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Formatting exported SVGs
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Brenton

Joined: 22 Jan 2013
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Link to postPosted: Mon Apr 13, 2015 1:42 amPost subject: Formatting exported SVGs Reply with quote

Hi, 

I have noticed that SVGs made using MarvinSketch's export to image tool include six blank spaces in all atom labels. Is there any way of getting MarvinSketch to automatically not add these blank spaces to atom labels? 

Thanks for your time,

Brenton

Eufrozina
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Link to postPosted: Mon Apr 13, 2015 5:12 pmPost subject: Reply with quote

Hi Brenton,

I was not able to reproduce this issue with our current (Marvin version 15.4.6. ) svg export, however we have fixed some svg related bugs recently. Could you check whether you see the blank spaces on the picture which I have generated and point out to them, please? Or can you send me an image on which these points are visible?

Thank you,

Efi




 Filename: atomlabels.svg    Filesize: 15.79 KB    Viewed: 23346 Time(s)
 Description:  
atomlabels.svg
Brenton

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Link to postPosted: Mon Apr 13, 2015 11:01 pmPost subject: Reply with quote

Here's the whitespace I'm talking about in your SVG. These spaces are why it's impossible for Inkscape to crop the SVGs that MarvinSketch produces as these spaces in the atom labels are interpreted as being part of the drawing.




 Filename: Atomiclabels.png    Filesize: 140.29 KB    Viewed: 23343 Time(s)
 Description:  
Atomiclabels.png
Eufrozina
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Link to postPosted: Tue Apr 14, 2015 1:33 pmPost subject: Reply with quote

Thank you. Now I could see the problem. I created a bug report in our issue tracking system, but unfortunately, I cannot promise a quick fix.

Best regards,

Efi

tfazekas
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Link to postPosted: Thu Apr 16, 2015 3:13 pmPost subject: Reply with quote

Hi Brenton,

We haven't been able to identify the root cause - yet - but until then, I can provide a workaround for removing the extra spaces in the svg files. 

Open the svg file with some text editor, since svg is a simple xml formatted text file. 

Find the <text ...> </text>  tags, and inside them there will be an attribute called xml:space set to "preserve". Remove them, and the extra spaces will disappear.

I hope that his is a possible solution for you, and we will report back, when this issue has been solved.

 

Regards, 

Tamas Fazekas-Vígh

Brenton

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Link to postPosted: Fri Apr 17, 2015 10:10 amPost subject: Pieces of exported SVGs being cut off Reply with quote

Thanks for your advice on how to correct this problem, sure beats removing these spaces manually in Inkscape. I was wondering if you might have a solution for the fact that MarvinSketch SVGs also has parts of it cut off (usually subscripts or hydrogens).  See the attached SVGs for examples of what I mean.

1st (Taurine.svg): notice how the H in the hydroxyl group is cut off. 

2nd (Glutamic acid (Glu, E).svg): notice how the 2 subscript is partially cut off. 




 Filename: Glutamic acid (Glu, E).svg    Filesize: 19.74 KB    Viewed: 23295 Time(s)
 Description:  
Glutamic acid (Glu, E).svg

 Filename: Taurine.svg    Filesize: 16.19 KB    Viewed: 23295 Time(s)
 Description:  
Taurine.svg
Eufrozina
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Link to postPosted: Fri Apr 17, 2015 3:07 pmPost subject: Reply with quote

Hello,

I would like to ask which Marvin version do you use? The good news that I was not able to reproduce this cut-off with the developer  version which will be released next week *15.4.20). In the new version, margin can be set on the dialog which appears when you generate an  svg image.

Best regards,

Efi

Brenton

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Link to postPosted: Fri Apr 17, 2015 3:42 pmPost subject: Reply with quote

Presently I'm using MarvinSketch 15.4.13. Ah that's good news, I've noticed this problem with versions back to the 6.x.x versions which was when I first started using ChemAxon software. Oh btw are there any plans on adding in-built updating capabilities for ChemAxon software (Marvin, JChem and Instant JChem included) such that the software can be set to automatically search for updates, download them and install them?

Eufrozina
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Link to postPosted: Fri Apr 17, 2015 5:08 pmPost subject: Reply with quote

We certainly plan to have an auto updater in Marvin, I will ask the other teams.

Regards,

Efi

Brenton

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Link to postPosted: Tue Apr 21, 2015 5:07 amPost subject: Release date of 15.4.20 Reply with quote

Hi, correct me if I'm wrong but isn't 15.4.20 meant to be released on 20 April 2015? If so it should have been released by now as it's presently 6 pm in Budapest (which as I understand it is where ChemAxon has its major headquarters) 21 April 2015. The other major headquarters of ChemAxon, as I understand it is on the East Coast of the U.S. where it just turned 12 pm 21 April 2015. 

