I did not intend this to be a project. Bob turned it into a project after the special topics were dismissed I believe. The original content is here: <a href="http://olcc.ccce.divched.org/Spring2017OLCCSpecialTopics-Molecular-Visualization-on-the-Web">http://olcc.ccce.divched.org/Spring2017OLCCSpecialTopics-Molecular-Visualization-on-the-Web</a>.
I am not sure what exactly this should be as a project. I would say the programming projects should be mostly up to the students where I (and you if you want) can have a supportive role. I don't believe in project assignments (strongly dislike getting them myself), the students should come up with something they love and then I can give some helpful directions. I could coin some rough ideas for inspiration.
While not the generator of this project, I do expect to get questions relating to it. I will
Q: What is the time frame for this project? Deadline?
Q: As it will be your project, do you have any ideas what you might want to visualize?
Hi Daniel, Damon and I are happy to see interest in this project as it is a topic that is quite important to us. We really feel that we can learn quite a bit from users exploring Reaxys. Let's see who else joins the project and then we can have a coordinated discussion about specific topics each person (or a team) would like to tackle. In the meantime, perhaps you can plan out a topic or type of search you want to focus on. Looking forward to working with you! Anja
I think what he wanted to do was to use the ID exchange service to get the isomeric SMILES of stereoisomers of a set of compounds and check the difference between them.
to make sense out of it, let me explain what is going on here for CID 1615 as an example. Please visit the Related Compounds section of the Compound Summary page of CID 1615.
137 compounds with the same connectivity as CID 1615.
134 compounds with the same stereo(chemistry) as CID 1615.
Click these links in a new tab or window, then you will see these compounds with thumbnail images. These docsum pages are not stored as Entrez history, so combine the results using "NOT", to get the compounds that have the same connectivity but not the same stereochemistry. (That is, the query looks like:
(History number for the 137 compound set) NOT (History number for the 134 compound set).
(that is, it should be something like #1 NOT #2)
This will give you three compounds (CIDs 102208935, 854031, 667458). In these compounds, the stereocenters are fully specified (either R or S). Remember that the query compound CID 1615 that we begin with have an unspecified stereo centers.
So, if you go back to the advanced search builder to take the intersection of the 137 and 134 compound sets, using "AND"
(History number for the 137 compound set) AND (History number fo the 134 compound set).
(That is, something like #1 AND #2)
Now you get 134 compounds that have the same connectivity and stereochemistry (with an unspecified stereocenter). Just open the five records on this DocSum page in new tabs or windows. You will see that these are all the same except that atoms at different positions are rare isotopes (like deterium (2H) or C-13). Basically, all 134 compounds are MDMA with different isotopic compositions, with varying positions of rare isotopes. This kind of cases occur quite often, when you search for very commonly studied molecules.
With that said, in the excel file you attached, you see many record pairs that involves CID 1615. For these record pairs, the returned isomeric SMILES strings contain many "2H"'s, meaning that they contain deuteriums at different positions. [If you selected CIDs as an output (instead of SMILES), you could've got the CIDs in the 137 or 134 compound set that I used in the example above.]
Considering that what you wanted was to compare SMILES strings between stereoisomers, you need to select the "Same, Isotope" option for the operator type. This will return compounds with the same isotopes as your query (but not necessarily the same stereochemistry). If you select "SMILES" as an output option, you will see what you expected to see.
What is the smartest way to open the JSON file in question number 6.d? I can open it and see the code, no problem. But is there a way I can open it so it looks readable?
Greetings,
My name is Daniel. I am one of Dr Belford students and i decided to choose Reaxys as my special project. After working at the start of the semester with Reaxys. I noticed that search strategies are quite important , especially for substances and materials that meet certain criteria. My focus will be on using screencasts to show my thought process and steps in searching Reaxys and also the difficulties i encountered in searching specific compounds. Thanks
I did not intend this to be a
Great
Welcome!
Hi Daniel, Damon and I are happy to see interest in this project as it is a topic that is quite important to us. We really feel that we can learn quite a bit from users exploring Reaxys. Let's see who else joins the project and then we can have a coordinated discussion about specific topics each person (or a team) would like to tackle. In the meantime, perhaps you can plan out a topic or type of search you want to focus on. Looking forward to working with you! Anja
What he wanted to do was
I think what he wanted to do was to use the ID exchange service to get the isomeric SMILES of stereoisomers of a set of compounds and check the difference between them.
Same CID
My understanding is that, if you want just to convert from one ID to another, you should use the "Same CID" operator. Best, Jordi
To make sense out it,
to make sense out of it, let me explain what is going on here for CID 1615 as an example. Please visit the Related Compounds section of the Compound Summary page of CID 1615.
https://pubchem.ncbi.nlm.nih.gov/compound/1615#section=Related-Compounds
In this section, you can see:
137 compounds with the same connectivity as CID 1615.
134 compounds with the same stereo(chemistry) as CID 1615.
Click these links in a new tab or window, then you will see these compounds with thumbnail images. These docsum pages are not stored as Entrez history, so combine the results using "NOT", to get the compounds that have the same connectivity but not the same stereochemistry. (That is, the query looks like:
(History number for the 137 compound set) NOT (History number for the 134 compound set).
(that is, it should be something like #1 NOT #2)
This will give you three compounds (CIDs 102208935, 854031, 667458). In these compounds, the stereocenters are fully specified (either R or S). Remember that the query compound CID 1615 that we begin with have an unspecified stereo centers.
So, if you go back to the advanced search builder to take the intersection of the 137 and 134 compound sets, using "AND"
(History number for the 137 compound set) AND (History number fo the 134 compound set).
(That is, something like #1 AND #2)
Now you get 134 compounds that have the same connectivity and stereochemistry (with an unspecified stereocenter). Just open the five records on this DocSum page in new tabs or windows. You will see that these are all the same except that atoms at different positions are rare isotopes (like deterium (2H) or C-13). Basically, all 134 compounds are MDMA with different isotopic compositions, with varying positions of rare isotopes. This kind of cases occur quite often, when you search for very commonly studied molecules.
With that said, in the excel file you attached, you see many record pairs that involves CID 1615. For these record pairs, the returned isomeric SMILES strings contain many "2H"'s, meaning that they contain deuteriums at different positions. [If you selected CIDs as an output (instead of SMILES), you could've got the CIDs in the 137 or 134 compound set that I used in the example above.]
Considering that what you wanted was to compare SMILES strings between stereoisomers, you need to select the "Same, Isotope" option for the operator type. This will return compounds with the same isotopes as your query (but not necessarily the same stereochemistry). If you select "SMILES" as an output option, you will see what you expected to see.
Opening JSON file
Opening JSON file
Having Problems
I am having some problems using the Identifier Exchange to convert CIDs to canonical smiles.
For input I use CIDs, and have a text file of the CIDs, which I will try and upload with this comment.
For operator type I have tried "Same, Sterochemistry" and "Same, Connectivity", thinking that would generate isomeric and canonical respectively.
For output method I used "Two column file showing input-output correspondence".
I am attaching the results that I saved to an Excel sheet. This makes no sense to me.
I am also attaching a linked Excel sheet that makes it easier to go to the PubChem pages.
I am also adding the txt file that I uploaded. Does anyone know what I am doing wrong?
Cheers,
Bob
Introduction