Developer's Notes and Design Decisions for pyopenbabel.py
---------------------------------------------------------

The Atom class
==============

To find all of the GetVar() methods of the Atom class:

import openbabel
b = [x for x in openbabel.OBAtom.__dict__.keys() if x.startswith("Get")]
b.sort()
for c in b:
	print c

GetAngle		"NotImplementedError: No matching function for overloaded 'OBAtom_GetAngle'"
GetAtomicMass		== atomicmass
GetAtomicNum		== atomicnum
GetBond			needs two arguments
GetCIdx			== cidx
GetCoordinate		replaced by a .coords attribute containing a tuple (x,y,z) (also "Segmentation fault")
GetCoordinateIdx	== coordidx
GetData			== data
GetDistance		"NotImplementedError: No matching function for overloaded 'OBAtom_GetDistance'"
GetExactMass		== exactmass
GetFormalCharge		== formalcharge
GetHeteroValence	== heterovalence
GetHvyValence		== heavyvalence (if hetero isn't abbreviated, then neither should heavy)
GetHyb			== hyb
GetIdx			== idx
GetImplicitValence	== implicitvalence
GetIsotope		== isotope
GetNewBondVector	needs three arguments
GetNextAtom		not required (given a Molecule, you can loop through the atoms)
GetPartialCharge	== partialcharge
GetResidue		"Segmentation fault"
GetSpinMultiplicity	== spin
GetType			== type
GetValence		== valence
GetVector		== vector
GetX			replaced by a .coords attribute containing a tuple (x,y,z)
GetY			replaced by a .coords attribute containing a tuple (x,y,z)
GetZ			replaced by a .coords attribute containing a tuple (x,y,z)

All attributes are calculated on-the-fly when you ask for them. They are also initialised when you create the Atom object, so that dir(myatom) gives a useful list of attributes.

The Molecule class
==================

To find all of the GetVar() methods of the Molecule class:

import openbabel
b = [x for x in openbabel.OBMol.__dict__.keys() if x.startswith("Get")]
b.sort()
for c in b:
	print c

GetAtom			replaced by a .atoms attributes containing a list of Atoms
GetBond			(to be)replaced by a .bonds attributes containing a list of Bonds
GetConformer		needs two arguments
GetConformers		== conformers
GetCoordinates		== coords
GetData			== data
GetDimension		== dim
GetEnergy		== energy
GetExactMass		== exactmass
GetFirstAtom		not required (can use .atoms attribute instead)
GetFlags		== flags
GetFormula		== formula
GetGIDVector		needs two arguments
GetGIVector		needs two arguments
GetGTDVector		== gtdvector
GetInternalCoord	== internalcoord (or internalcoords??)
GetMod			== mod
GetMolWt		== molwt
GetResidue		needs two arguments
GetSSSR			== sssr
GetTitle		== title
GetTorsion		"NotImplementedError: No matching function for overloaded 'OBMol_GetTorsion'"
GetTotalCharge		== charge
GetTotalSpinMultiplicity	== spin

All attributes are calculated on-the-fly when you ask for them. They are also initialised when you create the Molecule object, so that dir(mymolecule) gives a useful list of attributes.

Added an iterator over the atoms of the molecule so that you can do things like:

for atom in mymol:
   print atom

Creating a Molecule from a String
=================================
Replaced:
from openbabel import *
mymol = OBMol()
obConversion = OBConversion()
obConversion.SetInFormat("smi")
obConversion.ReadString(mymol,"C1=CC=CS1")

With:
from pyopenbabel import *
mymol = readstring("smi","C1=CC=CS1")

Reading a Molecule From a File
==============================

TODO

Writing a Molecule To a File (continued from either of the examples above)
============================

Replaced:
obConversion.SetOutFormat("smi")
obConversion.WriteFile(mymol,"tmp.txt")

With:
mymol.write("smi",tmp.txt")

Bug Converting To and From Smiles Strings?
==========================================
from openbabel import *
mymol = OBMol()
obConversion = OBConversion()
obConversion.SetInAndOutFormats("smi","smi")
obConversion.ReadString(mymol,"C1=CC=CS1")
print obConversion.WriteString(mymol)
'c1sccc1\t\n'
-- should remove the \t and \n