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core::pack::scmin::CartSCMinMinimizerMap Class Reference

#include <CartSCMinMinimizerMap.hh>

Inheritance diagram for core::pack::scmin::CartSCMinMinimizerMap:
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Public Types

typedef optimization::DOF_Node DOF_Node
 
typedef optimization::DOF_NodeOP DOF_NodeOP
 
- Public Types inherited from core::kinematics::MinimizerMapBase
typedef id::AtomID AtomID
 
typedef id::DOF_ID DOF_ID
 
typedef id::DOF_Type DOF_Type
 

Public Member Functions

 CartSCMinMinimizerMap ()
 
 ~CartSCMinMinimizerMap () override
 
void set_total_residue (Size total_residue) override
 the CartSCMinMinimizerMap has to know how many residues are in the pose; this allows it to do O(1) updates to its DomainMap – this function costs O(N). More...
 
void clear_active_dofs () override
 Disable the minimization for all residues. Ammortized O(1). More...
 
void activate_residue_dofs (Size resindex) override
 Activate all the dofs for a particular residue. Ammortized O(1). More...
 
void add_torsion (DOF_ID const &new_torsion, DOF_ID const &parent) override
 Invoked during the depth-first traversal through the AtomTree. The AtomTree is indicating that a particular torsion is dependent on another torsion. Record that fact. More...
 
void add_atom (AtomID const &atom_id, DOF_ID const &dof_id) override
 Invoked during the depth-first traversal through the AtomTree; the atom tree is indicating that a given atom is controlled by a particular DOF. Record that fact. More...
 
void setup (AtomTreeCollectionOP trees) override
 Traverse the atom trees in preparation for minimization to tie together all the DOFs and the atoms they control. More...
 
Size nactive_residues () const
 Accessors. More...
 
Size active_residue (Size index) const
 
kinematics::DomainMap const & domain_map () const override
 MinimizerMapBase class virtual accessor. More...
 
kinematics::DomainMap const & dm () const
 Inline accessor. More...
 
Size n_dof_nodes () const override
 
void starting_dofs (optimization::Multivec &dofs) const override
 Initialize a multivec with the dofs reflected in the current residue(s) More...
 
void assign_dofs_to_mobile_residues (optimization::Multivec const &dofs) override
 Assign the chi values to the residue(s) More...
 
optimization::DOF_Nodedof_node (Size index) override
 
conformation::Residue const & residue (Size seqpos) const override
 Convenience lookup – turns over the request to the AtomTreeCollection. More...
 
basic::datacache::BasicDataCache & residue_data (Size seqpos) const override
 
optimization::DOF_Node const & dof_node_for_chi (Size resid, Size chiid) const override
 
id::TorsionID tor_for_dof (id::DOF_ID const &dofid) const override
 
kinematics::tree::Atom const & atom (AtomID const &atid) const override
 
void zero_atom_derivative_vectors () override
 
void link_torsion_vectors () override
 propagate f1/f2's up from children to parents More...
 
void set_natoms_for_residue (Size resid, Size natoms) override
 
Size get_atom_index (id::AtomID const &atm)
 
id::AtomID const & get_atom (Size idx)
 
optimization::MultifuncOP make_multifunc (pose::Pose &p, utility::vector1< conformation::ResidueCOP > const &bg_residues, scoring::ScoreFunction const &sfxn, scoring::MinimizationGraph &mingraph) override
 
- Public Member Functions inherited from core::pack::scmin::SCMinMinimizerMap
 SCMinMinimizerMap ()
 
 ~SCMinMinimizerMap () override
 
Size nactive_residues () const
 Accessors. More...
 
Size active_residue (Size index) const
 
kinematics::DomainMap const & domain_map () const override
 MinimizerMapBase class virtual accessor. More...
 
kinematics::DomainMap const & dm () const
 Inline accessor. More...
 
utility::vector1
< scoring::DerivVectorPair > & 
atom_derivatives (Size resid)
 
void set_nonideal (bool val_in)
 
- Public Member Functions inherited from core::kinematics::MinimizerMapBase
 MinimizerMapBase ()
 default ctor; noop More...
 
