Re: [Bkchem-user] pdb export

[Beda Kosata]

Hello,

Fabien wrote:
> Hello,
> 
> I would like to know if a way to export to pdb files was forseen?
> 

I do not plan to include it. It is now possible to use BKChem (OASA)
together with OpenBabel, so this could be one way forward. However, the
topmost layer that actually exposes OpenBabel to the user is still
missing and I have no idea when and if it will be finished.
It would be great if you could try to add PDB support yourself.

> Also I wanted to see something in the code but when I tried to use tla
> (from Fedora) it gives me this:
> $ tla register-archive http://bkchem.zirael.org/arch/2004
> Failed to access file '.archive-version'
> Could not determine archive format, guessing to be tla 1.0
> Registering archive: address@hidden
> $ tla get -A address@hidden bkchem-dist--devel bkchem-dev
> Failed to access file '.archive-version'
> Could not determine archive format, guessing to be tla 1.0
> * from import revision:
> address@hidden/bkchem-dist--mainline--0.9.0--base-0
> tar: The --preserve option is deprecated, use --preserve-permissions
> --preserve-order instead
> * patching for revision:
> address@hidden/bkchem-dist--devel--0.1.0--base-0
> tar: The --preserve option is deprecated, use --preserve-permissions
> --preserve-order instead
> * patching for revision:
> address@hidden/bkchem-dist--devel--0.1.0--patch-1
> tar: The --preserve option is deprecated, use --preserve-permissions
> --preserve-order instead
> * patching for revision:
> address@hidden/bkchem-dist--devel--0.1.0--patch-2
> tar: The --preserve option is deprecated, use --preserve-permissions
> --preserve-order instead
> * patching for revision:
> address@hidden/bkchem-dist--devel--0.1.0--patch-3
> tar: The --preserve option is deprecated, use --preserve-permissions
> --preserve-order instead
> * patching for revision:
> address@hidden/bkchem-dist--devel--0.1.0--patch-4
> tar: The --preserve option is deprecated, use --preserve-permissions
> --preserve-order instead
> * making pristine copy
> * tree version set address@hidden/bkchem-dist--devel--0.1.0
> $ cd bkchem-dev
> $ tla build-config distribution.arch
> Failed to access file '.archive-version'
> Could not determine archive format, guessing to be tla 1.0
> tar: The --preserve option is deprecated, use --preserve-permissions
> --preserve-order instead
> [Many Outputs]
> 
> Is this normal? I tried to see on the web but did not find many clues. I
> was still able to import everything I think.
> 

I am not sure. tla does not seem to be maintained very well. I plan to
switch to git in the near future, so it should improve.

> I can speak of the things I have seen in the code of the version
> 0.14.0-1.pre1 that seems to be hardcoded links which I think should not
> be there. I did not find if it provoked some problems.
> 
> Here are the files:
> bkchem/oasa/oasa/graph/graph.py:  def _read_file( self,
> name="/home/beda/oasa/oasa/mol.graph"):
> doc/api/bkchem/molecule/molecule.html:flush_graph_to_file ( self, 
> name="/home/beda/oasa/oasa/mol.graph" )
> bkchem/oasa/oasa/config.py:  inchi_binary_path =
> "/home/beda/bin/cInChI-1-102b"
> bkchem/oasa/oasa/inchi.py:      print "  inchi:  ", generate_inchi( mol,
> fixed_hs=False, program="/home/beda/bin/stdinchi-1")
> bkchem/oasa/oasa/inchi.py:    print generate_inchi_and_inchikey( mol,
> fixed_hs=False, program="/home/beda/bin/stdinchi-1")
> bkchem/oasa/oasa/molecule.py:  def _read_file( self,
> name="/home/beda/oasa/oasa/mol.graph"):
> bkchem/oasa/oasa/svg_out.py:  mol = molfile.file_to_mol( file(
> "/home/beda/bkchem/bkchem/untitled0.mol", "r"))
> bkchem/molecule.py:  def flush_graph_to_file( self,
> name="/home/beda/oasa/oasa/mol.graph"):
> dtd/cdml.xsd:<!DOCTYPE xsd:schema SYSTEM
> "/home/beda/xml/schema/schema.dtd" [
> 
> Fabien
> 

It should be only in places where normal user would not get, but you are
right that it should not be there at all. I will try to minimize it :)

        Best regards

                Beda


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