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6. JOBTYPE point_energy and JOBTYPE sasa_calc

6.1 Overview

JOBTYPE point_energy prints to stdout the energy components for an inputted TEMPLATE_PDB structure. Defining OUTPUT_PREFIX is not necessary, since the output is printed to stdout. JOBTYPE sasa_calc is the same, except that SASA also are printed out on a per-residue basis.

If REBUILD_FLAG 0 (default), a WARNING is printed to stderr, since hydrogens may be missing, resulting in incorrect energies.

See examples/point_energy/point_energy_without_rebuild.output and examples/point_energy/point_energy_with_rebuild.output for sample output with and without rebuilding (REBUILD_FLAG 1). The energy outputs are similar to those described below in the ouput pdb file section. For JOBTYPE sasa_calc, see examples/sasa_calc/.

The differences between rebuilding and not rebuilding can be significant. In general, for the sake of consistency with other jobs that rebuild sidechains with ideal bond geometry and hydrogens, it is best to use REBUILD_FLAG 1. However, since this jobtype is used primarily for diagnostics, it was felt that it would be best to leave that decision to the user.

6.2 Implementation details

In main, after protein has returned from input_stuff.cpp: input_stuff, if protein->parameters.algorithm is "POINT_ENERGY", protein->mini_Template is sent to energy_functions.cpp: energy_calc. The components of the returned ENERGY struct are printed to stdout, along with the SASA components stored in SASA_SUM_TEMP.

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