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- builtins.object
-
- MMBondAngleLibrary
- MMBondAngleResidueTypeParam
- MMBondAngleResidueTypeParamSet
- MMBondAngleScore
- MMBondLengthLibrary
- MMBondLengthScore
- MMLJEnergyTable
- MMLJLibrary
- MMLJScore
- MMTorsionLibrary
- MMTorsionScore
class MMBondAngleLibrary(builtins.object) |
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(self : rosetta.core.scoring.mm.MMBondAngleLibrary, filename : str, mm_atom_set : rosetta.std.weak_ptr_const_core_chemical_MMAtomTypeSet_t) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.scoring.mm.MMBondAngleLibrary, : rosetta.core.scoring.mm.MMBondAngleLibrary) -> rosetta.core.scoring.mm.MMBondAngleLibrary
- pretty_print(...) from builtins.PyCapsule
- pretty_print(*args, **kwargs)
Overloaded function.
1. pretty_print(rosetta.core.scoring.mm.MMBondAngleLibrary) -> NoneType
pretty print / debug
2. pretty_print(self : rosetta.core.scoring.mm.MMBondAngleLibrary, atom1 : int, atom2 : int, atom3 : int) -> NoneType
3. pretty_print(self : rosetta.core.scoring.mm.MMBondAngleLibrary, atom1 : str, atom2 : str, atom3 : str) -> NoneType
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class MMBondAngleResidueTypeParam(builtins.object) |
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Methods defined here:
- Ktheta(...) from builtins.PyCapsule
- Ktheta(self : rosetta.core.scoring.mm.MMBondAngleResidueTypeParam, bondang : int) -> float
get Ktheta for a particular intraresidue angle
- __init__(...) from builtins.PyCapsule
- __init__(rosetta.core.scoring.mm.MMBondAngleResidueTypeParam) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- __str__(...) from builtins.PyCapsule
- __str__(rosetta.core.scoring.mm.MMBondAngleResidueTypeParam) -> str
- bondangle(...) from builtins.PyCapsule
- bondangle(self : rosetta.core.scoring.mm.MMBondAngleResidueTypeParam, bondang : int) -> rosetta.utility.keys.Key3Tuple_unsigned_long_unsigned_long_unsigned_long_t
Return the indices for the set of atoms that define a particular
intraresidue angle
- bondangle_index(...) from builtins.PyCapsule
- bondangle_index(self : rosetta.core.scoring.mm.MMBondAngleResidueTypeParam, atom_set : rosetta.utility.keys.Key3Tuple_unsigned_long_unsigned_long_unsigned_long_t) -> int
Returns the index of the intraresidue bond angle, 0 if not found
- bondangles_for_atom(...) from builtins.PyCapsule
- bondangles_for_atom(self : rosetta.core.scoring.mm.MMBondAngleResidueTypeParam, atomno : int) -> rosetta.utility.vector1_unsigned_long
Returns the list of all of the indices of all the intraresidue
bond angles a particular atom is involved in.
Useful for calculating the derivatives for an atom.
- connection_index(...) from builtins.PyCapsule
- connection_index(self : rosetta.core.scoring.mm.MMBondAngleResidueTypeParam, connection : int, atom_set : rosetta.utility.keys.Key2Tuple_unsigned_long_unsigned_long_t) -> int
Returns the index of the interresidue bond angle, 0 if not found
- connection_pair(...) from builtins.PyCapsule
- connection_pair(self : rosetta.core.scoring.mm.MMBondAngleResidueTypeParam, connection : int, bondang : int) -> rosetta.utility.keys.Key2Tuple_unsigned_long_unsigned_long_t
Return the indices for the set of two atoms that form part of a interresidue bond angle
- connection_theta0(...) from builtins.PyCapsule
- connection_theta0(self : rosetta.core.scoring.mm.MMBondAngleResidueTypeParam, connection : int, bondang : int) -> float
Return ResidueType derived theta0 for a interresidue bond angle
- connection_use_theta0(...) from builtins.PyCapsule
- connection_use_theta0(self : rosetta.core.scoring.mm.MMBondAngleResidueTypeParam, connection : int, bondang : int) -> bool
Return whether to use ResidueType derived theta0 for a interresidue bond angle
- init(...) from builtins.PyCapsule
- init(self : rosetta.core.scoring.mm.MMBondAngleResidueTypeParam, residue_type : rosetta.core.chemical.ResidueType, mm_bondangle_library : rosetta.core.scoring.mm.MMBondAngleLibrary, use_residue_type_theta0 : bool, central_atoms_to_score : rosetta.utility.vector1_std_string) -> NoneType
initialize the parameters
- n_connection_pairs(...) from builtins.PyCapsule
- n_connection_pairs(self : rosetta.core.scoring.mm.MMBondAngleResidueTypeParam, connection : int) -> int
number of ResidueConnections, counting polymeric residue connections
- n_possible_residue_connections(...) from builtins.PyCapsule
- n_possible_residue_connections(rosetta.core.scoring.mm.MMBondAngleResidueTypeParam) -> int
number of ResidueConnections, counting polymeric residue connections
- num_bondangles(...) from builtins.PyCapsule
- num_bondangles(rosetta.core.scoring.mm.MMBondAngleResidueTypeParam) -> int
get number of intraresidue bond angles
- theta0(...) from builtins.PyCapsule
- theta0(self : rosetta.core.scoring.mm.MMBondAngleResidueTypeParam, bondang : int) -> float
get Ktheta for a particular intraresidue angle
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class MMBondAngleResidueTypeParamSet(builtins.object) |
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.core.scoring.mm.MMBondAngleResidueTypeParamSet) -> NoneType
2. __init__(self : rosetta.core.scoring.mm.MMBondAngleResidueTypeParamSet, src : rosetta.core.scoring.mm.MMBondAngleResidueTypeParamSet) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.scoring.mm.MMBondAngleResidueTypeParamSet, : rosetta.core.scoring.mm.MMBondAngleResidueTypeParamSet) -> rosetta.core.scoring.mm.MMBondAngleResidueTypeParamSet
- central_atoms_to_score(...) from builtins.PyCapsule
- central_atoms_to_score(*args, **kwargs)
Overloaded function.
