Rosetta 3.4
Namespaces | Typedefs | Functions | Variables
core Namespace Reference

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

Namespaces

namespace  chemical
namespace  coarse
namespace  conformation
namespace  fragment
namespace  graph
namespace  grid
namespace  id
namespace  import_pose
namespace  io
namespace  kinematics
 

See AtomTree overview and FoldTree overview for details.


namespace  optimization
namespace  pack
namespace  pose
namespace  scoring
namespace  sequence
namespace  util

Typedefs

typedef platform::Size Size
typedef platform::SSize SSize
typedef platform::uint uint
typedef platform::Real Real
typedef unsigned short ShortSize
typedef Real Length
typedef Real LengthSquared
typedef Real Distance
typedef Real DistanceSquared
typedef Real Volume
typedef Real Angle
typedef Real Trig
typedef Real Mass
typedef Real Charge
typedef Real Energy
typedef Real EnergyDerivative
typedef float PackerEnergy
typedef numeric::xyzVector
< Length
PointPosition
typedef numeric::xyzVector
< Length
Vector
typedef numeric::xyzVector
< EnergyDerivative
EnergyGradient

Functions

static basic::Tracer TR ("core.init")
void init (int argc, char *argv[])
 Init basic core systems: options system, random system.
void init (utility::vector1< std::string > const &args)
 wrapper for core system Init
void init_random_generators (int const start_seed, RND_RunType run_type, std::string const &RGtype)
 Initialize random generator systems (and send debug io to tracer with seed/mode info).
void init_random_generators (int const start_seed, numeric::random::RND_RunType run_type, std::string const &RGtype)
 Initialize random generator systems (and send debug io to tracer with seed/mode info).
std::string minirosetta_svn_version ()
std::string minirosetta_svn_url ()

