mm¶

mmtrie

Bindings for core::scoring::mm namespace

class pyrosetta.rosetta.core.scoring.mm.MMBondAngleScore¶

Bases: pybind11_builtins.pybind11_object

Calculates scores of mm bond angle paramater sets given an angle

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.core.scoring.mm.MMBondAngleScore) -> None
__init__(self: pyrosetta.rosetta.core.scoring.mm.MMBondAngleScore, mmtl: pyrosetta.rosetta.core.scoring.mm.MMBondAngleLibrary) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

dscore(self: pyrosetta.rosetta.core.scoring.mm.MMBondAngleScore, Ktheta: float, theta0: float, angle: float) → float¶

Returns a derivative given an mm_bondangle_atom_trie and an angle in radians

C++: core::scoring::mm::MMBondAngleScore::dscore(double, double, double) const –> double

score(self: pyrosetta.rosetta.core.scoring.mm.MMBondAngleScore, Ktheta: float, theta0: float, angle: float) → float¶

Returns energy given an mm_bondangle_atom_tri and an angle in radians

C++: core::scoring::mm::MMBondAngleScore::score(double, double, double) const –> double

class pyrosetta.rosetta.core.scoring.mm.MMLJEnergyTable¶

Bases: pybind11_builtins.pybind11_object

blah

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(self: pyrosetta.rosetta.core.scoring.mm.MMLJEnergyTable) → None¶

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

deriv_score(self: pyrosetta.rosetta.core.scoring.mm.MMLJEnergyTable, atom1: int, atom2: int, path_distance: int, squared_distance: float, rep: float, atr: float) → None¶

blah

C++: core::scoring::mm::MMLJEnergyTable::deriv_score(unsigned long, unsigned long, unsigned long, double, double &, double &) const –> void

max_dist(self: pyrosetta.rosetta.core.scoring.mm.MMLJEnergyTable) → float¶

blah

C++: core::scoring::mm::MMLJEnergyTable::max_dist() const –> double

mm_lj_score(self: pyrosetta.rosetta.core.scoring.mm.MMLJEnergyTable) → pyrosetta.rosetta.core.scoring.mm.MMLJScore¶

blah

C++: core::scoring::mm::MMLJEnergyTable::mm_lj_score() const –> const class core::scoring::mm::MMLJScore &

score(self: pyrosetta.rosetta.core.scoring.mm.MMLJEnergyTable, atom1: int, atom2: int, path_distance: int, squared_distance: float, rep: float, atr: float) → None¶

blah

C++: core::scoring::mm::MMLJEnergyTable::score(unsigned long, unsigned long, unsigned long, double, double &, double &) const –> void

class pyrosetta.rosetta.core.scoring.mm.MMLJLibrary¶

Bases: pybind11_builtins.pybind11_object

A class to maintain a set of MM LJ paramaters.

blah

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(self: pyrosetta.rosetta.core.scoring.mm.MMLJLibrary, mm_atom_set: pyrosetta.rosetta.core.chemical.MMAtomTypeSet) → None¶

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

assign(self: pyrosetta.rosetta.core.scoring.mm.MMLJLibrary, : pyrosetta.rosetta.core.scoring.mm.MMLJLibrary) → pyrosetta.rosetta.core.scoring.mm.MMLJLibrary¶: C++: core::scoring::mm::MMLJLibrary::operator=(const class core::scoring::mm::MMLJLibrary &) –> class core::scoring::mm::MMLJLibrary &

lookup(*args, **kwargs)¶

Overloaded function.

lookup(self: pyrosetta.rosetta.core.scoring.mm.MMLJLibrary, atom: int) -> pyrosetta.rosetta.utility.keys.Key2Tuple_double_double_t

blah

C++: core::scoring::mm::MMLJLibrary::lookup(unsigned long) const –> class utility::keys::Key2Tuple<double, double>

lookup(self: pyrosetta.rosetta.core.scoring.mm.MMLJLibrary, atom: str) -> pyrosetta.rosetta.utility.keys.Key2Tuple_double_double_t

blah

C++: core::scoring::mm::MMLJLibrary::lookup(class std::basic_string<char>) const –> class utility::keys::Key2Tuple<double, double>

lookup_three_bond(*args, **kwargs)¶

Overloaded function.

