Fix to various solvation display issues

[jonwzheng]

Issue - Solvent + Solute Molecular Displays

Currently there is a glitch s.t. in the entry view for solvents, the structure is never given. Also solvation data views only displays structure for solutes (such as here).

Proposed Solution Fixed the small error that was causing solvent molecules to not get rendered. Here is an example of the new entry page, compared to the old one. And here is a new solvation data page and another one when solvent_temp == 'None.

Current Issues

If the solvent SMILES string is too large (such as in the case of squalane) then the solvent structure fails to properly render.

For the vast majority of solvents this shouldn't be an issue, but still the issue exists for a few implemented solvents.

On molecule pages like this one, for solvents,, perhaps we can try to automatically link "Solvation" as one of the auto-linked properties.

Here is the table list view of all solvents, and of all solutes.

More commits added by Yunsie:

1. Fixing TypeError glitch related to missing solvent properties

• For some solvents that are missing viscosity parameters, we got TypeError. Now, RMG-website displays 'not available' or 'N/A' if any of the solvent parameters are missing.
• You can check this by opening database/solvation/libraries/solvent/27/ (solvent library entry 27. methanol_50_water_50)

2. Display more solvent, solute, and solvation group information

• Some of the solvents have stereoisomers (e.g. trans- and cis- 1,2-dichloroethene), which RMG cannot distinguish when it draws the molecule structure. The SMILES strings are now displayed for solvent and solute entries, so the user can see that the SMILES are different between trans- and cis- stereoisomers.
• Check this by comparing 152. cis-1,2-dichloroethene and 190. trans-1,2-dichloroethene in the solvation solvent library.
• In addition, some of the solvent entries and solute group entries data have a new attribute called "data_count", which stores the number of data used to fit the parameters. For solvents, it also stores the mean absolute error associated with the fitted solvent parameters. These are now displayed for each library entry if it exists.
• Check this by looking at some of the solvent entries in the solvent library, e.g. 1. water.

3. Update how solvation group database entries are displayed for special groups

• Some of the solvation groups use the group values of a similiar of child group (reference group). Now, these special solvation groups will show the name of the reference groups that they are using. If the user clicks the reference group name, it directs to the reference group entry page.
• Check this by looking at some of the solvation groups that 'Other' as Data Format. For example, you can look at database/solvation/groups/halogen/19/ (solvation halogen group 19. F-(Cs-CbZZ)).
• Some of the solvation groups are the top nodes or general parent groups that do not need the groups values. RMG-website used to directs these groups to completely wrong group entries. Now it is fixed, and these groups will display the message: 'This group is one of the top nodes or general parent groups that do not need the group values.'.
• Check this by looking at some of the top nodes groups. e.g. database/solvation/groups/ring/1/ (solvation ring group 1. Ring).

4. Display detailed info for solvation group additivity

• The solvation search tool originally only displayed the estimated Abraham solute parameter values for the input solute compound. Now, if the group additivity method is used to estimate the solute parameter data, it displays a list of all groups used to estimate the solute parameters for the given solute compound. If a user clicks the individual group name, it links to the group entry page.
• If the solute parameter data are coming from the solute library, then it displays the solute label, which is linked to the original solute entry page.
• Check this by inputting any solute compounds in solvation search tool. e.g. CCCCC

5. Miscellaneous changes

• 'group' is displayed for solvation, statmech, and transport groups.
• The standard state information for solvation free energy is added on solvation search page.
• Change the VLE ratio result to scientific notation.
• Add a blank line between each solute data results to make them look nicer.

[yunsiechung]

@xiaoruiDong @jonwzheng I added some changes for solvation. I explained my changes on top and also explained why these changes can be tested. Do you mind reviewing this PR?

If everything looks okay, I will auto-squash the fixup commit and also add the python files created from making migrations.

[jonwzheng]

@yunsiechung, the changes look really good to me, awesome add-ons and fixups! A couple of small things before we approve. (1) We could merge parseThermoComment and parseSoluteDataComment. From what I can see, it looks like the changes between them are minor.
(2) When you do a solvation search it looks like the solvent info is no longer shown. Is this the intended display? (see old vs. new). (It looks like the solvent data is not recognized as an Entry in render_solvation_math, so its data is skipped.)

[yunsiechung]

@jonwzheng Thanks for the comments. (1) The way ThermoComment and SoluteDataComment are parsed are a bit different, especially for those that come from the library. So I would prefer to separate them into two different functions for now. (2) I actually forgot to display the solvent info for the solvation search. Instead of displaying the solvent data, I will create a link that directs the user to the solvent data page.

[yunsiechung]

@jonwzheng I added the change for your second comment.

I also added one more commit to edit some minor thing for solvation search. Previously, we only listed the solvents with both Abraham and Mintz parameters for solvation search. Now, we list all solvents for solvation search, and if the solvents only have some parameters, it will display only available results (e.g. if the solvent only has the Abraham parameters, it will only give the solvation free energy result and print 'N/A' for solvation enthalpy and entropy).

If everything looks good, I can also add the python files created from make migrations and push again.

[yunsiechung]

@jonwzheng I squashed the fixups. You can merge this PR now!

[jonwzheng]

Thanks! Before we merge, @xiaoruiDong do you know if we need to include the migrations files with this PR? I see we've done this in the past when models are updated, but our current workflow for updating the website seems to be designed not to include these files. Edit (7/19/21) - it looks like we do need to include these migrations files. There was a conflict when merging these files into the dev website, but it looks like the conflicting migration's changes are are already included in the migrations files in this PR. So the conflict was just from a mismatch in the names rather than content - which python manage.py makemigrations --merge fixed up automatically.