Variables

static EnergyMethodRegistrator
< scoring::constraints::ConstraintsEnergyCreator
ConstraintsEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::disulfides::CentroidDisulfideEnergyCreator
CentroidDisulfideEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::disulfides::DisulfideMatchingEnergyCreator
DisulfideMatchingEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::disulfides::FullatomDisulfideEnergyCreator
FullatomDisulfideEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::etable::EtableEnergyCreator
EtableEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::hbonds::HBondEnergyCreator
HBondEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::methods::ChainbreakEnergyCreator
ChainbreakEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::methods::CenPairEnergyCreator
CenPairEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::methods::ContactOrderEnergyCreator
ContactOrderEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::methods::EnvEnergyCreator
EnvEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::methods::EnvSmoothEnergyCreator
EnvSmoothEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::methods::OmegaTetherEnergyCreator
OmegaTetherEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::methods::P_AA_EnergyCreator
P_AA_EnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::methods::P_AA_pp_EnergyCreator
P_AA_pp_EnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::methods::PackStatEnergyCreator
PackStatEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::methods::PairEnergyCreator
PairEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::methods::PeptideBondEnergyCreator
PeptideBondEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::methods::ProClosureEnergyCreator
ProClosureEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::methods::BurialEnergyCreator
BurialCreator_registrator
static EnergyMethodRegistrator
< scoring::methods::RG_Energy_FastCreator
RG_Energy_FastCreator_registrator
static EnergyMethodRegistrator
< scoring::methods::SA_EnergyCreator
SA_EnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::methods::RMS_EnergyCreator
RMS_EnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::methods::RamachandranEnergy2BCreator
RamachandranEnergy2BCreator_registrator
static EnergyMethodRegistrator
< scoring::methods::RamachandranEnergyCreator
RamachandranEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::methods::ReferenceEnergyCreator
ReferenceEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::methods::SecondaryStructureEnergyCreator
SecondaryStructureEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::methods::VDW_EnergyCreator
VDW_EnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::methods::dfire::DFIRE_EnergyCreator
DFIRE_EnergyCreator_registrator
static EnergyMethodRegistrator
< pack::dunbrack::DunbrackEnergyCreator
DunbrackEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::nv::NVscoreCreator
NVscoreCreator_registrator
static EnergyMethodRegistrator
< scoring::orbitals::OrbitalsScoreCreator
OrbitalsScoreCreator_registrator
static EnergyMethodRegistrator
< scoring::interface::DDPscoreCreator
DDPscoreCreator_registrator
static EnergyMethodRegistrator
< scoring::carbon_hbonds::CarbonHBondEnergyCreator
CarbonHBondEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::custom_pair_distance::FullatomCustomPairDistanceEnergyCreator
FullatomCustomPairDistanceEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::methods::CustomAtomPairEnergyCreator
CustomAtomPairEnergy_registrator
static EnergyMethodRegistrator
< scoring::electron_density::FastDensEnergyCreator
FastDensEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::electron_density::ElecDensCenEnergyCreator
ElecDensCenEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::electron_density::ElecDensAllAtomCenEnergyCreator
ElecDensAllAtomCenEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::electron_density::ElecDensEnergyCreator
ElecDensEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::electron_density::PattersonCorrEnergyCreator
PattersonCorrEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::electron_density_atomwise::ElecDensAtomwiseEnergyCreator
ElecDensAtomwiseEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::geometric_solvation::ExactOccludedHbondSolEnergyCreator
ExactOccludedHbondSolEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::geometric_solvation::GeometricSolEnergyCreator
GeometricSolEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::geometric_solvation::ContextIndependentGeometricSolEnergyCreator
ContextIndependentGeometricSolEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::geometric_solvation::OccludedHbondSolEnergyCreator
OccludedHbondSolEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::geometric_solvation::OccludedHbondSolEnergy_onebodyCreator
OccludedHbondSolEnergy_onebodyCreator_registrator
static EnergyMethodRegistrator
< scoring::hackelec::HackElecEnergyCreator
HackElecEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::hackelec::RNAHackElecEnergyCreator
RNAHackElecEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::hackelec::HackElecEnergyAroAroCreator
HackElecEnergyAroAroCreator_registrator
static EnergyMethodRegistrator
< scoring::hackelec::HackElecEnergyAroAllCreator
HackElecEnergyAroAllCreator_registrator
static EnergyMethodRegistrator
< scoring::hackaro::HackAroEnergyCreator
HackAroEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::methods::DNA_BaseEnergyCreator
DNA_BaseEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::methods::DirectReadoutEnergyCreator
DirectReadoutEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::methods::DistanceChainbreakEnergyCreator
DistanceChainbreakEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::methods::Fa_MbenvEnergyCreator
Fa_MbenvEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::methods::Fa_MbsolvEnergyCreator
Fa_MbsolvEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::methods::GenBornEnergyCreator
GenBornEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::methods::HybridVDW_EnergyCreator
HybridVDW_EnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::methods::LK_CosThetaEnergyCreator
LK_CosThetaEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::methods::LK_hackCreator
LK_hackCreator_registrator
static EnergyMethodRegistrator
< scoring::methods::LK_BallEnergyCreator
LK_BallEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::methods::LinearChainbreakEnergyCreator
LinearChainbreakEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::methods::MMBondAngleEnergyCreator
MMBondAngleEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::methods::CartesianBondedEnergyCreator
CartesianBondedEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::methods::MMBondLengthEnergyCreator
MMBondLengthEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::methods::MMTorsionEnergyCreator
MMTorsionEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::methods::MMLJEnergyInterCreator
MMLJEnergyInterCreator_registrator
static EnergyMethodRegistrator
< scoring::methods::MMLJEnergyIntraCreator
MMLJEnergyIntraCreator_registrator
static EnergyMethodRegistrator
< scoring::methods::MembraneCbetaEnergyCreator
MembraneCbetaEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::methods::MembraneCenPairEnergyCreator
MembraneCenPairEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::methods::MembraneEnvEnergyCreator
MembraneEnvEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::methods::MembraneEnvPenaltiesCreator
MembraneEnvPenaltiesCreator_registrator
static EnergyMethodRegistrator
< scoring::methods::SmoothCenPairEnergyCreator
SmoothCenPairEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::methods::SmoothEnvEnergyCreator
SmoothEnvEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::methods::CenHBEnergyCreator
CenHBEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::methods::MembraneLipoCreator
MembraneLipoCreator_registrator
static EnergyMethodRegistrator
< scoring::methods::MembraneEnvSmoothEnergyCreator
MembraneEnvSmoothEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::methods::pHEnergyCreator
pHEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::methods::ResidualDipolarCouplingEnergyCreator
ResidualDipolarCouplingEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::methods::ResidualDipolarCouplingEnergy_RohlCreator
ResidualDipolarCouplingEnergy_RohlCreator_registrator
static EnergyMethodRegistrator
< scoring::methods::SuckerEnergyCreator
SuckerEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::methods::YHHPlanarityEnergyCreator
YYHPlanarityEnergyCreator_registrator
static EnergyMethodRegistrator
< pack::interaction_graph::SurfaceEnergyCreator
SurfaceEnergyCreator_registrator
static EnergyMethodRegistrator
< pack::interaction_graph::HPatchEnergyCreator
HPatchEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::methods::SymmetricLigandEnergyCreator
SymmetricLigandEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::methods::UnfoldedStateEnergyCreator
UnfoldedStateEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::methods::WaterAdductHBondEnergyCreator
WaterAdductHBondEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::methods::WaterAdductIntraEnergyCreator
WaterAdductIntraEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::packing::HolesEnergyCreator
HolesEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::packing::SurfVolEnergyCreator
SurfVolEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::packing::SurfEnergyCreator
SurfEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::rna::RG_Energy_RNACreator
RG_Energy_RNACreator_registrator
static EnergyMethodRegistrator
< scoring::rna::RNA_BulgeEnergyCreator
RNA_BulgeEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::rna::RNA_DataBackboneEnergyCreator
RNA_DataBackboneEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::rna::RNA_FullAtomStackingEnergyCreator
RNA_FullAtomStackingEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::rna::RNA_LJ_BaseEnergyCreator
RNA_LJ_BaseEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::rna::RNA_PairwiseLowResolutionEnergyCreator
RNA_PairwiseLowResolutionEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::rna::RNA_SugarCloseEnergyCreator
RNA_SugarCloseEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::rna::RNA_TorsionEnergyCreator
RNA_TorsionEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::rna::RNA_VDW_EnergyCreator
RNA_VDW_EnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::rna::RNA_FullAtomVDW_BasePhosphateCreator
RNA_FullAtomVDW_BasePhosphateCreator_registrator
static EnergyMethodRegistrator
< scoring::sym_e::symECreator
symECreator_registrator
static EnergyMethodRegistrator
< scoring::methods::PoissonBoltzmannEnergyCreator
PoissonBoltzmannEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::saxs::FastSAXSEnergyCreator
FastSAXSEnergyCreator_registrator
static EnergyMethodRegistrator
< scoring::saxs::SAXSEnergyCreatorCEN
SAXSEnergyCreatorCEN_registrator
static EnergyMethodRegistrator
< scoring::saxs::SAXSEnergyCreatorFA
SAXSEnergyCreatorFA_registrator
static EnergyMethodRegistrator
< scoring::saxs::SAXSEnergyCreator
SAXSEnergyCreator_registrator
static ConstraintRegistrator
< core::scoring::constraints::AmbiguousConstraintCreator
AmbiguousConstraintCreator_registrator
static ConstraintRegistrator
< core::scoring::constraints::AmbiguousNMRConstraintCreator
AmbiguousNMRConstraintCreator_registrator
static ConstraintRegistrator
< core::scoring::constraints::AmbiguousNMRDistanceConstraintCreator
AmbiguousNMRDistanceConstraintCreator_registrator
static ConstraintRegistrator
< core::scoring::constraints::AngleConstraintCreator
AngleConstraintCreator_registrator
static ConstraintRegistrator
< core::scoring::constraints::AtomPairConstraintCreator
AtomPairConstraintCreator_registrator
static ConstraintRegistrator
< core::scoring::constraints::BigBinConstraintCreator
BigBinConstraintCreator_registrator
static ConstraintRegistrator
< core::scoring::constraints::CoordinateConstraintCreator
CoordinateConstraintCreator_registrator
static ConstraintRegistrator
< core::scoring::constraints::DihedralConstraintCreator
DihedralConstraintCreator_registrator
static ConstraintRegistrator
< core::scoring::constraints::DihedralPairConstraintCreator
DihedralPairConstraintCreator_registrator
static ConstraintRegistrator
< core::scoring::constraints::KofNConstraintCreator
KofNConstraintCreator_registrator
static ConstraintRegistrator
< core::scoring::constraints::LocalCoordinateConstraintCreator
LocalCoordinateConstraintCreator_registrator
static ConstraintRegistrator
< core::scoring::constraints::MultiConstraintCreator
MultiConstraintCreator_registrator
static ConstraintRegistrator
< core::pack::dunbrack::DunbrackConstraintCreator
DunbrackConstraintCreator_registrator
static ConstraintRegistrator
< core::scoring::constraints::SiteConstraintCreator
SiteConstraintCreator_registrator
static ConstraintRegistrator
< core::scoring::constraints::SequenceProfileConstraintCreator
SequenceProfileConstraintCreator_registrator
static SilentStructRegistrator
< core::io::silent::ProteinSilentStructCreator
ProteinSilentStructCreator_registrator
static SilentStructRegistrator
< core::io::silent::ProteinSilentStruct_SinglePrecCreator
ProteinSilentStruct_SinglePrecCreator_registrator
static SilentStructRegistrator
< core::io::silent::RNA_SilentStructCreator
RNA_SilentStructCreator_registrator
static SilentStructRegistrator
< core::import_pose::PDBSilentStructCreator
PDBSilentStructCreator_registrator
static SilentStructRegistrator
< core::io::silent::BinaryProteinSilentStructCreator
BinaryProteinSilentStructCreator_registrator
static SilentStructRegistrator
< core::io::silent::ScoreFileSilentStructCreator
ScoreFileSilentStructCreator_registrator
static SilentStructRegistrator
< core::io::silent::BinaryRNASilentStructCreator
BinaryRNASilentStructCreator_registrator
static SequenceRegistrator
< core::sequence::SimpleSequenceCreator
SimpleSequenceCreator_registrator
static SequenceRegistrator
< core::sequence::SequenceProfileCreator
SequenceProfileCreator_registrator
static SequenceRegistrator
< core::sequence::SequenceCouplingCreator
SequenceCouplingCreator_registrator
static SequenceRegistrator
< core::sequence::CompositeSequenceCreator
CompositeSequenceCreator_registrator
static
TaskOperationRegistrator
< RestrictYSDesignCreator
RestrictYSDesignCreator_registrator
static
TaskOperationRegistrator
< PreventRepackingCreator
PreventRepackingCreator_registrator
static
TaskOperationRegistrator
< PreserveCBetaCreator
PreserveCBetaCreator_registrator
static
TaskOperationRegistrator
< AppendRotamerSetCreator
AppendRotamerSetCreator_registrator
static
TaskOperationRegistrator
< AppendRotamerCreator
AppendRotamerCreator_registrator
static
TaskOperationRegistrator
< SetRotamerCouplingsCreator
SetRotamerCouplingsCreator_registrator
static
TaskOperationRegistrator
< SetRotamerLinksCreator
SetRotamerLinksCreator_registrator
static
TaskOperationRegistrator
< ReadResfileCreator
ReadResfileCreator_registrator
static
TaskOperationRegistrator
< ReadResfileAndObeyLengthEventsCreator
ReadResfileAndObeyLengthEventsCreator_registrator
static
TaskOperationRegistrator
< IncludeCurrentCreator
IncludeCurrentCreator_registrator
static
TaskOperationRegistrator
< InitializeExtraRotsFromCommandlineCreator
InitializeExtraRotsFromCommandlineCreator_registrator
static
TaskOperationRegistrator
< InitializeFromCommandlineCreator
InitializeFromCommandlineCreator_registrator
static
TaskOperationRegistrator
< ExtraRotamersGenericCreator
ExtraRotamersGenericCreator_registrator
static
TaskOperationRegistrator
< RotamerExplosionCreator
RotamerExplosionCreator_registrator
static
TaskOperationRegistrator
< RestrictAbsentCanonicalAASCreator
RestrictAbsentCanonicalAASCreator_registrator
static
TaskOperationRegistrator
< DisallowIfNonnativeCreator
DisallowIfNonnativeCreator_registrator
static
TaskOperationRegistrator
< RestrictResidueToRepackingCreator
RestrictResidueToRepackingCreator_registrator
static
TaskOperationRegistrator
< RestrictToRepackingCreator
RestrictToRepackingCreator_registrator
static
TaskOperationRegistrator
< OperateOnCertainResiduesCreator
OperateOnCertainResiduesCreator_registrator
static
TaskOperationRegistrator
< NoRepackDisulfidesCreator
NoRepackDisulfidesCreator_registrator
static
TaskOperationRegistrator
< ReplicateTaskCreator
ReplicateTaskCreator_registrator
static
TaskOperationRegistrator
< OptCysHGCreator
OptCysHGCreator_registrator
static
TaskOperationRegistrator
< OptHCreator
OptHCreator_registrator
static
ResLvlTaskOperationRegistrator
< RestrictToRepackingRLTCreator
RestrictToRepackingRLTCreator_registrator
static
ResLvlTaskOperationRegistrator
< RestrictAbsentCanonicalAASRLTCreator
RestrictAbsentCanonicalAASRLTCreator_registrator
static
ResLvlTaskOperationRegistrator
< DisallowIfNonnativeRLTCreator
DisallowIfNonnativeRLTCreator_registrator
static
ResLvlTaskOperationRegistrator
< PreventRepackingRLTCreator
PreventRepackingRLTCreator_registrator
static
ResLvlTaskOperationRegistrator
< AddBehaviorRLTCreator
AddBehaviorRLTCreator_registrator
static ResFilterRegistrator
< ResidueHasPropertyCreator
ResidueHasPropertyCreator_registrator
static ResFilterRegistrator
< ResidueLacksPropertyCreator
ResidueLacksPropertyCreator_registrator
static ResFilterRegistrator
< ResidueName3IsCreator
ResidueName3IsCreator_registrator
static ResFilterRegistrator
< ResidueName3IsntCreator
ResidueName3IsntCreator_registrator
static ResFilterRegistrator
< ResidueIndexIsCreator
ResidueIndexIsCreator_registrator
static ResFilterRegistrator
< ResidueIndexIsntCreator
ResidueIndexIsntCreator_registrator
static ResFilterRegistrator
< ResiduePDBIndexIsCreator
ResiduePDBIndexIsCreator_registrator
static ResFilterRegistrator
< ResiduePDBIndexIsntCreator
ResiduePDBIndexIsntCreator_registrator
static ResFilterRegistrator
< ChainIsCreator
ChainIsCreator_registrator
static ResFilterRegistrator
< ChainIsntCreator
ChainIsntCreator_registrator
static const Size SZ_MIN = std::numeric_limits<Size>::min()
static const Size SZ_MAX = std::numeric_limits<Size>::max()

