tree

Bindings for core::kinematics::tree namespace

class pyrosetta.rosetta.core.kinematics.tree.Atom

Bases: pybind11_builtins.pybind11_object

Kinematics Atom interface class

append_atom(self: pyrosetta.rosetta.core.kinematics.tree.Atom, : pyrosetta.rosetta.core.kinematics.tree.Atom) None

C++: core::kinematics::tree::Atom::append_atom(class std::shared_ptr<class core::kinematics::tree::Atom>) –> void

atom_id(self: pyrosetta.rosetta.core.kinematics.tree.Atom) pyrosetta.rosetta.core.id.AtomID

Atom identifier

C++: core::kinematics::tree::Atom::atom_id() const –> const class core::id::AtomID &

atom_is_on_path_from_root(self: pyrosetta.rosetta.core.kinematics.tree.Atom, atm: pyrosetta.rosetta.core.kinematics.tree.Atom) bool

C++: core::kinematics::tree::Atom::atom_is_on_path_from_root(class std::shared_ptr<const class core::kinematics::tree::Atom>) const –> bool

atoms_begin(self: pyrosetta.rosetta.core.kinematics.tree.Atom) __gnu_cxx::__normal_iterator<std::shared_ptr<core::kinematics::tree::Atom>*, std::vector<std::shared_ptr<core::kinematics::tree::Atom>, std::allocator<std::shared_ptr<core::kinematics::tree::Atom> > > >

C++: core::kinematics::tree::Atom::atoms_begin() –> class __gnu_cxx::__normal_iterator<class std::shared_ptr<class core::kinematics::tree::Atom> *, class std::vector<class std::shared_ptr<class core::kinematics::tree::Atom>, class std::allocator<class std::shared_ptr<class core::kinematics::tree::Atom> > > >

atoms_end(self: pyrosetta.rosetta.core.kinematics.tree.Atom) __gnu_cxx::__normal_iterator<std::shared_ptr<core::kinematics::tree::Atom>*, std::vector<std::shared_ptr<core::kinematics::tree::Atom>, std::allocator<std::shared_ptr<core::kinematics::tree::Atom> > > >

C++: core::kinematics::tree::Atom::atoms_end() –> class __gnu_cxx::__normal_iterator<class std::shared_ptr<class core::kinematics::tree::Atom> *, class std::vector<class std::shared_ptr<class core::kinematics::tree::Atom>, class std::allocator<class std::shared_ptr<class core::kinematics::tree::Atom> > > >

child(self: pyrosetta.rosetta.core.kinematics.tree.Atom, k: int) pyrosetta.rosetta.core.kinematics.tree.Atom

C++: core::kinematics::tree::Atom::child(const unsigned long) –> class std::shared_ptr<class core::kinematics::tree::Atom>

child_index(self: pyrosetta.rosetta.core.kinematics.tree.Atom, child: pyrosetta.rosetta.core.kinematics.tree.Atom) int

the atom-index of this child

C++: core::kinematics::tree::Atom::child_index(class std::shared_ptr<const class core::kinematics::tree::Atom>) const –> unsigned long

clone(self: pyrosetta.rosetta.core.kinematics.tree.Atom, parent_in: pyrosetta.rosetta.std.weak_ptr_core_kinematics_tree_Atom_t, atom_pointer: pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t) pyrosetta.rosetta.core.kinematics.tree.Atom

copy atom with new memory allocation

C++: core::kinematics::tree::Atom::clone(class std::weak_ptr<class core::kinematics::tree::Atom>, class core::id::AtomID_Map<class std::shared_ptr<class core::kinematics::tree::Atom> > &) const –> class std::shared_ptr<class core::kinematics::tree::Atom>

copy_coords(self: pyrosetta.rosetta.core.kinematics.tree.Atom, src: pyrosetta.rosetta.core.kinematics.tree.Atom) None

copy DOFs and xyz coords from src Atom

C++: core::kinematics::tree::Atom::copy_coords(const class core::kinematics::tree::Atom &) –> void

delete_atom(self: pyrosetta.rosetta.core.kinematics.tree.Atom, : pyrosetta.rosetta.core.kinematics.tree.Atom) None

C++: core::kinematics::tree::Atom::delete_atom(class std::shared_ptr<class core::kinematics::tree::Atom>) –> void

dfs(self: pyrosetta.rosetta.core.kinematics.tree.Atom, changeset: pyrosetta.rosetta.utility.vector1_core_kinematics_AtomWithDOFChange, res_change_list: core::kinematics::ResidueCoordinateChangeList, start_atom_index: int) None
Perform a depth-first traversal of the tree that would be effected by

a DOF change from this atom. Stop at atoms that have already been traversed.

C++: core::kinematics::tree::Atom::dfs(class utility::vector1<class core::kinematics::AtomWithDOFChange, class std::allocator<class core::kinematics::AtomWithDOFChange> > &, class core::kinematics::ResidueCoordinateChangeList &, const unsigned long) const –> void

dihedral_between_bonded_children(self: pyrosetta.rosetta.core.kinematics.tree.Atom, child1: pyrosetta.rosetta.core.kinematics.tree.Atom, child2: pyrosetta.rosetta.core.kinematics.tree.Atom) float

dihedral angle between two bonded children to this atom

C++: core::kinematics::tree::Atom::dihedral_between_bonded_children(const class core::kinematics::tree::Atom &, const class core::kinematics::tree::Atom &) const –> double

distance(self: pyrosetta.rosetta.core.kinematics.tree.Atom, atom: pyrosetta.rosetta.core.kinematics.tree.Atom) float

Distance to an Atom

C++: core::kinematics::tree::Atom::distance(const class core::kinematics::tree::Atom &) const –> double

distance_squared(self: pyrosetta.rosetta.core.kinematics.tree.Atom, atom: pyrosetta.rosetta.core.kinematics.tree.Atom) float

Distance squared to an Atom

C++: core::kinematics::tree::Atom::distance_squared(const class core::kinematics::tree::Atom &) const –> double

dof(self: pyrosetta.rosetta.core.kinematics.tree.Atom, type: pyrosetta.rosetta.core.id.DOF_Type) float

get dof

C++: core::kinematics::tree::Atom::dof(const enum core::id::DOF_Type) const –> double

downstream(self: pyrosetta.rosetta.core.kinematics.tree.Atom, atom1: pyrosetta.rosetta.core.kinematics.tree.Atom) bool

C++: core::kinematics::tree::Atom::downstream(class std::shared_ptr<const class core::kinematics::tree::Atom>) const –> bool

get_dof_axis_and_end_pos(self: pyrosetta.rosetta.core.kinematics.tree.Atom, axis: pyrosetta.rosetta.numeric.xyzVector_double_t, end_pos: pyrosetta.rosetta.numeric.xyzVector_double_t, type: pyrosetta.rosetta.core.id.DOF_Type) None

C++: core::kinematics::tree::Atom::get_dof_axis_and_end_pos(class numeric::xyzVector<double> &, class numeric::xyzVector<double> &, const enum core::id::DOF_Type) const –> void

get_input_stub(self: pyrosetta.rosetta.core.kinematics.tree.Atom) pyrosetta.rosetta.core.kinematics.Stub

C++: core::kinematics::tree::Atom::get_input_stub() const –> class core::kinematics::Stub

get_nonjump_atom(self: pyrosetta.rosetta.core.kinematics.tree.Atom, i: int) pyrosetta.rosetta.core.kinematics.tree.Atom

C++: core::kinematics::tree::Atom::get_nonjump_atom(const unsigned long) const –> class std::shared_ptr<const class core::kinematics::tree::Atom>

get_self_ptr(self: pyrosetta.rosetta.core.kinematics.tree.Atom) pyrosetta.rosetta.core.kinematics.tree.Atom

C++: core::kinematics::tree::Atom::get_self_ptr() –> class std::shared_ptr<class core::kinematics::tree::Atom>

get_self_weak_ptr(self: pyrosetta.rosetta.core.kinematics.tree.Atom) pyrosetta.rosetta.std.weak_ptr_core_kinematics_tree_Atom_t

C++: core::kinematics::tree::Atom::get_self_weak_ptr() –> class std::weak_ptr<class core::kinematics::tree::Atom>

get_stub(self: pyrosetta.rosetta.core.kinematics.tree.Atom) pyrosetta.rosetta.core.kinematics.Stub

Get stub information

C++: core::kinematics::tree::Atom::get_stub() const –> class core::kinematics::Stub

id(*args, **kwargs)

Overloaded function.

  1. id(self: pyrosetta.rosetta.core.kinematics.tree.Atom) -> pyrosetta.rosetta.core.id.AtomID

Atom identifier

C++: core::kinematics::tree::Atom::id() const –> const class core::id::AtomID &

  1. id(self: pyrosetta.rosetta.core.kinematics.tree.Atom, id_in: pyrosetta.rosetta.core.id.AtomID) -> None

AtomID assignment

C++: core::kinematics::tree::Atom::id(const class core::id::AtomID &) –> void

input_stub_atom0(self: pyrosetta.rosetta.core.kinematics.tree.Atom) pyrosetta.rosetta.core.kinematics.tree.Atom

C++: core::kinematics::tree::Atom::input_stub_atom0() const –> class std::shared_ptr<const class core::kinematics::tree::Atom>

input_stub_atom0_id(self: pyrosetta.rosetta.core.kinematics.tree.Atom) pyrosetta.rosetta.core.id.AtomID

C++: core::kinematics::tree::Atom::input_stub_atom0_id() const –> const class core::id::AtomID &

input_stub_atom1(self: pyrosetta.rosetta.core.kinematics.tree.Atom) pyrosetta.rosetta.core.kinematics.tree.Atom

C++: core::kinematics::tree::Atom::input_stub_atom1() const –> class std::shared_ptr<const class core::kinematics::tree::Atom>

input_stub_atom1_id(self: pyrosetta.rosetta.core.kinematics.tree.Atom) pyrosetta.rosetta.core.id.AtomID

C++: core::kinematics::tree::Atom::input_stub_atom1_id() const –> const class core::id::AtomID &

input_stub_atom2(self: pyrosetta.rosetta.core.kinematics.tree.Atom) pyrosetta.rosetta.core.kinematics.tree.Atom

C++: core::kinematics::tree::Atom::input_stub_atom2() const –> class std::shared_ptr<const class core::kinematics::tree::Atom>

input_stub_atom2_id(self: pyrosetta.rosetta.core.kinematics.tree.Atom) pyrosetta.rosetta.core.id.AtomID

C++: core::kinematics::tree::Atom::input_stub_atom2_id() const –> const class core::id::AtomID &

input_stub_atom3(self: pyrosetta.rosetta.core.kinematics.tree.Atom) pyrosetta.rosetta.core.kinematics.tree.Atom

C++: core::kinematics::tree::Atom::input_stub_atom3() const –> class std::shared_ptr<const class core::kinematics::tree::Atom>

input_stub_atom3_id(self: pyrosetta.rosetta.core.kinematics.tree.Atom) pyrosetta.rosetta.core.id.AtomID

C++: core::kinematics::tree::Atom::input_stub_atom3_id() const –> const class core::id::AtomID &

insert_atom(*args, **kwargs)

Overloaded function.

  1. insert_atom(self: pyrosetta.rosetta.core.kinematics.tree.Atom, : pyrosetta.rosetta.core.kinematics.tree.Atom) -> None

C++: core::kinematics::tree::Atom::insert_atom(class std::shared_ptr<class core::kinematics::tree::Atom>) –> void

  1. insert_atom(self: pyrosetta.rosetta.core.kinematics.tree.Atom, : pyrosetta.rosetta.core.kinematics.tree.Atom, : int) -> None

C++: core::kinematics::tree::Atom::insert_atom(class std::shared_ptr<class core::kinematics::tree::Atom>, const int) –> void

is_jump(self: pyrosetta.rosetta.core.kinematics.tree.Atom) bool

atom is a jump atom?

C++: core::kinematics::tree::Atom::is_jump() const –> bool

jump(*args, **kwargs)

Overloaded function.

  1. jump(self: pyrosetta.rosetta.core.kinematics.tree.Atom) -> pyrosetta.rosetta.core.kinematics.Jump

get Jump

C++: core::kinematics::tree::Atom::jump() const –> const class core::kinematics::Jump &

  1. jump(self: pyrosetta.rosetta.core.kinematics.tree.Atom, jump_in: pyrosetta.rosetta.core.kinematics.Jump) -> None

set Jump

C++: core::kinematics::tree::Atom::jump(const class core::kinematics::Jump &) –> void

  1. jump(self: pyrosetta.rosetta.core.kinematics.tree.Atom, jump_in: pyrosetta.rosetta.core.kinematics.Jump, set: pyrosetta.rosetta.utility.vector1_core_kinematics_AtomWithDOFChange) -> None

set Jump – for use in output-sensitive refolding

C++: core::kinematics::tree::Atom::jump(const class core::kinematics::Jump &, class utility::vector1<class core::kinematics::AtomWithDOFChange, class std::allocator<class core::kinematics::AtomWithDOFChange> > &) –> void

keep_1st_child_pos(self: pyrosetta.rosetta.core.kinematics.tree.Atom) bool
when other atoms are inserted insert after 1st child if available.

