Rosetta  2021.16
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
core::pack::scmin::SCMinMinimizerMap Class Referenceabstract

#include <SCMinMinimizerMap.hh>

Inheritance diagram for core::pack::scmin::SCMinMinimizerMap:
Inheritance graph
[legend]

Public Member Functions

 SCMinMinimizerMap ()
 
 ~SCMinMinimizerMap () override
 
virtual void set_total_residue (Size total_residue)=0
 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). More...
 
virtual void clear_active_dofs ()=0
 Disable the minimization for all residues. Ammortized O(1). More...
 
virtual void activate_residue_dofs (Size resindex)=0
 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=0
 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=0
 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...
 
virtual void setup (AtomTreeCollectionOP trees)=0
 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...
 
virtual conformation::Residue
const & 
residue (Size seqpos) const =0
 Convenience lookup – turns over the request to the AtomTreeCollection. More...
 
virtual
basic::datacache::BasicDataCache & 
residue_data (Size seqpos) const =0
 
virtual Size n_dof_nodes () const =0
 
virtual void starting_dofs (optimization::Multivec &dofs) const =0
 Initialize a multivec with the dofs reflected in the current residue(s) More...
 
virtual void assign_dofs_to_mobile_residues (optimization::Multivec const &dofs)=0
 Assign the chi values to the residue(s) More...
 
virtual optimization::DOF_Nodedof_node (Size index)=0
 
virtual optimization::DOF_Node
const & 
dof_node_for_chi (Size resid, Size chiid) const =0
 
virtual id::TorsionID tor_for_dof (id::DOF_ID const &dofid) const =0
 
virtual kinematics::tree::Atom
const & 
atom (AtomID const &atid) const =0
 
virtual void zero_atom_derivative_vectors ()=0
 
virtual void link_torsion_vectors ()=0
 propagate f1/f2's up from children to parents More...
 
virtual void set_natoms_for_residue (Size resid, Size natoms)=0
 
utility::vector1
< scoring::DerivVectorPair > & 
atom_derivatives (Size resid)
 
void set_nonideal (bool val_in)
 
virtual optimization::MultifuncOP make_multifunc (pose::Pose &p, utility::vector1< conformation::ResidueCOP > const &bg_residues, scoring::ScoreFunction const &sfxn, scoring::MinimizationGraph &mingraph)=0
 
- Public Member Functions inherited from core::kinematics::MinimizerMapBase
 MinimizerMapBase ()
 default ctor; noop More...
 
 ~MinimizerMapBase () override
 dstor More...
 

Protected Member Functions

virtual void reset_dof_nodes ()=0
 

Protected Attributes

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_
 

Additional Inherited Members

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

Constructor & Destructor Documentation

core::pack::scmin::SCMinMinimizerMap::SCMinMinimizerMap ( )
inline
core::pack::scmin::SCMinMinimizerMap::~SCMinMinimizerMap ( )
inlineoverride

Member Function Documentation

virtual void core::pack::scmin::SCMinMinimizerMap::activate_residue_dofs ( Size  resindex)
pure virtual
Size core::pack::scmin::SCMinMinimizerMap::active_residue ( Size  index) const
inline
void core::pack::scmin::SCMinMinimizerMap::add_atom ( AtomID const &  atom_id,
DOF_ID const &  dof_id 
)
overridepure 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.

Implemented in core::pack::scmin::AtomTreeSCMinMinimizerMap, and core::pack::scmin::CartSCMinMinimizerMap.

void core::pack::scmin::SCMinMinimizerMap::add_torsion ( DOF_ID const &  new_torsion,
DOF_ID const &  parent 
)
overridepure 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.

Implemented in core::pack::scmin::AtomTreeSCMinMinimizerMap, and core::pack::scmin::CartSCMinMinimizerMap.

