[chimera-dev] residue.atoms, atom.bonds, coords, static class methods

[Eric Pettersen]

This is a heads up that the next release of Chimera (ETA some time this 
summer) will have had a major reworking of the internals, which will 
have some visible effects in the Python layer.  There will be four 
important Python-layer changes:

1)  The Residue class method atoms() will return a list of Atoms.
	Currently atoms() returns a dictionary keyed with atom names that 
yields a list of Atoms with the corresponding name.  This makes it 
awkward to simply iterate through the atoms of a residue, although the 
somewhat-obscure method oslChildren() of Residue does currently return 
a list of Atoms (and will continue to do so).
	A list of the atom names will be available as atomNames().
	The name->atom-list dictionary will remain available, but will be 
named atomsMap().

2) The Atom class method bonds() will return a list of Bonds.
	Currently bonds() is a dictionary whose keys are the Atoms bound to 
this atom, and whose values are the Bonds connecting them.  Instead, 
the bonds() method will return a list of the Bonds, and the neighbors() 
method will return a list of the bonded Atoms (in the same order).  The 
old bonds() functionality will remain available as the bondsMap() 
method.

3) Coord goes away
	The coord() and xformCoord() methods will return Points instead of 
Coords.  Relevant methods of Coord (e.g. dist(), sqDist()) will be 
added to Point.

4) Class method renaming
	Class methods names were indicated by a leading class name and 
underscore (e.g. Xform_identity()).  Now they are indicated with the 
class name followed by a dot (e.g. Xform.identity()).

	
                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         pett at cgl.ucsf.edu
                         http://www.cgl.ucsf.edu
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