–> this enables us to keep a stub of Downstream Jump atoms inside a single residue

C++: core::kinematics::tree::Atom::keep_1st_child_pos() const –> bool

keep_dof_fixed(self: pyrosetta.rosetta.core.kinematics.tree.Atom, : pyrosetta.rosetta.core.id.DOF_Type) bool

DoF should be fixed for this atom?

for DoFs that must be kept fixed due to topology of tree e.g., phi of stub_atoms for jump_atoms

C++: core::kinematics::tree::Atom::keep_dof_fixed(const enum core::id::DOF_Type) const –> bool

n_atom(self: pyrosetta.rosetta.core.kinematics.tree.Atom) int

C++: core::kinematics::tree::Atom::n_atom() const –> unsigned long

n_children(self: pyrosetta.rosetta.core.kinematics.tree.Atom) int

C++: core::kinematics::tree::Atom::n_children() const –> unsigned long

n_nonjump_children(self: pyrosetta.rosetta.core.kinematics.tree.Atom) int

C++: core::kinematics::tree::Atom::n_nonjump_children() const –> unsigned long

next_child(self: pyrosetta.rosetta.core.kinematics.tree.Atom, child: pyrosetta.rosetta.core.kinematics.tree.Atom) pyrosetta.rosetta.core.kinematics.tree.Atom

C++: core::kinematics::tree::Atom::next_child(class std::shared_ptr<const class core::kinematics::tree::Atom>) –> class std::shared_ptr<class core::kinematics::tree::Atom>

parent(*args, **kwargs)

Overloaded function.

  1. parent(self: pyrosetta.rosetta.core.kinematics.tree.Atom, parent_in: pyrosetta.rosetta.std.weak_ptr_core_kinematics_tree_Atom_t) -> None

parent assignment

C++: core::kinematics::tree::Atom::parent(class std::weak_ptr<class core::kinematics::tree::Atom>) –> void

  1. parent(self: pyrosetta.rosetta.core.kinematics.tree.Atom) -> pyrosetta.rosetta.core.kinematics.tree.Atom

Parent atom pointer, NULL for root atom

C++: core::kinematics::tree::Atom::parent() –> class std::shared_ptr<class core::kinematics::tree::Atom>

position(*args, **kwargs)

Overloaded function.

  1. position(self: pyrosetta.rosetta.core.kinematics.tree.Atom) -> pyrosetta.rosetta.numeric.xyzVector_double_t

Position

C++: core::kinematics::tree::Atom::position() const –> const class numeric::xyzVector<double> &

  1. position(self: pyrosetta.rosetta.core.kinematics.tree.Atom, position_a: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

Position assignment

C++: core::kinematics::tree::Atom::position(const class numeric::xyzVector<double> &) –> void

previous_child(self: pyrosetta.rosetta.core.kinematics.tree.Atom, child: pyrosetta.rosetta.core.kinematics.tree.Atom) pyrosetta.rosetta.core.kinematics.tree.Atom

C++: core::kinematics::tree::Atom::previous_child(class std::shared_ptr<const class core::kinematics::tree::Atom>) const –> class std::shared_ptr<const class core::kinematics::tree::Atom>

previous_sibling(self: pyrosetta.rosetta.core.kinematics.tree.Atom) pyrosetta.rosetta.core.kinematics.tree.Atom

C++: core::kinematics::tree::Atom::previous_sibling() const –> class std::shared_ptr<const class core::kinematics::tree::Atom>

raw_child_index(self: pyrosetta.rosetta.core.kinematics.tree.Atom, child: pyrosetta.rosetta.core.kinematics.tree.Atom) int

the atom-index of this child

C++: core::kinematics::tree::Atom::raw_child_index(const class core::kinematics::tree::Atom *) const –> unsigned long

raw_get_nonjump_atom(self: pyrosetta.rosetta.core.kinematics.tree.Atom, i: int) pyrosetta.rosetta.core.kinematics.tree.Atom
Rapid (increment-of-reference-count-avoiding) access to the ith non-jump atom in this atom’s

list of children.

C++: core::kinematics::tree::Atom::raw_get_nonjump_atom(const unsigned long) const –> const class core::kinematics::tree::Atom *

raw_input_stub_atom0(self: pyrosetta.rosetta.core.kinematics.tree.Atom) pyrosetta.rosetta.core.kinematics.tree.Atom

Rapid (increment-of-reference-count-avoiding) access to the 0th input stub atom;

C++: core::kinematics::tree::Atom::raw_input_stub_atom0() const –> const class core::kinematics::tree::Atom *

raw_input_stub_atom1(self: pyrosetta.rosetta.core.kinematics.tree.Atom) pyrosetta.rosetta.core.kinematics.tree.Atom

Rapid (increment-of-reference-count-avoiding) access to the 1st input stub atom;

C++: core::kinematics::tree::Atom::raw_input_stub_atom1() const –> const class core::kinematics::tree::Atom *

raw_input_stub_atom2(self: pyrosetta.rosetta.core.kinematics.tree.Atom) pyrosetta.rosetta.core.kinematics.tree.Atom

Rapid (increment-of-reference-count-avoiding) access to the 2nd input stub atom;

C++: core::kinematics::tree::Atom::raw_input_stub_atom2() const –> const class core::kinematics::tree::Atom *

raw_input_stub_atom3(self: pyrosetta.rosetta.core.kinematics.tree.Atom) pyrosetta.rosetta.core.kinematics.tree.Atom

Rapid (increment-of-reference-count-avoiding) access to the 3rd input stub atom;

C++: core::kinematics::tree::Atom::raw_input_stub_atom3() const –> const class core::kinematics::tree::Atom *

raw_parent(self: pyrosetta.rosetta.core.kinematics.tree.Atom) pyrosetta.rosetta.core.kinematics.tree.Atom

Rapid (increment-of-reference-count-avoiding) access to the parent atom pointer

C++: core::kinematics::tree::Atom::raw_parent() const –> const class core::kinematics::tree::Atom *

raw_previous_child(self: pyrosetta.rosetta.core.kinematics.tree.Atom, child: pyrosetta.rosetta.core.kinematics.tree.Atom) pyrosetta.rosetta.core.kinematics.tree.Atom

Rapid (increment-of-reference-count-avoiding) access to the previous child pointer;

C++: core::kinematics::tree::Atom::raw_previous_child(const class core::kinematics::tree::Atom *) const –> const class core::kinematics::tree::Atom *

raw_previous_sibling(self: pyrosetta.rosetta.core.kinematics.tree.Atom) pyrosetta.rosetta.core.kinematics.tree.Atom
Rapid (increment-of-reference-count-avoiding) access to the previous sibling pointer,

i.e. the first child in the parent’s children list to precede this atom.

C++: core::kinematics::tree::Atom::raw_previous_sibling() const –> const class core::kinematics::tree::Atom *

raw_stub_atom1(self: pyrosetta.rosetta.core.kinematics.tree.Atom) pyrosetta.rosetta.core.kinematics.tree.Atom

Rapid (increment-of-reference-count-avoiding) access to the fist stub atom

C++: core::kinematics::tree::Atom::raw_stub_atom1() const –> const class core::kinematics::tree::Atom *

raw_stub_atom2(self: pyrosetta.rosetta.core.kinematics.tree.Atom) pyrosetta.rosetta.core.kinematics.tree.Atom

Rapid (increment-of-reference-count-avoiding) access to the second stub atom

C++: core::kinematics::tree::Atom::raw_stub_atom2() const –> const class core::kinematics::tree::Atom *

raw_stub_atom3(self: pyrosetta.rosetta.core.kinematics.tree.Atom) pyrosetta.rosetta.core.kinematics.tree.Atom

Rapid (increment-of-reference-count-avoiding) access to the third stub atom

C++: core::kinematics::tree::Atom::raw_stub_atom3() const –> const class core::kinematics::tree::Atom *

replace_atom(self: pyrosetta.rosetta.core.kinematics.tree.Atom, old_atom: pyrosetta.rosetta.core.kinematics.tree.Atom, new_atom: pyrosetta.rosetta.core.kinematics.tree.Atom) None

C++: core::kinematics::tree::Atom::replace_atom(const class std::shared_ptr<class core::kinematics::tree::Atom>, const class std::shared_ptr<class core::kinematics::tree::Atom>) –> void

set_dof(*args, **kwargs)

Overloaded function.

  1. set_dof(self: pyrosetta.rosetta.core.kinematics.tree.Atom, type: pyrosetta.rosetta.core.id.DOF_Type, value: float) -> None

set dof, use “set_” syntax since we have multiple dof’s

C++: core::kinematics::tree::Atom::set_dof(const enum core::id::DOF_Type, const double) –> void

  1. set_dof(self: pyrosetta.rosetta.core.kinematics.tree.Atom, type: pyrosetta.rosetta.core.id.DOF_Type, value: float, set: pyrosetta.rosetta.utility.vector1_core_kinematics_AtomWithDOFChange) -> None

set dof, use “set_” syntax since we have multiple dof’s – for use in output-sensitive refold routine

C++: core::kinematics::tree::Atom::set_dof(const enum core::id::DOF_Type, const double, class utility::vector1<class core::kinematics::AtomWithDOFChange, class std::allocator<class core::kinematics::AtomWithDOFChange> > &) –> void

setup_min_map(self: pyrosetta.rosetta.core.kinematics.tree.Atom, last_torsion: pyrosetta.rosetta.core.id.DOF_ID, move_map: pyrosetta.rosetta.core.id.DOF_ID_Map_bool_t, min_map: core::kinematics::MinimizerMapBase) None

C++: core::kinematics::tree::Atom::setup_min_map(class core::id::DOF_ID &, const class core::id::DOF_ID_Map<bool> &, class core::kinematics::MinimizerMapBase &) const –> void

show(*args, **kwargs)

Overloaded function.

  1. show(self: pyrosetta.rosetta.core.kinematics.tree.Atom) -> None

dump out AtomID for this atom, its parent and all its offspring

C++: core::kinematics::tree::Atom::show() const –> void

  1. show(self: pyrosetta.rosetta.core.kinematics.tree.Atom, : int) -> None

dump out AtomID for this atom, its parent and all its offspring up to n_level

C++: core::kinematics::tree::Atom::show(const int &) const –> void

steal_inversion(self: pyrosetta.rosetta.core.kinematics.tree.Atom, : pyrosetta.rosetta.core.kinematics.tree.Atom) None

C++: core::kinematics::tree::Atom::steal_inversion(class std::shared_ptr<class core::kinematics::tree::Atom>) –> void

stub_atom1(self: pyrosetta.rosetta.core.kinematics.tree.Atom) pyrosetta.rosetta.core.kinematics.tree.Atom

C++: core::kinematics::tree::Atom::stub_atom1() const –> class std::shared_ptr<const class core::kinematics::tree::Atom>

stub_atom1_id(self: pyrosetta.rosetta.core.kinematics.tree.Atom) pyrosetta.rosetta.core.id.AtomID

C++: core::kinematics::tree::Atom::stub_atom1_id() const –> const class core::id::AtomID &

stub_atom2(self: pyrosetta.rosetta.core.kinematics.tree.Atom) pyrosetta.rosetta.core.kinematics.tree.Atom

C++: core::kinematics::tree::Atom::stub_atom2() const –> class std::shared_ptr<const class core::kinematics::tree::Atom>

stub_atom2_id(self: pyrosetta.rosetta.core.kinematics.tree.Atom) pyrosetta.rosetta.core.id.AtomID

C++: core::kinematics::tree::Atom::stub_atom2_id() const –> const class core::id::AtomID &

stub_atom3(self: pyrosetta.rosetta.core.kinematics.tree.Atom) pyrosetta.rosetta.core.kinematics.tree.Atom

C++: core::kinematics::tree::Atom::stub_atom3() const –> class std::shared_ptr<const class core::kinematics::tree::Atom>

stub_atom3_id(self: pyrosetta.rosetta.core.kinematics.tree.Atom) pyrosetta.rosetta.core.id.AtomID

C++: core::kinematics::tree::Atom::stub_atom3_id() const –> const class core::id::AtomID &

stub_defined(self: pyrosetta.rosetta.core.kinematics.tree.Atom) bool

C++: core::kinematics::tree::Atom::stub_defined() const –> bool

transform_Ax_plus_b_recursive(self: pyrosetta.rosetta.core.kinematics.tree.Atom, A: pyrosetta.rosetta.numeric.xyzMatrix_double_t, b: pyrosetta.rosetta.numeric.xyzVector_double_t, res_change_list: core::kinematics::ResidueCoordinateChangeList) None

Transform atom and children by linear transformation

C++: core::kinematics::tree::Atom::transform_Ax_plus_b_recursive(const class numeric::xyzMatrix<double> &, const class numeric::xyzVector<double> &, class core::kinematics::ResidueCoordinateChangeList &) –> void

update_domain_map(self: pyrosetta.rosetta.core.kinematics.tree.Atom, current_color: int, biggest_color: int, domain_map: pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t, dof_moved: pyrosetta.rosetta.core.id.AtomID_Map_bool_t, atom_moved: pyrosetta.rosetta.core.id.AtomID_Map_bool_t) None

C++: core::kinematics::tree::Atom::update_domain_map(int &, int &, class ObjexxFCL::FArray1D<int> &, const class core::id::AtomID_Map<bool> &, const class core::id::AtomID_Map<bool> &) const –> void

update_internal_coords(*args, **kwargs)

Overloaded function.

  1. update_internal_coords(self: pyrosetta.rosetta.core.kinematics.tree.Atom, stub: pyrosetta.rosetta.core.kinematics.Stub) -> None

  2. update_internal_coords(self: pyrosetta.rosetta.core.kinematics.tree.Atom, stub: pyrosetta.rosetta.core.kinematics.Stub, recursive: bool) -> None

Update internal coordinates for this atom and possibly all children.

If recursive is true, we update children, grandchildren, great-grandchildren, etc., but we don’t use a recursive algorithm.

Vikram K. Mulligan (vmulligan.org).