 ~MinimizerMapBase () override
 dstor More...
 

Protected Member Functions

void reset_dof_nodes () override
 

Private Attributes

utility::vector1
< utility::vector1< id::AtomID > > 
moving_atoms_
 
utility::vector1< core::Sizenactive_moving_atoms_
 
core::Size nactive_moving_atoms_total_
 
utility::vector1< id::AtomIDdofid_to_atoms_
 
utility::vector1
< utility::vector1< Size > > 
atoms_to_dofid_
 
utility::vector1< core::Vectorresidue_coord_workspace_
 
AtomTreeCollectionOP atom_tree_collection_
 
utility::vector1
< ResidueAtomTreeCollectionOP
atcs_for_residues_
 
kinematics::DomainMap domain_map_
 

Additional Inherited Members

- Protected Attributes inherited from core::pack::scmin::SCMinMinimizerMap
Size focused_residue_
 
Size nactive_residues_
 
utility::vector1
< utility::vector1
< scoring::DerivVectorPair > > 
atom_derivatives_
 
utility::vector1< Sizeactive_residue_index_for_res_
 
utility::vector1< Sizeactive_residues_
 
kinematics::DomainMap domain_map_
 
bool nonideal_
 

Member Typedef Documentation

Constructor & Destructor Documentation

core::pack::scmin::CartSCMinMinimizerMap::CartSCMinMinimizerMap ( )
core::pack::scmin::CartSCMinMinimizerMap::~CartSCMinMinimizerMap ( )
overridedefault

Member Function Documentation

void core::pack::scmin::CartSCMinMinimizerMap::activate_residue_dofs ( Size  resindex)
overridevirtual

Activate all the dofs for a particular residue. Ammortized O(1).

This should be called at most once per residue between calls to "clear_active_chi"

Implements core::pack::scmin::SCMinMinimizerMap.

References core::pack::scmin::SCMinMinimizerMap::active_residue_index_for_res_, core::pack::scmin::SCMinMinimizerMap::active_residues_, domain_map_, and core::pack::scmin::SCMinMinimizerMap::nactive_residues_.

Size core::pack::scmin::CartSCMinMinimizerMap::active_residue ( Size  index) const
inline
void core::pack::scmin::CartSCMinMinimizerMap::add_atom ( AtomID const &  atom_id,
DOF_ID const &  dof_id 
)
overridevirtual

Invoked during the depth-first traversal through the AtomTree; the atom tree is indicating that a given atom is controlled by a particular DOF. Record that fact.

Implements core::pack::scmin::SCMinMinimizerMap.

void core::pack::scmin::CartSCMinMinimizerMap::add_torsion ( DOF_ID const &  new_torsion,
DOF_ID const &  parent 
)
overridevirtual

Invoked during the depth-first traversal through the AtomTree. The AtomTree is indicating that a particular torsion is dependent on another torsion. Record that fact.

Implements core::pack::scmin::SCMinMinimizerMap.

void core::pack::scmin::CartSCMinMinimizerMap::assign_dofs_to_mobile_residues ( optimization::Multivec const &  dofs)
overridevirtual
kinematics::tree::Atom const & core::pack::scmin::CartSCMinMinimizerMap::atom ( AtomID const &  atid) const
overridevirtual
void core::pack::scmin::CartSCMinMinimizerMap::clear_active_dofs ( )
overridevirtual
kinematics::DomainMap const& core::pack::scmin::CartSCMinMinimizerMap::dm ( ) const
inline
optimization::DOF_Node & core::pack::scmin::CartSCMinMinimizerMap::dof_node ( Size  index)
overridevirtual
CartSCMinMinimizerMap::DOF_Node const & core::pack::scmin::CartSCMinMinimizerMap::dof_node_for_chi ( Size  resid,
Size  chiid 
) const
overridevirtual
kinematics::DomainMap const& core::pack::scmin::CartSCMinMinimizerMap::domain_map ( ) const
inlineoverridevirtual

MinimizerMapBase class virtual accessor.

