Gromacs
2024.5
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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, 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... | |
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const gmx::EnumerationArray<BackboneAtomTypes, const char*> gmx::analysismodules::anonymous_namespace{dssp.cpp}::c_backboneAtomTypeNames |
String values corresponding to backbone atom types.
const gmx::EnumerationArray<HBondDefinition, const char*> gmx::analysismodules::anonymous_namespace{dssp.cpp}::c_HBondDefinition |
String values corresponding to hydrogen bond definition modes.
const gmx::EnumerationArray<HydrogenMode, const char*> gmx::analysismodules::anonymous_namespace{dssp.cpp}::c_HydrogenModeNames |
String values corresponding to hydrogen-assignment modes.
const gmx::EnumerationArray<PPStretches, const char*> gmx::analysismodules::anonymous_namespace{dssp.cpp}::c_PPStretchesNames |
String values corresponding to neighbor-search modes.
const gmx::EnumerationArray<SecondaryStructureTypes, const char> gmx::analysismodules::anonymous_namespace{dssp.cpp}::c_secondaryStructureTypeNames |
String values (symbols) corresponding to secondary structures' types.
const gmx::EnumerationArray<SecondaryStructureTypes, const char*> gmx::analysismodules::anonymous_namespace{dssp.cpp}::c_secondaryStructureTypeNamesFull |
String values (full) corresponding to secondary structures' types.