C++: core::kinematics::tree::Atom::update_internal_coords(class core::kinematics::Stub &, const bool) –> void

  1. update_internal_coords(self: pyrosetta.rosetta.core.kinematics.tree.Atom, recursive: bool) -> None

calculate my input_stub from the current xyz’s and use that input_stub to update my torsions

C++: core::kinematics::tree::Atom::update_internal_coords(const bool) –> void

update_stub(self: pyrosetta.rosetta.core.kinematics.tree.Atom, stub: pyrosetta.rosetta.core.kinematics.Stub) None

update the stub without actually updating coordinates

C++: core::kinematics::tree::Atom::update_stub(class core::kinematics::Stub &) const –> void

update_xyz_coords(*args, **kwargs)

Overloaded function.

  1. update_xyz_coords(self: pyrosetta.rosetta.core.kinematics.tree.Atom) -> None

The atom must retrieve an appropriate stub from its parent; it is the root

of the subtree being refolded

C++: core::kinematics::tree::Atom::update_xyz_coords() –> void

  1. update_xyz_coords(self: pyrosetta.rosetta.core.kinematics.tree.Atom, stub: pyrosetta.rosetta.core.kinematics.Stub) -> None

update xyz coords from stub and internal coords and

C++: core::kinematics::tree::Atom::update_xyz_coords(class core::kinematics::Stub &) –> void

x(self: pyrosetta.rosetta.core.kinematics.tree.Atom) float

x coordinate

C++: core::kinematics::tree::Atom::x() const –> const double &

xyz(*args, **kwargs)

Overloaded function.

  1. xyz(self: pyrosetta.rosetta.core.kinematics.tree.Atom) -> pyrosetta.rosetta.numeric.xyzVector_double_t

Position

C++: core::kinematics::tree::Atom::xyz() const –> const class numeric::xyzVector<double> &

  1. xyz(self: pyrosetta.rosetta.core.kinematics.tree.Atom, position_a: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

Position assignment

C++: core::kinematics::tree::Atom::xyz(const class numeric::xyzVector<double> &) –> void

y(self: pyrosetta.rosetta.core.kinematics.tree.Atom) float

y coordinate

C++: core::kinematics::tree::Atom::y() const –> const double &

z(self: pyrosetta.rosetta.core.kinematics.tree.Atom) float

z coordinate

C++: core::kinematics::tree::Atom::z() const –> const double &

class pyrosetta.rosetta.core.kinematics.tree.Atom_

Bases: pyrosetta.rosetta.core.kinematics.tree.Atom

Kinematics Atom abstract base class

append_atom(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, : pyrosetta.rosetta.core.kinematics.tree.Atom) None

append an atom as this atom’s child

C++: core::kinematics::tree::Atom_::append_atom(class std::shared_ptr<class core::kinematics::tree::Atom>) –> void

atom_id(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.id.AtomID

Atom identifier

C++: core::kinematics::tree::Atom_::atom_id() const –> const class core::id::AtomID &

atom_is_on_path_from_root(self: pyrosetta.rosetta.core.kinematics.tree.Atom, atm: pyrosetta.rosetta.core.kinematics.tree.Atom) bool

C++: core::kinematics::tree::Atom::atom_is_on_path_from_root(class std::shared_ptr<const class core::kinematics::tree::Atom>) const –> bool

atoms_begin(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) __gnu_cxx::__normal_iterator<std::shared_ptr<core::kinematics::tree::Atom>*, std::vector<std::shared_ptr<core::kinematics::tree::Atom>, std::allocator<std::shared_ptr<core::kinematics::tree::Atom> > > >

starting iterator of the children atom list

C++: core::kinematics::tree::Atom_::atoms_begin() –> class __gnu_cxx::__normal_iterator<class std::shared_ptr<class core::kinematics::tree::Atom> *, class std::vector<class std::shared_ptr<class core::kinematics::tree::Atom>, class std::allocator<class std::shared_ptr<class core::kinematics::tree::Atom> > > >

atoms_end(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) __gnu_cxx::__normal_iterator<std::shared_ptr<core::kinematics::tree::Atom>*, std::vector<std::shared_ptr<core::kinematics::tree::Atom>, std::allocator<std::shared_ptr<core::kinematics::tree::Atom> > > >

ending iterator of the children atom list

C++: core::kinematics::tree::Atom_::atoms_end() –> class __gnu_cxx::__normal_iterator<class std::shared_ptr<class core::kinematics::tree::Atom> *, class std::vector<class std::shared_ptr<class core::kinematics::tree::Atom>, class std::allocator<class std::shared_ptr<class core::kinematics::tree::Atom> > > >

child(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, k: int) pyrosetta.rosetta.core.kinematics.tree.Atom

get a child atom by index

C++: core::kinematics::tree::Atom_::child(const unsigned long) –> class std::shared_ptr<class core::kinematics::tree::Atom>

child_index(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, child: pyrosetta.rosetta.core.kinematics.tree.Atom) int

the atom-index of this child

C++: core::kinematics::tree::Atom_::child_index(class std::shared_ptr<const class core::kinematics::tree::Atom>) const –> unsigned long

clone(self: pyrosetta.rosetta.core.kinematics.tree.Atom, parent_in: pyrosetta.rosetta.std.weak_ptr_core_kinematics_tree_Atom_t, atom_pointer: pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t) pyrosetta.rosetta.core.kinematics.tree.Atom

copy atom with new memory allocation

C++: core::kinematics::tree::Atom::clone(class std::weak_ptr<class core::kinematics::tree::Atom>, class core::id::AtomID_Map<class std::shared_ptr<class core::kinematics::tree::Atom> > &) const –> class std::shared_ptr<class core::kinematics::tree::Atom>

copy_coords(self: pyrosetta.rosetta.core.kinematics.tree.Atom, src: pyrosetta.rosetta.core.kinematics.tree.Atom) None

copy DOFs and xyz coords from src Atom

C++: core::kinematics::tree::Atom::copy_coords(const class core::kinematics::tree::Atom &) –> void

delete_atom(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, : pyrosetta.rosetta.core.kinematics.tree.Atom) None

remove an atom from this atom’s children

C++: core::kinematics::tree::Atom_::delete_atom(class std::shared_ptr<class core::kinematics::tree::Atom>) –> void

dfs(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, changeset: pyrosetta.rosetta.utility.vector1_core_kinematics_AtomWithDOFChange, res_change_list: pyrosetta.rosetta.core.kinematics.ResidueCoordinateChangeList, start_atom_index: int) None
base class implementation that traverses the subtree routed at this node

in the depth-first traversal of the atoms requiring coordinate updates.

C++: core::kinematics::tree::Atom_::dfs(class utility::vector1<class core::kinematics::AtomWithDOFChange, class std::allocator<class core::kinematics::AtomWithDOFChange> > &, class core::kinematics::ResidueCoordinateChangeList &, const unsigned long) const –> void

dihedral_between_bonded_children(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, child1: pyrosetta.rosetta.core.kinematics.tree.Atom, child2: pyrosetta.rosetta.core.kinematics.tree.Atom) float

dihedral angle between two bonded children to this atom

C++: core::kinematics::tree::Atom_::dihedral_between_bonded_children(const class core::kinematics::tree::Atom &, const class core::kinematics::tree::Atom &) const –> double

distance(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, atom: pyrosetta.rosetta.core.kinematics.tree.Atom) float

Distance to an Atom

C++: core::kinematics::tree::Atom_::distance(const class core::kinematics::tree::Atom &) const –> double

distance_squared(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, atom: pyrosetta.rosetta.core.kinematics.tree.Atom) float

Distance squared to an Atom

C++: core::kinematics::tree::Atom_::distance_squared(const class core::kinematics::tree::Atom &) const –> double

dof(self: pyrosetta.rosetta.core.kinematics.tree.Atom, type: pyrosetta.rosetta.core.id.DOF_Type) float

get dof

C++: core::kinematics::tree::Atom::dof(const enum core::id::DOF_Type) const –> double

downstream(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, atom1: pyrosetta.rosetta.core.kinematics.tree.Atom) bool

whether atom1 is downstream of this atom.

C++: core::kinematics::tree::Atom_::downstream(class std::shared_ptr<const class core::kinematics::tree::Atom>) const –> bool

get_dof_axis_and_end_pos(self: pyrosetta.rosetta.core.kinematics.tree.Atom, axis: pyrosetta.rosetta.numeric.xyzVector_double_t, end_pos: pyrosetta.rosetta.numeric.xyzVector_double_t, type: pyrosetta.rosetta.core.id.DOF_Type) None

C++: core::kinematics::tree::Atom::get_dof_axis_and_end_pos(class numeric::xyzVector<double> &, class numeric::xyzVector<double> &, const enum core::id::DOF_Type) const –> void

get_input_stub(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.kinematics.Stub

stub used to build this atom

C++: core::kinematics::tree::Atom_::get_input_stub() const –> class core::kinematics::Stub

get_nonjump_atom(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, i: int) pyrosetta.rosetta.core.kinematics.tree.Atom

get non-jump atom by its index from the children atoms list

C++: core::kinematics::tree::Atom_::get_nonjump_atom(const unsigned long) const –> class std::shared_ptr<const class core::kinematics::tree::Atom>

get_self_ptr(self: pyrosetta.rosetta.core.kinematics.tree.Atom) pyrosetta.rosetta.core.kinematics.tree.Atom

C++: core::kinematics::tree::Atom::get_self_ptr() –> class std::shared_ptr<class core::kinematics::tree::Atom>

get_self_weak_ptr(self: pyrosetta.rosetta.core.kinematics.tree.Atom) pyrosetta.rosetta.std.weak_ptr_core_kinematics_tree_Atom_t

C++: core::kinematics::tree::Atom::get_self_weak_ptr() –> class std::weak_ptr<class core::kinematics::tree::Atom>

get_stub(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.kinematics.Stub

stub centerd at this atom

C++: core::kinematics::tree::Atom_::get_stub() const –> class core::kinematics::Stub

id(*args, **kwargs)

Overloaded function.

  1. id(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) -> pyrosetta.rosetta.core.id.AtomID

Atom identifier

C++: core::kinematics::tree::Atom_::id() const –> const class core::id::AtomID &

  1. id(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, id_in: pyrosetta.rosetta.core.id.AtomID) -> None

AtomID assignment

C++: core::kinematics::tree::Atom_::id(const class core::id::AtomID &) –> void

input_stub_atom0(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.kinematics.tree.Atom
the center of the input stub for refolding this atom

it is its parent

C++: core::kinematics::tree::Atom_::input_stub_atom0() const –> class std::shared_ptr<const class core::kinematics::tree::Atom>

input_stub_atom0_id(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.id.AtomID

input stub atom0’s id

C++: core::kinematics::tree::Atom_::input_stub_atom0_id() const –> const class core::id::AtomID &

input_stub_atom1(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.kinematics.tree.Atom
the first atom to construct the input stub for refolding this atom

it is its parent’s stub_atom1, which normally the parent itself

C++: core::kinematics::tree::Atom_::input_stub_atom1() const –> class std::shared_ptr<const class core::kinematics::tree::Atom>

input_stub_atom1_id(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.id.AtomID

input stub atom1’s id

C++: core::kinematics::tree::Atom_::input_stub_atom1_id() const –> const class core::id::AtomID &

input_stub_atom2(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.kinematics.tree.Atom
the second atom to construct the input stub for refolding this atom

it is its parent’s stub_atom2, which normally the parent’s parent

C++: core::kinematics::tree::Atom_::input_stub_atom2() const –> class std::shared_ptr<const class core::kinematics::tree::Atom>

input_stub_atom2_id(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.id.AtomID

input stub atom2’s id

C++: core::kinematics::tree::Atom_::input_stub_atom2_id() const –> const class core::id::AtomID &

input_stub_atom3(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.kinematics.tree.Atom
the third atom to construct the input stub for refolding this atom

it is either its previous sibling or its parent’s stub_atom3,

C++: core::kinematics::tree::Atom_::input_stub_atom3() const –> class std::shared_ptr<const class core::kinematics::tree::Atom>

input_stub_atom3_id(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.id.AtomID

input stub atom3’s id

C++: core::kinematics::tree::Atom_::input_stub_atom3_id() const –> const class core::id::AtomID &

insert_atom(*args, **kwargs)

Overloaded function.

  1. insert_atom(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, : pyrosetta.rosetta.core.kinematics.tree.Atom) -> None

insert an atom as this atom’s child

C++: core::kinematics::tree::Atom_::insert_atom(class std::shared_ptr<class core::kinematics::tree::Atom>) –> void

  1. insert_atom(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, : pyrosetta.rosetta.core.kinematics.tree.Atom, : int) -> None

tries to insert at the position specified by the second argument

C++: core::kinematics::tree::Atom_::insert_atom(class std::shared_ptr<class core::kinematics::tree::Atom>, const int) –> void

is_jump(self: pyrosetta.rosetta.core.kinematics.tree.Atom) bool

atom is a jump atom?

C++: core::kinematics::tree::Atom::is_jump() const –> bool

jump(*args, **kwargs)

Overloaded function.

  1. jump(self: pyrosetta.rosetta.core.kinematics.tree.Atom) -> pyrosetta.rosetta.core.kinematics.Jump

get Jump

C++: core::kinematics::tree::Atom::jump() const –> const class core::kinematics::Jump &

  1. jump(self: pyrosetta.rosetta.core.kinematics.tree.Atom, jump_in: pyrosetta.rosetta.core.kinematics.Jump) -> None

set Jump

C++: core::kinematics::tree::Atom::jump(const class core::kinematics::Jump &) –> void

  1. jump(self: pyrosetta.rosetta.core.kinematics.tree.Atom, jump_in: pyrosetta.rosetta.core.kinematics.Jump, set: pyrosetta.rosetta.utility.vector1_core_kinematics_AtomWithDOFChange) -> None

set Jump – for use in output-sensitive refolding

C++: core::kinematics::tree::Atom::jump(const class core::kinematics::Jump &, class utility::vector1<class core::kinematics::AtomWithDOFChange, class std::allocator<class core::kinematics::AtomWithDOFChange> > &) –> void

keep_1st_child_pos(self: pyrosetta.rosetta.core.kinematics.tree.Atom) bool
when other atoms are inserted insert after 1st child if available.

