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MPDomainAssembly Class Reference
Inheritance diagram for MPDomainAssembly:
Inheritance graph
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Public Member Functions

 MPDomainAssembly ()
 Constructors ///. More...
 
 MPDomainAssembly (MPDomainAssembly const &src)
 Copy Constructor. More...
 
MPDomainAssemblyoperator= (MPDomainAssembly const &src)
 Assignment Operator. More...
 
 ~MPDomainAssembly () override
 Destructor. More...
 
std::string get_name () const override
 Mover Methods ///. More...
 
void apply (Pose &pose) override
 Get Membrane protein interface statistics. More...
 

Private Member Functions

void register_options ()
 Rosetta Scripts Methods ///. More...
 
void init_from_cmd ()
 Initialize Mover options from the comandline. More...
 
ResidueOP create_residue_from_olc (char olc)
 
Residue create_residue_from_resn (Pose &pose, core::Size resnumber)
 
void set_random_torsion (Pose &pose, Size resn)
 
void print_score (Pose &pose, core::scoring::ScoreFunctionOP sfxn)
 Print score to cout. More...
 

Private Attributes

std::string frag9_fn_
 Fragment filename. More...
 
std::string frag3_fn_
 Fragment filename. More...
 
std::string full_seq_
 Sequence of the full-length protein: given as fasta. More...
 
core::Size tmpdb_ {}
 Number of the pose in the -in:file:l list that is the TM domain. More...
 
utility::vector1< std::string > infiles_
 Vector of pose input files. More...
 
utility::vector1
< core::pose::Pose
poses_
 Vector of poses_ that are read in from PDB files. More...
 
utility::vector1< std::string > sequences_
 Vector of sequences_ in poses_. More...
 
utility::vector1< core::Size > offsets_
 Vector of offsets_, i.e. residue numbers along the full-length sequence for which the PDB poses_ start. More...
 
utility::vector1< core::Size > in_pdb_
 Vector of length (nres of full-length pose), describing whether the residue exists in a pose (0 = no, 1 = yes, >1 = overlap) More...
 
utility::vector1< std::string > linkers_
 Vectors of linker sequences_ to model. More...
 
core::kinematics::MoveMap movemap_
 Movemap of which residues can move (i.e. are in linkers_ +/-1 residue) More...
 
core::scoring::ScoreFunctionOP sfxn_
 scorefunction (i.e. membrane sfxn_) More...
 

Constructor & Destructor Documentation

MPDomainAssembly::MPDomainAssembly ( )

Constructors ///.

Construct a Default Mover

Construct a Default Membrane Position Mover

Referenced by main(), and operator=().

MPDomainAssembly::MPDomainAssembly ( MPDomainAssembly const &  src)

Copy Constructor.

Make a deep copy of this mover object

MPDomainAssembly::~MPDomainAssembly ( )
overridedefault

Destructor.

Member Function Documentation

void MPDomainAssembly::apply ( Pose pose)
override

Get Membrane protein interface statistics.

run domain assembly protocol for membrane proteins

References relax::range::angle_max(), utility::argmax(), create_residue_from_olc(), create_residue_from_resn(), pyrosetta::create_score_function, frag3_fn_, frag9_fn_, full_seq_, in_pdb_, infiles_, init_from_cmd(), basic::options::OptionKeys::ddg::iterations, basic::options::OptionKeys::frags::j, basic::options::OptionKeys::relax::range::kT, linkers_, test.T110_numeric::m, DRRAFTER::matches(), basic::options::OptionKeys::mc::mc, basic::options::OptionKeys::abinitio::membrane, basic::options::OptionKeys::MonteCarlo::MonteCarlo, movemap_, in::file::native(), basic::options::OptionKeys::in::file::native, basic::options::OptionKeys::mp::quickrelax::nmoves, basic::options::OptionKeys::rna::denovo::offset, offsets_, option, options, utility::vectorL< SSize, T, A >::pop(), pyrosetta.distributed.io::pose_from_file, poses_, print_score(), register_options(), basic::options::OptionKeys::casp::repack, basic::options::OptionKeys::AnchoredDesign::rmsd, test.T200_Scoring::rsd1, basic::options::OptionKeys::frags::scoring::scoring, local::secstruct, basic::options::OptionKeys::relax::sequence, sequences_, set_random_torsion(), sfxn_, amino_acids::size, basic::options::OptionKeys::mp::setup::spanfiles, test.G200_Module_Region::task, basic::options::OptionKeys::membrane::thickness, tmpdb_, TR, basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

Referenced by pyrosetta.distributed.tasks.rosetta_scripts.BaseRosettaScriptsTask::execute().

ResidueOP MPDomainAssembly::create_residue_from_olc ( char  olc)
private
Residue MPDomainAssembly::create_residue_from_resn ( Pose pose,
core::Size  resnumber 
)
private
std::string MPDomainAssembly::get_name ( ) const
override

Mover Methods ///.

Get the name of this mover

void MPDomainAssembly::init_from_cmd ( )
private
MPDomainAssembly & MPDomainAssembly::operator= ( MPDomainAssembly const &  src)

Assignment Operator.

Make a deep copy of this mover object, overriding the assignment operator

References MPDomainAssembly().

void MPDomainAssembly::print_score ( Pose pose,
core::scoring::ScoreFunctionOP  sfxn 
)
private

Print score to cout.

References demo.D010_Pose_structure::pose, and TR.

Referenced by apply().

void MPDomainAssembly::register_options ( )
private
void MPDomainAssembly::set_random_torsion ( Pose pose,
Size  resn 
)
private

References numeric::random::uniform().

Referenced by apply().

Member Data Documentation

std::string MPDomainAssembly::frag3_fn_
private

Fragment filename.

Referenced by apply(), and init_from_cmd().

std::string MPDomainAssembly::frag9_fn_
private

Fragment filename.

Referenced by apply(), and init_from_cmd().

std::string MPDomainAssembly::full_seq_
private

Sequence of the full-length protein: given as fasta.

Referenced by apply(), and init_from_cmd().

utility::vector1< core::Size > MPDomainAssembly::in_pdb_
private

Vector of length (nres of full-length pose), describing whether the residue exists in a pose (0 = no, 1 = yes, >1 = overlap)

Referenced by apply().

utility::vector1< std::string > MPDomainAssembly::infiles_
private

Vector of pose input files.

Referenced by apply(), and init_from_cmd().

utility::vector1< std::string > MPDomainAssembly::linkers_
private

Vectors of linker sequences_ to model.

Referenced by apply().

core::kinematics::MoveMap MPDomainAssembly::movemap_
private

Movemap of which residues can move (i.e. are in linkers_ +/-1 residue)

Referenced by apply().

utility::vector1< core::Size > MPDomainAssembly::offsets_
private

Vector of offsets_, i.e. residue numbers along the full-length sequence for which the PDB poses_ start.

Referenced by apply().

utility::vector1< core::pose::Pose > MPDomainAssembly::poses_
private

Vector of poses_ that are read in from PDB files.

Referenced by apply().

utility::vector1< std::string > MPDomainAssembly::sequences_
private

Vector of sequences_ in poses_.

Referenced by apply().

core::scoring::ScoreFunctionOP MPDomainAssembly::sfxn_
private

scorefunction (i.e. membrane sfxn_)

Referenced by apply().

core::Size MPDomainAssembly::tmpdb_ {}
private

Number of the pose in the -in:file:l list that is the TM domain.

Referenced by apply(), and init_from_cmd().


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