Detailed Description

A class for defining atom parameters, known as atom_types.

Package Headers.

Utility headers.

A class for generating statistics from orbitals.

you cannot #include yourself #include <core/scoring/mm/MMBondLengthScore.hh>

REPLACE THIS WITH .fwd.hh.

#include <core/pack/rotamer_set/RotamerSetFactory.hh>

Unit Headers.

A class for generating the table for fa_atr/rep and fa_sol.

#define APL_TEMP_DEBUG

A class for scoring fa_atr, fa_rep, fa_sol.

cant get to compile w/ Func.fwd.hh

Declaration of the base class for TaskOperation factory registration and creation.

Base class for TaskOperation factory-registration and creation classes.

Declaration of the base class for ResLvlTaskOperation factory registration and creation.

Base class for ResLvlTaskOperation factory-registration and creation classes.

Declaration of the base class for ResFilter factory registration and creation.

Base class for ResFilter factory-registration and creation classes.

ObjexxFCL.

Debugging headers.

#include <core/pack/dunbrack/SingleResidueDunbrackLibrary.tmpl.hh>

Numeric headers.

Unit headers.

Utility Headers.

Project Headers.

Project headers.

some utils for fragments

some utilities for fragments

right now there isnt a canonical mapping from nodes back to atom objects.

The conformation class of the atom object.

RNA specific properties.

A class for defining residue.

implementation class for abstract class Residue

A class that contains orbital parameters.

A class for reading in the orbital type properties.

Chemical manager class.

A class for reading in the atom type properties.

AtomType

Detailed:
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, hybridzation, and orbital paramaters.
Authors:
Phil Bradley Steven Combs - comments
Last Modified: December 6 2010

AtomTypeSet

Detailed:
This class reads in the atom_properties.txt file which contains the "chemical" information for atoms. This does not contain the actual properties, but sets the properties through the AtomType class. This class is called by the ChemicalManager
Authors:
Phil Bradley Steven Combs - comments
Last Modified: December 6 2010

ChemicalManager

Detailed:
The Chemical Manager is a singleton class, which means that it can only been initialized once (exist once in memory). Once initialized, you can call it by simply access it via:

core::chemical::AtomTypeSetCAP atom_types = core::chemical::ChemicalManager::get_instance()->atom_type_set("fa_standard");

You can substitute AtomTypeSet, with whatever is seen below (residue_type_set, mm_atom_type_set, orbital_type_set). In the below functions, the "tag_in" refers to fullatom, centroid, which basically tells what type of set to load in. The chemical manager will call functions within the AtomTypeSet, MMAtomTypeSet, ResidueTypeSet, etc etc. The classes type set reads in files from the database to create atom types, residue types, and mmatom types. The information from those files are stored in the type class.

Authors:
Andrew Leaver-Fay (leaverfa@email.unc.edu) Steven Combs - comments
Last Modified: December 6 2010

AtomTypeSet

Detailed:
This class contains the ORBITALS INTERNAL_ICOOR data that is read in from residue_io.cc. Actually, the data is set when residue_io.cc calls the command from residuetype.cc set_orbital_icoor. The data is set and chills out in memory until needed. The actual xyz coordinates are not stored at this point. xyz coordinates are constructed when conformation/Residue.hh asks for the build function in this class. At that point, the coordinates are built and returned.

But wait, you say, why do you store the names of the atoms instead of the index of the atoms!? Well, the problem occurs when residuetype reorders the indices of the atoms. When this occurrs, the indices for the icoor are not reordered here. Another problem ocurs because orbital indices are not reordered in this process because orbital indices are seperate from the atom indices. Regardless, when you build the xyz coords, this step is transparent because the function orbital_xyz() in residue.hh takes care of this conversion of indice to string.

Note:
NOTE!!!!!!!!!!! The internal coordinates cannot contain an orbital as the stub1, stub2, or stub3 atom. This is because the xyz coordinates are not updated when the conformation changes. The stub1, stub2, stub2 atoms must be actual atoms and not orbitals!!!!! (design feature or flaw? you decide)
Authors:
Steven Combs
Last Modified: December 12 2010

OrbitalType.cc

Detailed:
This class contains the "chemical" information for orbitals. This does not contain the actual xyz coordinates of the class which is managed by the conformation/Residue.hh. The orbital_type properties are assigned by the class OrbitalTypeSet which is initiated from the ChemicalManager. Orbital type properties are currently are read in from the file located chemical/orbital_type_sets/fa_standard/orbital_properties.txt. These properties contain the the parameters of distance, but can be modified. Currently this is a very small class that will be added on as more and more properties are identified and added. Note that information about the atomtype is stored along with the orbital type. This may or may not be useful later. Just adding the functionality for shits and giggles.