–> this enables us to keep a stub of Downstream Jump atoms inside a single residue

C++: core::kinematics::tree::Atom::keep_1st_child_pos() const –> bool

keep_dof_fixed(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, : pyrosetta.rosetta.core.id.DOF_Type) bool
for DOFs which must be kept fixed due to topology of tree

eg, phi of stub_atoms for jump_atoms

C++: core::kinematics::tree::Atom_::keep_dof_fixed(const enum core::id::DOF_Type) const –> bool

n_atom(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) int

number of children atoms

C++: core::kinematics::tree::Atom_::n_atom() const –> unsigned long

n_children(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) int

number of the child atoms

C++: core::kinematics::tree::Atom_::n_children() const –> unsigned long

n_nonjump_children(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) int

number of the non-jump child atoms

C++: core::kinematics::tree::Atom_::n_nonjump_children() const –> unsigned long

next_child(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, child: pyrosetta.rosetta.core.kinematics.tree.Atom) pyrosetta.rosetta.core.kinematics.tree.Atom

find the child atom after this child in the list

C++: core::kinematics::tree::Atom_::next_child(class std::shared_ptr<const class core::kinematics::tree::Atom>) –> class std::shared_ptr<class core::kinematics::tree::Atom>

parent(*args, **kwargs)

Overloaded function.

  1. parent(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) -> pyrosetta.rosetta.core.kinematics.tree.Atom

Parent atom pointer

C++: core::kinematics::tree::Atom_::parent() –> class std::shared_ptr<class core::kinematics::tree::Atom>

  1. parent(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, parent_in: pyrosetta.rosetta.std.weak_ptr_core_kinematics_tree_Atom_t) -> None

C++: core::kinematics::tree::Atom_::parent(class std::weak_ptr<class core::kinematics::tree::Atom>) –> void

position(*args, **kwargs)

Overloaded function.

  1. position(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) -> pyrosetta.rosetta.numeric.xyzVector_double_t

Position

C++: core::kinematics::tree::Atom_::position() const –> const class numeric::xyzVector<double> &

  1. position(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, position_a: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

Position assignment

C++: core::kinematics::tree::Atom_::position(const class numeric::xyzVector<double> &) –> void

previous_child(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, child: pyrosetta.rosetta.core.kinematics.tree.Atom) pyrosetta.rosetta.core.kinematics.tree.Atom

find the child atom before this child in the list

C++: core::kinematics::tree::Atom_::previous_child(class std::shared_ptr<const class core::kinematics::tree::Atom>) const –> class std::shared_ptr<const class core::kinematics::tree::Atom>

previous_sibling(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.kinematics.tree.Atom
routines for navigating the tree

find the sibling atom before itself

C++: core::kinematics::tree::Atom_::previous_sibling() const –> class std::shared_ptr<const class core::kinematics::tree::Atom>

raw_child_index(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, child: pyrosetta.rosetta.core.kinematics.tree.Atom) int

the atom-index of this child

C++: core::kinematics::tree::Atom_::raw_child_index(const class core::kinematics::tree::Atom *) const –> unsigned long

raw_get_nonjump_atom(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, i: int) pyrosetta.rosetta.core.kinematics.tree.Atom

C++: core::kinematics::tree::Atom_::raw_get_nonjump_atom(const unsigned long) const –> const class core::kinematics::tree::Atom *

raw_input_stub_atom0(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.kinematics.tree.Atom

C++: core::kinematics::tree::Atom_::raw_input_stub_atom0() const –> const class core::kinematics::tree::Atom *

raw_input_stub_atom1(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.kinematics.tree.Atom

C++: core::kinematics::tree::Atom_::raw_input_stub_atom1() const –> const class core::kinematics::tree::Atom *

raw_input_stub_atom2(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.kinematics.tree.Atom

C++: core::kinematics::tree::Atom_::raw_input_stub_atom2() const –> const class core::kinematics::tree::Atom *

raw_input_stub_atom3(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.kinematics.tree.Atom

C++: core::kinematics::tree::Atom_::raw_input_stub_atom3() const –> const class core::kinematics::tree::Atom *

raw_parent(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.kinematics.tree.Atom

C++: core::kinematics::tree::Atom_::raw_parent() const –> const class core::kinematics::tree::Atom *

raw_previous_child(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, child: pyrosetta.rosetta.core.kinematics.tree.Atom) pyrosetta.rosetta.core.kinematics.tree.Atom

C++: core::kinematics::tree::Atom_::raw_previous_child(const class core::kinematics::tree::Atom *) const –> const class core::kinematics::tree::Atom *

raw_previous_sibling(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.kinematics.tree.Atom

C++: core::kinematics::tree::Atom_::raw_previous_sibling() const –> const class core::kinematics::tree::Atom *

raw_stub_atom1(self: pyrosetta.rosetta.core.kinematics.tree.Atom) pyrosetta.rosetta.core.kinematics.tree.Atom

Rapid (increment-of-reference-count-avoiding) access to the fist stub atom

C++: core::kinematics::tree::Atom::raw_stub_atom1() const –> const class core::kinematics::tree::Atom *

raw_stub_atom2(self: pyrosetta.rosetta.core.kinematics.tree.Atom) pyrosetta.rosetta.core.kinematics.tree.Atom

Rapid (increment-of-reference-count-avoiding) access to the second stub atom

C++: core::kinematics::tree::Atom::raw_stub_atom2() const –> const class core::kinematics::tree::Atom *

raw_stub_atom3(self: pyrosetta.rosetta.core.kinematics.tree.Atom) pyrosetta.rosetta.core.kinematics.tree.Atom

Rapid (increment-of-reference-count-avoiding) access to the third stub atom

C++: core::kinematics::tree::Atom::raw_stub_atom3() const –> const class core::kinematics::tree::Atom *

replace_atom(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, old_atom: pyrosetta.rosetta.core.kinematics.tree.Atom, new_atom: pyrosetta.rosetta.core.kinematics.tree.Atom) None

replace the old atom by the new atom in the child atom list

C++: core::kinematics::tree::Atom_::replace_atom(const class std::shared_ptr<class core::kinematics::tree::Atom>, const class std::shared_ptr<class core::kinematics::tree::Atom>) –> void

set_dof(*args, **kwargs)

Overloaded function.

  1. set_dof(self: pyrosetta.rosetta.core.kinematics.tree.Atom, type: pyrosetta.rosetta.core.id.DOF_Type, value: float) -> None

set dof, use “set_” syntax since we have multiple dof’s

C++: core::kinematics::tree::Atom::set_dof(const enum core::id::DOF_Type, const double) –> void

  1. set_dof(self: pyrosetta.rosetta.core.kinematics.tree.Atom, type: pyrosetta.rosetta.core.id.DOF_Type, value: float, set: pyrosetta.rosetta.utility.vector1_core_kinematics_AtomWithDOFChange) -> None

set dof, use “set_” syntax since we have multiple dof’s – for use in output-sensitive refold routine

C++: core::kinematics::tree::Atom::set_dof(const enum core::id::DOF_Type, const double, class utility::vector1<class core::kinematics::AtomWithDOFChange, class std::allocator<class core::kinematics::AtomWithDOFChange> > &) –> void

setup_min_map(self: pyrosetta.rosetta.core.kinematics.tree.Atom, last_torsion: pyrosetta.rosetta.core.id.DOF_ID, move_map: pyrosetta.rosetta.core.id.DOF_ID_Map_bool_t, min_map: core::kinematics::MinimizerMapBase) None

C++: core::kinematics::tree::Atom::setup_min_map(class core::id::DOF_ID &, const class core::id::DOF_ID_Map<bool> &, class core::kinematics::MinimizerMapBase &) const –> void

show(*args, **kwargs)

Overloaded function.

  1. show(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) -> None

dump out AtomID for this atom, its parent and all its offspring

C++: core::kinematics::tree::Atom_::show() const –> void

  1. show(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, n_level: int) -> None

dump out AtomID for this atom, its parent and all its offspring up to n_level

C++: core::kinematics::tree::Atom_::show(const int &) const –> void

steal_inversion(self: pyrosetta.rosetta.core.kinematics.tree.Atom, : pyrosetta.rosetta.core.kinematics.tree.Atom) None

C++: core::kinematics::tree::Atom::steal_inversion(class std::shared_ptr<class core::kinematics::tree::Atom>) –> void

stub_atom1(self: pyrosetta.rosetta.core.kinematics.tree.Atom) pyrosetta.rosetta.core.kinematics.tree.Atom

C++: core::kinematics::tree::Atom::stub_atom1() const –> class std::shared_ptr<const class core::kinematics::tree::Atom>

stub_atom1_id(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.id.AtomID

stub atom1 ‘s id

C++: core::kinematics::tree::Atom_::stub_atom1_id() const –> const class core::id::AtomID &

stub_atom2(self: pyrosetta.rosetta.core.kinematics.tree.Atom) pyrosetta.rosetta.core.kinematics.tree.Atom

C++: core::kinematics::tree::Atom::stub_atom2() const –> class std::shared_ptr<const class core::kinematics::tree::Atom>

stub_atom2_id(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.id.AtomID

stub atom2’s id

C++: core::kinematics::tree::Atom_::stub_atom2_id() const –> const class core::id::AtomID &

stub_atom3(self: pyrosetta.rosetta.core.kinematics.tree.Atom) pyrosetta.rosetta.core.kinematics.tree.Atom

C++: core::kinematics::tree::Atom::stub_atom3() const –> class std::shared_ptr<const class core::kinematics::tree::Atom>

stub_atom3_id(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.id.AtomID

stub atom3’s id

C++: core::kinematics::tree::Atom_::stub_atom3_id() const –> const class core::id::AtomID &

stub_defined(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) bool

whether a Stub can be defined for this atom

C++: core::kinematics::tree::Atom_::stub_defined() const –> bool

transform_Ax_plus_b_recursive(self: pyrosetta.rosetta.core.kinematics.tree.Atom, A: pyrosetta.rosetta.numeric.xyzMatrix_double_t, b: pyrosetta.rosetta.numeric.xyzVector_double_t, res_change_list: core::kinematics::ResidueCoordinateChangeList) None

Transform atom and children by linear transformation

C++: core::kinematics::tree::Atom::transform_Ax_plus_b_recursive(const class numeric::xyzMatrix<double> &, const class numeric::xyzVector<double> &, class core::kinematics::ResidueCoordinateChangeList &) –> void

update_domain_map(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, current_color: int, biggest_color: int, domain_map: pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t, dof_moved: pyrosetta.rosetta.core.id.AtomID_Map_bool_t, atom_moved: pyrosetta.rosetta.core.id.AtomID_Map_bool_t) None

update domain map

C++: core::kinematics::tree::Atom_::update_domain_map(int &, int &, class ObjexxFCL::FArray1D<int> &, const class core::id::AtomID_Map<bool> &, const class core::id::AtomID_Map<bool> &) const –> void

update_internal_coords(*args, **kwargs)

Overloaded function.

  1. update_internal_coords(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, recursive: bool) -> None

update internal coords of this atom and its offspring atoms (if recursive)

C++: core::kinematics::tree::Atom_::update_internal_coords(const bool) –> void

  1. update_internal_coords(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, stub: pyrosetta.rosetta.core.kinematics.Stub) -> None

  2. update_internal_coords(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, stub: pyrosetta.rosetta.core.kinematics.Stub, recursive: bool) -> None

Update internal coordinates for this atom and possibly all children.

If recursive is true, we update children, grandchildren, great-grandchildren, etc., but we don’t use a recursive algorithm.

Vikram K. Mulligan (vmulligan.org).

C++: core::kinematics::tree::Atom_::update_internal_coords(class core::kinematics::Stub &, const bool) –> void

update_stub(self: pyrosetta.rosetta.core.kinematics.tree.Atom, stub: pyrosetta.rosetta.core.kinematics.Stub) None

update the stub without actually updating coordinates

C++: core::kinematics::tree::Atom::update_stub(class core::kinematics::Stub &) const –> void

update_xyz_coords(*args, **kwargs)

Overloaded function.

  1. update_xyz_coords(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, stub: pyrosetta.rosetta.core.kinematics.Stub) -> None

  2. update_xyz_coords(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) -> None

update xyz position of this atom and its offspring atoms

C++: core::kinematics::tree::Atom_::update_xyz_coords() –> void

x(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) float

x coordinate

C++: core::kinematics::tree::Atom_::x() const –> const double &

xyz(*args, **kwargs)

Overloaded function.

