On Jan 23, 2010, at 11:36 AM, Noel O'Boyle wrote:
> (Questions on the API are best sent to the devel list or the scripting list.)
There's a scripting list? I had no idea.
I was influenced by the python-dev list, which is only concerned
with implementation questions, while using the API is left to
the general list. While I didn't check the list purposes first,
I read now:
About OpenBabel-discuss
A list for discussion on all aspects of Open Babel,
including use, development, bugs, future goals, etc.
About OpenBabel-Devel
This list is for discussion of development plans, etc. of Open Babel.
> Getting Python/SWIG to handle streams is difficult. I haven't done it
> (contributions welcome here). I could add a convenience function
> ReadFromStdin().
Another option is to have ob.cin, ob.cout and ob.cerr variables
with the correct type signatures. SWIG will treat them as opaque
pointers and allow them to be passed to functions which take
those types.
> However that would not solve the general problem,
> just your specific one. Can you describe the use case?
You are asking why someone wants to read SMILES from stdin?
My specific case is I'm working on my fingerprint format code.
I have a program which uses OB to read structures and generate
OB fingerprints.
I want it to handle being part of the standard Unix workflow.
For example, suppose "dump_smiles" is a program which
connects to a database and dumps the compounds in SMILES
format, and I want to convert them to a set of fingerprints
in my new format:
dump_smiles mysql://chem:ad...@localhost/test | ob2fps --FP3
> Will look into the version question. I could try to set this in the
> Python interface if all else fails.
Daylight used to only support the version via a compile-time
value. It was tricky for me to get the value through the SWIG
interface in PyDaylight.
I pointed out that because of shared libraries, a program
might be compiled against one version but run using another
version. They later made it a function to make those cases
easier. I think the same is true here.
Cheers!
Andrew
[email protected]
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