Orbital type name: the orbital type name contains the hybridization, orbital name, and element associated with the orbital

Hybridization: the hybridiztion of the atom that the orbital is bonded to (sp, sp2, sp3)

Orbital Name: the name of the orbital. This usually is p, d, pi, sigma. The orbital name is different than the orbital type name

Atom Type Name: the type of atom associated with an orbital

Distance: distance the orbital comes off of the atom. Currently, for residues, the distance is the Bohr radius of Hydrogen+element

Donor: does the orbital donate electrons? currently not implemented

Acceptor: is the orbital accept electrons? currently not implemented

Authors:
Steven Combs
Last Modified: December 15 2010

OrbitalType.cc

Detailed:
This class contains the "chemical" information for orbitals. This does not contain the actual xyz coordinates of the class which is managed by the conformation/Residue.hh. The orbital_type properties are assigned by the class OrbitalTypeSet which is initiated from the ChemicalManager. Orbital type properties are currently are read in from the file located chemical/orbital_type_sets/fa_standard/orbital_properties.txt. These properties contain the the parameters of distance, but can be modified. Currently this is a very small class that will be added on as more and more properties are identified and added. Note that information about the atomtype is stored along with the orbital type. This may or may not be useful later. Just adding the functionality for shits and giggles.

Orbital type name: the orbital type name contains the hybridization, orbital name, and element associated with the orbital

Hybridization: the hybridiztion of the atom that the orbital is bonded to (sp, sp2, sp3)

Orbital Name: the name of the orbital. This usually is p, d, pi, sigma. The orbital name is different than the orbital type name

Atom Type Name: the type of atom associated with an orbital

Distance: distance the orbital comes off of the atom. Currently, for residues, the distance is the Bohr radius of Hydrogen+element

Authors:
Steven Combs
Last Modified: December 15 2010

AtomTypeSet

Detailed:
This class reads in the orbital_properties.txt file which contains the "chemical" information for orbitals. This does not contain the actual properties, but sets the properties through the OrbitalType class. This class is called by the ChemicalManager. Modeled off of atomtypeset.
Authors:
Steven Combs
Last Modified: December 12 2010

Patch.cc

Detailed:
My understanding of this piece of code comes from various conversations with Oliver Lang, Summer Thyme, and Andrew Leaver-Fay. If the ideas are incorrect, feel free to correct, but I doubt you will, because no one ever comments code.

General Overview

What are patches? Patches are modifications to the original amino acid residues. These modifications include capping the N and C terminus, adding phosphorylation to residues, etc, etc. The actually files that are read and used are found in: minirosetta_database/chemical/residue_type_sets/fa_standard/patches All of these patches are read at the beginning of a Rosetta application and are applied to all residues that are identified as needing to be patched (full of explanation on identification of residues is explained later). Identification of residues that need to be patched varies by what is in the actual patch file. For example, residues that are C and N terminus are patched with the N and C terminus patch, which is defined in the files NtermProteinFull.txt and CtermProteinFull.txt.

Overview of a Patch File

Lets look at a patch file to see what goes on. File we are looking at is NtermProteinFull.txt. The file is shortened to make it easier to read. Important parts are shown:

NAME NtermProteinFull #actual name of the patch TYPES LOWER_TERMINUS #the type that this patch belongs to. Types are defined in VariantTypes.cc/.hh

#This section is for general selection rules to apply the patch. BEGIN_SELECTOR #Here is where we define how to select amino acids for the patch. Properties/variant types needed for the patch are found between the BEGIN_SELECTOR and END_SELECTOR "titles" PROPERTY PROTEIN for this patch to apply, the residue must be a protein, as defined in the paramaters file NOT VARIANT_TYPE LOWER_TERMINUS #We do not want to patch the variant type LOWER_TERMINUS. This is because, we do not want to double patch a residue (if the residue is already variant type lower_terminus) END_SELECTOR #ending the selection process for the patch

#This section is to modify specific residues that the patch encounters BEGIN_CASE ## PROLINE # Within the BEGIN_CASE and END_CASE section is where the residue is modified. These are the operations that occur to apply the patch BEGIN_SELECTOR #Once again, we are defining what to do in this specific BEGIN_CASE/END_CASE block by using the selctor AA PRO #We only want to modify aa PRO in the following way between the BEGIN_CASE and END_CASE block END_SELECTOR #end selection requirements

ADD_ATOM 1H Hpol HC 0.24 #straight forward, add atoms 1H ADD_ATOM 2H Hpol HC 0.24 ADD_BOND N 1H #atoms need bonds, add those bonds ADD_BOND N 2H SET_POLYMER_CONNECT LOWER NONE # setting a property

## totally making these up: SET_ICOOR 1H 120 60 1 N CA C ## like to use CD but CD's parent is CG #Once new atoms are placed, new Icoor need to be made SET_ICOOR 2H 120 60 1 N CA 1H

## modify properties of existing atoms SET_ATOM_TYPE N Nlys SET_MM_ATOM_TYPE N NP SET_ATOMIC_CHARGE N -0.07 SET_ATOMIC_CHARGE CA 0.16 SET_ATOMIC_CHARGE HA 0.09 SET_ATOMIC_CHARGE CD 0.16 SET_ATOMIC_CHARGE 1HD 0.09 SET_ATOMIC_CHARGE 2HD 0.09 ADD_PROPERTY LOWER_TERMINUS ## implies terminus END_CASE

BEGIN_CASE ### THE GENERAL CASE # Here is the general case, that is specified at the very begining of the patch file

## these are the operations involved DELETE_ATOM H ## deletes all bonds to this atom ADD_ATOM 1H Hpol HC 0.33 ADD_ATOM 2H Hpol HC 0.33 ADD_ATOM 3H Hpol HC 0.33 ADD_BOND N 1H ADD_BOND N 2H ADD_BOND N 3H SET_POLYMER_CONNECT LOWER NONE

## totally making these up: SET_ICOOR 1H 120 60 1 N CA C SET_ICOOR 2H 120 60 1 N CA 1H SET_ICOOR 3H 120 60 1 N CA 2H

## modify properties of existing atoms SET_ATOM_TYPE N Nlys SET_MM_ATOM_TYPE N NH3 SET_ATOMIC_CHARGE N -0.3 SET_ATOMIC_CHARGE CA 0.21 SET_ATOMIC_CHARGE HA 0.10 ADD_PROPERTY LOWER_TERMINUS ## implies terminus END_CASE

