How should I use "cansmi" and "cansmiNS" descriptors?
I tried in pybel:
In [44]: import pybel
In [45]: mol = pybel.readstring("smi", "c1ccccc1O")
In [46]: mol.calcdesc(["cansmi", "cansmiNS"])
Out[46]: {'cansmi': nan, 'cansmiNS': nan}
In [47]:
I tried stepping through the pybel implementation manually
In [35]: import openbabel as ob
In [36]: mol = ob.OBMol()
In [37]: obconv = ob.OBConversion()
In [38]: obconv.SetInFormat("smi")
Out[38]: True
([39] was an oopsie)
In [40]: obconv.ReadString(mol, "c1ccccc1O")
Out[40]: True
In [41]: ob.OBDescriptor.FindType("cansmi").Predict(mol)
Out[41]: nan
The descriptor framework does work:
In [42]: ob.OBDescriptor.FindType("MR").Predict(mol)
Out[42]: 28.465
Since the function returns a string instead of a float,
it appears that I should call GetStringValue(). But how?
In [70]: ob.OBDescriptor.FindType("cansmi").GetStringValue(mol.OBMol)
---------------------------------------------------------------------------
NotImplementedError Traceback (most recent call last)
/Users/dalke/cvses/propbox/<ipython console> in <module>()
NotImplementedError: Wrong number of arguments for overloaded function
'OBDescriptor_GetStringValue'.
Possible C/C++ prototypes are:
GetStringValue(OpenBabel::OBDescriptor *,OpenBabel::OBBase *,std::string
&,std::string *)
GetStringValue(OpenBabel::OBDescriptor *,OpenBabel::OBBase *,std::string &)
I can't figure out what I should use to pass in a std::string& from Python.
So my questions are:
- how do I figure out which return type is expected, so I know
which descriptor method to call, and
- how do I get string value from the descriptor API?
Best regards,
Andrew
[email protected]
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