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protocols::mainchain_potential::GenerateMainchainPotential Class Reference

A generator for mainchain potentials. Inputs are a noncanonical residue type with an already-generated sidechain potential; outputs are a potential file suitable for use by the RamaPrePro scoreterm. More...

#include <GenerateMainchainPotential.hh>

Inheritance diagram for protocols::mainchain_potential::GenerateMainchainPotential:
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Public Member Functions

 GenerateMainchainPotential (GenerateMainchainPotentialOptionsCOP options=nullptr)
 Default constructor. More...
 
 GenerateMainchainPotential (GenerateMainchainPotential const &src)
 Copy constructor. More...
 
 ~GenerateMainchainPotential () override
 Destructor. More...
 
GenerateMainchainPotentialOP clone () const
 Clone function: make a copy of this object and return an owning pointer to the copy. More...
 
void run ()
 Entry point into protocol execution. More...
 
void write_last_generated_to_disk () const
 Write the last generated mainchain potential to disk. The output filename is given in the options_ object. More...
 

Private Member Functions

core::scoring::ScoreFunctionOP generate_sfxn () const
 Get the scorefunction that we'll be using. More...
 
core::pose::PoseOP generate_pose () const
 Generate the one-residue pose, based on options. More...
 
bool protein_patches_can_apply (core::chemical::ResidueTypeCOP restype) const
 Can this residue type take protein terminal patches? More...
 
bool patches_can_apply (core::chemical::ResidueTypeCOP restype, utility::vector1< core::chemical::VariantType > const &vartypes) const
 Can this residue type take specified terminal patches? More...
 
void apply_protein_patches (core::pose::Pose &pose) const
 Given a one-residue pose, apply acetylated N-terminus and aminomethylated C-terminus patches. More...
 
void generate_mainchain_potential (core::pose::PoseCOP pose, core::scoring::ScoreFunctionOP sfxn, core::chemical::mainchain_potential::MainchainScoreTableOP newtable, std::map< core::scoring::ScoreType, core::chemical::mainchain_potential::MainchainScoreTableOP > &last_generated_scoretables_by_scoreterm) const
 Given a pose, cycle through mainchain dihedrals and generate the mainchain potential. More...
 

Private Attributes

GenerateMainchainPotentialOptionsOP options_
 This protocol's options. More...
 
core::chemical::mainchain_potential::MainchainScoreTableCOP last_generated_scoretable_
 The last mainchain potential that this object generated. Nullptr if nothing has been generated. More...
 
std::map
< core::scoring::ScoreType,
core::chemical::mainchain_potential::MainchainScoreTableOP
last_generated_scoretables_by_scoreterm_
 Mainchain potentials for each scoreterm, separately. More...
 

Friends

class ::GenerateMainchainPotentialTests
 

Detailed Description

A generator for mainchain potentials. Inputs are a noncanonical residue type with an already-generated sidechain potential; outputs are a potential file suitable for use by the RamaPrePro scoreterm.

Constructor & Destructor Documentation

protocols::mainchain_potential::GenerateMainchainPotential::GenerateMainchainPotential ( GenerateMainchainPotentialOptionsCOP  options = nullptr)

Default constructor.

Optionally takes a GenerageMainchainPotentialOptions const-owning pointer. If null, this object initializes itself to default values.

protocols::mainchain_potential::GenerateMainchainPotential::GenerateMainchainPotential ( GenerateMainchainPotential const &  src)

Copy constructor.

References last_generated_scoretables_by_scoreterm_.

protocols::mainchain_potential::GenerateMainchainPotential::~GenerateMainchainPotential ( )
override

Destructor.

Member Function Documentation

void protocols::mainchain_potential::GenerateMainchainPotential::apply_protein_patches ( core::pose::Pose pose) const
private

Given a one-residue pose, apply acetylated N-terminus and aminomethylated C-terminus patches.

Applies aminomethylated or aminodimethylated C-terminus patches depending on settings in options.

References core::chemical::ACETYLATED_NTERMINUS_VARIANT, core::pose::add_variant_type_to_pose_residue(), core::chemical::DIMETHYLATED_CTERMINUS_VARIANT, core::chemical::ResidueTypeBase::has_variant_type(), core::chemical::METHYLATED_CTERMINUS_VARIANT, options_, core::pose::Pose::residue_type(), and core::pose::Pose::update_residue_neighbors().

Referenced by generate_pose().

GenerateMainchainPotentialOP protocols::mainchain_potential::GenerateMainchainPotential::clone ( ) const

Clone function: make a copy of this object and return an owning pointer to the copy.

void protocols::mainchain_potential::GenerateMainchainPotential::generate_mainchain_potential ( core::pose::PoseCOP  pose,
core::scoring::ScoreFunctionOP  sfxn,
core::chemical::mainchain_potential::MainchainScoreTableOP  newtable,
std::map< core::scoring::ScoreType, core::chemical::mainchain_potential::MainchainScoreTableOP > &  last_generated_scoretables_by_scoreterm 
) const
private

Given a pose, cycle through mainchain dihedrals and generate the mainchain potential.

References core::id::BB, core::pack::create_packer_graph(), core::scoring::n_score_types, options_, and protocols::TR().

Referenced by run().

core::pose::PoseOP protocols::mainchain_potential::GenerateMainchainPotential::generate_pose ( ) const
private
core::scoring::ScoreFunctionOP protocols::mainchain_potential::GenerateMainchainPotential::generate_sfxn ( ) const
private

Get the scorefunction that we'll be using.

References core::scoring::ScoreFunctionFactory::create_score_function(), options_, and protocols::TR().

Referenced by run().

bool protocols::mainchain_potential::GenerateMainchainPotential::patches_can_apply ( core::chemical::ResidueTypeCOP  restype,
utility::vector1< core::chemical::VariantType > const &  vartypes 
) const
private
bool protocols::mainchain_potential::GenerateMainchainPotential::protein_patches_can_apply ( core::chemical::ResidueTypeCOP  restype) const
private

Can this residue type take protein terminal patches?

References core::chemical::ACETYLATED_NTERMINUS_VARIANT, core::chemical::METHYLATED_CTERMINUS_VARIANT, and patches_can_apply().

Referenced by generate_pose().

void protocols::mainchain_potential::GenerateMainchainPotential::run ( )
void protocols::mainchain_potential::GenerateMainchainPotential::write_last_generated_to_disk ( ) const

Write the last generated mainchain potential to disk. The output filename is given in the options_ object.

If we're writing individual scoretables for individual scoreterms, that happens here, too.

References last_generated_scoretable_, last_generated_scoretables_by_scoreterm_, core::scoring::name_from_score_type(), options_, and protocols::TR().

Friends And Related Function Documentation

friend class ::GenerateMainchainPotentialTests
friend

Member Data Documentation

core::chemical::mainchain_potential::MainchainScoreTableCOP protocols::mainchain_potential::GenerateMainchainPotential::last_generated_scoretable_
private

The last mainchain potential that this object generated. Nullptr if nothing has been generated.

Referenced by run(), and write_last_generated_to_disk().

std::map< core::scoring::ScoreType, core::chemical::mainchain_potential::MainchainScoreTableOP > protocols::mainchain_potential::GenerateMainchainPotential::last_generated_scoretables_by_scoreterm_
private

Mainchain potentials for each scoreterm, separately.

Note that these will be kept unnormalized. Moreover, each scoreterm's weight is treated as though it were 1.0.

Referenced by GenerateMainchainPotential(), run(), and write_last_generated_to_disk().

GenerateMainchainPotentialOptionsOP protocols::mainchain_potential::GenerateMainchainPotential::options_
private

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