So, lets go through what was put up there. In general, you name your patch and assign it a type. Then, you tell the patch system in the BEGIN_SELECTOR / END_SELECTOR block what type of properties that you are looking for to apply the patch. You then in the BEGIN_CASE / END_CASE block add operations to the residue. You can specify specific selectors within the BEGIN_CASE / END_CASE by having another BEGIN_SELECTOR / END_SELECTOR block. People generally specify specific amino acids within the BEGIN_SELECTOR / END_SELECTOR blocks within the BEGIN_CASE / END_CASE blocks. At the end, there is one last BEGIN_CASE / END_CASE with no BEGIN_SELECTOR / END_SELECTOR block. This block is used to specify what to do with the general case, which was defined at the very begining of the file. A little more detail follows below

First, you must name your patch. Then you have to give it a "type". This type is defined in VariantType.cc/.hh. All the type does is adds a name that can be used later on in different protocols. It also helps the patch system keep track of what residues are patched with what type. The type has no magical meaning, its a name that you give it that is "defined" in the variantType.cc. In short, its a name handler. Once the name and type have been assigned, you must define a general case in which your patch applies. Generally, this means that you want it to apply to a specific type of aa, or all residues of a specific type or property. After this block comes the BEGIN_CASE / END_CASE statements. In these statements, you specify what modifications you want to apply to the residues. If you have different requirements for different amino acids, you must specify this in a BEGIN_SELECTOR / END_SELECTOR block within the BEGIN_CASE / END_CASE block. You must specify specific amino acids first, then in a new BEGIN_CASE / END_CASE block, you specify the general modfications defined by the first selector. Confusing, huh? The reason for having specific selectors defined before the general case is because...I dont know. I suspect its because of how the file is read in and applied. Regardless, if you want to do something to a specific amino acid/ residue before you get to the general case, you need to have a BEGIN_CASE / END_CASE block with a selector in there before you get to the general BEGIN_CASE / END_CASE block.

Using Patch Selector to Specify Application of a patch to specific residues

Woah there! Now that you know how to use patches, you dont need to go all gun whole crazy and create a ton of patches. This is because all patches are read at the begging of Rosetta and applied. This creates overhead if you have a ton of patch files. To circumvent this, Someone wrote an option called -residues:patch_selectors. I dont know who wrote it, or where its located, sorry. This option allows you to create patches that are only loaded when you use the option -residues:patch_selectors. To get this to work, you create a patch like normal. Then, in the BEGIN_SELECTOR / END_SELECTOR line, you add a line CMDLINE_SELECTOR <name of="" command="" line>="">. This means, if you use the CMDLINE_SELECTOR sc_orbitals, your patch will only be loaded if you use the option -residues:patch_selectors sc_orbitals. Cool, huh?

Trouble Shooting!!! so, you added a new patch and used cmd line selector and nothing happens. Did you modify VariantTypes.cc to have your new type? Did you name things correctly? Did you edit the patches.txt to include your patch? Are you trying to use a command that does not exist? Look at patchoperations.cc for commands that exist. These are all things to check for.

so, you have added a new patch and you get segmentation faults. Most common seg fault for me is in the stub atom. This is because your patch might add atoms/delete atoms that are used in other patches. In order to fix this, you must modify other patches to include your modifications. Remember patches are all loaded at the beginning of Rosetta startup! If you have conflicts with other patches in your patch, even if you are using cmd line selector, you must resolve those problems. Write an integration test so that people wont screw up your patches.

Author:
Phil Bradely Steven Combs only added comments
Last Modified: October 22 2010

ResidueType

Detailed:
This class contains the "chemical" information for residues. This does not contain the actual xyz coordinates of the class (xyz found in core/conformation/Residue.hh). A residue in Rosetta can be a ligand, DNA, amino acid, or basically anything. A residue is read in through residue_io.cc and read from parameter files, generally located in the database chemical/residuetypes. For ligands, or anything that is not the natural 20 aa, a parameter has to be provided to rosetta through the -extra_res_fa flag. Residue_io sets private member data in ResidueType. The primary data that are set are: atoms, mmatoms, orbitals, properties of residues. These properties can be modified through patches, which is controlled through PatchOperations.cc. If the residuetype is modified, the indices of atoms and mmatoms and everything associated with those indices must be redefined. This redordering of indices is taken care of with the function reorder_primary_data().

Setting of primary data and then reordering is important. Primary data for the following are described:

atoms: setting of atoms includes indexing the atoms into vectors, saving their names into vectors/maps, saving the associated mm_atom_type into a vector, saving bond connections into vectors, etc, etc. Since everything is allocated into vectors, it is easy to reorder those vectors. On any given residue, the heavy atoms are put into the vector first (their indices are first) and hydrogens are put in last.

properties: properties of a residue include things like DNA, PROTEIN, SC_ORBITALS, CHARGED, etc. These properties indicate the type of residue it is and what properties that are asscociated with the residue. They are set when read in. Several lines of code must be modified to get them to work, all found in residuetype.cc

orbitals: orbitals are indexed seperate from atoms. They function much the same way as atoms, except for some key differences. To find atoms bonded to orbitals, you must provide the atom index, not the orbital index. I havent figured out how to get the reverse to work because of the seperate indices. Orbital xyz coordinates are not updated when atom coordinates are. This is to keep speed consistent with just having atoms. To output the orbitals, use the flag -output_orbitals

Authors:
Phil Bradley Steven Combs - these comments::include <core/pack/dunbrack/RotamerLibrary.fwd.hh>

RNA_residueType

Author:
Parin Sripakdeevong (sripakpa@stanford.edu)

Atom.hh

Detailed:
This atom class differs from the AtomType/AtomTypeSet class in that it only contains the information about the xyz coordinates, the index of the atom, and the index of the atomtype. This information is generally initialized and set by conformation/Residue.hh. Steven Combs - comments
Authors:
Phil Bradley
Last Modified: December 9 2010
Author:
Phil Bradley, Ingemar Andre
Oliver Lange (olange@u.washington.edu)
Christopher Miles (cmiles@uw.edu)
Oliver Lange
Oliver Lange (olange@u.washington.edu)
Date:
Wed Oct 20 12:08:31 2007

Utility headers

Utility headers C++ headers

A temporary copy of the pose_from_pdb code from the demo directory. Will be phased out in favor of file_data routines soon.