Eufrozina
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Link to postPosted: Tue Apr 21, 2015 10:11 amPost subject: Reply with quote

We release the program weekly, the version number is always the data of the given Monday even if the actual release was on Friday.  Marvin 15.3.20 will be released today afternoon or tomorrow.

However, some doubt have arisen in the team whether we understand your workflow and problem correctly or not. Do you save the picture from MSketch UI or by Molconvert?  Do you modify the original Height and Width of the picture on the "Export of svg image" dialog? Or from code? ( It works properly with the default settings on my laptop. This leads to my next question: what kind of computer/OSX do you have?)

I am looking forward to your reply.

Efi

Brenton

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Link to postPosted: Tue Apr 21, 2015 10:39 amPost subject: Mechanism of SVG creation Reply with quote

I use the GUI, not the command-line. My method & settings are shown in the screenshots. Ask if any additional info is desired. 

 

EDIT: Sorry, I didn't see your question about OS. My OS is 64 bit Windows 7 SP1 (I've changed the theme settings if you're wondering why it looks Mac OS X-like). Intel Core i5-3230M CPU @ 2.6 GHz, if needed. My PC's brand is Lenovo, if relevant. 




 Filename: MarvinSketch export window.png    Filesize: 23.42 KB    Viewed: 23196 Time(s)
 Description:  
MarvinSketch export window.png

 Filename: MarvinSketch structure exports.png    Filesize: 50.97 KB    Viewed: 23196 Time(s)
 Description:  
MarvinSketch structure exports.png
Brenton

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Link to postPosted: Tue Apr 21, 2015 11:19 amPost subject: Timezones Reply with quote

Is that today afternoon/tomorrow in Budapest time (UTC+1)? 

Eufrozina
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Link to postPosted: Tue Apr 21, 2015 11:33 amPost subject: Reply with quote

Yes. And thank you for the example.

Unfortunately with this settings the bug still exists. I am sorry. If you set the margin to 10.0, the cut off will not appear. 

Best regards,

Efi

Brenton

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Link to postPosted: Tue Apr 21, 2015 11:41 amPost subject: Setting default text font Reply with quote

Is there any way to set the default text font in the GUI so that whenever one tries to insert text (e.g., labels under skeletal structures) into a drawing in MarvinSketch it'll be the font-size and family that was set to default automatically? 

Eufrozina
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Link to postPosted: Wed Apr 22, 2015 9:02 amPost subject: Reply with quote

Unfortunately there is no way to set this currently. We are understand that this is an important issue and will work on it in the Q3/Q4 this year.

Best regards,

Efi

Eufrozina
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Link to postPosted: Wed Apr 22, 2015 9:10 amPost subject: Reply with quote

Sorry that I was not clear. If everything goes according to the current plans, we will work on this issue between August and December this year.

Regards,

Efi

Brenton

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Link to postPosted: Wed Apr 22, 2015 2:41 pmPost subject: One other issue with MarvinSketch Reply with quote

Hi,

I've noticed another issue with MarvinSketch, isoleucine (3 letter code: Xle)'s symbol in the Advanced Templates toolbar is larger and otherwise differently-formatted (without the blue square brackets) than the symbols of the other amino acids in the toolbar. Attached is a screenshot I've taken showing what I mean. 




 Filename: MarvinSketch Xle screenshot.png    Filesize: 37.4 KB    Viewed: 23133 Time(s)
 Description:  
MarvinSketch Xle screenshot.png
nmihala
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Link to postPosted: Thu Apr 23, 2015 3:49 pmPost subject: Reply with quote

Dear Fusion 809,

 

thank you very much for your comment.

Could you summarize briefly how the amino acids were added to the Advanced Tool panel please?

Best regards,

Nikolett Mihala

Brenton

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Link to postPosted: Thu Apr 23, 2015 4:18 pmPost subject: Reply with quote

Not sure, I honestly thought this was just how the "Advanced Templates" (View->Toolbars->Advanced Templates was how I enabled it) toolbar appeared by default. I added this toolbar probably over a year ago, so I must confess if there was some sort of configuration that was needed to be done I probably have completely forgotten it. Attached is the template library entry for the amino acid isoleucine which is represented abnormally in the toolbar. 




 Filename: MarvinSketch & template library manager.png    Filesize: 59.61 KB    Viewed: 23103 Time(s)
 Description:  
MarvinSketch & template library manager.png
nmihala
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Link to postPosted: Mon Apr 27, 2015 10:14 amPost subject: Reply with quote

It's OK, thank you. 

The bug report was created in our issue tracking system and you will be informed in due course.

Thank you again.

Best regards,

Nikolett Mihala

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