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core::pack::scmin::AtomTreeSCMinMinimizerMap Class Reference

#include <AtomTreeSCMinMinimizerMap.hh>

Inheritance diagram for core::pack::scmin::AtomTreeSCMinMinimizerMap:
Inheritance graph
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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

 AtomTreeSCMinMinimizerMap ()
 
 ~AtomTreeSCMinMinimizerMap () override
 
void set_total_residue (Size total_residue) override
 the AtomTreeSCMinMinimizerMap 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
 Convenience lookup – turns over the request to the AtomTreeCollection. More...
 
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
 
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
< ResidueAtomTreeCollectionOP
atcs_for_residues_
 
id::DOF_ID_Mask dof_mask_
 
utility::vector1
< optimization::DOF_NodeOP
dof_nodes_
 
Size n_active_dof_nodes_
 
AtomTreeCollectionOP atom_tree_collection_
 
utility::vector1< Sizeatoms_representing_chis_
 
utility::vector1< Sizeatoms_representing_ds_
 
utility::vector1< Sizeatoms_representing_thetas_
 
utility::vector1< Sizechi_start_for_active_residue_
 
utility::vector1
< utility::vector1< Size > > 
active_residue_atom_to_dofnode_index_
 
Size dof_start_for_focused_residue_
 For parent_dof lookup: track which dofs a particular atom are responsible for. More...
 
Size ndofs_added_for_focused_residue_
 

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

Member Function Documentation

void core::pack::scmin::AtomTreeSCMinMinimizerMap::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_, core::pack::scmin::SCMinMinimizerMap::domain_map_, and core::pack::scmin::SCMinMinimizerMap::nactive_residues_.

Size core::pack::scmin::AtomTreeSCMinMinimizerMap::active_residue ( Size  index) const
inline
void core::pack::scmin::AtomTreeSCMinMinimizerMap::add_atom ( AtomID const &  atom_id,
DOF_ID const &  dof_id 
)
overridevirtual
void core::pack::scmin::AtomTreeSCMinMinimizerMap::add_torsion ( DOF_ID const &  new_torsion,
DOF_ID const &  parent 
)
overridevirtual
void core::pack::scmin::AtomTreeSCMinMinimizerMap::assign_dofs_to_mobile_residues ( optimization::Multivec const &  dofs)
overridevirtual
kinematics::tree::Atom const & core::pack::scmin::AtomTreeSCMinMinimizerMap::atom ( AtomID const &  atid) const
overridevirtual
void core::pack::scmin::AtomTreeSCMinMinimizerMap::clear_active_dofs ( )
overridevirtual
kinematics::DomainMap const& core::pack::scmin::AtomTreeSCMinMinimizerMap::dm ( ) const
inline
optimization::DOF_Node& core::pack::scmin::AtomTreeSCMinMinimizerMap::dof_node ( Size  index)
inlineoverridevirtual
AtomTreeSCMinMinimizerMap::DOF_Node const & core::pack::scmin::AtomTreeSCMinMinimizerMap::dof_node_for_chi ( Size  resid,
Size  chiid 
) const
overridevirtual
kinematics::DomainMap const& core::pack::scmin::AtomTreeSCMinMinimizerMap::domain_map ( ) const
inlineoverridevirtual

MinimizerMapBase class virtual accessor.

Implements core::kinematics::MinimizerMapBase.

References core::pack::scmin::SCMinMinimizerMap::domain_map_.

void core::pack::scmin::AtomTreeSCMinMinimizerMap::link_torsion_vectors ( )
overridevirtual

propagate f1/f2's up from children to parents

super simple – no need for a sort (nor is there a need in the optimization::MinimizerMap for that matter).