virtual void core::pack::scmin::SCMinMinimizerMap::assign_dofs_to_mobile_residues ( optimization::Multivec const &  dofs)
pure virtual
virtual kinematics::tree::Atom const& core::pack::scmin::SCMinMinimizerMap::atom ( AtomID const &  atid) const
pure virtual
utility::vector1< scoring::DerivVectorPair >& core::pack::scmin::SCMinMinimizerMap::atom_derivatives ( Size  resid)
inline
virtual void core::pack::scmin::SCMinMinimizerMap::clear_active_dofs ( )
pure virtual
kinematics::DomainMap const& core::pack::scmin::SCMinMinimizerMap::dm ( ) const
inline
virtual optimization::DOF_Node& core::pack::scmin::SCMinMinimizerMap::dof_node ( Size  index)
pure virtual
virtual optimization::DOF_Node const& core::pack::scmin::SCMinMinimizerMap::dof_node_for_chi ( Size  resid,
Size  chiid 
) const
pure virtual
kinematics::DomainMap const& core::pack::scmin::SCMinMinimizerMap::domain_map ( ) const
inlineoverridevirtual

MinimizerMapBase class virtual accessor.

Implements core::kinematics::MinimizerMapBase.

References domain_map_.

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

propagate f1/f2's up from children to parents

Implemented in core::pack::scmin::AtomTreeSCMinMinimizerMap, and core::pack::scmin::CartSCMinMinimizerMap.

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

virtual optimization::MultifuncOP core::pack::scmin::SCMinMinimizerMap::make_multifunc ( pose::Pose p,
utility::vector1< conformation::ResidueCOP > const &  bg_residues,
scoring::ScoreFunction const &  sfxn,
scoring::MinimizationGraph mingraph 
)
pure virtual
virtual Size core::pack::scmin::SCMinMinimizerMap::n_dof_nodes ( ) const
pure virtual
Size core::pack::scmin::SCMinMinimizerMap::nactive_residues ( ) const
inline
virtual void core::pack::scmin::SCMinMinimizerMap::reset_dof_nodes ( )
protectedpure virtual
virtual conformation::Residue const& core::pack::scmin::SCMinMinimizerMap::residue ( Size  seqpos) const
pure virtual
virtual basic::datacache::BasicDataCache& core::pack::scmin::SCMinMinimizerMap::residue_data ( Size  seqpos) const
pure virtual
virtual void core::pack::scmin::SCMinMinimizerMap::set_natoms_for_residue ( Size  resid,
Size  natoms 
)
pure virtual
void core::pack::scmin::SCMinMinimizerMap::set_nonideal ( bool  val_in)
inline

References nonideal_.

virtual void core::pack::scmin::SCMinMinimizerMap::set_total_residue ( Size  total_residue)
pure virtual

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).

Implemented in core::pack::scmin::AtomTreeSCMinMinimizerMap, and core::pack::scmin::CartSCMinMinimizerMap.

virtual void core::pack::scmin::SCMinMinimizerMap::setup ( AtomTreeCollectionOP  trees)
pure virtual

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

Implemented in core::pack::scmin::AtomTreeSCMinMinimizerMap, and core::pack::scmin::CartSCMinMinimizerMap.

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

virtual void core::pack::scmin::SCMinMinimizerMap::starting_dofs ( optimization::Multivec dofs) const
pure virtual
virtual id::TorsionID core::pack::scmin::SCMinMinimizerMap::tor_for_dof ( id::DOF_ID const &  dofid) const
pure virtual
virtual void core::pack::scmin::SCMinMinimizerMap::zero_atom_derivative_vectors ( )
pure virtual

Member Data Documentation

utility::vector1< Size > core::pack::scmin::SCMinMinimizerMap::active_residue_index_for_res_
protected
utility::vector1< Size > core::pack::scmin::SCMinMinimizerMap::active_residues_
protected
utility::vector1< utility::vector1< scoring::DerivVectorPair > > core::pack::scmin::SCMinMinimizerMap::atom_derivatives_
protected
kinematics::DomainMap core::pack::scmin::SCMinMinimizerMap::domain_map_
protected
Size core::pack::scmin::SCMinMinimizerMap::focused_residue_
protected

each atom tree in the AtomTreeCollection will tell us that it represents residue 1. this variable tells us which residue is actually being represented.

Referenced by core::pack::scmin::AtomTreeSCMinMinimizerMap::add_atom(), core::pack::scmin::AtomTreeSCMinMinimizerMap::add_torsion(), core::pack::scmin::CartSCMinMinimizerMap::setup(), and core::pack::scmin::AtomTreeSCMinMinimizerMap::setup().

Size core::pack::scmin::SCMinMinimizerMap::nactive_residues_
protected
bool core::pack::scmin::SCMinMinimizerMap::nonideal_
protected

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