Rosetta Core  2014.35
Public Types | Public Member Functions | Protected Member Functions | Private Attributes | List of all members
core::pack::scmin::CartSCMinMinimizerMap Class Reference

#include <CartSCMinMinimizerMap.hh>

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 ()
 
virtual ~CartSCMinMinimizerMap ()
 
virtual void set_total_residue (Size total_residue)
 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...
 
virtual void clear_active_dofs ()
 Disable the minimization for all residues. Ammortized O(1). More...
 
virtual void activate_residue_dofs (Size resindex)
 Activate all the dofs for a particular residue. Ammortized O(1). More...
 
virtual void add_torsion (DOF_ID const &new_torsion, DOF_ID const &parent)
 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...
 
virtual void add_atom (AtomID const &atom_id, DOF_ID const &dof_id)
 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)
 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
 
virtual kinematics::DomainMap
const & 		domain_map () const
 MinimizerMapBase class virtual accessor. More...
 
kinematics::DomainMap const & dm () const
 Inline accessor. More...
 
Size n_dof_nodes () const
 
void starting_dofs (optimization::Multivec &dofs) const
 Initialize a multivec with the dofs reflected in the current residue(s) More...
 
void assign_dofs_to_mobile_residues (optimization::Multivec const &dofs)
 Assign the chi values to the residue(s) More...
 
optimization::DOF_Node & dof_node (Size index)
 
virtual conformation::Residue
const & 		residue (Size seqpos) const
 Convenience lookup – turns over the request to the AtomTreeCollection. More...
 
optimization::DOF_Node const & dof_node_for_chi (Size resid, Size chiid) const
 
id::TorsionID tor_for_dof (id::DOF_ID const &dofid) const
 
kinematics::tree::Atom const & atom (AtomID const &atid) const
 
void zero_atom_derivative_vectors ()
 
void link_torsion_vectors ()
 propagate f1/f2's up from children to parents More...
 
void set_natoms_for_residue (Size resid, Size natoms)
 
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)
 
- Public Member Functions inherited from core::pack::scmin::SCMinMinimizerMap
 SCMinMinimizerMap ()
 
virtual ~SCMinMinimizerMap ()
 
Size nactive_residues () const
 Accessors. More...
 
Size active_residue (Size index) const
 
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...
 
virtual ~MinimizerMapBase ()
 dstor More...
 

Protected Member Functions

void reset_dof_nodes ()
 

Private Attributes

utility::vector1
< utility::vector1< id::AtomID > > 		moving_atoms_
 
utility::vector1< core::Size > nactive_moving_atoms_
 
core::Size nactive_moving_atoms_total_
 
utility::vector1< id::AtomID > dofid_to_atoms_
 
utility::vector1
< utility::vector1< Size > > 		atoms_to_dofid_
 
utility::vector1< core::Vector > residue_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< Size > active_residue_index_for_res_
 
utility::vector1< Size > active_residues_
 
kinematics::DomainMap domain_map_
 
bool nonideal_
 

Member Typedef Documentation

typedef optimization::DOF_Node core::pack::scmin::CartSCMinMinimizerMap::DOF_Node
typedef optimization::DOF_NodeOP core::pack::scmin::CartSCMinMinimizerMap::DOF_NodeOP

Constructor & Destructor Documentation

core::pack::scmin::CartSCMinMinimizerMap::CartSCMinMinimizerMap ( )

References residue_coord_workspace_.

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

Member Function Documentation

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

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

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

Referenced by core::pack::scmin::CartSCMinMultifunc::dfunc(), core::pack::scmin::CartSCMinMultifunc::operator()(), setup(), and starting_dofs().

void core::pack::scmin::CartSCMinMinimizerMap::add_atom ( AtomID const &  atom_id,
DOF_ID const &  dof_id 
)
virtual

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 
)
virtual

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)
virtual

Assign the chi values to the residue(s)

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

References core::pack::scmin::SCMinMinimizerMap::active_residues_, atcs_for_residues_, moving_atoms_, nactive_moving_atoms_total_, core::pack::scmin::SCMinMinimizerMap::nactive_residues_, and residue_coord_workspace_.

