PoissonBoltzmannPotential.cc File Reference

PoissonBoltzmann potential class implementation. More...

#include <basic/Tracer.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/pb_potential.OptionKeys.gen.hh>
#include <core/scoring/PoissonBoltzmannPotential.hh>
#include <core/scoring/electron_density/util.hh>
#include <core/chemical/ResidueType.hh>
#include <core/conformation/Residue.hh>
#include <core/pose/Pose.hh>
#include <core/pose/init_id_map.hh>
#include <utility/file/file_sys_util.hh>
#include <utility/io/izstream.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/FArray3D.hh>
#include <numeric/xyzMatrix.hh>
#include <numeric/xyzVector.hh>
#include <utility/vector1.hh>
#include <ctime>
#include <fstream>

Namespaces
	core
	A class for reading in the atom type properties.
	core::scoring

Typedefs
using	core::scoring::PB = PoissonBoltzmannPotential

Functions
static basic::Tracer	TR ("core.scoring.PoissonBoltzmannPotential")
static std::string const	chr_chains ("ABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789!@#$&.<>?]{}|-_\\~=%zyxwvutsrqponmlkjihgfedcbaABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789!@#$&.<>?]{}|-_\\~=%zyxwvutsrqponmlkjihgfedcbaABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789!@#$&.<>?]{}|-_\\~=%zyxwvutsrqponmlkjihgfedcbaABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789!@#$&.<>?]{}|-_\\~=%zyxwvutsrqponmlkjihgfedcbaABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789!@#$&.<>?]{}|-_\\~=%zyxwvutsrqponmlkjihgfedcbaABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789!@#$&.<>?]{}|-_\\~=%zyxwvutsrqponmlkjihgfedcbaABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789!@#$&.<>?]{}|-_\\~=%zyxwvutsrqponmlkjihgfedcbaABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789!@#$&.<>?]{}|-_\\~=%zyxwvutsrqponmlkjihgfedcba")

Detailed Description

PoissonBoltzmann potential class implementation.

Compute electrostatic.

Options:

vector1<Integer> pb_potential::charged_chain The chain numbers (>=1) of which charge is non-zero. The electrostatic will be computed for the atoms in these chains.

Author

Yifan Song (yfson.nosp@m.g@uw.nosp@m..edu)

Function Documentation

chr_chains()

static std::string const chr_chains ( )

static

Referenced by core::import_pose::RNA_DeNovoSetup::de_novo_setup_from_options(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_residue_information(), core::pose::PDBInfo::PDBInfo(), and core::scoring::PoissonBoltzmannPotential::write_pqr().

TR()

static basic::Tracer TR ( "core.scoring.PoissonBoltzmannPotential"  )

static