.g. exact sequences of commands) whenever
something non-standard comes up.

On Fri, Oct 10, 2014 at 4:13 PM, Lee-Ping [email protected] wrote:

Would it be okay if you changed it? You could probably do it much faster.
:)

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#6 (comment).

from freesolv.

No problem! I'm still learning aspects of Git and GitHub as well. I'd be happy to provide pointers for any step of the process.

from freesolv.

Hi, all,

OK, so on this, we should remove mobley_4689084, as the calculated value is older/slightly less reliable, among other reasons. 

I can easily make that change on my end. But can you help me out with github commands? At this point the only way I’ve interacted with github is through the web interface, so presumably I need to know how to:

• check out (?) the repository from github
• once I’ve made the change, put it back into github (pull request?)
• merge pull request from command line 

Can you guys help me out with terminology/sequence of commands?

Thanks.

David Mobley
[email protected]
949-385-2436

On Fri, Oct 10, 2014 at 1:59 PM, Lee-Ping [email protected]
wrote:

No problem! I'm still learning aspects of Git and GitHub as well.

Reply to this email directly or view it on GitHub:
#6 (comment)

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Calculated or experimental value?

from freesolv.

Experimental values are the same. Calculated value.

On Thu, Oct 23, 2014 at 5:50 PM, John Chodera [email protected]
wrote:

Calculated or experimental value?

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#6 (comment)

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Hi David,

For directly updating the master branch (requires write permissions to the repository):

== On the web ==
0) Make sure your SSH public key is stored in your GitHub account
== In the terminal ==

1. Clone the repository using git clone [email protected]:choderalab/FreeSolv.git, then cd FreeSolv
   1a) If the repository already exists, cd FreeSolv and run git pull origin master to get updates
2. Make the changes
3. Commit the changes using git commit -a
4. Push the changes using git push origin master.

To make a pull request:

== On the web ==
0) Make sure your SSH public key is stored in your GitHub account

1. Fork the repository to your user account,
   == In the terminal ==
2. Clone your repository using git clone [email protected]:davidlmobley/FreeSolv.git, then cd FreeSolv
   2a) If the repository already exists, cd FreeSolv and run git pull origin master to get updates
3. Make the changes
4. Commit the changes using git commit -a
5. Push the changes using git push origin master.
   == Back on the web ==
6. In your repository, click the "Compare and Pull Request" button
7. Type in a description and create the pull request, which opens the discussion thread
8. The administrator can then merge the changes

The pull request system is helpful because it always opens up a discussion thread, so you can always do this even if you're the admin.

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This was resolved 10/24/14 but I did not close the issue. Closing now.

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