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

[Beda Kosata]

You are welcome :)

        Beda

David García Aristegui wrote:
> 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.
>>>
>>>
>>>
>>> _______________________________________________
>>> Bkchem-user mailing list
>>> address@hidden
>>> http://lists.nongnu.org/mailman/listinfo/bkchem-user
>>>
>>
> 


-- 
Bedrich Kosata
Laboratory of Informatics and Chemistry
ICT Prague
Czech Republic

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