lookup_three_bond(self: pyrosetta.rosetta.core.scoring.mm.MMLJLibrary, atom: int) -> pyrosetta.rosetta.utility.keys.Key2Tuple_double_double_t

blah

C++: core::scoring::mm::MMLJLibrary::lookup_three_bond(unsigned long) const –> class utility::keys::Key2Tuple<double, double>

lookup_three_bond(self: pyrosetta.rosetta.core.scoring.mm.MMLJLibrary, atom: str) -> pyrosetta.rosetta.utility.keys.Key2Tuple_double_double_t

blah

C++: core::scoring::mm::MMLJLibrary::lookup_three_bond(class std::basic_string<char>) const –> class utility::keys::Key2Tuple<double, double>

mm_atom_set(self: pyrosetta.rosetta.core.scoring.mm.MMLJLibrary) → pyrosetta.rosetta.std.weak_ptr_const_core_chemical_MMAtomTypeSet_t¶

blah

C++: core::scoring::mm::MMLJLibrary::mm_atom_set() const –> class std::weak_ptr<const class core::chemical::MMAtomTypeSet>

nblist_dis2_cutoff_HH(self: pyrosetta.rosetta.core.scoring.mm.MMLJLibrary) → float¶

blah

C++: core::scoring::mm::MMLJLibrary::nblist_dis2_cutoff_HH() const –> double

nblist_dis2_cutoff_XH(self: pyrosetta.rosetta.core.scoring.mm.MMLJLibrary) → float¶

blah

C++: core::scoring::mm::MMLJLibrary::nblist_dis2_cutoff_XH() const –> double

nblist_dis2_cutoff_XX(self: pyrosetta.rosetta.core.scoring.mm.MMLJLibrary) → float¶

blah

C++: core::scoring::mm::MMLJLibrary::nblist_dis2_cutoff_XX() const –> double

class pyrosetta.rosetta.core.scoring.mm.MMLJScore¶

Bases: pybind11_builtins.pybind11_object

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

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.core.scoring.mm.MMLJScore) -> None
__init__(self: pyrosetta.rosetta.core.scoring.mm.MMLJScore, mmljl: core::scoring::mm::MMLJLibrary) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

deriv_score(self: pyrosetta.rosetta.core.scoring.mm.MMLJScore, atom1: int, atom2: int, path_distance: int, distance: float) → float¶

blah

C++: core::scoring::mm::MMLJScore::deriv_score(unsigned long, unsigned long, unsigned long, double) const –> double

min_dist(self: pyrosetta.rosetta.core.scoring.mm.MMLJScore, atom1: int, atom2: int, path_distance: int) → float¶

blah

C++: core::scoring::mm::MMLJScore::min_dist(unsigned long, unsigned long, unsigned long) const –> double

mm_lj_library(self: pyrosetta.rosetta.core.scoring.mm.MMLJScore) → core::scoring::mm::MMLJLibrary¶

blah

C++: core::scoring::mm::MMLJScore::mm_lj_library() const –> const class core::scoring::mm::MMLJLibrary &

score(self: pyrosetta.rosetta.core.scoring.mm.MMLJScore, atom1: int, atom2: int, path_distance: int, distance: float) → float¶

blah

C++: core::scoring::mm::MMLJScore::score(unsigned long, unsigned long, unsigned long, double) const –> double

class pyrosetta.rosetta.core.scoring.mm.MMTorsionLibrary¶

Bases: pybind11_builtins.pybind11_object

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.

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(self: pyrosetta.rosetta.core.scoring.mm.MMTorsionLibrary, filename: str, mm_atom_set: pyrosetta.rosetta.core.chemical.MMAtomTypeSet) → None¶

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

assign(self: pyrosetta.rosetta.core.scoring.mm.MMTorsionLibrary, : pyrosetta.rosetta.core.scoring.mm.MMTorsionLibrary) → pyrosetta.rosetta.core.scoring.mm.MMTorsionLibrary¶: C++: core::scoring::mm::MMTorsionLibrary::operator=(const class core::scoring::mm::MMTorsionLibrary &) –> class core::scoring::mm::MMTorsionLibrary &

class pyrosetta.rosetta.core.scoring.mm.MMTorsionScore¶

Bases: pybind11_builtins.pybind11_object

Calculates scores of mm torsion paramater sets given an angle

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.core.scoring.mm.MMTorsionScore) -> None
__init__(self: pyrosetta.rosetta.core.scoring.mm.MMTorsionScore, mmtl: pyrosetta.rosetta.core.scoring.mm.MMTorsionLibrary) -> None
__init__(self: pyrosetta.rosetta.core.scoring.mm.MMTorsionScore, arg0: pyrosetta.rosetta.core.scoring.mm.MMTorsionScore) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

pyrosetta.rosetta.core.scoring.mm.mm_bond_angle_residue_type_param_set(scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → pyrosetta.rosetta.core.scoring.mm.MMBondAngleResidueTypeParamSet¶

extract a MMBondAngleResidueTypeParamSet from a ScoreFunction, returning NULL if none exists

C++: core::scoring::mm::mm_bond_angle_residue_type_param_set(const class core::scoring::ScoreFunction &) –> class std::shared_ptr<const class core::scoring::mm::MMBondAngleResidueTypeParamSet>