Package headers Project headers Utility headers

Package headers Project headers Utility headers Numeric headers

Package headers

Package headers ObjexxFCL headers C++ headers

Package headers ObjexxFCL headers

rearrange the dunbrack arrays:

mapping from aa to single-residue-rotamer-library

to preserve current interpolation scheme, need ability to (quickly) lookup the probability/chi-means/chi-sdevs for a given rotamer in several torsion-angle bins.

so how to store prob/mean/sd for alt rotamers at different pp bins

quick conversion from rotno-tuple to index?

rotamer_data: probability, chi-mean, chi-sd

C++ headers

This layer of abstraction between the InteractionGraphBase and the various fixed-backbone interaction graphs is primarily to allow outside users to READ from an interaction graph -- to grab data that the interaction graph stores. This is not so much for the writing of information -- in particular, edge energies -- to an interaction graph.

Author:
ashworth
stranges
Andrew Leaver-Fay (aleaverfay@gmail.com)
ashworth

Be very careful with #includes in this file. As almost every file in mini #includes Pose.hh, any header file #included here will produce a huge recompile when modified. I pledge a personally delivered, hand crafted ass whooping for any fool that #includes an unneccessary .hh file in Pose.hh. Allowed .hh files are few: Residue, ResidueType, Conformation, Energies AtomID and NamedAtomID. Everything else should be forward included, or not included at all. The above pledge applies to any header file unnecessarily #included in the .hh files #included here. If Pose were to hold a ConformationOP and an EnergiesOP, and not inline their access, then Residue.hh, ResidueType.hh, Conformation.hh and Energies.hh could be replaced with .fwd.hh's instead.

atom_pair_energy_inline.hh

Detailed:
This class is invoked when scoring. The terms that it is responsible for are fa_atr, fa_rep, fa_sol. The class is highly optimized for speed and will break if you are not careful. It calls functions within BaseEtableEnergy, which actually does the scoring. It passes an energy map, which contains the energy for that residue for the atr, rep, and sol terms. This is modified once the scores are tallied in BaseEtableEnergy.
Authors:
Stuart G. Mentzer (Stuart_Mentzer@objexx.com) Kevin P. Hinshaw (KevinHinshaw@gmail.com) Andrew Leaver-Fay (leaverfa@email.unc.edu) Steven Combs - comments and skipping of virtual atoms
Last Modified: December 6 2010

Etable.hh

Detailed:
This class is called upon by the ScoringManager. Since actual calculating of the LJ potential is time consuming if done multiple times, this class precomputes and discritizes the potential (meaning that the potential is broken down into bins). Once the bins have been created, it will smooth out the bins, for better interpolation.
Authors:
I dont know? Steven Combs - comments and skipping of virtual atoms
Last Modified: December 6 2010

This is a reimplementation of Jim Havranek's original rosetta++ Gen Born code. source files: rosetta++/gb_elec*

Hacky (hence the name) implementation of distance dependant dielectric electrostatics, with near and far distance cutoffs.

Hacky (hence the name) implementation of 10r dielectric model, cutoff at 5.5A

Package Headers

To add an additional option for hydrogen bonds do the following:

In HBondOptions.hh: 1) add it to the default constructor 2) add it to the copy constructor 3) add a getter and a setter 4) add it to operator== 5) add it to the private data 6) add it to HBondOptions::show

To add an additional option for hydrogen bonds do the following: 1) add it to the default constructor 2) add it to the copy constructor 3) add a getter and a setter 4) add it to operator== 5) add it to the private data 6) add it to HBondOptions::show

NOTE-- this file includes both string and map, use .fwd.hh if you can! Utility headers

The Two Body Energy Method specifies an interface for all two body methods: both long and short range, both context dependent and independent. Any two body method must implement this interface as well as the EnergyMethod interface.

In this inheritance heirarchy, a common interface is defined for both context dependent and context independent two body energies. Context dependent two body energies require a Pose as context to evaluate the energy and so the interface includes a Pose for all energy evaluation calls.

However, context independent methods do not require a pose, and could conceivably be evaluated in the absence of one. Is the design compromised by demanding a common interface between context independent and context dependent two-body methods? Yes and no. The alternatives are 1) to demand separate, but nearly identical interfaces for ci2b and cd2b classes in which case, the design is compromised by the presence of duplicated code, 2) to use multiple inherritance so that the CI2B class could derive from a two-body interface (shared with the CD2B class) as well as a contex-independent interface (not shared with the CD2B class). The problem is that most of the "shared" interface involves evaluating energies, and for the CD classes, this requires a Pose. The truely shared interface between CI and CD classes would be empty and problem 1 has resurfaced. Moreover, multiple inherritance is difficult to work with and should be avoided.

What is the drawback of requiring a pose for a CI2B method evaluation? It makes it less clear to the energy-method user (not the energy-method writer) that the Pose does not play a role in the evaluation of the ci2b energy. It also makes it possible for the energy-method writer to define a context dependent two body method while declaring it to be context independent: such an act would produce bizzare (wrong) behavior as the innards of the ScoreFunction and the Energies class tried to re-use cached scores that were no longer correct. So the warning must be made:

DANGER! DANGER! DANGER! If the EnergyMethod writer declares a method to be context independent, it had better be!

Author:
Andrew Leaver-Fay (aleaverfay@gmail.com)
Andrew Leaver-Fay

OrbitalStatistics

Detailed:
This is an attempt to be transparent in how the orbital-hydrogen interactions were converted into a KBP. In general terms, a set of proteins from PDB were taken and the shortest distance from an orbital to a polar or aromatic hydrogen was recorded and binned. In addition to the shortest distance, an angle was taken. The angle considered is the angle between the base atom that contains the orbital, the orbital, and the hydrogen. For polar hydrogens, only sidechain polar hydrogens were considered.

For protein interactions, there are 7 classes (orbital types) of orbitals that statistics are generated. These 7 types are mapped using a map to enum data structure. For each sidechain interaction, only the shortest distance between any given orbital type to a hydrogen is calculated. That means, that for each sidechain interaction only 1 distance, 1 angle, and 1 class is recorded.

