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protocols::toolbox::match_enzdes_util::InvrotTree Class Referenceabstract

#include <InvrotTree.hh>

Inheritance diagram for protocols::toolbox::match_enzdes_util::InvrotTree:
Inheritance graph
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Public Types

typedef core::Size Size
 

Public Member Functions

 InvrotTree ()
 
 ~InvrotTree () override
 
core::scoring::constraints::ConstraintCOP get_constraint_for_target_state (core::Size target_state) const
 
void generate_inverse_rotamer_constraints (core::pose::Pose const &pose, AllowedSeqposForGeomCstCOP geomcst_seqpos)
 the main function, generate the constraints More...
 
utility::vector1
< InvrotCollectorCOP
collect_all_inverse_rotamers () const
 convenience access function to the inverse rotamers in the tree note: the returned invrots can contain duplications, as every unique definition of the tree is returned More...
 
void dump_invrots_tree_as_multimodel_pdbs (std::string filename_base) const
 visualization this can lead to several files being written, depending on the ambiguities in the tree More...
 
virtual void generate_targets_and_inverse_rotamers ()=0
 important function 1: populate the tree should be called before folding a chain obviously see TheozymeInvrotTree below for example More...
 
virtual bool check_pose_tree_compatibility (core::pose::Pose &pose) const =0
 important function 2: after a chain/pose has been generated, check whether it's compatible with the inverse rotamers in the tree this can change the pose again More...
 
core::Size num_target_states () const
 

Protected Member Functions

void clear_target_states ()
 
void add_to_targets (InvrotTargetOP invrot_target)
 

Private Attributes

utility::vector1< InvrotTargetOPinvrot_targets_
 
utility::vector1
< core::scoring::constraints::ConstraintCOP
invrot_tree_constraints_
 

Detailed Description

abstract base class for the inverse rotamer tree is abstract so that in the future inverse rots could be generated in different ways than throug the enz cst machinery

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::toolbox::match_enzdes_util::InvrotTree::InvrotTree ( )
protocols::toolbox::match_enzdes_util::InvrotTree::~InvrotTree ( )
overridedefault

Member Function Documentation

void protocols::toolbox::match_enzdes_util::InvrotTree::add_to_targets ( InvrotTargetOP  invrot_target)
protected
virtual bool protocols::toolbox::match_enzdes_util::InvrotTree::check_pose_tree_compatibility ( core::pose::Pose pose) const
pure virtual

important function 2: after a chain/pose has been generated, check whether it's compatible with the inverse rotamers in the tree this can change the pose again

Implemented in protocols::toolbox::match_enzdes_util::TheozymeInvrotTree.

void protocols::toolbox::match_enzdes_util::InvrotTree::clear_target_states ( )
protected
utility::vector1< InvrotCollectorCOP > protocols::toolbox::match_enzdes_util::InvrotTree::collect_all_inverse_rotamers ( ) const

convenience access function to the inverse rotamers in the tree note: the returned invrots can contain duplications, as every unique definition of the tree is returned

References invrot_targets_.

Referenced by dump_invrots_tree_as_multimodel_pdbs().

void protocols::toolbox::match_enzdes_util::InvrotTree::dump_invrots_tree_as_multimodel_pdbs ( std::string  filename_base) const

visualization this can lead to several files being written, depending on the ambiguities in the tree

References collect_all_inverse_rotamers(), core::io::pdb::dump_pdb_residue(), core::sequence::end, protocols::abinitio::filename(), core::id::to_string(), and protocols::toolbox::match_enzdes_util::tr().

void protocols::toolbox::match_enzdes_util::InvrotTree::generate_inverse_rotamer_constraints ( core::pose::Pose const &  pose,
AllowedSeqposForGeomCstCOP  geomcst_seqpos 
)

the main function, generate the constraints

References invrot_targets_, and invrot_tree_constraints_.

virtual void protocols::toolbox::match_enzdes_util::InvrotTree::generate_targets_and_inverse_rotamers ( )
pure virtual

important function 1: populate the tree should be called before folding a chain obviously see TheozymeInvrotTree below for example

Implemented in protocols::toolbox::match_enzdes_util::TheozymeInvrotTree.

core::scoring::constraints::ConstraintCOP protocols::toolbox::match_enzdes_util::InvrotTree::get_constraint_for_target_state ( core::Size  target_state) const
core::Size protocols::toolbox::match_enzdes_util::InvrotTree::num_target_states ( ) const
inline

Member Data Documentation

utility::vector1< InvrotTargetOP > protocols::toolbox::match_enzdes_util::InvrotTree::invrot_targets_
private
utility::vector1< core::scoring::constraints::ConstraintCOP > protocols::toolbox::match_enzdes_util::InvrotTree::invrot_tree_constraints_
private

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