Brilliant, many thanks for this Chris.
Two further questions:
- Will this change be released with the next version of open babel?
- How do you make your molecules in a grid like in your attached example?
Many Thanks,
-
Jean-Paul Ebejer
Early Stage Researcher
On 19 November 2011 14:05, Chris Morley <c.mor...@gaseq.co.uk> wrote:
> On 11/11/2011 09:38, JP wrote:
>
>> Is it possible to have a transparent background (or user specified) when
>> converting to an svg?
>> The choice of black and white looks very arbitrary.
>>
>
> Well, minimalist. So to bring some color back to your life, in the
> development code you can now specify the background color by name or rgb:
> -xb yellow, or -xb #ccff00, or -xb none (transparent). Just -xb is as
> before, white on black. -xB similarly specifies the bond color.
>
> With multiple molecules, the -xh option highlights those which meet a
> condition in its parameter. This is the same as in the --filter option
> http://openbabel.org/docs/**current/Command-line_tools/**
> babel.html#filtering-**molecules-from-a-**multimolecule-file<http://openbabel.org/docs/current/Command-line_tools/babel.html#filtering-molecules-from-a-multimolecule-file>and
> is constructed from descriptors and properties. The highlight color is
> an optional second parameter. The svg file at http://gaseq.co.uk/OB/hl.svgwas
> made by:
>
> obabel chembl_02.sdf.gz -O out.svg -xh !L5 -xl -l64
>
> and displays the first 64 molecules in a grid, with those not meeting the
> Lipinski Rule of Five highlighted.
>
> Chris
>
>
>
> ------------------------------------------------------------------------------
> All the data continuously generated in your IT infrastructure
> contains a definitive record of customers, application performance,
> security threats, fraudulent activity, and more. Splunk takes this
> data and makes sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-novd2d
> _______________________________________________
> OpenBabel-discuss mailing list
> OpenBabel-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
>
------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure
contains a definitive record of customers, application performance,
security threats, fraudulent activity, and more. Splunk takes this
data and makes sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-novd2d
_______________________________________________
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
