1. Fall 2015 Course
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Discussion

Ben Brown (not verified) | Sun, 11/29/2015 - 18:55
In module eight, we learned how to format URLs for sites like PubChem in order to look up specific pieces of information about a compound. For my project I need to look up dissociation constants online in order to use in my program. As it stands right now, I'm having to use a less robust database to search for dissociation constants. I would like to use PubChem for this search, but I don't know how to format the URL to access that information. The compounds have dissociation constants on the PubChem page, but I don't know how to access it via the PUG REST interface.

Ben Brown (not verified) | Fri, 11/27/2015 - 20:54
I'm working on my project with Java and I was having trouble finding ways to incorporate the database I want into my code. I can figure out how to generate the right inputs, but I'm confused as to how I query the database in the first place. The modules we learned about used Javascript, but not Java. How might I go about coding in functionality that lets me access databases?

Jordi Cuadros's picture
Jordi Cuadros | Sat, 11/21/2015 - 00:11
Although there is fair level of compatibility between Google Spreadsheets and common desktop spreadsheet programs (Excel, Calc, Numbers, Gnumeric...), this does not hold for their macros or scripts. How to use webservices from desktop spreadsheet programs is discussed in the first part of 8.6.

Judat Yazigi (not verified) | Fri, 11/20/2015 - 20:45
I'm just confused on how I would add the webservices into excel, and would it work with Excel 2016?? Like how would I add gONS into excel 2016 or gChem???

Andrew Lang's picture
Andrew Lang | Fri, 11/20/2015 - 14:44
The correct link is: <a href="https://docs.google.com/spreadsheets/d/1YqDxTF2B2D-jlevY1NVcFdP5-UoHAISHKcI1tIRyPcU/copy">https://docs.google.com/spreadsheets/d/1YqDxTF2B2D-jlevY1NVcFdP5-UoHAISHKcI1tIRyPcU/copy</a>

Joshua Henrich (not verified) | Thu, 11/19/2015 - 17:32
I'm curious as to how you can access a molecular fingerprint directly from structure using the Chemistry Development Kit? The link provided for the latest spreadsheet doesn't lead to anything.

Jordi Cuadros's picture
Jordi Cuadros | Tue, 11/17/2015 - 16:44
Hi Andrew, I am unsure whether we have made this differentiation before in this course but I would say we need to take apart algorithmic identifiers (the ones that can be calculated) from arbitrary identifiers (the ones that are just given). If you plan to cover only algorithmic identifiers open babel in the back end may work better than querying online databases. For arbitrary identifiers like PubChem sid and cid, ChemSpider csid, ChEMBL number, CAS registry number... you will have to look them up. An online database (via a web API) would be preferred in this case. Jordi

Jordi Cuadros's picture
Jordi Cuadros | Tue, 11/17/2015 - 16:33
Hi Daniel, Although ChemSpider and CHEMnetBASE allow searching by boiling point, these databases don't offer a RESTful web API to make this search. ChemSpider seems to offers a SOAP access to this type of search but I haven't tested it. Alternatives that could work are: - web scrapping Kaye & Laby (table 3.3): <a href="http://www.kayelaby.npl.co.uk/chemistry/3_3/3_3.html">http://www.kayelaby.npl.co.uk/chemistry/3_3/3_3.html</a> - using The Organic Compound Database at <a href="http://www.colby.edu/chemistry/cmp/cmp.html">http://www.colby.edu/chemistry/cmp/cmp.html</a>. Search by boiling point can be automated like <a href="http://www.colby.edu/chemistry/cmp/fd.cgi?BP=320">http://www.colby.edu/chemistry/cmp/fd.cgi?BP=320</a> (Replace the last number for your boiling point in Celsius) Jordi

Jordi Cuadros's picture
Jordi Cuadros | Tue, 11/17/2015 - 15:26
Hi Alex, Tokens are a form of user authentication. I nice explanation of their use can be found at <a href="https://scotch.io/tutorials/the-ins-and-outs-of-token-based-authentication">https://scotch.io/tutorials/the-ins-and-outs-of-token-based-authentication</a>. They allow for an stateless (RESTful) authentication when some services need to be restricted to some users, use of the service wants to be monitored or for-a-fee services are involved. Jordi

Jordi Cuadros's picture
Jordi Cuadros | Tue, 11/17/2015 - 15:25
Hi Alex, Information about making HTTP request in Java can be found at <a href="http://docs.oracle.com/javase/tutorial/networking/urls/readingWriting.html">http://docs.oracle.com/javase/tutorial/networking/urls/readingWriting.html</a>. In example on using Cactus API to pull SMILES from a name is given in part 8.3 (<a href="http://cactus.nci.nih.gov/chemical/structure/aspirin/smiles">http://cactus.nci.nih.gov/chemical/structure/aspirin/smiles</a>). The response is plain text so there is no need for parsing. Jordi Jordi