1. central_atoms_to_score(rosetta.core.scoring.mm.MMBondAngleResidueTypeParamSet) -> rosetta.utility.vector1_std_string
get central atoms to score in newly created ResidueTypeParam objects
2. central_atoms_to_score(self : rosetta.core.scoring.mm.MMBondAngleResidueTypeParamSet, value : rosetta.utility.vector1_std_string) -> NoneType
set central atoms to score in newly created ResidueTypeParam objects
- get(...) from builtins.PyCapsule
- get(*args, **kwargs)
Overloaded function.
1. get(self : rosetta.core.scoring.mm.MMBondAngleResidueTypeParamSet, residue_type : rosetta.core.chemical.ResidueType) -> core::scoring::mm::MMBondAngleResidueTypeParam
lookup a param object for a given ResidueType
2. get(self : rosetta.core.scoring.mm.MMBondAngleResidueTypeParamSet, residue_type : rosetta.core.chemical.ResidueType) -> core::scoring::mm::MMBondAngleResidueTypeParam
lookup a param object for a given ResidueType, does not auto-create
- lookup(...) from builtins.PyCapsule
- lookup(self : rosetta.core.scoring.mm.MMBondAngleResidueTypeParamSet, conformation : rosetta.core.conformation.Conformation, atomid1 : rosetta.core.id.AtomID, atomid2 : rosetta.core.id.AtomID, atomid3 : rosetta.core.id.AtomID, Ktheta : float, theta0 : float) -> NoneType
lookup Ktheta and theta0 for any bond angle in a conformation
- mm_bondangle_library(...) from builtins.PyCapsule
- mm_bondangle_library(*args, **kwargs)
Overloaded function.
1. mm_bondangle_library(rosetta.core.scoring.mm.MMBondAngleResidueTypeParamSet) -> rosetta.core.scoring.mm.MMBondAngleLibrary
get bond angle library for newly created ResidueTypeParam objects
2. mm_bondangle_library(self : rosetta.core.scoring.mm.MMBondAngleResidueTypeParamSet, value : rosetta.core.scoring.mm.MMBondAngleLibrary) -> NoneType
set bond angle library for newly created ResidueTypeParam objects
- use_residue_type_theta0(...) from builtins.PyCapsule
- use_residue_type_theta0(*args, **kwargs)
Overloaded function.
1. use_residue_type_theta0(rosetta.core.scoring.mm.MMBondAngleResidueTypeParamSet) -> bool
get use of ResidueType theta0 in newly created ResidueTypeParam objects
2. use_residue_type_theta0(self : rosetta.core.scoring.mm.MMBondAngleResidueTypeParamSet, value : bool) -> NoneType
set use of ResidueType theta0 in newly created ResidueTypeParam objects
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class MMLJEnergyTable(builtins.object) |
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blah
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(rosetta.core.scoring.mm.MMLJEnergyTable) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- deriv_score(...) from builtins.PyCapsule
- deriv_score(self : rosetta.core.scoring.mm.MMLJEnergyTable, atom1 : int, atom2 : int, path_distance : int, squared_distance : float, rep : float, atr : float) -> NoneType
blah
- max_dist(...) from builtins.PyCapsule
- max_dist(rosetta.core.scoring.mm.MMLJEnergyTable) -> float
blah
- mm_lj_score(...) from builtins.PyCapsule
- mm_lj_score(rosetta.core.scoring.mm.MMLJEnergyTable) -> rosetta.core.scoring.mm.MMLJScore
blah
- score(...) from builtins.PyCapsule
- score(self : rosetta.core.scoring.mm.MMLJEnergyTable, atom1 : int, atom2 : int, path_distance : int, squared_distance : float, rep : float, atr : float) -> NoneType
blah
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class MMLJScore(builtins.object) |
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Calculates scores of mm lj paramater sets given two mm atom types,
the path distance of the 2 atoms and actual distance between the two atoms
blah
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.core.scoring.mm.MMLJScore) -> NoneType
2. __init__(self : rosetta.core.scoring.mm.MMLJScore, mmljl : core::scoring::mm::MMLJLibrary) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- deriv_score(...) from builtins.PyCapsule
- deriv_score(self : rosetta.core.scoring.mm.MMLJScore, atom1 : int, atom2 : int, path_distance : int, distance : float) -> float
blah
- min_dist(...) from builtins.PyCapsule
- min_dist(self : rosetta.core.scoring.mm.MMLJScore, atom1 : int, atom2 : int, path_distance : int) -> float
blah
- mm_lj_library(...) from builtins.PyCapsule
- mm_lj_library(rosetta.core.scoring.mm.MMLJScore) -> core::scoring::mm::MMLJLibrary
blah
- score(...) from builtins.PyCapsule
- score(self : rosetta.core.scoring.mm.MMLJScore, atom1 : int, atom2 : int, path_distance : int, distance : float) -> float
blah
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class MMTorsionLibrary(builtins.object) |
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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.
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(self : rosetta.core.scoring.mm.MMTorsionLibrary, filename : str, mm_atom_set : rosetta.core.chemical.MMAtomTypeSet) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.scoring.mm.MMTorsionLibrary, : rosetta.core.scoring.mm.MMTorsionLibrary) -> rosetta.core.scoring.mm.MMTorsionLibrary
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