  1. xyz(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) -> pyrosetta.rosetta.numeric.xyzVector_double_t

Position

C++: core::kinematics::tree::Atom_::xyz() const –> const class numeric::xyzVector<double> &

  1. xyz(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, position_a: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

Position assignment

C++: core::kinematics::tree::Atom_::xyz(const class numeric::xyzVector<double> &) –> void

y(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) float

y coordinate

C++: core::kinematics::tree::Atom_::y() const –> const double &

z(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) float

z coordinate

C++: core::kinematics::tree::Atom_::z() const –> const double &

class pyrosetta.rosetta.core.kinematics.tree.BondedAtom

Bases: pyrosetta.rosetta.core.kinematics.tree.Atom_

an atom which are bonded to its parent, derived from Atom_

See

append_atom(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, : pyrosetta.rosetta.core.kinematics.tree.Atom) None

append an atom as this atom’s child

C++: core::kinematics::tree::Atom_::append_atom(class std::shared_ptr<class core::kinematics::tree::Atom>) –> void

assign(self: pyrosetta.rosetta.core.kinematics.tree.BondedAtom, : pyrosetta.rosetta.core.kinematics.tree.BondedAtom) pyrosetta.rosetta.core.kinematics.tree.BondedAtom

C++: core::kinematics::tree::BondedAtom::operator=(const class core::kinematics::tree::BondedAtom &) –> class core::kinematics::tree::BondedAtom &

atom_id(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.id.AtomID

Atom identifier

C++: core::kinematics::tree::Atom_::atom_id() const –> const class core::id::AtomID &

atom_is_on_path_from_root(self: pyrosetta.rosetta.core.kinematics.tree.Atom, atm: pyrosetta.rosetta.core.kinematics.tree.Atom) bool

C++: core::kinematics::tree::Atom::atom_is_on_path_from_root(class std::shared_ptr<const class core::kinematics::tree::Atom>) const –> bool

atoms_begin(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) __gnu_cxx::__normal_iterator<std::shared_ptr<core::kinematics::tree::Atom>*, std::vector<std::shared_ptr<core::kinematics::tree::Atom>, std::allocator<std::shared_ptr<core::kinematics::tree::Atom> > > >

starting iterator of the children atom list

C++: core::kinematics::tree::Atom_::atoms_begin() –> class __gnu_cxx::__normal_iterator<class std::shared_ptr<class core::kinematics::tree::Atom> *, class std::vector<class std::shared_ptr<class core::kinematics::tree::Atom>, class std::allocator<class std::shared_ptr<class core::kinematics::tree::Atom> > > >

atoms_end(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) __gnu_cxx::__normal_iterator<std::shared_ptr<core::kinematics::tree::Atom>*, std::vector<std::shared_ptr<core::kinematics::tree::Atom>, std::allocator<std::shared_ptr<core::kinematics::tree::Atom> > > >

ending iterator of the children atom list

C++: core::kinematics::tree::Atom_::atoms_end() –> class __gnu_cxx::__normal_iterator<class std::shared_ptr<class core::kinematics::tree::Atom> *, class std::vector<class std::shared_ptr<class core::kinematics::tree::Atom>, class std::allocator<class std::shared_ptr<class core::kinematics::tree::Atom> > > >

child(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, k: int) pyrosetta.rosetta.core.kinematics.tree.Atom

get a child atom by index

C++: core::kinematics::tree::Atom_::child(const unsigned long) –> class std::shared_ptr<class core::kinematics::tree::Atom>

child_index(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, child: pyrosetta.rosetta.core.kinematics.tree.Atom) int

the atom-index of this child

C++: core::kinematics::tree::Atom_::child_index(class std::shared_ptr<const class core::kinematics::tree::Atom>) const –> unsigned long

clone(self: pyrosetta.rosetta.core.kinematics.tree.BondedAtom, parent_in: pyrosetta.rosetta.std.weak_ptr_core_kinematics_tree_Atom_t, atom_pointer: pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t) pyrosetta.rosetta.core.kinematics.tree.Atom

copy this atom

C++: core::kinematics::tree::BondedAtom::clone(class std::weak_ptr<class core::kinematics::tree::Atom>, class core::id::AtomID_Map<class std::shared_ptr<class core::kinematics::tree::Atom> > &) const –> class std::shared_ptr<class core::kinematics::tree::Atom>

copy_coords(self: pyrosetta.rosetta.core.kinematics.tree.BondedAtom, src: pyrosetta.rosetta.core.kinematics.tree.Atom) None

copy DOFs, xyz’s

C++: core::kinematics::tree::BondedAtom::copy_coords(const class core::kinematics::tree::Atom &) –> void

delete_atom(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, : pyrosetta.rosetta.core.kinematics.tree.Atom) None

remove an atom from this atom’s children

C++: core::kinematics::tree::Atom_::delete_atom(class std::shared_ptr<class core::kinematics::tree::Atom>) –> void

dfs(self: pyrosetta.rosetta.core.kinematics.tree.BondedAtom, changeset: pyrosetta.rosetta.utility.vector1_core_kinematics_AtomWithDOFChange, res_change_list: pyrosetta.rosetta.core.kinematics.ResidueCoordinateChangeList, start_atom_index: int) None
Perform a depth-first traversal of the tree that would be effected by

a DOF change from this atom. Stop at atoms that have already been traversed. Will recurse on younger siblings if a phi on this atom has changed.

C++: core::kinematics::tree::BondedAtom::dfs(class utility::vector1<class core::kinematics::AtomWithDOFChange, class std::allocator<class core::kinematics::AtomWithDOFChange> > &, class core::kinematics::ResidueCoordinateChangeList &, const unsigned long) const –> void

dihedral_between_bonded_children(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, child1: pyrosetta.rosetta.core.kinematics.tree.Atom, child2: pyrosetta.rosetta.core.kinematics.tree.Atom) float

dihedral angle between two bonded children to this atom

C++: core::kinematics::tree::Atom_::dihedral_between_bonded_children(const class core::kinematics::tree::Atom &, const class core::kinematics::tree::Atom &) const –> double

distance(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, atom: pyrosetta.rosetta.core.kinematics.tree.Atom) float

Distance to an Atom

C++: core::kinematics::tree::Atom_::distance(const class core::kinematics::tree::Atom &) const –> double

distance_squared(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, atom: pyrosetta.rosetta.core.kinematics.tree.Atom) float

Distance squared to an Atom

C++: core::kinematics::tree::Atom_::distance_squared(const class core::kinematics::tree::Atom &) const –> double

dof(self: pyrosetta.rosetta.core.kinematics.tree.BondedAtom, type: pyrosetta.rosetta.core.id.DOF_Type) float

get degrees of freedom

C++: core::kinematics::tree::BondedAtom::dof(const enum core::id::DOF_Type) const –> double

downstream(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, atom1: pyrosetta.rosetta.core.kinematics.tree.Atom) bool

whether atom1 is downstream of this atom.

C++: core::kinematics::tree::Atom_::downstream(class std::shared_ptr<const class core::kinematics::tree::Atom>) const –> bool

get_dof_axis_and_end_pos(self: pyrosetta.rosetta.core.kinematics.tree.BondedAtom, axis: pyrosetta.rosetta.numeric.xyzVector_double_t, end_pos: pyrosetta.rosetta.numeric.xyzVector_double_t, type: pyrosetta.rosetta.core.id.DOF_Type) None

get rotation axis and end_pos for a BondedAtom.

C++: core::kinematics::tree::BondedAtom::get_dof_axis_and_end_pos(class numeric::xyzVector<double> &, class numeric::xyzVector<double> &, const enum core::id::DOF_Type) const –> void

get_input_stub(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.kinematics.Stub

stub used to build this atom

C++: core::kinematics::tree::Atom_::get_input_stub() const –> class core::kinematics::Stub

get_inversion(self: pyrosetta.rosetta.core.kinematics.tree.BondedAtom) bool

C++: core::kinematics::tree::BondedAtom::get_inversion() –> bool

get_nonjump_atom(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, i: int) pyrosetta.rosetta.core.kinematics.tree.Atom

get non-jump atom by its index from the children atoms list

C++: core::kinematics::tree::Atom_::get_nonjump_atom(const unsigned long) const –> class std::shared_ptr<const class core::kinematics::tree::Atom>

get_self_ptr(self: pyrosetta.rosetta.core.kinematics.tree.Atom) pyrosetta.rosetta.core.kinematics.tree.Atom

C++: core::kinematics::tree::Atom::get_self_ptr() –> class std::shared_ptr<class core::kinematics::tree::Atom>

get_self_weak_ptr(self: pyrosetta.rosetta.core.kinematics.tree.Atom) pyrosetta.rosetta.std.weak_ptr_core_kinematics_tree_Atom_t

C++: core::kinematics::tree::Atom::get_self_weak_ptr() –> class std::weak_ptr<class core::kinematics::tree::Atom>

get_stub(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.kinematics.Stub

stub centerd at this atom

C++: core::kinematics::tree::Atom_::get_stub() const –> class core::kinematics::Stub

id(*args, **kwargs)

Overloaded function.

  1. id(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) -> pyrosetta.rosetta.core.id.AtomID

Atom identifier

C++: core::kinematics::tree::Atom_::id() const –> const class core::id::AtomID &

  1. id(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, id_in: pyrosetta.rosetta.core.id.AtomID) -> None

AtomID assignment

C++: core::kinematics::tree::Atom_::id(const class core::id::AtomID &) –> void

input_stub_atom0(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.kinematics.tree.Atom
the center of the input stub for refolding this atom

it is its parent

C++: core::kinematics::tree::Atom_::input_stub_atom0() const –> class std::shared_ptr<const class core::kinematics::tree::Atom>

input_stub_atom0_id(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.id.AtomID

input stub atom0’s id

C++: core::kinematics::tree::Atom_::input_stub_atom0_id() const –> const class core::id::AtomID &

input_stub_atom1(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.kinematics.tree.Atom
the first atom to construct the input stub for refolding this atom

it is its parent’s stub_atom1, which normally the parent itself

C++: core::kinematics::tree::Atom_::input_stub_atom1() const –> class std::shared_ptr<const class core::kinematics::tree::Atom>

input_stub_atom1_id(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.id.AtomID

input stub atom1’s id

C++: core::kinematics::tree::Atom_::input_stub_atom1_id() const –> const class core::id::AtomID &

input_stub_atom2(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.kinematics.tree.Atom
the second atom to construct the input stub for refolding this atom

it is its parent’s stub_atom2, which normally the parent’s parent

C++: core::kinematics::tree::Atom_::input_stub_atom2() const –> class std::shared_ptr<const class core::kinematics::tree::Atom>

input_stub_atom2_id(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.id.AtomID

input stub atom2’s id

C++: core::kinematics::tree::Atom_::input_stub_atom2_id() const –> const class core::id::AtomID &

input_stub_atom3(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.kinematics.tree.Atom
the third atom to construct the input stub for refolding this atom

it is either its previous sibling or its parent’s stub_atom3,

C++: core::kinematics::tree::Atom_::input_stub_atom3() const –> class std::shared_ptr<const class core::kinematics::tree::Atom>

input_stub_atom3_id(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.id.AtomID

input stub atom3’s id

C++: core::kinematics::tree::Atom_::input_stub_atom3_id() const –> const class core::id::AtomID &

insert_atom(*args, **kwargs)

Overloaded function.

  1. insert_atom(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, : pyrosetta.rosetta.core.kinematics.tree.Atom) -> None

insert an atom as this atom’s child

C++: core::kinematics::tree::Atom_::insert_atom(class std::shared_ptr<class core::kinematics::tree::Atom>) –> void

  1. insert_atom(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, : pyrosetta.rosetta.core.kinematics.tree.Atom, : int) -> None

tries to insert at the position specified by the second argument

C++: core::kinematics::tree::Atom_::insert_atom(class std::shared_ptr<class core::kinematics::tree::Atom>, const int) –> void

is_jump(self: pyrosetta.rosetta.core.kinematics.tree.BondedAtom) bool

bonded atom is a jump? of course not!!!

C++: core::kinematics::tree::BondedAtom::is_jump() const –> bool

jump(*args, **kwargs)

Overloaded function.

  1. jump(self: pyrosetta.rosetta.core.kinematics.tree.BondedAtom) -> pyrosetta.rosetta.core.kinematics.Jump

abort if attempt to get jump for a bonded atom

C++: core::kinematics::tree::BondedAtom::jump() const –> const class core::kinematics::Jump &

  1. jump(self: pyrosetta.rosetta.core.kinematics.tree.BondedAtom, : pyrosetta.rosetta.core.kinematics.Jump) -> None

abort if attempt to set jump for a bonded atom

C++: core::kinematics::tree::BondedAtom::jump(const class core::kinematics::Jump &) –> void

  1. jump(self: pyrosetta.rosetta.core.kinematics.tree.BondedAtom, : pyrosetta.rosetta.core.kinematics.Jump, : pyrosetta.rosetta.utility.vector1_core_kinematics_AtomWithDOFChange) -> None

abort if attempt to set jump for a bonded atom

C++: core::kinematics::tree::BondedAtom::jump(const class core::kinematics::Jump &, class utility::vector1<class core::kinematics::AtomWithDOFChange, class std::allocator<class core::kinematics::AtomWithDOFChange> > &) –> void

keep_1st_child_pos(self: pyrosetta.rosetta.core.kinematics.tree.BondedAtom) bool
when other atoms are inserted insert after 1st child if available.

–> this enables us to keep a stub of Downstream Jump atoms inside a single residue

C++: core::kinematics::tree::BondedAtom::keep_1st_child_pos() const –> bool

keep_dof_fixed(self: pyrosetta.rosetta.core.kinematics.tree.BondedAtom, type: pyrosetta.rosetta.core.id.DOF_Type) bool

whether a DOF for this atom should be fixed?

