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protocols::toolbox::match_enzdes_util::TheozymeInvrotTree Class Reference

This class takes an EnzConstraintIO object and generates a 3D model of the theozyme in it, where inverse rotamers are generated for every block in the cstfile. It gets complicated when ambiguous interactions are specified and other residues are interacting (possibly in ambiguous fashion) with these ambiguous residues... More...

#include <InvrotTree.hh>

Inheritance diagram for protocols::toolbox::match_enzdes_util::TheozymeInvrotTree:
Inheritance graph
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Public Member Functions

 TheozymeInvrotTree (EnzConstraintIOCOP enzcst_io)
 
 ~TheozymeInvrotTree () override
 
void generate_targets_and_inverse_rotamers () override
 this function generates the 'target' for the inverse rotamers, i.e. in the case of enzdes, simply the coordinates for the ligand if in the future somebody wants to use this to build inverse rotamers against a protein, this function can be reimplemented. called from the constructor, is this really the best idea? More...
 
bool check_pose_tree_compatibility (core::pose::Pose &pose) const override
 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...
 
- Public Member Functions inherited from protocols::toolbox::match_enzdes_util::InvrotTree
 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...
 
core::Size num_target_states () const
 

Private Attributes

EnzConstraintIOCOP enzcst_io_
 

Additional Inherited Members

- Public Types inherited from protocols::toolbox::match_enzdes_util::InvrotTree
typedef core::Size Size
 
- Protected Member Functions inherited from protocols::toolbox::match_enzdes_util::InvrotTree
void clear_target_states ()
 
void add_to_targets (InvrotTargetOP invrot_target)
 

Detailed Description

This class takes an EnzConstraintIO object and generates a 3D model of the theozyme in it, where inverse rotamers are generated for every block in the cstfile. It gets complicated when ambiguous interactions are specified and other residues are interacting (possibly in ambiguous fashion) with these ambiguous residues...

Constructor & Destructor Documentation

protocols::toolbox::match_enzdes_util::TheozymeInvrotTree::TheozymeInvrotTree ( EnzConstraintIOCOP  enzcst_io)
protocols::toolbox::match_enzdes_util::TheozymeInvrotTree::~TheozymeInvrotTree ( )
overridedefault

Member Function Documentation

bool protocols::toolbox::match_enzdes_util::TheozymeInvrotTree::check_pose_tree_compatibility ( core::pose::Pose pose) const
overridevirtual

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

Implements protocols::toolbox::match_enzdes_util::InvrotTree.

void protocols::toolbox::match_enzdes_util::TheozymeInvrotTree::generate_targets_and_inverse_rotamers ( )
overridevirtual

this function generates the 'target' for the inverse rotamers, i.e. in the case of enzdes, simply the coordinates for the ligand if in the future somebody wants to use this to build inverse rotamers against a protein, this function can be reimplemented. called from the constructor, is this really the best idea?

Implements protocols::toolbox::match_enzdes_util::InvrotTree.

References protocols::toolbox::match_enzdes_util::InvrotTree::add_to_targets(), core::pack::rotamer_set::bb_independent_rotamers(), protocols::toolbox::match_enzdes_util::InvrotTree::clear_target_states(), core::conformation::ResidueFactory::create_residue(), enzcst_io_, protocols::toolbox::match_enzdes_util::InvrotTree::num_target_states(), and protocols::toolbox::match_enzdes_util::tr().

Member Data Documentation

EnzConstraintIOCOP protocols::toolbox::match_enzdes_util::TheozymeInvrotTree::enzcst_io_
private

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