Re: [openbabel-scripting] GetData

[Noel O'B. <no...@ca...>]

On Tue, 2006-02-21 at 10:38 -0500, Geoffrey Hutchison wrote:
> On Feb 21, 2006, at 5:54 AM, Noel O'Boyle wrote:
> 
> > I've just CVS updated my openbabel, but I'm just wondering about some
> > changes to the API that I've found.
> >
> > Both OBMolecule and OBAtom no longer have a wrapped GetData() method.
> 
> Oops. This was brought into the base class OBBase, so that other  
> classes can store data too (e.g., OBReaction, OBResidue...).
> 
> On that subject, are there other headers/classes that I should be  
> adding to the wrapper?
This I cannot say, as I do not have experience with the C++ classes.
Personally, I am first concerned with allowing access to basic chemical
information. Until people start using the scripting interfaces, we won't
know what people will want to use it for.


BTW, it might be nice to have a bit more non-API documentation on the
Open Babel classes. Some kind of tutorial to show the sort of thing that
can be achieved with the library. For instance, I don't know much about
the capabilities of OpenBabel beyond file format translation. Now that
there are scripting interfaces, these other uses of OpenBabel should be
more heavily 'promoted'.

> Thanks,
> -Geoff
> 
> P.S. Yes, I think it's good to have documentation (e.g., in the wiki)  
> on which classes are accessible from the scripting wrapper. I guess  
> eventually everything would be available, but some headers seem to  
> generate errors when first trying to wrap them.

>>> dir(openbabel.OBAtom)
['AddBond', 'AverageBondAngle', 'BOSum', 'BeginBond', 'BeginBonds',
'BeginNbrAtom', 'Clear', 'ClearBond', 'ClearCoordPtr',
'CountBondsOfOrder', 'CountFreeOxygens', 'DecrementImplicitValence',
'DeleteBond', 'DeleteResidue', 'EndBonds', 'ExplicitHydrogenCount',
'GetAngle', 'GetAtomicMass', 'GetAtomicNum', 'GetBond', 'GetCIdx',
'GetCoordinate', 'GetCoordinateIdx', 'GetDistance', 'GetExactMass',
'GetFormalCharge', 'GetHeteroValence', 'GetHvyValence', 'GetHyb',
'GetIdx', 'GetImplicitValence', 'GetIsotope', 'GetNewBondVector',
'GetNextAtom', 'GetPartialCharge', 'GetResidue', 'GetSpinMultiplicity',
'GetType', 'GetValence', 'GetVector', 'GetX', 'GetY', 'GetZ',
'HasAlphaBetaUnsat', 'HasAromaticBond', 'HasBondOfOrder',
'HasChiralVolume', 'HasChiralitySpecified', 'HasDoubleBond',
'HasNonSingleBond', 'HasResidue', 'HasSingleBond', 'HtoMethyl',
'ImplicitHydrogenCount', 'IncrementImplicitValence', 'InsertBond',
'IsAmideNitrogen', 'IsAntiClockwise', 'IsAromatic', 'IsAromaticNOxide',
'IsAxial', 'IsCarbon', 'IsCarboxylOxygen', 'IsChiral', 'IsClockwise',
'IsConnected', 'IsHbondAcceptor', 'IsHbondDonor', 'IsHbondDonorH',
'IsHeteroatom', 'IsHydrogen', 'IsInRing', 'IsInRingSize',
'IsNegativeStereo', 'IsNitroOxygen', 'IsNitrogen', 'IsNonPolarHydrogen',
'IsNotCorH', 'IsOneFour', 'IsOneThree', 'IsOxygen', 'IsPhosphateOxygen',
'IsPhosphorus', 'IsPolarHydrogen', 'IsPositiveStereo',
'IsSulfateOxygen', 'IsSulfur', 'KBOSum', 'MatchesSMARTS',
'MemberOfRingCount', 'MemberOfRingSize', 'NewResidue', 'NextBond',
'NextNbrAtom', 'SetAntiClockwiseStereo', 'SetAromatic', 'SetAtomicNum',
'SetChiral', 'SetClockwiseStereo', 'SetCoordPtr', 'SetFormalCharge',
'SetHyb', 'SetHybAndGeom', 'SetIdx', 'SetImplicitValence', 'SetInRing',
'SetIsotope', 'SetNegativeStereo', 'SetPartialCharge',
'SetPositiveStereo', 'SetResidue', 'SetSpinMultiplicity', 'SetType',
'SetVector', 'SmallestBondAngle', 'UnsetAromatic', 'UnsetStereo',
'__class__', '__del__', '__delattr__', '__dict__', '__doc__',
'__getattribute__', '__hash__', '__init__', '__module__', '__new__',
'__reduce__', '__reduce_ex__', '__repr__', '__setattr__', '__str__',
'__weakref__', 'x', 'y', 'z']

Is this useful documentation?

> 
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