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
*** ../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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