MPDomainAssembly Class Reference

Inheritance diagram for MPDomainAssembly:

Public Member Functions
	MPDomainAssembly ()
	Constructors ///. More...
	MPDomainAssembly (MPDomainAssembly const &src)
	Copy Constructor. More...
MPDomainAssembly &	operator= (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() [1/2]

MPDomainAssembly::MPDomainAssembly

(

)

Constructors ///.

Construct a Default Mover

Construct a Default Membrane Position Mover

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

MPDomainAssembly() [2/2]

MPDomainAssembly::MPDomainAssembly

(

MPDomainAssembly const &

src

)

Copy Constructor.

Make a deep copy of this mover object

~MPDomainAssembly()

MPDomainAssembly::~MPDomainAssembly ( )

overridedefault

Destructor.

Member Function Documentation

apply()

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_, create_a3b_hbs::i, in_pdb_, infiles_, init_from_cmd(), autocorrelation::iterations, create_a3b_hbs::j, create_a3b_hbs::k, basic::options::OptionKeys::relax::range::kT, linkers_, kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, DRRAFTER_util::matches(), mc, basic::options::OptionKeys::abinitio::membrane, basic::options::OptionKeys::MonteCarlo::MonteCarlo, movemap_, in::file::native(), surface_app::native, basic::options::OptionKeys::mp::quickrelax::nmoves, offset, offsets_, option, utility::vectorL< L, T, A >::pop(), beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, poses_, pyrosetta.io::poses_from_files(), print_score(), register_options(), basic::options::OptionKeys::casp::repack, average_rmsds::rmsd, test.T200_Scoring::rsd1, basic::options::OptionKeys::frags::scoring::scoring, secstruct(), basic::options::OptionKeys::relax::sequence, sequences_, set_random_torsion(), sfxn_, subloop_histogram::size, basic::options::OptionKeys::mp::setup::spanfiles, vancomycin::task, thickness, tmpdb_, TR, basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

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

create_residue_from_olc()

ResidueOP MPDomainAssembly::create_residue_from_olc ( char  olc )

private

References basic::options::OptionKeys::chemical::chemical, res, and basic::options::OptionKeys::in::file::residue_type_set.

Referenced by apply().

create_residue_from_resn()

Residue MPDomainAssembly::create_residue_from_resn ( Pose &  pose, core::Size  resnumber  )

private

References beta_sc_scan::name3, beta_nonlocal::pose, basic::options::OptionKeys::in::file::residue_type_set, and test.T200_Scoring::rsd1.

Referenced by apply().

get_name()

std::string MPDomainAssembly::get_name ( ) const

override

Mover Methods ///.

Get the name of this mover

init_from_cmd()

void MPDomainAssembly::init_from_cmd ( )

private

Initialize Mover options from the comandline.

References CREATE_EXCEPTION, basic::options::OptionKeys::in::file::fasta, basic::options::OptionKeys::in::file::frag3, frag3_fn_, basic::options::OptionKeys::in::file::frag9, frag9_fn_, full_seq_, infiles_, surface_app::native, basic::options::option, option, mp::assembly::poses(), basic::options::OptionKeys::mp::setup::spanfiles, basic::options::OptionKeys::mp::assembly::TM_pose_number, tmpdb_, TR, and basic::options::OptionKeys::inout::dbms::user.

Referenced by apply().

operator=()

MPDomainAssembly & MPDomainAssembly::operator=

(

MPDomainAssembly const &

src

)

Assignment Operator.

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

References MPDomainAssembly().

print_score()

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

private

Print score to cout.

References beta_nonlocal::pose, and TR.

Referenced by apply().

register_options()

void MPDomainAssembly::register_options ( )

private

Rosetta Scripts Methods ///.

Register Options with JD2.

Register Options with JD2

References basic::options::OptionKeys::mp::quickrelax::angle_max, basic::options::OptionKeys::in::file::fasta, basic::options::OptionKeys::in::file::frag3, basic::options::OptionKeys::in::file::frag9, surface_app::native, option, basic::options::OptionKeys::mp::assembly::poses, basic::options::OptionKeys::mp::setup::spanfiles, and basic::options::OptionKeys::mp::assembly::TM_pose_number.

Referenced by apply().

set_random_torsion()

void MPDomainAssembly::set_random_torsion ( Pose &  pose, Size  resn  )

private

References beta_nonlocal::pose, and numeric::random::uniform().

Referenced by apply().

Member Data Documentation

frag3_fn_

std::string MPDomainAssembly::frag3_fn_

private

Fragment filename.

Referenced by apply(), and init_from_cmd().

frag9_fn_

std::string MPDomainAssembly::frag9_fn_

private

Fragment filename.

Referenced by apply(), and init_from_cmd().

full_seq_

std::string MPDomainAssembly::full_seq_

private

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

Referenced by apply(), and init_from_cmd().

in_pdb_

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().

infiles_

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

private

Vector of pose input files.

Referenced by apply(), and init_from_cmd().

linkers_

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

private

Vectors of linker sequences_ to model.

Referenced by apply().

movemap_

core::kinematics::MoveMap MPDomainAssembly::movemap_

private

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

Referenced by apply().

offsets_

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().

poses_

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

private

Vector of poses_ that are read in from PDB files.

Referenced by apply().

sequences_

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

private

Vector of sequences_ in poses_.

Referenced by apply().

sfxn_

core::scoring::ScoreFunctionOP MPDomainAssembly::sfxn_

private

scorefunction (i.e. membrane sfxn_)

Referenced by apply().

tmpdb_

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:

• src/apps/public/membrane/mp_domain_assembly.cc