gmx::analysismodules::anonymous_namespace{dssp.cpp} Namespace Reference

Classes
struct	DsspStorageFrame
	Structure that contains storage information from different frames. More...
class	DsspStorage
	Class that stores frame information in storage and, upon request, can return it. More...
struct	ResInfo
	Structure of residues' information that can operate with atoms' indices. More...
class	SecondaryStructuresData
	Describes and manipulates secondary structure attributes of a residue. More...
class	SecondaryStructures
	Class that provides search of specific h-bond patterns within residues. More...

Enumerations
enum	BackboneAtomTypes : std::size_t {   AtomCA, AtomC, AtomO, AtomN,   AtomH, AtomHN, Count }
	Enum of backbone atoms' types.
enum	SecondaryStructureTypes : std::size_t {   Loop = 0, SecondaryStructureTypes::Break, SecondaryStructureTypes::Bend, SecondaryStructureTypes::Turn,   SecondaryStructureTypes::Helix_PP, SecondaryStructureTypes::Helix_5, SecondaryStructureTypes::Helix_3, SecondaryStructureTypes::Strand,   SecondaryStructureTypes::Bridge, SecondaryStructureTypes::Helix_4, SecondaryStructureTypes::Count }
	Enum of secondary structures' types. More...
enum	TurnsTypes : std::size_t {   Turn_3 = 0, Turn_4, Turn_5, Turn_PP,   Count }
	Enum of turns' types.
enum	HelixPositions : std::size_t {   None = 0, Start, Middle, End,   StartAndEnd, Count }
	Enum of different possible helix positions' types.
enum	BridgeTypes : std::size_t { None = 0, AntiParallelBridge, ParallelBridge, Count }
	Enum of bridges' types.
enum	HydrogenMode : std::size_t { Gromacs = 0, Dssp, Count }
	Enum of various modes of use of hydrogen atoms. Gromacs mode strictly uses hydrogen atoms from the protein structure, while Dssp mode exclusively uses non-existent hydrogen atoms with coordinates calculated from the positions of carbon and oxygen atoms in residues.
enum	PPStretches : std::size_t { Shortened = 0, Default, Count }
	Enum of various size of stretch of polyproline helices.
enum	HBondDefinition : std::size_t { Energy = 0, Geometry, Count }
	Enum of various modes of hydrogen bond definition.

Variables
const gmx::EnumerationArray < BackboneAtomTypes, const char * >	c_backboneAtomTypeNames
	String values corresponding to backbone atom types. More...
const gmx::EnumerationArray < SecondaryStructureTypes, const char >	c_secondaryStructureTypeNames
	String values (symbols) corresponding to secondary structures' types. More...
const gmx::EnumerationArray < SecondaryStructureTypes, const char * >	c_secondaryStructureTypeNamesFull
	String values (full) corresponding to secondary structures' types. More...
const gmx::EnumerationArray < HydrogenMode, const char * >	c_HydrogenModeNames
	String values corresponding to hydrogen-assignment modes. More...
const gmx::EnumerationArray < PPStretches, const char * >	c_PPStretchesNames
	String values corresponding to neighbor-search modes. More...
const gmx::EnumerationArray < HBondDefinition, const char * >	c_HBondDefinition
	String values corresponding to hydrogen bond definition modes. More...

Enumeration Type Documentation

enum gmx::analysismodules::anonymous_namespace{dssp.cpp}::SecondaryStructureTypes : std::size_t

strong

Enum of secondary structures' types.

Enumerator
Break	~
Bend	=
Turn	S.
Helix_PP	T.
Helix_5	P.
Helix_3	I.
Strand	G.
Bridge	E.
Helix_4	B.
Count	H.

Variable Documentation

const gmx::EnumerationArray<BackboneAtomTypes, const char*> gmx::analysismodules::anonymous_namespace{dssp.cpp}::c_backboneAtomTypeNames

Initial value:

= {
    { "CA", "C", "O", "N", "H", "HN" }
}

String values corresponding to backbone atom types.

const gmx::EnumerationArray<HBondDefinition, const char*> gmx::analysismodules::anonymous_namespace{dssp.cpp}::c_HBondDefinition

Initial value:

= { { "energy",
                                                                                  "geometry" } }

String values corresponding to hydrogen bond definition modes.

const gmx::EnumerationArray<HydrogenMode, const char*> gmx::analysismodules::anonymous_namespace{dssp.cpp}::c_HydrogenModeNames

Initial value:

= { { "gromacs",
                                                                                 "dssp" } }

String values corresponding to hydrogen-assignment modes.

const gmx::EnumerationArray<PPStretches, const char*> gmx::analysismodules::anonymous_namespace{dssp.cpp}::c_PPStretchesNames

Initial value:

= { { "shortened",
                                                                               "default" } }

String values corresponding to neighbor-search modes.

const gmx::EnumerationArray<SecondaryStructureTypes, const char> gmx::analysismodules::anonymous_namespace{dssp.cpp}::c_secondaryStructureTypeNames

Initial value:

= {
    { '~', '=', 'S', 'T', 'P', 'I', 'G', 'E', 'B', 'H' }
}

String values (symbols) corresponding to secondary structures' types.

const gmx::EnumerationArray<SecondaryStructureTypes, const char*> gmx::analysismodules::anonymous_namespace{dssp.cpp}::c_secondaryStructureTypeNamesFull

Initial value:

= {
    { "Loops",
      "Breaks",
      "Bends",
      "Turns",
      "PP\\sII\\N-Helices",
      "\\xp\\f{}-Helices",
      "3\\s10\\N-Helices",
      "\\xb\\f{}-Strands",
      "\\xb\\f{}-Bridges",
      "\\xa\\f{}-Helices" }
}

String values (full) corresponding to secondary structures' types.