Implements core::kinematics::MinimizerMapBase.

References domain_map_.

id::AtomID const& core::pack::scmin::CartSCMinMinimizerMap::get_atom ( Size  idx)
inline
Size core::pack::scmin::CartSCMinMinimizerMap::get_atom_index ( id::AtomID const &  atm)
inline
void core::pack::scmin::CartSCMinMinimizerMap::link_torsion_vectors ( )
overridevirtual

propagate f1/f2's up from children to parents

Implements core::pack::scmin::SCMinMinimizerMap.

optimization::MultifuncOP core::pack::scmin::CartSCMinMinimizerMap::make_multifunc ( pose::Pose p,
utility::vector1< conformation::ResidueCOP > const &  bg_residues,
scoring::ScoreFunction const &  sfxn,
scoring::MinimizationGraph mingraph 
)
inlineoverridevirtual
Size core::pack::scmin::CartSCMinMinimizerMap::n_dof_nodes ( ) const
inlineoverridevirtual
Size core::pack::scmin::CartSCMinMinimizerMap::nactive_residues ( ) const
inline
void core::pack::scmin::CartSCMinMinimizerMap::reset_dof_nodes ( )
overrideprotectedvirtual
conformation::Residue const & core::pack::scmin::CartSCMinMinimizerMap::residue ( Size  seqpos) const
overridevirtual
basic::datacache::BasicDataCache & core::pack::scmin::CartSCMinMinimizerMap::residue_data ( Size  seqpos) const
overridevirtual
void core::pack::scmin::CartSCMinMinimizerMap::set_natoms_for_residue ( Size  resid,
Size  natoms 
)
overridevirtual
void core::pack::scmin::CartSCMinMinimizerMap::set_total_residue ( Size  total_residue)
overridevirtual
void core::pack::scmin::CartSCMinMinimizerMap::setup ( AtomTreeCollectionOP  trees)
overridevirtual
void core::pack::scmin::CartSCMinMinimizerMap::starting_dofs ( optimization::Multivec dofs) const
overridevirtual
id::TorsionID core::pack::scmin::CartSCMinMinimizerMap::tor_for_dof ( id::DOF_ID const &  dofid) const
overridevirtual
void core::pack::scmin::CartSCMinMinimizerMap::zero_atom_derivative_vectors ( )
overridevirtual

Member Data Documentation

utility::vector1< ResidueAtomTreeCollectionOP > core::pack::scmin::CartSCMinMinimizerMap::atcs_for_residues_
private
AtomTreeCollectionOP core::pack::scmin::CartSCMinMinimizerMap::atom_tree_collection_
private

Referenced by setup().

utility::vector1< utility::vector1< Size > > core::pack::scmin::CartSCMinMinimizerMap::atoms_to_dofid_
private
utility::vector1< id::AtomID > core::pack::scmin::CartSCMinMinimizerMap::dofid_to_atoms_
private

Referenced by get_atom(), set_total_residue(), and setup().

kinematics::DomainMap core::pack::scmin::CartSCMinMinimizerMap::domain_map_
private
utility::vector1< utility::vector1< id::AtomID > > core::pack::scmin::CartSCMinMinimizerMap::moving_atoms_
private
utility::vector1< core::Size > core::pack::scmin::CartSCMinMinimizerMap::nactive_moving_atoms_
private
core::Size core::pack::scmin::CartSCMinMinimizerMap::nactive_moving_atoms_total_
private
utility::vector1< core::Vector > core::pack::scmin::CartSCMinMinimizerMap::residue_coord_workspace_
private

The documentation for this class was generated from the following files: