scmin

Bindings for core::pack::scmin namespace

class pyrosetta.rosetta.core.pack.scmin.AtomTreeCollection

Bases: pybind11_builtins.pybind11_object

A collection of ResidueAtomTreeCollection objects for an entire design task.

__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.

1. __init__(self: pyrosetta.rosetta.core.pack.scmin.AtomTreeCollection, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets) -> None
2. __init__(self: pyrosetta.rosetta.core.pack.scmin.AtomTreeCollection, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask) -> None
3. __init__(self: pyrosetta.rosetta.core.pack.scmin.AtomTreeCollection, pose: pyrosetta.rosetta.core.pose.Pose, rset: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet, resid: int) -> None
4. __init__(self: pyrosetta.rosetta.core.pack.scmin.AtomTreeCollection, pose: pyrosetta.rosetta.core.pose.Pose, rltask: pyrosetta.rosetta.core.pack.task.ResidueLevelTask, resid: int) -> 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.pack.scmin.AtomTreeCollection, : pyrosetta.rosetta.core.pack.scmin.AtomTreeCollection) → pyrosetta.rosetta.core.pack.scmin.AtomTreeCollection

C++: core::pack::scmin::AtomTreeCollection::operator=(const class core::pack::scmin::AtomTreeCollection &) –> class core::pack::scmin::AtomTreeCollection &

moltenres_atomtree_collection(self: pyrosetta.rosetta.core.pack.scmin.AtomTreeCollection, moltenresid: int) → pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection

C++: core::pack::scmin::AtomTreeCollection::moltenres_atomtree_collection(unsigned long) –> class core::pack::scmin::ResidueAtomTreeCollection &

residue_atomtree_collection(self: pyrosetta.rosetta.core.pack.scmin.AtomTreeCollection, resid: int) → pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection

C++: core::pack::scmin::AtomTreeCollection::residue_atomtree_collection(unsigned long) –> class core::pack::scmin::ResidueAtomTreeCollection &

residue_atomtree_collection_op(self: pyrosetta.rosetta.core.pack.scmin.AtomTreeCollection, resid: int) → pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection

C++: core::pack::scmin::AtomTreeCollection::residue_atomtree_collection_op(unsigned long) –> class std::shared_ptr<class core::pack::scmin::ResidueAtomTreeCollection>

class pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection

Bases: pybind11_builtins.pybind11_object

The conformation::Residues and kinematics::AtomTrees for a single collection of rotamers (e.g. a RotamerSet). Each chemical::ResidueType gets its own residue/atomtree pair. A particular AtomTree/Residue pair can be set as “active” and manipulated by setter and getters for either the coordinates of the Residues or the chi dihedrals of the AtomTree.

__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.

1. __init__(self: pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection, rltask: pyrosetta.rosetta.core.pack.task.ResidueLevelTask, conformation: pyrosetta.rosetta.core.conformation.Conformation, orig_res: pyrosetta.rosetta.core.conformation.Residue) -> None
2. __init__(self: pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection, rset: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet, resid: int) -> 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).

active_atom_tree(self: pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection) → pyrosetta.rosetta.core.kinematics.AtomTree

Inline accessor for the active atom tree.

asserts atom_tree_uptodate_ – make sure that update_atom_tree is called first

C++: core::pack::scmin::ResidueAtomTreeCollection::active_atom_tree() const –> const class core::kinematics::AtomTree &

active_residue(self: pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection) → pyrosetta.rosetta.core.conformation.Residue

Inline accessor for the active residue.

asserts residue_uptodate_ – make sure that update_residue is called first

C++: core::pack::scmin::ResidueAtomTreeCollection::active_residue() const –> const class core::conformation::Residue &

active_residue_cop(self: pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection) → pyrosetta.rosetta.core.conformation.Residue

C++: core::pack::scmin::ResidueAtomTreeCollection::active_residue_cop() const –> class std::shared_ptr<const class core::conformation::Residue>

active_residue_data(self: pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection) → pyrosetta.rosetta.basic.datacache.BasicDataCache

Accessor for the active residue’s data cache

asserts residue_uptodate_ – make sure that update_residue is called first

C++: core::pack::scmin::ResidueAtomTreeCollection::active_residue_data() –> class basic::datacache::BasicDataCache &

active_restype(self: pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection) → pyrosetta.rosetta.core.chemical.ResidueType

C++: core::pack::scmin::ResidueAtomTreeCollection::active_restype() const –> const class core::chemical::ResidueType &

active_restype_index(self: pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection) → int

C++: core::pack::scmin::ResidueAtomTreeCollection::active_restype_index() const –> unsigned long

dof(self: pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection, dofid: pyrosetta.rosetta.core.id.DOF_ID) → float

fpd get dof value by DOF_ID

NOTE input resid must be 1

C++: core::pack::scmin::ResidueAtomTreeCollection::dof(const class core::id::DOF_ID &) –> double

save_momento(self: pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection, momento: pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento) → None

C++: core::pack::scmin::ResidueAtomTreeCollection::save_momento(class core::pack::scmin::ResidueAtomTreeCollectionMomento &) const –> void

set_active_restype_index(self: pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection, restype_index: int) → None

C++: core::pack::scmin::ResidueAtomTreeCollection::set_active_restype_index(unsigned long) –> void

set_chi(self: pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection, chi_index: int, value: float) → None

Assigns the chi dihedral for the active restype. Must be followed by a call to

update_residue() before the next call to active_residue()

C++: core::pack::scmin::ResidueAtomTreeCollection::set_chi(unsigned long, double) –> void

set_d(self: pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection, chi_index: int, value: float) → None

fpd bondlength analog to set_chi

like set_chi, assumes changes propagate to atomtree keyed off of chi#, so we only allow distances corresponding to chi angles to refine distance corresponds to the distance between atoms 3 and 4 defining the chi chino==0 ==> CA-CB distance, which allows us to refine ALA CB position for example

C++: core::pack::scmin::ResidueAtomTreeCollection::set_d(unsigned long, double) –> void

set_rescoords(*args, **kwargs)

Overloaded function.

