Rosetta 3.4
Public Types | Public Member Functions
core::pack::scmin::SCMinMinimizerMap Class Reference

#include <SCMinMinimizerMap.hh>

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List of all members.

Public Types

typedef optimization::DOF_Node DOF_Node
typedef optimization::DOF_NodeOP DOF_NodeOP

Public Member Functions

 SCMinMinimizerMap ()
virtual ~SCMinMinimizerMap ()
void set_total_residue (Size total_residue)
 the SCMinMinimizerMap 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).
void clear_active_chi ()
 Disable the minimization for all residues. Ammortized O(1).
void activate_residue_chi (Size resindex)
 Activate all the chi for a particular residue. Ammortized O(1).
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.
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.
void setup (AtomTreeCollectionOP trees)
 Traverse the atom trees in preparation for minimization to tie together all the DOFs and the atoms they control.
Size nactive_residues () const
 Accessors.
Size active_residue (Size index) const
virtual kinematics::DomainMap
const & 
domain_map () const
 MinimizerMapBase class virtual accessor.
kinematics::DomainMap const & dm () const
 Inline accessor.
conformation::Residue const & residue (Size seqpos) const
 Convenience lookup -- turns over the request to the AtomTreeCollection.
Size n_dof_nodes () const
void starting_dofs (optimization::Multivec &chi) const
 Initialize a multivec with the chi reflected in the current residue(s)
void assign_dofs_to_mobile_residues (optimization::Multivec const &chi)
 Assign the chi values to the residue(s)
optimization::DOF_Nodedof_node (Size index)
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
void set_natoms_for_residue (Size resid, Size natoms)
utility::vector1
< scoring::DerivVectorPair > & 
atom_derivatives (Size resid)

Member Typedef Documentation


Constructor & Destructor Documentation

core::pack::scmin::SCMinMinimizerMap::SCMinMinimizerMap ( )
core::pack::scmin::SCMinMinimizerMap::~SCMinMinimizerMap ( ) [virtual]

Member Function Documentation

void core::pack::scmin::SCMinMinimizerMap::activate_residue_chi ( Size  resindex)

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

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

Referenced by core::pack::get_residue_current_energy(), core::pack::get_total_energy_for_state(), and core::pack::minimize_alt_rotamer().

Size core::pack::scmin::SCMinMinimizerMap::active_residue ( Size  index) const [inline]

Referenced by setup().

void core::pack::scmin::SCMinMinimizerMap::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::kinematics::MinimizerMapBase.

References core::id::AtomID::atomno(), core::id::DOF_ID::atomno(), and core::id::DOF_ID::valid().

void core::pack::scmin::SCMinMinimizerMap::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::kinematics::MinimizerMapBase.

References core::id::DOF_ID::atomno(), core::id::DOF_ID::type(), and core::id::DOF_ID::valid().

void core::pack::scmin::SCMinMinimizerMap::assign_dofs_to_mobile_residues ( optimization::Multivec const &  chi)

Assign the chi values to the residue(s)

References core::optimization::DOF_Node::atomno(), and core::optimization::DOF_Node::rsd().

kinematics::tree::Atom const & core::pack::scmin::SCMinMinimizerMap::atom ( AtomID const &  atid) const
utility::vector1< scoring::DerivVectorPair >& core::pack::scmin::SCMinMinimizerMap::atom_derivatives ( Size  resid) [inline]
void core::pack::scmin::SCMinMinimizerMap::clear_active_chi ( )
kinematics::DomainMap const& core::pack::scmin::SCMinMinimizerMap::dm ( ) const [inline]

Inline accessor.

optimization::DOF_Node& core::pack::scmin::SCMinMinimizerMap::dof_node ( Size  index) [inline]
SCMinMinimizerMap::DOF_Node const & core::pack::scmin::SCMinMinimizerMap::dof_node_for_chi ( Size  resid,
Size  chiid 
) const
virtual kinematics::DomainMap const& core::pack::scmin::SCMinMinimizerMap::domain_map ( ) const [inline, virtual]

MinimizerMapBase class virtual accessor.

Implements core::kinematics::MinimizerMapBase.

void core::pack::scmin::SCMinMinimizerMap::link_torsion_vectors ( )

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).

Size core::pack::scmin::SCMinMinimizerMap::n_dof_nodes ( ) const [inline]
Size core::pack::scmin::SCMinMinimizerMap::nactive_residues ( ) const [inline]

Accessors.

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

Convenience lookup -- turns over the request to the AtomTreeCollection.

Referenced by tor_for_dof().

void core::pack::scmin::SCMinMinimizerMap::set_natoms_for_residue ( Size  resid,
Size  natoms 
)
void core::pack::scmin::SCMinMinimizerMap::set_total_residue ( Size  total_residue)

the SCMinMinimizerMap 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).

void core::pack::scmin::SCMinMinimizerMap::setup ( AtomTreeCollectionOP  trees)
void core::pack::scmin::SCMinMinimizerMap::starting_dofs ( optimization::Multivec chi) const

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

References core::optimization::DOF_Node::atomno(), and core::optimization::DOF_Node::rsd().

id::TorsionID core::pack::scmin::SCMinMinimizerMap::tor_for_dof ( id::DOF_ID const &  dofid) const
void core::pack::scmin::SCMinMinimizerMap::zero_atom_derivative_vectors ( )

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