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

References dof_nodes_, and n_active_dof_nodes_.

optimization::MultifuncOP core::pack::scmin::AtomTreeSCMinMinimizerMap::make_multifunc ( pose::Pose p,
utility::vector1< conformation::ResidueCOP > const &  bg_residues,
scoring::ScoreFunction const &  sfxn,
scoring::MinimizationGraph mingraph 
)
inlineoverridevirtual
Size core::pack::scmin::AtomTreeSCMinMinimizerMap::n_dof_nodes ( ) const
inlineoverridevirtual
Size core::pack::scmin::AtomTreeSCMinMinimizerMap::nactive_residues ( ) const
inline
void core::pack::scmin::AtomTreeSCMinMinimizerMap::reset_dof_nodes ( )
overrideprotectedvirtual
conformation::Residue const & core::pack::scmin::AtomTreeSCMinMinimizerMap::residue ( Size  seqpos) const
overridevirtual

Convenience lookup – turns over the request to the AtomTreeCollection.

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

References atcs_for_residues_.

Referenced by tor_for_dof().

basic::datacache::BasicDataCache & core::pack::scmin::AtomTreeSCMinMinimizerMap::residue_data ( Size  seqpos) const
overridevirtual

Convenience lookup – turns over the request to the AtomTreeCollection.

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

References atcs_for_residues_.

void core::pack::scmin::AtomTreeSCMinMinimizerMap::set_natoms_for_residue ( Size  resid,
Size  natoms 
)
overridevirtual
void core::pack::scmin::AtomTreeSCMinMinimizerMap::set_total_residue ( Size  total_residue)
overridevirtual
void core::pack::scmin::AtomTreeSCMinMinimizerMap::setup ( AtomTreeCollectionOP  trees)
overridevirtual
void core::pack::scmin::AtomTreeSCMinMinimizerMap::starting_dofs ( optimization::Multivec dofs) const
overridevirtual
id::TorsionID core::pack::scmin::AtomTreeSCMinMinimizerMap::tor_for_dof ( id::DOF_ID const &  dofid) const
overridevirtual
void core::pack::scmin::AtomTreeSCMinMinimizerMap::zero_atom_derivative_vectors ( )
overridevirtual

Member Data Documentation

utility::vector1< utility::vector1< Size > > core::pack::scmin::AtomTreeSCMinMinimizerMap::active_residue_atom_to_dofnode_index_
private
utility::vector1< ResidueAtomTreeCollectionOP > core::pack::scmin::AtomTreeSCMinMinimizerMap::atcs_for_residues_
private
AtomTreeCollectionOP core::pack::scmin::AtomTreeSCMinMinimizerMap::atom_tree_collection_
private

Referenced by setup().

utility::vector1< Size > core::pack::scmin::AtomTreeSCMinMinimizerMap::atoms_representing_chis_
private

Referenced by add_atom(), add_torsion(), and setup().

utility::vector1< Size > core::pack::scmin::AtomTreeSCMinMinimizerMap::atoms_representing_ds_
private

Referenced by add_atom(), add_torsion(), and setup().

utility::vector1< Size > core::pack::scmin::AtomTreeSCMinMinimizerMap::atoms_representing_thetas_
private

Referenced by add_atom(), add_torsion(), and setup().

utility::vector1< Size > core::pack::scmin::AtomTreeSCMinMinimizerMap::chi_start_for_active_residue_
private
id::DOF_ID_Mask core::pack::scmin::AtomTreeSCMinMinimizerMap::dof_mask_
private

Referenced by setup().

utility::vector1< optimization::DOF_NodeOP > core::pack::scmin::AtomTreeSCMinMinimizerMap::dof_nodes_
private
Size core::pack::scmin::AtomTreeSCMinMinimizerMap::dof_start_for_focused_residue_
private

For parent_dof lookup: track which dofs a particular atom are responsible for.

Referenced by add_atom(), add_torsion(), and setup().

Size core::pack::scmin::AtomTreeSCMinMinimizerMap::n_active_dof_nodes_
private
Size core::pack::scmin::AtomTreeSCMinMinimizerMap::ndofs_added_for_focused_residue_
private

Referenced by add_torsion(), and setup().


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