1. set_rescoords(self: pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection, res: pyrosetta.rosetta.core.conformation.Residue) -> None

Assigns the coordinates for a residue. Must be followed by a call to

update_atom_tree() before the next cal to active_atom_tree().

C++: core::pack::scmin::ResidueAtomTreeCollection::set_rescoords(const class core::conformation::Residue &) –> void

2. set_rescoords(self: pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection, coords: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t) -> None

C++: core::pack::scmin::ResidueAtomTreeCollection::set_rescoords(const class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &) –> void

3. set_rescoords(self: pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection, atms: pyrosetta.rosetta.utility.vector1_core_id_AtomID, coords: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t) -> None

C++: core::pack::scmin::ResidueAtomTreeCollection::set_rescoords(const class utility::vector1<class core::id::AtomID, class std::allocator<class core::id::AtomID> > &, const class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &) –> void

set_theta(self: pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection, chi_index: int, value: float) → None

fpd bondangle analog to set_chi

same idea as set_d

C++: core::pack::scmin::ResidueAtomTreeCollection::set_theta(unsigned long, double) –> void

update_atom_tree(self: pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection) → None

See comments for update_residue(). After a call to “set_rescoords”, the user must

call update_atomtree() to make sure the atomtree and the residue are in synch.

C++: core::pack::scmin::ResidueAtomTreeCollection::update_atom_tree() –> void

update_from_momento(self: pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection, momento: pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento) → None

C++: core::pack::scmin::ResidueAtomTreeCollection::update_from_momento(const class core::pack::scmin::ResidueAtomTreeCollectionMomento &) –> void

update_residue(self: pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection) → None

The responsibility for making sure that the active residue and the active atomtree

are in synch is offloaded to an external class so that the calls to “active_residue()” and “active_atom_tree()” are as fast as possible (and bitwise const for future multithreaded use). After a round of set_chi() calls, the user for this class must update the residue coordinates.

C++: core::pack::scmin::ResidueAtomTreeCollection::update_residue() –> void

class pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento

Bases: pybind11_builtins.pybind11_object

Class to save the state for a ResidueAtomTreeCollection

__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.

1. __init__(self: pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento) -> None
2. __init__(self: pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento, arg0: pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento) -> 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.pack.scmin.ResidueAtomTreeCollectionMomento, : pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento) → pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento

C++: core::pack::scmin::ResidueAtomTreeCollectionMomento::operator=(const class core::pack::scmin::ResidueAtomTreeCollectionMomento &) –> class core::pack::scmin::ResidueAtomTreeCollectionMomento &

coord(self: pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento, ind: int) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::pack::scmin::ResidueAtomTreeCollectionMomento::coord(unsigned long) const –> const class numeric::xyzVector<double> &

copy_coords(self: pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento, : pyrosetta.rosetta.core.conformation.Residue) → None

C++: core::pack::scmin::ResidueAtomTreeCollectionMomento::copy_coords(const class core::conformation::Residue &) –> void

restype_index(self: pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento) → int

C++: core::pack::scmin::ResidueAtomTreeCollectionMomento::restype_index() const –> unsigned long

set_restype_index(self: pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento, setting: int) → None

C++: core::pack::scmin::ResidueAtomTreeCollectionMomento::set_restype_index(unsigned long) –> void

class pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment

Bases: pybind11_builtins.pybind11_object

A simple class for tracking a network state and its energy where each sidechain’s state is described by a series of chi angles.

__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.

1. __init__(self: pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment, nmoltenres: int) -> None
2. __init__(self: pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment, arg0: pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment) -> 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).

any_unassigned(self: pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment) → bool

C++: core::pack::scmin::SidechainStateAssignment::any_unassigned() const –> bool

assign(self: pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment, : pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment) → pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment

C++: core::pack::scmin::SidechainStateAssignment::operator=(const class core::pack::scmin::SidechainStateAssignment &) –> class core::pack::scmin::SidechainStateAssignment &

assign_energy(self: pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment, energy: float) → None

C++: core::pack::scmin::SidechainStateAssignment::assign_energy(double) –> void

assign_state(self: pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment, moltenresid: int, orig_rotid: int) → None

C++: core::pack::scmin::SidechainStateAssignment::assign_state(unsigned long, unsigned long) –> void

energy(self: pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment) → float

C++: core::pack::scmin::SidechainStateAssignment::energy() const –> double

momento_for_moltenres(self: pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment, moltenresid: int) → pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento

C++: core::pack::scmin::SidechainStateAssignment::momento_for_moltenres(unsigned long) const –> const class core::pack::scmin::ResidueAtomTreeCollectionMomento &

n_unassigned(self: pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment) → int

C++: core::pack::scmin::SidechainStateAssignment::n_unassigned() const –> unsigned long

nmoltenres(self: pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment) → int

C++: core::pack::scmin::SidechainStateAssignment::nmoltenres() const –> unsigned long

orig_rotamer_id_for_moltenres(self: pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment, moltenres: int) → int

C++: core::pack::scmin::SidechainStateAssignment::orig_rotamer_id_for_moltenres(unsigned long) const –> unsigned long

state_momento(self: pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment, moltenresid: int) → pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento

C++: core::pack::scmin::SidechainStateAssignment::state_momento(unsigned long) –> class core::pack::scmin::ResidueAtomTreeCollectionMomento &