C++: core::kinematics::tree::BondedAtom::keep_dof_fixed(const enum core::id::DOF_Type) const –> bool

n_atom(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) int

number of children atoms

C++: core::kinematics::tree::Atom_::n_atom() const –> unsigned long

n_children(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) int

number of the child atoms

C++: core::kinematics::tree::Atom_::n_children() const –> unsigned long

n_nonjump_children(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) int

number of the non-jump child atoms

C++: core::kinematics::tree::Atom_::n_nonjump_children() const –> unsigned long

next_child(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, child: pyrosetta.rosetta.core.kinematics.tree.Atom) pyrosetta.rosetta.core.kinematics.tree.Atom

find the child atom after this child in the list

C++: core::kinematics::tree::Atom_::next_child(class std::shared_ptr<const class core::kinematics::tree::Atom>) –> class std::shared_ptr<class core::kinematics::tree::Atom>

parent(*args, **kwargs)

Overloaded function.

  1. parent(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) -> pyrosetta.rosetta.core.kinematics.tree.Atom

Parent atom pointer

C++: core::kinematics::tree::Atom_::parent() –> class std::shared_ptr<class core::kinematics::tree::Atom>

  1. parent(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, parent_in: pyrosetta.rosetta.std.weak_ptr_core_kinematics_tree_Atom_t) -> None

C++: core::kinematics::tree::Atom_::parent(class std::weak_ptr<class core::kinematics::tree::Atom>) –> void

position(*args, **kwargs)

Overloaded function.

  1. position(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) -> pyrosetta.rosetta.numeric.xyzVector_double_t

Position

C++: core::kinematics::tree::Atom_::position() const –> const class numeric::xyzVector<double> &

  1. position(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, position_a: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

Position assignment

C++: core::kinematics::tree::Atom_::position(const class numeric::xyzVector<double> &) –> void

previous_child(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, child: pyrosetta.rosetta.core.kinematics.tree.Atom) pyrosetta.rosetta.core.kinematics.tree.Atom

find the child atom before this child in the list

C++: core::kinematics::tree::Atom_::previous_child(class std::shared_ptr<const class core::kinematics::tree::Atom>) const –> class std::shared_ptr<const class core::kinematics::tree::Atom>

previous_sibling(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.kinematics.tree.Atom
routines for navigating the tree

find the sibling atom before itself

C++: core::kinematics::tree::Atom_::previous_sibling() const –> class std::shared_ptr<const class core::kinematics::tree::Atom>

raw_child_index(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, child: pyrosetta.rosetta.core.kinematics.tree.Atom) int

the atom-index of this child

C++: core::kinematics::tree::Atom_::raw_child_index(const class core::kinematics::tree::Atom *) const –> unsigned long

raw_get_nonjump_atom(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, i: int) pyrosetta.rosetta.core.kinematics.tree.Atom

C++: core::kinematics::tree::Atom_::raw_get_nonjump_atom(const unsigned long) const –> const class core::kinematics::tree::Atom *

raw_input_stub_atom0(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.kinematics.tree.Atom

C++: core::kinematics::tree::Atom_::raw_input_stub_atom0() const –> const class core::kinematics::tree::Atom *

raw_input_stub_atom1(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.kinematics.tree.Atom

C++: core::kinematics::tree::Atom_::raw_input_stub_atom1() const –> const class core::kinematics::tree::Atom *

raw_input_stub_atom2(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.kinematics.tree.Atom

C++: core::kinematics::tree::Atom_::raw_input_stub_atom2() const –> const class core::kinematics::tree::Atom *

raw_input_stub_atom3(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.kinematics.tree.Atom

C++: core::kinematics::tree::Atom_::raw_input_stub_atom3() const –> const class core::kinematics::tree::Atom *

raw_parent(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.kinematics.tree.Atom

C++: core::kinematics::tree::Atom_::raw_parent() const –> const class core::kinematics::tree::Atom *

raw_previous_child(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, child: pyrosetta.rosetta.core.kinematics.tree.Atom) pyrosetta.rosetta.core.kinematics.tree.Atom

C++: core::kinematics::tree::Atom_::raw_previous_child(const class core::kinematics::tree::Atom *) const –> const class core::kinematics::tree::Atom *

raw_previous_sibling(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.kinematics.tree.Atom

C++: core::kinematics::tree::Atom_::raw_previous_sibling() const –> const class core::kinematics::tree::Atom *

raw_stub_atom1(self: pyrosetta.rosetta.core.kinematics.tree.BondedAtom) pyrosetta.rosetta.core.kinematics.tree.Atom

C++: core::kinematics::tree::BondedAtom::raw_stub_atom1() const –> const class core::kinematics::tree::Atom *

raw_stub_atom2(self: pyrosetta.rosetta.core.kinematics.tree.BondedAtom) pyrosetta.rosetta.core.kinematics.tree.Atom

C++: core::kinematics::tree::BondedAtom::raw_stub_atom2() const –> const class core::kinematics::tree::Atom *

raw_stub_atom3(self: pyrosetta.rosetta.core.kinematics.tree.BondedAtom) pyrosetta.rosetta.core.kinematics.tree.Atom

C++: core::kinematics::tree::BondedAtom::raw_stub_atom3() const –> const class core::kinematics::tree::Atom *

replace_atom(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, old_atom: pyrosetta.rosetta.core.kinematics.tree.Atom, new_atom: pyrosetta.rosetta.core.kinematics.tree.Atom) None

replace the old atom by the new atom in the child atom list

C++: core::kinematics::tree::Atom_::replace_atom(const class std::shared_ptr<class core::kinematics::tree::Atom>, const class std::shared_ptr<class core::kinematics::tree::Atom>) –> void

set_dof(*args, **kwargs)

Overloaded function.

  1. set_dof(self: pyrosetta.rosetta.core.kinematics.tree.BondedAtom, type: pyrosetta.rosetta.core.id.DOF_Type, value: float) -> None

set degrees of freedom (internal coordinates)

C++: core::kinematics::tree::BondedAtom::set_dof(const enum core::id::DOF_Type, const double) –> void

  1. set_dof(self: pyrosetta.rosetta.core.kinematics.tree.BondedAtom, type: pyrosetta.rosetta.core.id.DOF_Type, value: float, changeset: pyrosetta.rosetta.utility.vector1_core_kinematics_AtomWithDOFChange) -> None

set degrees of freedom (internal coordinates). For use in

output-sensitive refold subroutine.

C++: core::kinematics::tree::BondedAtom::set_dof(const enum core::id::DOF_Type, const double, class utility::vector1<class core::kinematics::AtomWithDOFChange, class std::allocator<class core::kinematics::AtomWithDOFChange> > &) –> void

setup_min_map(self: pyrosetta.rosetta.core.kinematics.tree.BondedAtom, last_torsion: pyrosetta.rosetta.core.id.DOF_ID, allow_move: pyrosetta.rosetta.core.id.DOF_ID_Map_bool_t, min_map: pyrosetta.rosetta.core.kinematics.MinimizerMapBase) None

for minimizing,add DOF(PHI,THETA,D) for a BondedAtom into the MinimizerMap

C++: core::kinematics::tree::BondedAtom::setup_min_map(class core::id::DOF_ID &, const class core::id::DOF_ID_Map<bool> &, class core::kinematics::MinimizerMapBase &) const –> void

show(*args, **kwargs)

Overloaded function.

  1. show(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) -> None

dump out AtomID for this atom, its parent and all its offspring

C++: core::kinematics::tree::Atom_::show() const –> void

  1. show(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, n_level: int) -> None

dump out AtomID for this atom, its parent and all its offspring up to n_level

C++: core::kinematics::tree::Atom_::show(const int &) const –> void

steal_inversion(self: pyrosetta.rosetta.core.kinematics.tree.BondedAtom, steal_from: pyrosetta.rosetta.core.kinematics.tree.Atom) None

C++: core::kinematics::tree::BondedAtom::steal_inversion(class std::shared_ptr<class core::kinematics::tree::Atom>) –> void

stub_atom1(self: pyrosetta.rosetta.core.kinematics.tree.BondedAtom) pyrosetta.rosetta.core.kinematics.tree.Atom

stub_atom1 of a bonded atom it is itself

C++: core::kinematics::tree::BondedAtom::stub_atom1() const –> class std::shared_ptr<const class core::kinematics::tree::Atom>

stub_atom1_id(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.id.AtomID

stub atom1 ‘s id

C++: core::kinematics::tree::Atom_::stub_atom1_id() const –> const class core::id::AtomID &

stub_atom2(self: pyrosetta.rosetta.core.kinematics.tree.BondedAtom) pyrosetta.rosetta.core.kinematics.tree.Atom

stub_atom2 of a bonded atom it is its parent

C++: core::kinematics::tree::BondedAtom::stub_atom2() const –> class std::shared_ptr<const class core::kinematics::tree::Atom>

stub_atom2_id(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.id.AtomID

stub atom2’s id

C++: core::kinematics::tree::Atom_::stub_atom2_id() const –> const class core::id::AtomID &

stub_atom3(self: pyrosetta.rosetta.core.kinematics.tree.BondedAtom) pyrosetta.rosetta.core.kinematics.tree.Atom

stub_atom3 of a bonded atom

  • if this atom’s parent is a bonded_atom it is this atom’s parent’s parent.

  • if this atom’s parent is a jump atom, it is this atom’s first non-jump

sibling or its second non-jump sibling (if it itself is the first) or its first non-jump child (if it does not have any sibling)

C++: core::kinematics::tree::BondedAtom::stub_atom3() const –> class std::shared_ptr<const class core::kinematics::tree::Atom>

stub_atom3_id(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.id.AtomID

stub atom3’s id

C++: core::kinematics::tree::Atom_::stub_atom3_id() const –> const class core::id::AtomID &

stub_defined(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) bool

whether a Stub can be defined for this atom

C++: core::kinematics::tree::Atom_::stub_defined() const –> bool

transform_Ax_plus_b_recursive(self: pyrosetta.rosetta.core.kinematics.tree.Atom, A: pyrosetta.rosetta.numeric.xyzMatrix_double_t, b: pyrosetta.rosetta.numeric.xyzVector_double_t, res_change_list: core::kinematics::ResidueCoordinateChangeList) None

Transform atom and children by linear transformation

C++: core::kinematics::tree::Atom::transform_Ax_plus_b_recursive(const class numeric::xyzMatrix<double> &, const class numeric::xyzVector<double> &, class core::kinematics::ResidueCoordinateChangeList &) –> void

update_domain_map(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, current_color: int, biggest_color: int, domain_map: pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t, dof_moved: pyrosetta.rosetta.core.id.AtomID_Map_bool_t, atom_moved: pyrosetta.rosetta.core.id.AtomID_Map_bool_t) None

update domain map

C++: core::kinematics::tree::Atom_::update_domain_map(int &, int &, class ObjexxFCL::FArray1D<int> &, const class core::id::AtomID_Map<bool> &, const class core::id::AtomID_Map<bool> &) const –> void

update_internal_coords(*args, **kwargs)

Overloaded function.

  1. update_internal_coords(self: pyrosetta.rosetta.core.kinematics.tree.BondedAtom, stub: pyrosetta.rosetta.core.kinematics.Stub) -> None

  2. update_internal_coords(self: pyrosetta.rosetta.core.kinematics.tree.BondedAtom, stub: pyrosetta.rosetta.core.kinematics.Stub, recursive: bool) -> None

  3. update_internal_coords(self: pyrosetta.rosetta.core.kinematics.tree.BondedAtom, recursive: bool) -> None

update_stub(self: pyrosetta.rosetta.core.kinematics.tree.BondedAtom, stub: pyrosetta.rosetta.core.kinematics.Stub) None

update the stub without actually updating coordinates

C++: core::kinematics::tree::BondedAtom::update_stub(class core::kinematics::Stub &) const –> void

update_xyz_coords(*args, **kwargs)

Overloaded function.

  1. update_xyz_coords(self: pyrosetta.rosetta.core.kinematics.tree.BondedAtom) -> None

The atom must retrieve an appropriate stub from its parent; it is the root

of the subtree being refolded. Valid only if this atom is the maximal root of a subtree requiring coordinate updates – if any ancestor of this atom requires a coordinate update, then the Stub this atom generates for itself will be invalid.

C++: core::kinematics::tree::BondedAtom::update_xyz_coords() –> void

  1. update_xyz_coords(self: pyrosetta.rosetta.core.kinematics.tree.BondedAtom, stub: pyrosetta.rosetta.core.kinematics.Stub) -> None

update cartesian coordinates for this atom from its input stub and internal cooridnates

C++: core::kinematics::tree::BondedAtom::update_xyz_coords(class core::kinematics::Stub &) –> void

x(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) float

x coordinate

C++: core::kinematics::tree::Atom_::x() const –> const double &

xyz(*args, **kwargs)

Overloaded function.

  1. xyz(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) -> pyrosetta.rosetta.numeric.xyzVector_double_t

Position

C++: core::kinematics::tree::Atom_::xyz() const –> const class numeric::xyzVector<double> &

  1. xyz(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, position_a: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

Position assignment

C++: core::kinematics::tree::Atom_::xyz(const class numeric::xyzVector<double> &) –> void

y(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) float

y coordinate

C++: core::kinematics::tree::Atom_::y() const –> const double &

z(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) float

z coordinate

C++: core::kinematics::tree::Atom_::z() const –> const double &

class pyrosetta.rosetta.core.kinematics.tree.JumpAtom

Bases: pyrosetta.rosetta.core.kinematics.tree.Atom_

an atom who are connected to its parent via rigid-body transformation “Jump”

See

append_atom(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, : pyrosetta.rosetta.core.kinematics.tree.Atom) None

append an atom as this atom’s child

C++: core::kinematics::tree::Atom_::append_atom(class std::shared_ptr<class core::kinematics::tree::Atom>) –> void

assign(self: pyrosetta.rosetta.core.kinematics.tree.JumpAtom, : pyrosetta.rosetta.core.kinematics.tree.JumpAtom) pyrosetta.rosetta.core.kinematics.tree.JumpAtom

C++: core::kinematics::tree::JumpAtom::operator=(const class core::kinematics::tree::JumpAtom &) –> class core::kinematics::tree::JumpAtom &

atom_id(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.id.AtomID

Atom identifier

C++: core::kinematics::tree::Atom_::atom_id() const –> const class core::id::AtomID &

atom_is_on_path_from_root(self: pyrosetta.rosetta.core.kinematics.tree.Atom, atm: pyrosetta.rosetta.core.kinematics.tree.Atom) bool

C++: core::kinematics::tree::Atom::atom_is_on_path_from_root(class std::shared_ptr<const class core::kinematics::tree::Atom>) const –> bool

atoms_begin(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) __gnu_cxx::__normal_iterator<std::shared_ptr<core::kinematics::tree::Atom>*, std::vector<std::shared_ptr<core::kinematics::tree::Atom>, std::allocator<std::shared_ptr<core::kinematics::tree::Atom> > > >

starting iterator of the children atom list

C++: core::kinematics::tree::Atom_::atoms_begin() –> class __gnu_cxx::__normal_iterator<class std::shared_ptr<class core::kinematics::tree::Atom> *, class std::vector<class std::shared_ptr<class core::kinematics::tree::Atom>, class std::allocator<class std::shared_ptr<class core::kinematics::tree::Atom> > > >

atoms_end(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) __gnu_cxx::__normal_iterator<std::shared_ptr<core::kinematics::tree::Atom>*, std::vector<std::shared_ptr<core::kinematics::tree::Atom>, std::allocator<std::shared_ptr<core::kinematics::tree::Atom> > > >

ending iterator of the children atom list

C++: core::kinematics::tree::Atom_::atoms_end() –> class __gnu_cxx::__normal_iterator<class std::shared_ptr<class core::kinematics::tree::Atom> *, class std::vector<class std::shared_ptr<class core::kinematics::tree::Atom>, class std::allocator<class std::shared_ptr<class core::kinematics::tree::Atom> > > >

child(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, k: int) pyrosetta.rosetta.core.kinematics.tree.Atom

get a child atom by index

C++: core::kinematics::tree::Atom_::child(const unsigned long) –> class std::shared_ptr<class core::kinematics::tree::Atom>

child_index(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, child: pyrosetta.rosetta.core.kinematics.tree.Atom) int

the atom-index of this child

C++: core::kinematics::tree::Atom_::child_index(class std::shared_ptr<const class core::kinematics::tree::Atom>) const –> unsigned long

clone(self: pyrosetta.rosetta.core.kinematics.tree.JumpAtom, parent_in: pyrosetta.rosetta.std.weak_ptr_core_kinematics_tree_Atom_t, atom_pointer: pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t) pyrosetta.rosetta.core.kinematics.tree.Atom

copy this atom

C++: core::kinematics::tree::JumpAtom::clone(class std::weak_ptr<class core::kinematics::tree::Atom>, class core::id::AtomID_Map<class std::shared_ptr<class core::kinematics::tree::Atom> > &) const –> class std::shared_ptr<class core::kinematics::tree::Atom>

copy_coords(self: pyrosetta.rosetta.core.kinematics.tree.JumpAtom, src: pyrosetta.rosetta.core.kinematics.tree.Atom) None

copy DOFs, xyz’s

C++: core::kinematics::tree::JumpAtom::copy_coords(const class core::kinematics::tree::Atom &) –> void

delete_atom(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, : pyrosetta.rosetta.core.kinematics.tree.Atom) None

remove an atom from this atom’s children

C++: core::kinematics::tree::Atom_::delete_atom(class std::shared_ptr<class core::kinematics::tree::Atom>) –> void

dfs(self: pyrosetta.rosetta.core.kinematics.tree.JumpAtom, changeset: pyrosetta.rosetta.utility.vector1_core_kinematics_AtomWithDOFChange, res_change_list: pyrosetta.rosetta.core.kinematics.ResidueCoordinateChangeList, start_atom_index: int) None
Perform a depth-first traversal of the tree that would be effected by

a DOF change from this atom. Stop at atoms that have already been traversed.

C++: core::kinematics::tree::JumpAtom::dfs(class utility::vector1<class core::kinematics::AtomWithDOFChange, class std::allocator<class core::kinematics::AtomWithDOFChange> > &, class core::kinematics::ResidueCoordinateChangeList &, const unsigned long) const –> void

dihedral_between_bonded_children(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, child1: pyrosetta.rosetta.core.kinematics.tree.Atom, child2: pyrosetta.rosetta.core.kinematics.tree.Atom) float

dihedral angle between two bonded children to this atom

C++: core::kinematics::tree::Atom_::dihedral_between_bonded_children(const class core::kinematics::tree::Atom &, const class core::kinematics::tree::Atom &) const –> double

distance(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, atom: pyrosetta.rosetta.core.kinematics.tree.Atom) float

Distance to an Atom

C++: core::kinematics::tree::Atom_::distance(const class core::kinematics::tree::Atom &) const –> double

distance_squared(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, atom: pyrosetta.rosetta.core.kinematics.tree.Atom) float

Distance squared to an Atom

C++: core::kinematics::tree::Atom_::distance_squared(const class core::kinematics::tree::Atom &) const –> double

dof(self: pyrosetta.rosetta.core.kinematics.tree.JumpAtom, type: pyrosetta.rosetta.core.id.DOF_Type) float

get a degree of freedom from jump

C++: core::kinematics::tree::JumpAtom::dof(const enum core::id::DOF_Type) const –> double

downstream(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, atom1: pyrosetta.rosetta.core.kinematics.tree.Atom) bool

whether atom1 is downstream of this atom.

C++: core::kinematics::tree::Atom_::downstream(class std::shared_ptr<const class core::kinematics::tree::Atom>) const –> bool

get_dof_axis_and_end_pos(self: pyrosetta.rosetta.core.kinematics.tree.JumpAtom, axis: pyrosetta.rosetta.numeric.xyzVector_double_t, end_pos: pyrosetta.rosetta.numeric.xyzVector_double_t, type: pyrosetta.rosetta.core.id.DOF_Type) None

get rotation axis and end_pos for a JumpAtom.

C++: core::kinematics::tree::JumpAtom::get_dof_axis_and_end_pos(class numeric::xyzVector<double> &, class numeric::xyzVector<double> &, const enum core::id::DOF_Type) const –> void

get_input_stub(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.kinematics.Stub

stub used to build this atom

C++: core::kinematics::tree::Atom_::get_input_stub() const –> class core::kinematics::Stub

get_inversion(self: pyrosetta.rosetta.core.kinematics.tree.JumpAtom) Tuple[bool, bool]

C++: core::kinematics::tree::JumpAtom::get_inversion() –> struct std::pair<bool, bool>

get_nonjump_atom(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, i: int) pyrosetta.rosetta.core.kinematics.tree.Atom

get non-jump atom by its index from the children atoms list

C++: core::kinematics::tree::Atom_::get_nonjump_atom(const unsigned long) const –> class std::shared_ptr<const class core::kinematics::tree::Atom>

get_self_ptr(self: pyrosetta.rosetta.core.kinematics.tree.Atom) pyrosetta.rosetta.core.kinematics.tree.Atom

C++: core::kinematics::tree::Atom::get_self_ptr() –> class std::shared_ptr<class core::kinematics::tree::Atom>

get_self_weak_ptr(self: pyrosetta.rosetta.core.kinematics.tree.Atom) pyrosetta.rosetta.std.weak_ptr_core_kinematics_tree_Atom_t

C++: core::kinematics::tree::Atom::get_self_weak_ptr() –> class std::weak_ptr<class core::kinematics::tree::Atom>

get_stub(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.kinematics.Stub

stub centerd at this atom

C++: core::kinematics::tree::Atom_::get_stub() const –> class core::kinematics::Stub

id(*args, **kwargs)

Overloaded function.

  1. id(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) -> pyrosetta.rosetta.core.id.AtomID

Atom identifier

C++: core::kinematics::tree::Atom_::id() const –> const class core::id::AtomID &

  1. id(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, id_in: pyrosetta.rosetta.core.id.AtomID) -> None

AtomID assignment

C++: core::kinematics::tree::Atom_::id(const class core::id::AtomID &) –> void

input_stub_atom0(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.kinematics.tree.Atom
the center of the input stub for refolding this atom

it is its parent

C++: core::kinematics::tree::Atom_::input_stub_atom0() const –> class std::shared_ptr<const class core::kinematics::tree::Atom>

input_stub_atom0_id(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.id.AtomID

input stub atom0’s id

C++: core::kinematics::tree::Atom_::input_stub_atom0_id() const –> const class core::id::AtomID &

input_stub_atom1(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.kinematics.tree.Atom
the first atom to construct the input stub for refolding this atom

it is its parent’s stub_atom1, which normally the parent itself

C++: core::kinematics::tree::Atom_::input_stub_atom1() const –> class std::shared_ptr<const class core::kinematics::tree::Atom>

input_stub_atom1_id(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.id.AtomID

input stub atom1’s id

C++: core::kinematics::tree::Atom_::input_stub_atom1_id() const –> const class core::id::AtomID &

input_stub_atom2(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.kinematics.tree.Atom
the second atom to construct the input stub for refolding this atom

it is its parent’s stub_atom2, which normally the parent’s parent

C++: core::kinematics::tree::Atom_::input_stub_atom2() const –> class std::shared_ptr<const class core::kinematics::tree::Atom>

input_stub_atom2_id(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.id.AtomID

input stub atom2’s id

C++: core::kinematics::tree::Atom_::input_stub_atom2_id() const –> const class core::id::AtomID &

input_stub_atom3(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.kinematics.tree.Atom
the third atom to construct the input stub for refolding this atom

it is either its previous sibling or its parent’s stub_atom3,

C++: core::kinematics::tree::Atom_::input_stub_atom3() const –> class std::shared_ptr<const class core::kinematics::tree::Atom>

input_stub_atom3_id(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.id.AtomID

input stub atom3’s id

C++: core::kinematics::tree::Atom_::input_stub_atom3_id() const –> const class core::id::AtomID &

insert_atom(*args, **kwargs)

Overloaded function.

  1. insert_atom(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, : pyrosetta.rosetta.core.kinematics.tree.Atom) -> None

insert an atom as this atom’s child

C++: core::kinematics::tree::Atom_::insert_atom(class std::shared_ptr<class core::kinematics::tree::Atom>) –> void

  1. insert_atom(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, : pyrosetta.rosetta.core.kinematics.tree.Atom, : int) -> None

tries to insert at the position specified by the second argument

C++: core::kinematics::tree::Atom_::insert_atom(class std::shared_ptr<class core::kinematics::tree::Atom>, const int) –> void

is_jump(self: pyrosetta.rosetta.core.kinematics.tree.JumpAtom) bool

a jump atom is a jump? of course yes!!!

C++: core::kinematics::tree::JumpAtom::is_jump() const –> bool

jump(*args, **kwargs)

Overloaded function.

  1. jump(self: pyrosetta.rosetta.core.kinematics.tree.JumpAtom) -> pyrosetta.rosetta.core.kinematics.Jump

access the jump

C++: core::kinematics::tree::JumpAtom::jump() const –> const class core::kinematics::Jump &

  1. jump(self: pyrosetta.rosetta.core.kinematics.tree.JumpAtom, jump_in: pyrosetta.rosetta.core.kinematics.Jump) -> None

set the jump

C++: core::kinematics::tree::JumpAtom::jump(const class core::kinematics::Jump &) –> void

  1. jump(self: pyrosetta.rosetta.core.kinematics.tree.JumpAtom, jump_in: pyrosetta.rosetta.core.kinematics.Jump, changeset: pyrosetta.rosetta.utility.vector1_core_kinematics_AtomWithDOFChange) -> None

set the jump. For use with output-sensitive refold subroutine.

C++: core::kinematics::tree::JumpAtom::jump(const class core::kinematics::Jump &, class utility::vector1<class core::kinematics::AtomWithDOFChange, class std::allocator<class core::kinematics::AtomWithDOFChange> > &) –> void

keep_1st_child_pos(self: pyrosetta.rosetta.core.kinematics.tree.JumpAtom) bool
when other atoms are inserted insert after 1st child if available.

–> this enables us to keep a stub of Downstream Jump atoms inside a single residue

C++: core::kinematics::tree::JumpAtom::keep_1st_child_pos() const –> bool

keep_dof_fixed(self: pyrosetta.rosetta.core.kinematics.tree.JumpAtom, type: pyrosetta.rosetta.core.id.DOF_Type) bool

whether a jump should be fixed in some special cases

C++: core::kinematics::tree::JumpAtom::keep_dof_fixed(const enum core::id::DOF_Type) const –> bool

n_atom(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) int

number of children atoms

C++: core::kinematics::tree::Atom_::n_atom() const –> unsigned long

n_children(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) int

number of the child atoms

C++: core::kinematics::tree::Atom_::n_children() const –> unsigned long

n_nonjump_children(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) int

number of the non-jump child atoms

C++: core::kinematics::tree::Atom_::n_nonjump_children() const –> unsigned long

next_child(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, child: pyrosetta.rosetta.core.kinematics.tree.Atom) pyrosetta.rosetta.core.kinematics.tree.Atom

find the child atom after this child in the list

C++: core::kinematics::tree::Atom_::next_child(class std::shared_ptr<const class core::kinematics::tree::Atom>) –> class std::shared_ptr<class core::kinematics::tree::Atom>

parent(*args, **kwargs)

Overloaded function.

