Rosetta Core  2014.35
Namespaces | Functions | Variables File Reference

A class for defining atom parameters, known as atom_types. More...

#include <core/chemical/AtomType.hh>
#include <utility/exit.hh>
#include <basic/Tracer.hh>
#include <algorithm>


 A class for reading in the atom type properties.


std::ostream & core::chemical::operator<< (std::ostream &out, const AtomType &atom_type)


Real const core::chemical::MAX_CHEMICAL_BOND_TO_HYDROGEN_LENGTH = { 1.35 }
 Maximum distance between a heavy atom and a hydrogen atom to which it is chemically bound Set in .cc file. More...

Detailed Description

A class for defining atom parameters, known as atom_types.

This class contains the "chemical" information for atoms. This does not contain the actual xyz coordinates of the class (xyz found in core/conformation/Atom.hh. The atom_type properties are assigned by the class AtomTypeSet which is initiated from the ChemicalManager. Atom type properties are currently are read in from the file located chemical/atom_type_sets/fa_standard/atom_properties.txt. These properties contain the the properties of LJ_RADIUS, LJ_WDEPTH, LK_DGRFREE, LK_LAMBDA, LK_VOLUME. These properties are used in the scoring function fa_atr, fa_rep, fa_sol, which is located in the Etable (core/scoring/etable/Etable.hh) Additional parameters are acceptor/donor, hybridization, and orbital parameters.

Phil Bradley
Steven Combs - comments