SVG does not have symbols but source MOL have it

Hi,

We use:

Oracle environment:

Oracle Database 10g Enterprise Edition Release 10.2.0.5.0 - 64bi

PL/SQL Release 10.2.0.5.0 - Production

CORE    10.2.0.5.0      Production

TNS for Linux: Version 10.2.0.5.0 - Production

NLSRTL Version 10.2.0.5.0 - Production

-------------------------------------------------------------
JChem Server environment:

Java VM vendor: Sun Microsystems Inc.

Java version: 1.6.0_23

Java VM version: 19.0-b09

JChem version: 5.6.0.0

JChem Index version: 5060000

JDBC driver version: 11.1.0.7.0-Production

I have moved this topic to the Visualization forum, as the problem described can be reproduced with the molconvert command line tool as well with version 5.6.0.1.

Peter

Hi,

can you send us the code snippet you use to generate the svg content, or describe the way of the creation of the marvin generated image? If it is considered to be confidetial, then you can send us it in an e-mail also.

Regards,
Istvan

On Windows using the molconvert command line tool:

C:\Users\pkovacs>chemaxon\packages\jchem-5.6.0.1\bin\molconvert svg C:\Users\pkovacs\Downloads\_misc\Wednesday\-2067844589.mol > C:\Users\pkovacs\a.svg

The input file -2067844589.mol is attached to the first post.

Peter

Thank you, I am checking it.

Hi,

first of all, sorry for the very late useful response.

It seems it is a very old issue in marvin svg export, and it seems it can be fixed in an upcoming release, 5.8 the latest.

The bug is that marvin does not calculates the fonts if the scale is less then a certain level, as i tracked it. If you set the scale manually to at least 5 (as i tested, maybe bigger a bit) then the atom labels does not generated into the svg. To set the scale use "svg:scale14" as the format specifier for example, as a workaround.

Regards,
Istvan

Thanks a lot, Istvan.

We've migrated to JChem from Accord last night and this workaround will be very useful.

Istvan,

It's start working with scale5.

Hi,

yes, i forgot to mention the scale5 limit, this limitation will disappear in 5.8, we delivered the fix in our main development branch, and 5.8 will contain it.

Regards,
Istvan

It's a good news, Istvan.

Thanks.