On 23 January 2010 14:46, Andrew Dalke <[email protected]> wrote:
> On Jan 23, 2010, at 1:06 PM, Noel O'Boyle wrote:
>> Gotcha. I'll see if that's possible (do you know of any example of a
>> SWIG library that has this?).
>
> I did some searching and experimentation just now.
>
> I think you only need to %include "std_iostream.i" and let SWIG's
> built-in templates handle it for you. Here's a one-line change
That's great Andrew (how did you find this out BTW?).
>
>
> *** ../openbabel-python.i 2010-01-23 15:05:32.000000000 +0100
> --- /Users/dalke/cvses/ob/scripts/openbabel-python.i 2009-11-20
> 18:09:52.000000000 +0100
> ***************
> *** 49,55 ****
> %include "std_map.i"
> %include "std_vector.i"
> %include "std_string.i"
> - %include "std_iostream.i"
>
> namespace std {
>
> --- 49,54 ----
>
>
> When that in place, I uncommented the Makefile code which regenerates
> the openbabel_python.cpp from the .i file, rebuilt it, compiled
> (which takes a while), then tested it with the following:
>
>
> [openbabel-2.2.3/scripts/python] dalke% cat use_stdin.py
> import
> openbabel as ob
>
> obconversion = ob.OBConversion()
> obconversion.SetInFormat("smi")
> obmol = ob.OBMol()
>
> obconversion.Read(obmol, ob.cvar.cin)
>
> print "title is:", obmol.GetTitle()
>
> [openbabel-2.2.3/scripts/python] dalke% echo "C methane" | env
> PYTHONPATH=build/lib.macosx-10.6-universal-2.6
> LD_LIBRARY_PATH=build/lib.macosx-10.6-universal-2.6 python use_stdin.py
> title is: methane
> [openbabel-2.2.3/scripts/python] dalke%
>
>
> The only other change would be the extra %pythoncode
>
> cin = cvar.cin
> cout = cvar.cout
> cerr = cvar.cerr
>
>
>>> dump_smiles mysql://chem:ad...@localhost/test | ob2fps --FP3
>>
>> In that case, why not use the code behind pybel.readstring()? You can
>> read strings from stdin in Python, and pass them to OpenBabel.
>
> Because I want to support all the formats which OpenBabel supports
>
> dump_sdf mysql://chem:ad...@localhost/test | ob2fps --FP3 --in sdf
>
> Including compressed versions, which OB auto-detects
>
> curl 'http://example.com/smiles_data.gz"; | ob2fps --FP2 --in smi
>
> Supporting these all through readstring() would be a lot of
> duplicated work.
>
>> Ok, I see. So you are requesting a global function, GetVersion() or
>> so, that returns the version string.
>
> If such a function doesn't already exist, then yes, I would like it.
>
> It's possible to get the information already, through roundabout means
>
> import openbabel as ob
>
> def GetVersion():
> obconversion = ob.OBConversion()
> obconversion.SetInFormat("smi")
> obconversion.SetOutFormat("pdb")
> obmol = ob.OBMol()
>
> obconversion.ReadString(obmol, "C")
> for line in obconversion.WriteString(obmol).splitlines():
> if "GENERATED BY OPEN BABEL" in line:
> return line.split()[-1]
> return "<unknown>"
>
> print GetVersion()
>
>
> I might just used this if no GetVersion() exists in ob.
>
>
> Andrew
> [email protected]
>
>
>
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world's best and brightest in the field, creating opportunities for Conference
attendees to learn about information security's most important issues through
interactions with peers, luminaries and emerging and established companies.
http://p.sf.net/sfu/rsaconf-dev2dev
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