correction, not 168 through 211 in brackets for the out: {} block, but
rather 168 through 183. Iterating over the bonds isn't part of the
iterations for computing electronegativity. All the more reason to enclose
in brackets :]
- Eric
On Wed, Dec 21, 2011 at 1:15 AM, Eric Jang <ericjang2...@gmail.com> wrote:
> Hello!
>
> Might I make a couple suggestions regarding
> the GasteigerMarsiliPartialCharges.java calculation....
>
> - it would be a good idea to enclose lines 168 through 211 in brackets.
> more easier to understand where the 'out:' label breaks out of.
>
> - starting from line 206:
> q = (gasteigerFactors[STEP_SIZE * atom1 + atom1 + 4] -
> gasteigerFactors[STEP_SIZE * atom2 + atom2 + 4]) / deoc;
> gasteigerFactors[STEP_SIZE * atom1 + atom1 + 5] -= (q*alpha);
> gasteigerFactors[STEP_SIZE * atom2 + atom2 + 5] += (q*alpha);
>
> I suggest that q should be renamed to deltaQ, because q is the symbol for
> the partial charge while deltaQ is the more accurate description. q is
> actually supposed to be gasteigerFactors[STEP_SIZE * atom1 + atom1 + 5]
>
> - in the beginning of the file, STEP_SIZE defined as 6; There are 6 values
> being stored per atom anyway, so we could represent, say, q
> using [STEP_SIZE * atom1 + 5]. Works out fine because the array starts at 0
> anyway.
>
> otherwise, thanks for this great implementation! Made my day today :]
>
> - Eric
>
------------------------------------------------------------------------------
Write once. Port to many.
Get the SDK and tools to simplify cross-platform app development. Create
new or port existing apps to sell to consumers worldwide. Explore the
Intel AppUpSM program developer opportunity. appdeveloper.intel.com/join
http://p.sf.net/sfu/intel-appdev
_______________________________________________
Cdk-user mailing list
Cdk-user@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/cdk-user