Referenced by core::pack::scmin::CartSCMinMultifunc::dfunc(), and core::pack::scmin::CartSCMinMultifunc::operator()().

kinematics::tree::Atom const & core::pack::scmin::CartSCMinMinimizerMap::atom ( AtomID const &  atid) const
virtual

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

References atcs_for_residues_, core::id::AtomID::atomno(), and core::id::AtomID::rsd().

void core::pack::scmin::CartSCMinMinimizerMap::clear_active_dofs ( )
virtual

Disable the minimization for all residues. Ammortized O(1).

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

References core::pack::scmin::SCMinMinimizerMap::active_residue_index_for_res_, core::pack::scmin::SCMinMinimizerMap::active_residues_, atcs_for_residues_, domain_map_, core::pack::scmin::SCMinMinimizerMap::nactive_residues_, and reset_dof_nodes().

kinematics::DomainMap const& core::pack::scmin::CartSCMinMinimizerMap::dm ( ) const
inline

Inline accessor.

References domain_map_.

Referenced by core::pack::scmin::CartSCMinMultifunc::dfunc(), and core::pack::scmin::CartSCMinMultifunc::operator()().

optimization::DOF_Node & core::pack::scmin::CartSCMinMinimizerMap::dof_node ( Size  index)
virtual

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

References core::pack::scmin::dummy_nodeop.

CartSCMinMinimizerMap::DOF_Node const & core::pack::scmin::CartSCMinMinimizerMap::dof_node_for_chi ( Size  resid,
Size  chiid 
) const
virtual

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

References core::pack::scmin::dummy_nodeop.

virtual kinematics::DomainMap const& core::pack::scmin::CartSCMinMinimizerMap::domain_map ( ) const
inlinevirtual

MinimizerMapBase class virtual accessor.

Reimplemented from core::pack::scmin::SCMinMinimizerMap.

References domain_map_.

id::AtomID const& core::pack::scmin::CartSCMinMinimizerMap::get_atom ( Size  idx)
inline

References dofid_to_atoms_.

Referenced by core::pack::scmin::CartSCMinMultifunc::dfunc().

Size core::pack::scmin::CartSCMinMinimizerMap::get_atom_index ( id::AtomID const &  atm)
inline

References core::id::AtomID::atomno(), atoms_to_dofid_, and core::id::AtomID::rsd().

Referenced by core::pack::scmin::CartSCMinMultifunc::dfunc().

void core::pack::scmin::CartSCMinMinimizerMap::link_torsion_vectors ( )
virtual

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 
)
inlinevirtual

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

Size core::pack::scmin::CartSCMinMinimizerMap::n_dof_nodes ( ) const
inlinevirtual

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

References nactive_moving_atoms_total_.

Referenced by core::pack::scmin::CartSCMinMultifunc::dfunc().

Size core::pack::scmin::CartSCMinMinimizerMap::nactive_residues ( ) const
inline

Accessors.

References core::pack::scmin::SCMinMinimizerMap::nactive_residues_.

Referenced by core::pack::scmin::CartSCMinMultifunc::dfunc(), and core::pack::scmin::CartSCMinMultifunc::operator()().

void core::pack::scmin::CartSCMinMinimizerMap::reset_dof_nodes ( )
protectedvirtual

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

References core::pack::scmin::SCMinMinimizerMap::active_residues_, nactive_moving_atoms_, nactive_moving_atoms_total_, and core::pack::scmin::SCMinMinimizerMap::nactive_residues_.

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

conformation::Residue const & core::pack::scmin::CartSCMinMinimizerMap::residue ( Size  seqpos) const
virtual

Convenience lookup – turns over the request to the AtomTreeCollection.

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

References atcs_for_residues_.

Referenced by core::pack::scmin::CartSCMinMultifunc::dfunc(), core::pack::scmin::CartSCMinMultifunc::operator()(), and tor_for_dof().

void core::pack::scmin::CartSCMinMinimizerMap::set_natoms_for_residue ( Size  resid,
Size  natoms 
)
virtual

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

References core::pack::scmin::SCMinMinimizerMap::atom_derivatives_, and core::io::serialization::size().

void core::pack::scmin::CartSCMinMinimizerMap::set_total_residue ( Size  total_residue)
virtual

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).