Bin sizes were calculated by .1A for distance and cos of 1 for angles. See below:

angle -1 -.9 -.8 -.7.......... d .1 | 0 0 0 0 i .2 | 500 0 0 0 s .3 | 25 0 0 0 t .4 | 0 30 5 0

This is not the original code that was used to generate the statistics. The original code was much more convoluted than this because I had no idea how to program. I wrote this piece for clarity. I have tested it and it produces the same results.

Authors:
Steven Combs

Package headers C++ Headers

Package headers Utility headers Numeric headers

Author:
Hetu Kamisetty

Typedef Documentation

typedef Real core::Angle
typedef Real core::Charge
typedef Real core::Energy
typedef Real core::Length
typedef Real core::Mass
typedef float core::PackerEnergy
typedef unsigned short core::ShortSize
typedef platform::SSize core::SSize
typedef Real core::Trig
typedef platform::uint core::uint
typedef Real core::Volume

Function Documentation

void core::init ( int  argc,
char *  argv[] 
)

Init basic core systems: options system, random system.

References init_random_generators(), minirosetta_svn_url(), minirosetta_svn_version(), protocols::wum::mpi_rank(), core::scoring::p_aa_pp, core::scoring::T(), and core::scoring::methods::TR().

Referenced by protocols::canonical_sampling::CanonicalSamplingMover::apply(), protocols::toolbox::KCluster::cluster(), protocols::LoopRebuild::desired_loops(), protocols::docking::DockingProtocol::DockingProtocol(), protocols::LoopRebuild::get_ccd_closure_exist(), protocols::LoopRebuild::get_chain_break_tolerance(), protocols::LoopRebuild::get_combine_if_fail_exist(), protocols::LoopRebuild::get_desired_loops_exist(), protocols::LoopRebuild::get_loop_combine_rate(), protocols::LoopRebuild::get_rmsd_tolerance(), protocols::wum::DatabaseQueryWorkUnitManager< T >::go(), protocols::loophash::MPI_LoopHashRefine_Master::go(), protocols::loophash::MPI_LoopHashRefine_Emperor::go(), init(), core::scoring::rna::initialize_non_main_chain_sugar_atoms(), core::scoring::input_sasa_dats(), core::scoring::packstat::old::input_sasa_dats(), protocols::LoopRebuild::loop_model(), main(), OPT_1GRP_KEY(), protocols::rna::RNA_Fragments::read_vall_torsions(), protocols::rna::FullAtomRNA_Fragments::read_vall_torsions(), core::io::silent::SilentStruct::rename_energies(), protocols::simple_moves::symmetry::SymShakeStructureMover::run_mc(), protocols::simple_moves::ShakeStructureMover::run_mc(), protocols::simple_moves::ShakeStructureMover::set_temp_based_on_ens_diversity(), and protocols::simple_filters::ScoreCutoffFilter::set_unweighted().

void core::init ( utility::vector1< std::string > const &  args)

wrapper for core system Init

References init().

void core::init_random_generators ( int const  start_seed,
RND_RunType  run_type,
std::string const &  RGtype 
)

Initialize random generator systems (and send debug io to tracer with seed/mode info).

References core::scoring::T().

Referenced by init().

void core::init_random_generators ( int const  start_seed,
numeric::random::RND_RunType  run_type,
std::string const &  RGtype 
)

Initialize random generator systems (and send debug io to tracer with seed/mode info).

std::string core::minirosetta_svn_url ( )
std::string core::minirosetta_svn_version ( )
static basic::Tracer core::TR ( "core.init"  ) [static]

Referenced by protocols::seeded_abinitio::GrowPeptides::apply(), protocols::protein_interface_design::filters::HbondsToResidueFilter::apply(), protocols::protein_interface_design::Revert::apply(), core::chemical::apply_adducts_to_residue(), protocols::docking::calc_Fnat(), protocols::docking::calc_Irmsd(), protocols::fldsgn::topology::calc_strand_pairing_set(), protocols::antibody2::CDR_H3_filter(), protocols::fldsgn::topology::check_kink_helix(), protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData::get_score(), protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::get_score(), hbonded(), protocols::loophash::LocalInserter_SimpleMin::make_local_bb_change(), protocols::loophash::LocalInserter_SimpleMin::make_local_bb_change_close_gaps(), protocols::loophash::LocalInserter_SimpleMin::make_local_bb_change_include_cut(), MinimizeInterface(), protocols::seeded_abinitio::GrowPeptides::parse_my_tag(), protocols::protein_interface_design::TerminusDistanceFilter::parse_my_tag(), protocols::protein_interface_design::BuriedUnsatHbondFilter::parse_my_tag(), protocols::protein_interface_design::EnergyPerResidueFilter::parse_my_tag(), protocols::protein_interface_design::HbondsToResidueFilter::parse_my_tag(), protocols::protein_interface_design::DdgFilter::parse_my_tag(), protocols::protein_interface_design::ResidueDistanceFilter::parse_my_tag(), protocols::protein_interface_design::ResidueBurialFilter::parse_my_tag(), protocols::protein_interface_design::NeighborTypeFilter::parse_my_tag(), protocols::protein_interface_design::AlaScan::parse_my_tag(), protocols::protein_interface_design::InterfaceSasaFilter::parse_my_tag(), protocols::protein_interface_design::ScoreTypeFilter::parse_my_tag(), protocols::protein_interface_design::ResiduesInInterfaceFilter::parse_my_tag(), protocols::protein_interface_design::filters::HbondsToResidueFilter::parse_my_tag(), protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData::process_score(), protocols::protein_interface_design::PatchdockReader::read_patchdock(), protocols::protein_interface_design::PatchdockReader::read_patchdock_entry(), protocols::protein_interface_design::PatchdockReader::read_poses(), protocols::protein_interface_design::ReportSequenceDifferences::report(), protocols::rna::setup_base_pair_constraints(), protocols::antibody2::setup_packer_task(), protocols::antibody2::setup_simple_fold_tree(), protocols::antibody2::simple_fold_tree(), protocols::antibody2::simple_one_loop_fold_tree(), and SymMinimizeInterface().


Variable Documentation

const Size core::SZ_MAX = std::numeric_limits<Size>::max() [static]
const Size core::SZ_MIN = std::numeric_limits<Size>::min() [static]
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Defines