Re: [Bkchem-user] Generating 2D structures images from 2D (.mol)

[David García Aristegui]

Thank you very much indeed!!!!
Best regards.

David.
El mié, 18-02-2009 a las 06:31 +0100, Beda Kosata escribió:
> Hello David,
> 
> it is indeed possible, but for molfiles it would be an overkill because,
> as you suggested, BKChem needs an X server for the drawing.
> However there is a simpler alternative - a library called OASA which is
> the basis of BKChem an can create pictures without the need of an X server.
> Here are some examples of its use:
> http://bkchem.zirael.org/oasa_en.html
> http://notimetolouse.blogspot.com/2009/02/pdf-and-svg-support-added-to-oasa.html
> 
> OASA is also used by pybel - the python bindings to OpenBabel:
> http://openbabel.org/wiki/Install_Python_bindings
> 
> Depending on what you prefer, you can read your molfiles either by pybel
> and draw them using OASA, or give both tasks to OASA.
> The code would look like this..
> 
> ---
> from oasa import cairo_out, molfile
> 
> m = molfile.converter()
> f = open("input.sdf","r")
> i = 1
> for mol in m.read_file( f):
>     mol.remove_unimportant_hydrogens()
>     mol.normalize_bond_length( 30)
>     cairo_out.mol_to_cairo( mol, "out%d.png" % i, "png")
>     i += 1
> f.close()
> ---
> 
> ..or like this..
> 
> ---
> import pybel
> 
> i = 1
> for mol in pybel.readfile( "sdf", "input.sdf"):
>   mol.draw( show=False, filename="out%d.png"%i)
>   i += 1
> ---
> 
> As you can see, the OASA code is actually longer, but is gives you more
> control of the output.
> You can for example control display of hydrogens, bond widths,
> background color, etc.
> 
> ---
>     cairo_out.mol_to_cairo( mol, "out%d.png" % i, "png",
>                             line_width=2, font_size=12,
>                           background_color=(0.9,0.8,0.8,1))
> ---
> 
> 
> You can also use OASA to export SVG or PDF.
> I hope this helps.
> 
>       Best regards
> 
>               Beda
> 
> 
> 
> David García Aristegui wrote:
> > Hello, is possible to use BKchem to generate 2D images (png, for
> > example) from MOL/SDF (2D) files? i see this issue was discussed before
> > http://www.mail-archive.com/address@hidden/msg00030.html
> > but i don't know how to implement this. Is available an example like
> > smi2png.py, but working with MOL files? 
> > 
> > BTW, i remember that the old xchemdraw calls the X server to generate
> > the PNGs, BKChem calls the X server too? 
> > 
> > Thank you in advanced, best regards.
> > 
> > 
> > 
> > _______________________________________________
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> > 
> 
>