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

References core::pack::scmin::SCMinMinimizerMap::active_residue_index_for_res_, core::pack::scmin::SCMinMinimizerMap::active_residues_, atcs_for_residues_, core::pack::scmin::SCMinMinimizerMap::atom_derivatives_, atoms_to_dofid_, dofid_to_atoms_, domain_map_, moving_atoms_, nactive_moving_atoms_, core::pack::scmin::SCMinMinimizerMap::nactive_residues_, and reset_dof_nodes().

void core::pack::scmin::CartSCMinMinimizerMap::setup ( AtomTreeCollectionOP  trees)
virtual

Traverse the atom trees in preparation for minimization to tie together all the DOFs and the atoms they control.

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

References active_residue(), core::pack::scmin::SCMinMinimizerMap::active_residues_, atcs_for_residues_, atom_tree_collection_, atoms_to_dofid_, dofid_to_atoms_, core::conformation::Residue::first_sidechain_atom(), core::conformation::Residue::first_sidechain_hydrogen(), core::pack::scmin::SCMinMinimizerMap::focused_residue_, moving_atoms_, nactive_moving_atoms_, nactive_moving_atoms_total_, core::pack::scmin::SCMinMinimizerMap::nactive_residues_, core::conformation::Residue::natoms(), core::conformation::Residue::nheavyatoms(), reset_dof_nodes(), and core::io::serialization::size().

void core::pack::scmin::CartSCMinMinimizerMap::starting_dofs ( optimization::Multivec &  dofs) const
virtual

Initialize a multivec with the dofs reflected in the current residue(s)

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

References active_residue(), core::pack::scmin::SCMinMinimizerMap::active_residues_, atcs_for_residues_, moving_atoms_, nactive_moving_atoms_total_, core::pack::scmin::SCMinMinimizerMap::nactive_residues_, and core::conformation::Residue::xyz().

id::TorsionID core::pack::scmin::CartSCMinMinimizerMap::tor_for_dof ( id::DOF_ID const &  dofid) const
virtual

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

References core::id::DOF_ID::atomno(), core::id::BOGUS_TORSION_ID, core::id::CHI, core::id::PHI, residue(), core::id::DOF_ID::rsd(), type, and core::id::DOF_ID::type().

void core::pack::scmin::CartSCMinMinimizerMap::zero_atom_derivative_vectors ( )
virtual

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

References core::pack::scmin::SCMinMinimizerMap::active_residues_, core::pack::scmin::SCMinMinimizerMap::atom_derivatives_, core::pack::scmin::SCMinMinimizerMap::nactive_residues_, and core::io::serialization::size().

Referenced by core::pack::scmin::CartSCMinMultifunc::dfunc().

Member Data Documentation

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

Referenced by assign_dofs_to_mobile_residues(), atom(), clear_active_dofs(), residue(), set_total_residue(), setup(), and starting_dofs().

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

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

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

Referenced by activate_residue_dofs(), clear_active_dofs(), dm(), domain_map(), and set_total_residue().

utility::vector1< utility::vector1< id::AtomID > > core::pack::scmin::CartSCMinMinimizerMap::moving_atoms_
private

Referenced by assign_dofs_to_mobile_residues(), set_total_residue(), setup(), and starting_dofs().

utility::vector1< core::Size > core::pack::scmin::CartSCMinMinimizerMap::nactive_moving_atoms_
private

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

core::Size core::pack::scmin::CartSCMinMinimizerMap::nactive_moving_atoms_total_
private

Referenced by assign_dofs_to_mobile_residues(), n_dof_nodes(), reset_dof_nodes(), setup(), and starting_dofs().

utility::vector1< core::Vector > core::pack::scmin::CartSCMinMinimizerMap::residue_coord_workspace_
private

Referenced by assign_dofs_to_mobile_residues(), and CartSCMinMinimizerMap().

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