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

[Beda Kosata]

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
>>
>>
>