docking-org/cartblanche22

A molecule shopping cart and ZINC-22 search tool

Cartblanche22 is a molecule shopping cart and ZINC-22 search tool.

Copyright Mar Castanon, Benjamin Tingle, Chinzo Dandar, John Irwin, and the UC Regents

cartblanche22's Issues

cosmetic changes to 3D and 2D browser

In the last column, I would like to get rid of 1/M400 leaving only the total.
This reduces it to one line, and means that we will get more info on the screen as each row will be roughly 50% of the size.
both 2d and 3d please

Issues with stereochemistry in smiles

Hi,
Using the "Download random molecules" from cartblanche22, I think I found an issue with the formatting of stereochemistry of smiles strings. When downloading some compounds, you can found an error with a double backslash instead of a simple backslash. Here is an example of a smiles extracted from the generated smiles file :
CO/C=C(\\C)C(=O)N1C[C@H]2Oc3cccc(NC(=O)Cc4ccccc4)c3[C@@H]2C1 ZINCtB000007oj1c

What is strange is that this problem does not seem to be present in the "substance" part of cartblanche22, nor in the cart, the checkout and the csv obtained during checkout. For the same example :
https://cartblanche22.docking.org/substance/ZINCtB000007oj1c

So I believe it's only using the "Download random molecules" tab.

Best regards,
Corentin

API : result doesn't include ZincID (Search by list of supplier code)

curl http://cartblanche22.docking.org/catlist -F supplier_code-in="s_1070__3705440__1080206"

{
"items":[
{
"catalogs":[
{
"catalog_name":"s",
"short_name":"s"
}
],
"smiles":"C=C1c2ccccc2NC(=O)N1CCCN1C(=O)CCC1=O",
"sub_id":83494,
"supplier_code":[
"s_1070__3705440__1080206"
]
}
]
}

Downloading local dump for ZINC22

Dear team,

Is there a way to download the Postgres database of ZINC locally? I have been looking for this dump on the Wiki page but wasn't successful in retrieving the location where I can directly download the dump. Please can you provide some guidance on this?

Thank you.

rename this report to cartblanche22

please, unless you advise against

Charge popup in 3D tranche browser

I am going to try this method of making requests. If this does not work, we can switch back to email.

In the popup for charge, it currently display All None J K L M N O P Q R
For each letter, I would like it to display the corresponding charge, in the popup only.
thus
J -4
K -3
L -2
M -1
N 0
O +1
P +2
Q +3
R +4

Thank you

more changes to 2D and 3D browsers

I would like to make logP more readable as follows.
In the title, put logP (up to) as we do for ZINC15.

instead of M500, put < -5.0
instead of M400 put -4.0
for M300 put -3.0
for M200 put -2.0
for M100 put -1.0
for M000 put < 0
for P000 put > 0
for P010 put 0.1
for P020 put 0.2
and so on
for P100 put 1.0
for P110 put 1.1
for P200 put 2.0
for P210 put 2.1
for P300 put 3.0
for P310 put 3.1
for P400 put 4.0
for P410 put 4.1
for P500 put 5.0
for P600 put 6.0
for P700 put 7.0
for P800 put 8.0
for P900 put 9.0

The tooltip should now be the old value and the single alphanumeric.
Thus for M500 ( now < -5.0) the tooltip should be "M500 (0)"
for P030 (now 0.3) the tooltip should be "P030 (9)"
and so on

I know this is a lot of work, but it will make the tranche browser much easier for people to understand.

I would love to have the tool tip for each square as follows, if you can compute it.
Thus if I hover over H14P250 for more than a second or two (say) then a tool tip comes up and it says
"H14P250 (ev)"
that would be really cool, but I realize might not be easy!
Thank you

Order of items in the Heavy Atom Count row

Layers is perfect.
I would like to try Charge next to layers. (left justified, Layers then Charge
I would like to try Download to the right of Predefined Subsets, thus in the top right corner.

I would like to try the toggle switch immediately to the right of Heavy Atom Count.

I might change my mind. I want to try it on an iPad, phone and other platforms to see how they are impacted.
Thank you

Search responses should have same structures

1. Search single zinc_id - > http://cartblanche22.docking.org/search.json?zinc_id=ZINCms000002NiP3
2. Search list of zinc_ids ->
   curl http://cartblanche22.docking.org/substances.json -F zinc_id-in=@/nfs/exd/zinc-22/H16/H16P220/H16P220-N.txt
3. Search list of supplier code -> curl http://cartblanche22.docking.org/catlist -F supplier_code-in="s_1070__3705440__1080206"
4. Search list of smiles -> curl http://cartblanche22.docking.org/smilelist -F smiles-in="[C+]2(=C1CCCCC1)=CC=CC=C2,C1=CC=CC=C1C2=CC=CC=C2" -F dist=0

They must include

1. smiles
2. zinc_ids
3. tranches
4. full catalog name
5. supplier code

delete contents of shopping cart / start again

Stefan suggests a button to delete the cart. We might want an "are you sure?" or (likely harder) make it reversible.
of course we can delete cart / create cart, and that might be how it is implemented. but can we have a button please?

square coloring in 2d/3d browser

There is something funny about the grey scale. the number 2 is not continuous with other low numbers so there are weird coloring effects. Would you look at how it is calculated and see if you can make it look a little less weird (discontinuous).

It is pretty good already, so don't worry too much!

in 3D tranche browser - download - get rid of SMILES. not available

we do not support SMILES in 3D tranche browser. please remove that option from the popup (bottom left in the download panel. thanks

Can you download a 3D structure as pdbqt based on ZINC ID?

Hi,

I am hoping it is possible to download 3D structures (as pdbqt) from ZINC22 based on a SMILES string or a ZINC ID, but I haven't yet found a way. Can it be done?

I am designing a screening library based on subsets from many tranches and would prefer not having to download everything just to delete the majority of the files. I select the relevant molecules from the tranches based on the SMILES alone.

Best,
Lucy

2D and 3D slider to change from K/M to full numbers

The slider is default left and the format is default K/M numbers
when we slide right, we still have K/M numbers
then we slide back to the original position and we get the full numbers.
This is confusing. Either the slider should start right OR the meanings of the two sides should be swapped.
I like K/M as a default.

Can you put a tool tip on the slider. If we hover over it the tool tip says
"Toggle between condensed and full numbers" (or your choice if you have better words)

3d tranche browser close after download

when we click on download, I would like the popup to close. Because I usually don't want to do it twice, so I find myself just closing it myself.

smile search result pictures were all the same

From: John

I looked for this smiles

BrC(CNCc1cccnn1)=C1CCOCC1

with dist=0
I got 52 matches but they were all the same (the pictures were all the same)

Please check it.
I agree with the last one. dist=1, I'm not sure why there are so many
other molecules. it seems wrong.

when i click on the code above the molecule I get
"we found 0 matches"
which does not seem right.
please check it

refresh vendors / assign vendors is slow

assign vendors is slow / does not work.
refresh vendors is fast.
I can't actually tell if it is doing anything at all.