Re: [Bkchem-user] Using BKChem as a library for generation of 2D structure images

[Beda Kosata]

I have just updated OASA (the development archive that can be accessed
using tla or baz) with some basic support for E/Z stereochemistry.
As for now, the only two parts that support it are SMILES reading (no
encoding yet) and coords generator.
The code is a result of only 3 hours of intensive coding, so there may
still be some problems, but it seems to work well in my test cases.

        Best regards

                Beda

Beda Kosata wrote:
> Unfortunately OASA does not support stereochemistry (yet). It is a
> feature that I would like to add soon (before summer), but as for now it
> is not supported.
> I will have a look at the code to see what can be done to avoid using a
> file for the image.
> 
>       Best regards
> 
>               Beda
> 
> Noel O'Boyle wrote:
>> I have not yet looked at the development code, but it seems to me that
>> the current release of OASA does not allow me to specify the
>> stereochemistry around a double bond, i.e. E/Z or in SMILES, F/C=C\F
>> vs. F\C=C\F. Is this true?
>>
>> I must say that the images look very nice. I have one request though -
>> it should be possible to get back the image itself as a Cairo surface
>> or even just as a string representing a PNG. At the moment the only
>> option is to create a PNG file. I want to display the image using
>> Tkinter so it's better for me if I don't need to write to disk.
>>
>> Noel
>>
>> On 28/03/2008, Beda Kosata <address@hidden> wrote:
>>> You are right, OSRA (http://cactus.nci.nih.gov/osra/) is great, but my
>>>  library is called OASA (as in Obviously Another Stupid Acronym) :)))
>>>  Please let me know if you stumble upon anything strange. The library is
>>>  not very well organized and presently undergoes some changes (mainly
>>>  additions of functionality).
>>>  You might want to try the development sources:
>>>
>>>  tla register-archive http://bkchem.zirael.org/arch/2004
>>>  tla get -A address@hidden oasa--develop oasa
>>>
>>>
>>>  Beda
>>>
>>>
>>>  p.s.- please be warned that some of the code might be "write-only".
>>>
>>>
>>>  Noel O'Boyle wrote:
>>>  > OSRA looks perfect for the job (particularly example2.py). I will
>>>  > carry out some tests with it over the weekend.
>>>  >
>>>  > Noel
>>>  >
>>>  > On 27/03/2008, Beda Kosata <address@hidden> wrote:
>>>  >> Noel O'Boyle wrote:
>>>  >>  >
>>>  >>  > Hmm...it seems that it's necessary to start the Application. Do you
>>>  >>  > have any plans to separate some of the functionality into a library
>>>  >>  > that could be accessed without starting the App? For example, I 
>>> simply
>>>  >>  > want to (1) build a molecule (using the information in the connection
>>>  >>  > table of a pybel molecule), (2) generate 2D layout, (3) create an
>>>  >>  > image (preferably stored in a string, rather than in a file).
>>>  >>
>>>  >>
>>>  >> The problem here is that the started App lets you measure exact (or
>>>  >>  almost exact) text size, thus enabling much nicer output.
>>>  >>  Also there is the whole machinery of the App behind you, so you can
>>>  >>  relatively easily work with color, fonts, etc.
>>>  >>  But its true that it is slow and ineffective.
>>>  >>
>>>  >>
>>>  >>  >
>>>  >>  > It would be great to have this as a library, not just for Pybel.
>>>  >>  > According to today's write up on Depth First, BKChem is one of only 4
>>>  >>  > available structure diagram generators...and the only one in Python
>>>  >>  > (see 
>>> http://depth-first.com/articles/2008/03/26/five-open-tools-for-2d-structure-layout-aka-structure-diagram-generation)
>>>  >>  >
>>>  >>
>>>  >>
>>>  >> Interesting. The 2D coordinate generation is done in the OASA library I
>>>  >>  mentioned. This particular part of the library was written some 3 or 4
>>>  >>  years ago when I was doing a postdoc in Germany and had plenty of free
>>>  >>  time in the evenings. I did not touch the code since and it has some
>>>  >>  weak points (such as possible overlaps of atoms in highly branched
>>>  >>  structures), etc.
>>>  >>
>>>  >>  This brings us nicely to the second option I mentioned - using OASA 
>>> (the
>>>  >>  library that is behind BKChem). I use it on http://inchi.info to
>>>  >>  generate pictures in the converter. It is not able to run without
>>>  >>  X-windows installed, because it uses cairo for picture generation and
>>>  >>  cairo does not work without X installed. However, you don't need X
>>>  >>  running. I use it for PNGs now, but cairo is capable of producing 
>>> PDF's,
>>>  >>  EPS's and SVG's as well.
>>>  >>  I attach two  small scripts that demonstrate what you can do. Just copy
>>>  >>  it to the bkchem directory where the oasa library resides and run it. 
>>> As
>>>  >>  you can see the OASA api is not that different from Pybel and it would
>>>  >>  be almost no effort to create a bridge between the two (as I intent to
>>>  >>  do in neat future :)
>>>  >>  The only problem here is that I did not put that much effort into the
>>>  >>  cairo output backend, so the result is not that nice. Also there is not
>>>  >>  much support for configuration of display options for atoms, fancy
>>>  >>  things like sub- and superscripts, etc. (In BKChem you can say "I want
>>>  >>  this atom rendered with symbol on and hydrogens on, I also want each
>>>  >>  nitrogen atom painted in green"; you cannot do this in OASA (without
>>>  >>  some hacking)).
>>>  >>  It all depends on what you need.
>>>  >>
>>>  >>
>>>  >>  > My other question is how stable is the BKChem API?
>>>  >>  >
>>>  >>
>>>  >>
>>>  >> Well, it depends. Some parts of the API are pretty stable, but I don't
>>>  >>  hesitate when I need to change something when I need to. I try to
>>>  >>  document changes in commit logs, but not very thoroughly because I am
>>>  >>  the only one working on BKChem.
>>>  >>  Maybe it is better to give an example - there are some batch scripts
>>>  >>  that I have created some two years ago that work even with recent
>>>  >>  versions. On the other hand there are a few that I had to tweak 
>>> slightly
>>>  >>  because they used things that changed slightly over the time.
>>>  >>
>>>  >>  Best regards
>>>  >>
>>>  >>
>>>  >>         Beda
>>>  >>
>>>  >>
>>>  >
>>>
>>>
>>>
>>> --
>>>
>>> Bedrich Kosata
>>>  Laboratory of Informatics and Chemistry
>>>  ICT Prague
>>>  Czech Republic
>>>
>>>
> 
> 
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-- 
Bedrich Kosata
Laboratory of Informatics and Chemistry
ICT Prague
Czech Republic

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