Find new names for confusing Atom attribute names (e.g., residId)

[charlestonchas]

Attributes of class Atom are currently named using camelCase and include the lowercase name of the class, which can be redundant or clumsy

For example, if an Atom object is named atom1, accessing its attributes involves writing atom twice. Also, because "resid" was chosen instead of "residue" or "res", one has the unfortunate attribute name residId. Here are some current examples of referencing these attributes:

• atom1.atomId # atom index number
• atom1.atomType # CA, N, HN1, ...
• atom1.atomElement # C, N, H, O, etc.
• atom1.residId # residue number of the residue the atom is in
• atom1.residType # LEU, ARG, ...
• atom1.chainId # A, B, etc.
• atom1.atomCharge # atom charge
• atom1.extra # extra data

Suggested changes:

• atom1.id # atom index number (*)
• atom1.type # CA, N, HN1, ...
• atom1.element # C, N, H, O, etc.
• atom1.resid # residue number of the residue the atom is in
• atom1.restype # LEU, ARG, ...
• atom1.chainid # A, B, etc.
• atom1.charge # atom charge
• atom1.extra # extra data

* Note that id and type technically clash with the reserved python words, but I don't think they introduce very much chance of confusion.

[chantalprevost]

This an be modified when modifying the nomenclature. resId was the most appropriate with the former nomenclature.