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Rosetta
2020.50
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A class to maintain a set of MM torsion paramaters. More...
#include <MMTorsionLibrary.hh>
Public Member Functions | |
MMTorsionLibrary (std::string filename, core::chemical::MMAtomTypeSetCOP mm_atom_set, utility::vector1< std::string > extra_mm_param_dirs=utility::vector1< std::string >()) | |
ctor More... | |
~MMTorsionLibrary () override | |
mm_torsion_library_citer_pair | lookup (int atom1, int atom2, int atom3, int atom4) const |
lookup by atom type ints More... | |
mm_torsion_library_citer_pair | lookup (std::string atom1, std::string atom2, std::string atom3, std::string atom4) const |
lookup by atom type strings More... | |
Private Attributes | |
mm_torsion_library | fully_assigned_mm_torsion_library_ |
library that contains torsion params for sets in which all mm atom types are specified for all 4 positions More... | |
mm_torsion_library | wildcard_mm_torsion_library_ |
library that contains torsion params for sets in which all mm atom types are NOT specified for all 4 positions More... | |
core::chemical::MMAtomTypeSetCAP | mm_atom_set_ |
the MMAtomTypeSet associated with the library More... | |
A class to maintain a set of MM torsion paramaters.
The MMTorsionLibrary class contains functions and data structures to initialize, store, and provide lookups for molecular mechanics torsional paramaters. The sets of 4 atom types that make up a dihedral angle are stored in an mm_torsion_atom_quad . The sets 3 parameters that act as values for the actual MM torsion potential are stored in an mm_torsion_param_set . The class maintains 2 libraries; one for set of torsion parameter for which all 4 atom types in the dihedral at defined ( fully_assigned_mm_torsion_library_ ), and a library that is only dependant on the two central atom types ( wildcard_mm_torsion_library_ ). Wildcar atom types are designated by 'X'. Lookups are done with MMAtomType indicies or strings that are converted to MMAtomType indicies. Lookup functions return pairs of iterators to the map. The same set of 4 atom types can corespond to multiple paramter sets with different multiplicities to more accuratly define the potential and is the reason multimaps are used instead of just maps.
core::scoring::mm::MMTorsionLibrary::MMTorsionLibrary | ( | std::string | filename, |
core::chemical::MMAtomTypeSetCOP | mm_atom_set, | ||
utility::vector1< std::string > | extra_mm_param_dirs = utility::vector1< std::string > () |
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ctor
Constructs a MMTorsionLibrary instance from a filename string and constant access pointer to an MMAtomTypeSet
References fully_assigned_mm_torsion_library_, mm_atom_set_, protocols::hybridization::score, core::scoring::mm::TR(), and wildcard_mm_torsion_library_.
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overridedefault |
mm_torsion_library_citer_pair core::scoring::mm::MMTorsionLibrary::lookup | ( | int | atom1, |
int | atom2, | ||
int | atom3, | ||
int | atom4 | ||
) | const |
lookup by atom type ints
The lookup function returns a pair of iterators to the first and last element in the multimap library that corespond to the set(s) of mm params that corespond to the 4 mm atom type indices. If non are found it exits.
References fully_assigned_mm_torsion_library_, mm_atom_set_, core::id::to_string(), core::scoring::mm::TR(), and wildcard_mm_torsion_library_.
Referenced by core::scoring::mm::MMTorsionScore::dscore(), core::scoring::mm::MMTorsionScore::score(), and protocols::simple_moves::CyclizationMover::setup_constraints().
mm_torsion_library_citer_pair core::scoring::mm::MMTorsionLibrary::lookup | ( | std::string | atom1, |
std::string | atom2, | ||
std::string | atom3, | ||
std::string | atom4 | ||
) | const |
lookup by atom type strings
References mm_atom_set_.
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private |
library that contains torsion params for sets in which all mm atom types are specified for all 4 positions
Referenced by lookup(), and MMTorsionLibrary().
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private |
the MMAtomTypeSet associated with the library
Referenced by lookup(), and MMTorsionLibrary().
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private |
library that contains torsion params for sets in which all mm atom types are NOT specified for all 4 positions
Referenced by lookup(), and MMTorsionLibrary().