Here are some ways to improve hbonds.cc from OptimizingRosetta.

• hbonds.cc: original hbonds.cc

The energy function

The function used comes from Kortemme et al., and sums independent functions on distance and angles of the AH bond.

• Kortemme-JMB-v326-p1239.pdf: An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes, Kortemme, T., Morozov, A. V., Baker, D., J Mol Biol 326: (4) 1239-59 Feb 28 2003
• Kortemme_suppl_tables.doc: Supplementary tables
• Polynomials are used to evaluate functions of distance and angles for hbonds.
  • PlotsofKortemme.doc: My plots of the polynomials used for hbond energies
  • hbondDB.m: MATLAB function to plot polynomials from hbond_db.cc

hbond_compute_energy()

Precompute unit vectors for cosine calculations

Normalized Donor-Hydrogen (DH) and Acceptor-Base (AA1) vectors are used to compute cosines for hydrogen bond energy. These can be precomputed, and only the normalized AH vector computed in the loop.

Precompute most of the bond classification

min/max cutoffs

The min/max cutoffs could depend on the type of bond. This would require classifying bonds first, however. On the other hand, the function now compares and clamps on output, which it can easily do on input.

Lower degree polynomials

Can we find lower degree polynomials with same interpolating power?

hbond_polynomial()

Include offset and scale with polynomial coefficients

There are some post-polynomial evaluations that could be pushed into the polynomial.

Jump table to unrolled polynomial evaluation

At the moment, the code computes one of 16 polynomials from coefficients in a table. Since the polynomials are of degree 2 or 7, we might unroll and inline this code, and select with a switch, which the compiler should make into a jump table.

Horner's rule

Horner's rule saves multiplications, and lets you compute polynomial and derivative at the same time. Changed

   int fdegree = poly_degree(table); // offset for arrays
   for ( int i = 1, l = coeff.index(i,table); i <= fdegree; ++i, ++l ) {
      value += coeff[ l ] * term; // coeff(i,table)
      term *= variable;
   }
   term = 1.0;
   for ( int i = 2, l = coeff.index(i,table); i <= fdegree; ++i, ++l ) {
      derivative += (i-1) * coeff[ l ] * term; // coeff(i,table)
      term *= variable;
   }
   value -= offset(table);

---

   int fdegree = poly_degree(table); // offset for arrays
  int i = fdegree, l = coeff.index(i,table);
   accum = daccum = coeff[l]; // initial value of poly & deriv;
   for (i--, l--; i > 1; i--, l-- ) { // jss assume at least 2 terms
         accum = coeff[l] + variable*accum; // Horner's rule
         daccum = accum + variable*daccum; //  " for derivs
   }
   accum = coeff[l] + variable*accum; // deriv stops one earlier; finish polynomial

-- JackSnoeyink - 24 Mar 2005

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