Hi Tim,
First off, it's good to hear from you again :-) I'm glad you're still
active in the community.
On Thu, Nov 10, 2011 at 11:23 AM, Tim Vandermeersch
<tim.vandermeer...@gmail.com> wrote:
> On Thu, Nov 10, 2011 at 4:32 PM, David Lonie <lonieda...@gmail.com> wrote:
>> In atom.h, there are the following three functions:
>>
>> //! \return the internal atom index (e.g., inside an OBMol)
>> unsigned int GetIdx() const { return((int)_idx); }
>> unsigned int GetIndex() const { return _idx - 1; }
>> unsigned long GetId() const { return _id; }
>>
>> Can someone explain and/or document these in a bit more detail? I was
>> quite surprised that GetIdx and GetIndex are defined differently. What
>> is the role of _idx vs _id? Is there a reason that in GetIdx _idx is
>> cast from uint->int, then (implicitly) back to a uint?
>
> The idx is an atom index that goes from 1 to N (N = number of atoms).
> This is the _idx field and can be retreived using GetIdx().
>
> The index (GetIndex()) is also an atom index but starts from 0 (0 to
> N-1). This is the _idx - 1 field. This function was added for more
> conformance to the bond indexes which start from 0.
>
> The _id (GetId()) field is a unique id that does not change if atoms
> are deleted and can be to identify atoms during an OBMol's lifespan.
>
>> The reason I ask is that I'm trying to limit an OBFF calculation with
>> OBForceField::AddInt[er,ra]Group[s], which takes the atom index, but
>> it's not clear to me whether this means the index, the idx, or the id.
>
> You usually have to see at the specific code.
That is much clearer. I'll add this to the docs later today.
Thanks,
Dave
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