Discussion | DivCHED CCCE: Cheminformatics OLCC

The Excel file seems zipped (so the extension is wrong)

I have been able to open the Excel file by downloading it and changing its extension to .zip. Uncompress and voilà! Does it work for you?

Interesting and maybe worth noting

I too am now having this problem, which is interesting, as it worked when the article was reviewed. I will look into this. But also, what we did was several years old, and there are different ways to do it now. That is, we wrote a script to interact with the API, and now there are functions in Excel, Libre Office and Google Sheets that do what the script did. You should still be able to watch the video, and there may be a message here. Which is, make videos, so that when something is degraded or no longer supported, you can still show what you did. What bothers me is that the sheet is now corrupt, and that makes no sense (I can see if an API changed that it would not work, but why become corrupt?)

More data

Yesterday I ran across a Kindle book with solubility data. I paid 99 cents for it. But it turns out you can get the book for free from the Internet Archive. And it turns out there is a second volume. You can get to both volumes on the Internet Archive (<a href="http://archive.org">http://archive.org</a>) with the title Solubilities of inorganic and organic compounds; a compilation of quantitative solubility data from the periodical literature. But maybe we already have more data that we could hope to use in this project.

Excel file and J Chem Inf

I had the same trouble as Perry with the Excel file. I thought it might be that I'm a Mac user. But Perry's not a Mac user. Here's the link to the JChemInf article, copied from above: <a href="http://www.jcheminf.com/content/7/1/22">http://www.jcheminf.com/content/7/1/22</a>

Broken Excel File

Hello, Dr. Belford I took a look at the MS word document, but for some reason the excel file is corrupt. I tried to look for the file on the JChemInf website but I could not find it. Is there anyway you could post a working link? Thank You

Response to clarification

Hi Perry, I do not think that is your project, as it has already been done. If you look above (into the body of this discussion), I link to a youtube that is supporting documents to a paper in JChemInf, where we did that. Now there may be something simliar, which is to scrape solubility data from various resources and compare it. But I think we all need some discussion on this. I suggest you look at the YouTube, and there is also an MS word document that describes the process, and an Excel spreadsheet that has the functions in it. You should be able to download the latter two from the JChemInf site (it is open access). But thanks for contacting us, and I am sure we will come up with something worth presenting at the ACS meeting. Cheers, Bob

Clarification

Hello everyone, I just wanted to clarify my current assignment for this project. If I am correct, I am supposed to create a script that uses web APIs to convert structures and names to InChI and compare them. Where am I supposed to get the structures and names? Are you referring to the figshare solubility dataset? If so, what is the best way to access the script editor for that excel file? Thank You Perry Sharma

Correction and addition

In my previous message, I happened to use the URL beginning with "<a href="https://testpubchem">https://testpubchem</a>..." (not "<a href="https://pubchem">https://pubchem</a>..."), which is for our test server. I've fixed the URL (in the previous message) to the correct one. By the way, you can actually download a "part" of the data displayed on the Compound Summary page through the PUG-REST-View (also called PUG-View), by suffixing the URL with an optional parameter for a particular section. For example, <a href="https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/compound/91757643/JSON?heading=Dissociation%20Constants">https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/compound/91757643/JSON?heading=Dissociation%20Constants</a> This will allow you to download the "Dissociation Constants" part of the data, but you still need to parse the data.

Need to use PUG-REST-View instead of PUG-REST

Hi, Ben, PUG-REST does not support programmatic access to pKa or pKb values. Instead, you need to use another protocol called PUG-REST-View, which allow you to access all data presented in the Compound Summary page for a particular compound. For example, the Compound Summary page of CID 91757643 can be accessed via the URL: <a href="https://pubchem.ncbi.nlm.nih.gov/compound/91757643">https://pubchem.ncbi.nlm.nih.gov/compound/91757643</a> And all the data presented in this Compound Summary page can be programatically accessed via the PUG-REST-View: <a href="https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/compound/91757643/JSON">https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/compound/91757643/JSON</a> Note that this PUG-REST-View request will give you *ALL* information on the Summary page, so you need to write a short program to extract dissociation constants from the downloaded data. Does you or your colleague have basic programming knowledge?

gChem-CDK link

I'm trying to work through the tutorial in 8.6 about CDK Descriptors. I see the same behavior that Vincent is reporting. Actually, it says: "Sorry, the file you have requested does not exist. Make sure that you have the correct URL and that the owner of the file hasn't deleted it." Does anyone have the updated link? I don't know how important the CDK Descriptors are for completing the tasks associated with Module 8b.