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
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