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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_Helices",
"π-Helices",
"3⏨-Helices",
"β-Strands",
"β-Bridges",
"α-Helices" }
}

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