> In C++
> std::string OBPlugin::ListAsString
> (const char* PluginID, const char* param=NULL);
> gives similar functionality, but I don't know whether it is exposed in
> Python.
I've been trying to figure out how to use it.
>>> openbabel.OBFingerprint.ListAsString("Fingerprint")
'Fingerprint is not a recognized plugin type. Those with instances of sub-types
loaded are:\n'
>>> openbabel.OBFingerprint.ListAsString("OBFingerprint")
'OBFingerprint is not a recognized plugin type. Those with instances of
sub-types loaded are:\n'
>>> openbabel.OBFingerprint.ListAsString("fp")
'fp is not a recognized plugin type. Those with instances of sub-types loaded
are:\n'
>>> openbabel.OBFingerprint.ListAsString("obfp")
'obfp is not a recognized plugin type. Those with instances of sub-types loaded
are:\n'
>>> openbabel.OBFingerprint.ListAsString("PatternFP")
'PatternFP is not a recognized plugin type. Those with instances of sub-types
loaded are:\n'
>>> openbabel.OBFingerprint.ListAsString("fingerprints")
'fingerprints is not a recognized plugin type. Those with instances of
sub-types loaded are:\n'
>>> openbabel.OBFingerprint.ListAsString("format")
'format is not a recognized plugin type. Those with instances of sub-types
loaded are:\n'
>>> openbabel.OBFingerprint.ListAsString("formats")
'formats is not a recognized plugin type. Those with instances of sub-types
loaded are:\n'
>>>
It seems I'm doing wrong. I can't find where the code uses ListAsString and I
can't find the list of supported PluginIDs. I did find
src/GUI/OBGUI.cpp:
OBPlugin::ListAsVector(NULL, NULL, topvec);//get 'formats', 'fingerprints', etc
but you can see that neither 'formats' nor 'fingerprints' works. I tried
looking for C++ code which uses ListAsVector but couldn't find anything - not
even a test.
I also can't get the Python interface to ListAsVector working
>>> openbabel.OBFingerprint.ListAsVector("formats", None, None)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ValueError: invalid null reference in method 'OBPlugin_ListAsVector', argument
3 of type 'std::vector< std::string,std::allocator< std::string > > &'
>>>
>>> q = openbabel.vectorString()
>>> openbabel.OBFingerprint.ListAsVector("formats", None, q)
False
>>> list(q)
[]
>>>
Any advice?
>> figure out how many bits they generate? For example, I don't see
>> any way to find that FP2 generates 1021 bits.
> The size of the vector returned by GetFingerprint() gives an
> indication (rounded up to a power of 2).
I did find that, but if someone's using the MACCS keys I think
they would expect a fingerprint of size 166 bits, and not something
which is 256 bits, of which the last 90 bits are always 0.
There are a number of scoring functions which are based on the fingerprint
length. A quick scan of
http://www.daylight.com/dayhtml/doc/theory/theory.finger.html
lists Euclidian, Forbes, Hamman, Manhattan, Matching, and Russell-Rao as ones
which depend on the total length (they have 'a+b+c+d' which is n, or the total
number of bits).
It doesn't seem right to use the implementation size (which is
a power of 2) rather than the specification size (which for
MACCS is 166 bits).
Andrew
da...@dalkescientific.com
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