  1. parent(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) -> pyrosetta.rosetta.core.kinematics.tree.Atom

Parent atom pointer

C++: core::kinematics::tree::Atom_::parent() –> class std::shared_ptr<class core::kinematics::tree::Atom>

  1. parent(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, parent_in: pyrosetta.rosetta.std.weak_ptr_core_kinematics_tree_Atom_t) -> None

C++: core::kinematics::tree::Atom_::parent(class std::weak_ptr<class core::kinematics::tree::Atom>) –> void

position(*args, **kwargs)

Overloaded function.

  1. position(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) -> pyrosetta.rosetta.numeric.xyzVector_double_t

Position

C++: core::kinematics::tree::Atom_::position() const –> const class numeric::xyzVector<double> &

  1. position(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, position_a: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

Position assignment

C++: core::kinematics::tree::Atom_::position(const class numeric::xyzVector<double> &) –> void

previous_child(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, child: pyrosetta.rosetta.core.kinematics.tree.Atom) pyrosetta.rosetta.core.kinematics.tree.Atom

find the child atom before this child in the list

C++: core::kinematics::tree::Atom_::previous_child(class std::shared_ptr<const class core::kinematics::tree::Atom>) const –> class std::shared_ptr<const class core::kinematics::tree::Atom>

previous_sibling(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.kinematics.tree.Atom
routines for navigating the tree

find the sibling atom before itself

C++: core::kinematics::tree::Atom_::previous_sibling() const –> class std::shared_ptr<const class core::kinematics::tree::Atom>

raw_child_index(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, child: pyrosetta.rosetta.core.kinematics.tree.Atom) int

the atom-index of this child

C++: core::kinematics::tree::Atom_::raw_child_index(const class core::kinematics::tree::Atom *) const –> unsigned long

raw_get_nonjump_atom(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, i: int) pyrosetta.rosetta.core.kinematics.tree.Atom

C++: core::kinematics::tree::Atom_::raw_get_nonjump_atom(const unsigned long) const –> const class core::kinematics::tree::Atom *

raw_input_stub_atom0(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.kinematics.tree.Atom

C++: core::kinematics::tree::Atom_::raw_input_stub_atom0() const –> const class core::kinematics::tree::Atom *

raw_input_stub_atom1(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.kinematics.tree.Atom

C++: core::kinematics::tree::Atom_::raw_input_stub_atom1() const –> const class core::kinematics::tree::Atom *

raw_input_stub_atom2(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.kinematics.tree.Atom

C++: core::kinematics::tree::Atom_::raw_input_stub_atom2() const –> const class core::kinematics::tree::Atom *

raw_input_stub_atom3(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.kinematics.tree.Atom

C++: core::kinematics::tree::Atom_::raw_input_stub_atom3() const –> const class core::kinematics::tree::Atom *

raw_parent(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.kinematics.tree.Atom

C++: core::kinematics::tree::Atom_::raw_parent() const –> const class core::kinematics::tree::Atom *

raw_previous_child(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, child: pyrosetta.rosetta.core.kinematics.tree.Atom) pyrosetta.rosetta.core.kinematics.tree.Atom

C++: core::kinematics::tree::Atom_::raw_previous_child(const class core::kinematics::tree::Atom *) const –> const class core::kinematics::tree::Atom *

raw_previous_sibling(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.kinematics.tree.Atom

C++: core::kinematics::tree::Atom_::raw_previous_sibling() const –> const class core::kinematics::tree::Atom *

raw_stub_atom1(self: pyrosetta.rosetta.core.kinematics.tree.JumpAtom) pyrosetta.rosetta.core.kinematics.tree.Atom

C++: core::kinematics::tree::JumpAtom::raw_stub_atom1() const –> const class core::kinematics::tree::Atom *

raw_stub_atom2(self: pyrosetta.rosetta.core.kinematics.tree.JumpAtom) pyrosetta.rosetta.core.kinematics.tree.Atom

C++: core::kinematics::tree::JumpAtom::raw_stub_atom2() const –> const class core::kinematics::tree::Atom *

raw_stub_atom3(self: pyrosetta.rosetta.core.kinematics.tree.JumpAtom) pyrosetta.rosetta.core.kinematics.tree.Atom

C++: core::kinematics::tree::JumpAtom::raw_stub_atom3() const –> const class core::kinematics::tree::Atom *

replace_atom(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, old_atom: pyrosetta.rosetta.core.kinematics.tree.Atom, new_atom: pyrosetta.rosetta.core.kinematics.tree.Atom) None

replace the old atom by the new atom in the child atom list

C++: core::kinematics::tree::Atom_::replace_atom(const class std::shared_ptr<class core::kinematics::tree::Atom>, const class std::shared_ptr<class core::kinematics::tree::Atom>) –> void

set_dof(*args, **kwargs)

Overloaded function.

  1. set_dof(self: pyrosetta.rosetta.core.kinematics.tree.JumpAtom, type: pyrosetta.rosetta.core.id.DOF_Type, value: float) -> None

set a degree of freedom for jump

C++: core::kinematics::tree::JumpAtom::set_dof(const enum core::id::DOF_Type, const double) –> void

  1. set_dof(self: pyrosetta.rosetta.core.kinematics.tree.JumpAtom, type: pyrosetta.rosetta.core.id.DOF_Type, value: float, changeset: pyrosetta.rosetta.utility.vector1_core_kinematics_AtomWithDOFChange) -> None

set degrees of freedom (internal coordinates). For use in

output-sensitive refold subroutine.

C++: core::kinematics::tree::JumpAtom::set_dof(const enum core::id::DOF_Type, const double, class utility::vector1<class core::kinematics::AtomWithDOFChange, class std::allocator<class core::kinematics::AtomWithDOFChange> > &) –> void

setup_min_map(self: pyrosetta.rosetta.core.kinematics.tree.JumpAtom, last_torsion: pyrosetta.rosetta.core.id.DOF_ID, allow_move: pyrosetta.rosetta.core.id.DOF_ID_Map_bool_t, min_map: pyrosetta.rosetta.core.kinematics.MinimizerMapBase) None

for minimizing, add DOF(RB) for a JumpAtom into the MinimizerMap

C++: core::kinematics::tree::JumpAtom::setup_min_map(class core::id::DOF_ID &, const class core::id::DOF_ID_Map<bool> &, class core::kinematics::MinimizerMapBase &) const –> void

show(*args, **kwargs)

Overloaded function.

  1. show(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) -> None

dump out AtomID for this atom, its parent and all its offspring

C++: core::kinematics::tree::Atom_::show() const –> void

  1. show(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, n_level: int) -> None

dump out AtomID for this atom, its parent and all its offspring up to n_level

C++: core::kinematics::tree::Atom_::show(const int &) const –> void

steal_inversion(self: pyrosetta.rosetta.core.kinematics.tree.JumpAtom, steal_from: pyrosetta.rosetta.core.kinematics.tree.Atom) None

C++: core::kinematics::tree::JumpAtom::steal_inversion(class std::shared_ptr<class core::kinematics::tree::Atom>) –> void

stub_atom1(self: pyrosetta.rosetta.core.kinematics.tree.JumpAtom) pyrosetta.rosetta.core.kinematics.tree.Atom

stub_atom1 of a jump-atom it is itself if a stub can be defined for it. Otherwise it is parent

C++: core::kinematics::tree::JumpAtom::stub_atom1() const –> class std::shared_ptr<const class core::kinematics::tree::Atom>

stub_atom1_id(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.id.AtomID

stub atom1 ‘s id

C++: core::kinematics::tree::Atom_::stub_atom1_id() const –> const class core::id::AtomID &

stub_atom2(self: pyrosetta.rosetta.core.kinematics.tree.JumpAtom) pyrosetta.rosetta.core.kinematics.tree.Atom

stub_atom2 of a jump-atom it is its first bonded child if a stub can be defined for it. Otherwise

it is parent’s stub_atom2.

C++: core::kinematics::tree::JumpAtom::stub_atom2() const –> class std::shared_ptr<const class core::kinematics::tree::Atom>

stub_atom2_id(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.id.AtomID

stub atom2’s id

C++: core::kinematics::tree::Atom_::stub_atom2_id() const –> const class core::id::AtomID &

stub_atom3(self: pyrosetta.rosetta.core.kinematics.tree.JumpAtom) pyrosetta.rosetta.core.kinematics.tree.Atom

stub_atom3 of a jump atom it is its child’s child or its second child if a stub can be defined for it,

otherwise it is its parent’s stub_atom3

C++: core::kinematics::tree::JumpAtom::stub_atom3() const –> class std::shared_ptr<const class core::kinematics::tree::Atom>

stub_atom3_id(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) pyrosetta.rosetta.core.id.AtomID

stub atom3’s id

C++: core::kinematics::tree::Atom_::stub_atom3_id() const –> const class core::id::AtomID &

stub_defined(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) bool

whether a Stub can be defined for this atom

C++: core::kinematics::tree::Atom_::stub_defined() const –> bool

transform_Ax_plus_b_recursive(self: pyrosetta.rosetta.core.kinematics.tree.Atom, A: pyrosetta.rosetta.numeric.xyzMatrix_double_t, b: pyrosetta.rosetta.numeric.xyzVector_double_t, res_change_list: core::kinematics::ResidueCoordinateChangeList) None

Transform atom and children by linear transformation

C++: core::kinematics::tree::Atom::transform_Ax_plus_b_recursive(const class numeric::xyzMatrix<double> &, const class numeric::xyzVector<double> &, class core::kinematics::ResidueCoordinateChangeList &) –> void

update_domain_map(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, current_color: int, biggest_color: int, domain_map: pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t, dof_moved: pyrosetta.rosetta.core.id.AtomID_Map_bool_t, atom_moved: pyrosetta.rosetta.core.id.AtomID_Map_bool_t) None

update domain map

C++: core::kinematics::tree::Atom_::update_domain_map(int &, int &, class ObjexxFCL::FArray1D<int> &, const class core::id::AtomID_Map<bool> &, const class core::id::AtomID_Map<bool> &) const –> void

update_internal_coords(*args, **kwargs)

Overloaded function.

  1. update_internal_coords(self: pyrosetta.rosetta.core.kinematics.tree.JumpAtom, stub: pyrosetta.rosetta.core.kinematics.Stub) -> None

  2. update_internal_coords(self: pyrosetta.rosetta.core.kinematics.tree.JumpAtom, stub: pyrosetta.rosetta.core.kinematics.Stub, recursive: bool) -> None

  3. update_internal_coords(self: pyrosetta.rosetta.core.kinematics.tree.JumpAtom, recursive: bool) -> None

update_stub(self: pyrosetta.rosetta.core.kinematics.tree.JumpAtom, : pyrosetta.rosetta.core.kinematics.Stub) None

update the stub without actually updating coordinates

C++: core::kinematics::tree::JumpAtom::update_stub(class core::kinematics::Stub &) const –> void

update_xyz_coords(*args, **kwargs)

Overloaded function.

  1. update_xyz_coords(self: pyrosetta.rosetta.core.kinematics.tree.JumpAtom) -> None

The atom must retrieve an appropriate stub from its parent; it is the root

of the subtree being refolded. Valid only if this atom is the maximal root of a subtree requiring coordinate updates – if any ancestor of this atom requires a coordinate update, then the Stub this atom generates for itself will be invalid.

C++: core::kinematics::tree::JumpAtom::update_xyz_coords() –> void

  1. update_xyz_coords(self: pyrosetta.rosetta.core.kinematics.tree.JumpAtom, stub: pyrosetta.rosetta.core.kinematics.Stub) -> None

update this atom’s xyz position

C++: core::kinematics::tree::JumpAtom::update_xyz_coords(class core::kinematics::Stub &) –> void

x(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) float

x coordinate

C++: core::kinematics::tree::Atom_::x() const –> const double &

xyz(*args, **kwargs)

Overloaded function.

  1. xyz(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) -> pyrosetta.rosetta.numeric.xyzVector_double_t

Position

C++: core::kinematics::tree::Atom_::xyz() const –> const class numeric::xyzVector<double> &

  1. xyz(self: pyrosetta.rosetta.core.kinematics.tree.Atom_, position_a: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

Position assignment

C++: core::kinematics::tree::Atom_::xyz(const class numeric::xyzVector<double> &) –> void

y(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) float

y coordinate

C++: core::kinematics::tree::Atom_::y() const –> const double &

z(self: pyrosetta.rosetta.core.kinematics.tree.Atom_) float

z coordinate

C++: core::kinematics::tree::Atom_::z() const –> const double &

pyrosetta.rosetta.core.kinematics.tree.distance(atom1: pyrosetta.rosetta.core.kinematics.tree.Atom, atom2: pyrosetta.rosetta.core.kinematics.tree.Atom) float

Distance between two Atoms

C++: core::kinematics::tree::distance(const class core::kinematics::tree::Atom &, const class core::kinematics::tree::Atom &) –> double

pyrosetta.rosetta.core.kinematics.tree.distance_squared(atom1: pyrosetta.rosetta.core.kinematics.tree.Atom, atom2: pyrosetta.rosetta.core.kinematics.tree.Atom) float

Distance squared between two Atoms

C++: core::kinematics::tree::distance_squared(const class core::kinematics::tree::Atom &, const class core::kinematics::tree::Atom &) –> double

pyrosetta.rosetta.core.kinematics.tree.is_collinear(atom1: pyrosetta.rosetta.core.kinematics.tree.Atom, atom2: pyrosetta.rosetta.core.kinematics.tree.Atom, atom3: pyrosetta.rosetta.core.kinematics.tree.Atom) bool

Check collinearity of three atoms

C++: core::kinematics::tree::is_collinear(const class core::kinematics::tree::Atom &, const class core::kinematics::tree::Atom &, const class core::kinematics::tree::Atom &) –> bool