I can't view the calculation results for anything when not logged in. I get a blank window, no user visible error. When I look at the console there are errors about e.origin not being defined. We should check it is valid before trying to use it, pop a warning if not present. It is probably a permission thing on the server that needs fixing to show molecular data. It can be tracked here though as it relates to the interface.

There is a migration guide here:
https://material-ui.com/guides/migration-v0x/

Figuring out if we can show/hide the D3 chart without breaking its rendering. I couldn't get it to work if I linked the ng-show to the vibrational modes.

Hitting refresh on a calculation, or pasting a link to a calculation is broken with 1.0 - the molecule state is lost, no data is shown in the 3D view.

When I choose to search by name, display more results per page etc, these should be remembered as preferred settings. In general it is irritating to keep selecting things, and most choices should be reasonably sticky in our web interface. They could be stored in some cookies or similar even for non-authenticated users ideally.

It now seems to be hard coded on here. This functionality must have been lost when the component was move the oc-web-components.

@cryos Does this want to be launched from a molecule, so we know which molecules to associate the calculation with?

We want to be able to filter molecule search results using arbitrary min/max values such as "heavy atom count > 10". This is partial fulfillment of this issue.

This is now possible on the mongochemserver side (as of this PR), but an interface for it needs to be added to the client. The current search setup is shown below. Perhaps it might be useful to have an advanced search box where users can specify a series of filters by keywords (like "mass <= 240 AND heavyAtomCount >= 10").

Show broadening so it is easier to compare with experiment, add scaling for displacements and calculate client side.

http://cactus.nci.nih.gov/chemical/structure

• Add support for looking up and importing structures by name
• Add support for looking up the common names of a give structure. This can be used to provide the user a list of names to select from when uploading a file.

Molecules can have a number of calculations associated with them, we need to support choosing which one to view, and displaying those results.

We should offer an admin view of all jobs running, and a user view of their calculations. When running a large number of jobs it would be great to have some counts on pending jobs, complete, failed, etc. We can start small with a listing of pending jobs, and running jobs.

Allow user to enter a PDB ID and import the structure into mongochem.

It shoudn't ...

Seems the same as #89

deprecated [email protected]: This project is no longer maintained.

I am thinking of the calculation page, where I see the download area:

on Firefox if I click CJSON when it is already selected I end up with a blank page, if I click download then I end up with a HTML mime type, and all the escaping to render it such as the below:

 >&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;],<br />&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;"occupations":&nbsp;[<br />&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;2,<br />&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;2,<br />&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;2,<br />&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;2,<br />&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;2,<br />&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;2,<br />&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;2,<br />&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;2,<br />&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;2,<br />&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0,<br />&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0,<br />&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0,<br />&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0,<br />&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0,<br />&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0,<br />&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0,<br />&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0,<br />&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0,<br />&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0,<br />&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0,<br />&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0,<br />&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0,<br />&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0,<br />&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0,<br />&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0,<br />&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0,<br />&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0,<br />&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0,<br />&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0,<br />&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0<br />&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;]<br />&nbsp;&nbsp;&nbsp;&nbsp;},<br />&nbsp;&nbsp;&nbsp;&nbsp;"properties":&nbsp;{<br />&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;"totalEnergy":&nbsp;-209548320.72014692<br />&nbsp;&nbsp;&nbsp;&nbsp;}<br />}</div>

This will be needed by 01/09/19 when it will be a requirement. The password passed to the server will then become password + MFA .

Formula: C24H51O39S6
INCHIKey: CAKDYPYEIQSZJT-UHFFFAOYSA-N

We currently have a check for atom count. However, we also need to check if the convertion fails. For example:

$ python mongochem.py ferrocene.cml ferrocene
{'name': 'ferrocene', 'filename': 'ferrocene.cml'}
==============================
*** Open Babel Warning  in GetAtomicNum
  Cannot understand the element label X.
==============================
*** Open Babel Warning  in GetAtomicNum
  Cannot understand the element label X.
==============================
*** Open Babel Warning  in InChI code
  m1 :Unknown element(s): Xx
==============================
*** Open Babel Error  in InChI code
  InChI generation failed
==============================
*** Open Babel Warning  in InChI code
  m1 :Unknown element(s): Xx
==============================
*** Open Babel Error  in InChI code
  InChI generation failed
JSON output follows:
[{"inchikey": "", "xyz": "23\nm1\nC          3.60742        1.17022
    1.70118\nC          2.45209        1.79763        2.19417\nC
   1.36958        1.40787        1.38882\nC          1.85638
0.53814        0.39997\nC          3.23919        0.39222
0.59286\nC          2.15027       -0.67100        4.09665\nC
3.14638       -1.40054        3.42840\nC          2.53860
-2.09663        2.37108\nC          1.16761       -1.79507
2.38537\nC          0.92800       -0.91485        3.45213\nFe
2.24399       -0.15862        2.19981\nXx         2.50493
1.06122        1.25540\nXx         1.98617       -1.37562
3.14673\nH          4.61389        1.26971        2.10767\nH
2.40402        2.46920        3.05136\nH          0.33369
1.72469        1.50995\nH          1.26456        0.06005
-0.38059\nH          3.90960       -0.21830       -0.01205\nH
2.29969       -0.02792        4.96395\nH          4.20544
-1.42263        3.68532\nH          3.04244       -2.75525
1.66364\nH          0.42022       -2.17733        1.69011\nH
-0.03811       -0.49429        3.73118\n", "inchi": "", "name":
"ferrocene"}]

While in Energy Type Mode, there is no way to click Vibrations Type as it lies over the 3D model of molecule.

I'm opening the issue here, but the fix may have to be done at the mongochemdeploy level.

On a ocdeploy stack freshly started, opening a notebook from the mongochemclient redirects to a 404 page by jupyter hub:

http://localhost:1234/jupyterhub/hub/spawn-pending/mongochemdev/tree/PSI4.ipynb

Going back to the client and opening the notebook again works

http://localhost:1234/jupyterhub/user/mongochemdev/lab/workspaces/auto-5/tree/PSI4.ipynb

Most of the new image manager features are now merged except the pop-up.

The user can currently register images by going to the image manager page and click "Register". However, it will be nice to have a pop-up when the user first logs in that asks if they want to register the images.

I'll try to get to this soon.

This will have a know on effect on oc-web-components. We will have to replace our use of redux-form as it don't plan on supporting react 17.

As a follow up to OpenChemistry/mongochemserver#162, we should make the necessary changes so this information is displayed along with the other calculation information.

I get this error when I log in, and it goes away if I refresh the page.

I know we can probably fix the error by changing this line to { user && user.admin. Is that an acceptable fix, or should user always not be null here?

We should add support for pasting a URL for a chemical data file too, probably let them specify the format/look at the file ending if it is in the URL?

What script/code will be required?

It is important to use the correct case for these terms, InChI (International Chemical Identifier), and SMILES (Simplified Molecular Input Line Entry System). This is just some simple tweaks to our frontend.