cannot download structures in chemicalize.org

I am able to...

-upload a pdf document

- view the structures

- but cannot download structures

lakella wrote:

I am able to... -upload a pdf document - view the structures - but cannot download structures

Hi Lakshmi,

Thanks for the report, this looks like a bug. I'll let you know once I deployed a fix!

Andras

Hi Lakshmi,

In the attached PDF, no chemical structures are found, this is why there's an empty structure toolbar at the top of the page. If there are hits (such as on www.chemaxon.com%2Fwp-content%2Fuploads%2F2011%2F09%2F1758-2946-3-S1-O3.pdf">this example page), the toolbar shows 2D structure images and names, and there is actually something to download. In this case there is nothing to download.

Do you have another example PDF where you do see structures in the toolbar and download doesn't work?

Andras

Hi Andras

Attached is the pdf.

lakella wrote:

Hi Andras Attached is the pdf.

Hi Lakshmi,

I can see 33 structures imported and displayed from this PDF and when I click on Download and select either SDF or MRV I get 33 structures in the downloaded file. Is this not what you're experiencing?

Andras

Hi Andras

I cannot download any structures.  Also, there are >200 strcutures in that document about 7 structures per page.  Is there a limit on file size when you upload on chemicalize.org?

Thanks

Lakshmi

lakella wrote:

Hi Andras I cannot download any structures.  Also, there are >200 strcutures in that document about 7 structures per page.  Is there a limit on file size when you upload on chemicalize.org? Thanks Lakshmi

Hi Lakshmi,

Document to Structure (which powers the PDF viewer on chemicalize.org) recognizes 33 out of the >200 structures from this PDF. The rest of the structures are only available as CAS numbers in the PDF, and CAS number importing is not yet enabled for PDF documents yet on chemicalize.org (this feature was only recently added to our toolkits in Marvin 5.7).

There is a file size limit for upload on chemicalize.org, but that's not an issue in this case.

The issue seems to be with Internet Explorer 7 only and I believe I managed to fix it, if you refresh the page now, you will see the download dialog.

In the coming weeks we will enable CAS number importing on chemicalize.org, with that, you should have a lot more extracted structures from these example PDFs. When this improvement is ready, I will let you know or you can keep an eye on the chemicalize.org blog where we post announcements.

Cheers,
Andras 

Hi Andras

I don't understand.  Are you parsing the name and then converting name into structure?  Are you saying that very soon you will convert CAS numbers into structures?  Does that mean that if I don't provide a name or CAS number conversion cannot be done?

I thought you were using OSRA (converting graphic into structure).

I was able to download 33 structues now.

Lakshmi

lakella wrote:

Hi Andras I don't understand.  Are you parsing the name and then converting name into structure?  Are you saying that very soon you will convert CAS numbers into structures?  Does that mean that if I don't provide a name or CAS number conversion cannot be done? I thought you were using OSRA (converting graphic into structure). I was able to download 33 structues now. Lakshmi

Hi Lakshmi,

I don't know where you got this information (please point me to it so I can correct it), but chemicalize.org doesn't do this.

chemicalize.org document viewer extracts all the text content of text based PDFs (scanned PDFs are not support) and we do name to structure conversion from this. If you don't provide a name in the text, conversion cannot be done.Soon, CAS numbers will be supported in addition to names.

chemicalize.org doesn't yet support OSRA, so structures can only be extracted from text.

Hi,

I seem to have a similar problem to the one posted here. When I click the download buttin after viewing the properties of a molecule, no pop-up shows up indicating download. The page reloads instead. Any solution for this?

Thank you.

Hi Jessica,

Could you share the link to that molecule so I can investigate?

Thanks,
Andras 

Thank you, the link is:

http://www.chemicalize.org/structure/#!mol=OC1%3DC%28CC%3DC%29C%3DCC%3DC1\C%3DN\NC1%3DC2C3%3DC%28CCCC3%29SC2%3DNC%3DN1&source=fp

But in reality I have had this issue with any SMILES string I input.

Hi Jessica

Thanks for the link!

I think the bug is now fixed on chemicalize.org. Please let me know if you still experience problems with downloading properties results.

Cheers,
Andras 

Dear Andras, I am still unable to download, the same thing occurs. Am I missing something? Are limitations for the number of categories you can have to download it? Is there anything else you can think that may be a problem?

Thank you!

jrathbun wrote:

Dear Andras, I am still unable to download, the same thing occurs. Am I missing something? Are limitations for the number of categories you can have to download it? Is there anything else you can think that may be a problem? Thank you!

Hi Jessica,

As we discussed it in email, the issue was cache related and its resolved now.

Cheers,

Andras

I see! Got it!

i have uploaded a pdf document containing approximately 50 structures and not able to retrieve any. i am able to upload and view all structures but when i click on download it just shows the format to download and then nothing happens. Pls help ASAP

i have uploaded a pdf document containing approximately 50 structures and not able to retrieve any. i am able to upload and view all structures but when i click on download it just shows the format to download and then nothing happens. Pls help ASAP