mp_parameters.cc File Reference

Checking options for MPframework. More...

#include <devel/init.hh>
#include <protocols/moves/Mover.hh>
#include <protocols/membrane/MembraneUnitTestMover.hh>
#include <core/types.hh>
#include <protocols/jd2/JobDistributor.hh>
#include <protocols/jd2/Job.hh>
#include <basic/Tracer.hh>
#include <protocols/viewer/viewers.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/mp.OptionKeys.gen.hh>
#include <numeric/xyzVector.hh>
#include <utility/file/file_sys_util.hh>
#include <utility/string_util.hh>
#include <utility/io/izstream.hh>
#include <cstdlib>
#include <string>

Functions
bool	no_interpolate_Mpair (false)
bool	Hbond_depth_correction (false)
bool	TMprojection (false)
bool	non_helix (false)
bool	termini (false)
bool	secstruct (false)
bool	spanning (false)
void	read_membrane ()
void	read_embeddings ()
void	read_parameters ()
void	read_penalties ()
void	read_options ()
void	user_overwrites_options ()
void	check_options ()
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("apps.pilot.jkleman.mp_parameters")
Vector	normal
Vector	center
Real	thickness
Vector	center_start
Real	center_delta
Real	center_search_cycles
Vector	normal_start
Real	normal_angle_start
Real	normal_angle_delta
Real	normal_search_cycles
Real	chain_normal_angle_max
Real	pose_normal_angle_max
Real	wt_TMprojection
Real	wt_non_helix
Real	wt_termini
Real	wt_secstruct
Real	wt_spanning

Detailed Description

Checking options for MPframework.

Checking options from database and user input for MPframework Last Modified: 3/24/14

Author

JKLeman (julia.nosp@m..koe.nosp@m.hler1.nosp@m.982@.nosp@m.gmail.nosp@m..com)

Function Documentation

check_options()

void check_options

(

)

References center, center_delta, center_search_cycles, center_start, chain_normal_angle_max, Hbond_depth_correction(), no_interpolate_Mpair(), non_helix(), normal, normal_angle_delta, normal_angle_start, normal_search_cycles, normal_start, pose_normal_angle_max, secstruct(), spanning(), termini(), TMprojection(), numeric::xyzVector< T >::to_string(), numeric::interpolation::to_string(), utility_exit_with_message, wt_non_helix, wt_secstruct, wt_spanning, wt_termini, and wt_TMprojection.

Referenced by main().

Hbond_depth_correction()

bool Hbond_depth_correction

(

false

)

Referenced by check_options(), read_parameters(), and user_overwrites_options().

main()

int main	(	int	argc,
		char *	argv[]
	)

References argv, check_options(), test.T009_Exceptions::e, basic::init(), read_options(), and user_overwrites_options().

no_interpolate_Mpair()

bool no_interpolate_Mpair

(

false

)

Referenced by check_options(), read_parameters(), and user_overwrites_options().

non_helix()

bool non_helix

(

false

)

Referenced by check_options(), read_penalties(), and user_overwrites_options().

read_embeddings()

void read_embeddings

(

)

References numeric::xyzVector< T >::assign(), center_delta, center_search_cycles, center_start, chain_normal_angle_max, utility::io::izstream::fail(), utility::file::file_exists(), getline(), line, normal_angle_delta, normal_angle_start, normal_search_cycles, normal_start, pose_normal_angle_max, tag, TR, utility_exit_with_message, x, numeric::xyzVector< T >::x(), predPRE::y, numeric::xyzVector< T >::y(), predPRE::z, and numeric::xyzVector< T >::z().

Referenced by read_options().

read_membrane()

void read_membrane

(

)

References numeric::xyzVector< T >::assign(), center, utility::io::izstream::fail(), utility::file::file_exists(), getline(), line, normal, tag, thickness, TR, utility_exit_with_message, x, numeric::xyzVector< T >::x(), predPRE::y, numeric::xyzVector< T >::y(), predPRE::z, and numeric::xyzVector< T >::z().

Referenced by read_options().

read_options()

void read_options

(

)

References read_embeddings(), read_membrane(), read_parameters(), and read_penalties().

Referenced by main().

read_parameters()

void read_parameters

(

)

References utility::io::izstream::fail(), utility::file::file_exists(), getline(), Hbond_depth_correction(), line, no_interpolate_Mpair(), tag, TR, utility_exit_with_message, x, predPRE::y, and predPRE::z.

Referenced by read_options().

read_penalties()

void read_penalties

(

)

References utility::io::izstream::fail(), utility::file::file_exists(), getline(), line, non_helix(), secstruct(), spanning(), tag, termini(), TMprojection(), TR, utility_exit_with_message, wt_non_helix, wt_secstruct, wt_spanning, wt_termini, wt_TMprojection, x, predPRE::y, and predPRE::z.

Referenced by read_options().

secstruct()

bool secstruct

(

false

)

Referenced by FoldTreeOutputter::apply(), MetalSiteFinderMover::apply(), MPDomainAssembly::apply(), check_options(), figure_out_secstruct(), get_fragment_sets(), zinc_stats::ZincStatisticGenerator::get_local_zn_positions_for_residue(), get_min_frag_rmsd(), get_sequence_and_secstruct_from_dssp(), homolog_finder(), zinc_stats::ZincStatisticGenerator::iterate_over_residues(), main(), obtain_secstruct_segments(), output_minipose_coords_test(), read_penalties(), rebuild_test(), rna_fullatom_minimize_test(), rna_stack_pdbstats_from_pose(), setup_fragment_mover(), setup_loops_fragment_libraries_with_ss(), spanfile_from_pdb(), split_pdb_into_ss_chunks(), DomainDescription::ss_match(), and user_overwrites_options().

spanning()

bool spanning

(

false

)

Referenced by check_options(), read_penalties(), and user_overwrites_options().

termini()

bool termini

(

false

)

Referenced by check_options(), TCDock::dump_pdb(), read_penalties(), and user_overwrites_options().

TMprojection()

bool TMprojection

(

false

)

Referenced by check_options(), read_penalties(), and user_overwrites_options().

user_overwrites_options()

void user_overwrites_options

(

)

References center_delta, mp::center_delta(), center_search_cycles, mp::center_search_cycles(), center_start, mp::center_start(), chain_normal_angle_max, mp::chain_normal_angle_max(), mp::Hbond_depth_correction(), Hbond_depth_correction(), mp::no_interpolate_Mpair(), no_interpolate_Mpair(), mp::non_helix(), non_helix(), normal_angle_delta, mp::normal_angle_delta(), normal_angle_start, mp::normal_angle_start(), normal_search_cycles, mp::normal_search_cycles(), normal_start, mp::normal_start(), option, pose_normal_angle_max, mp::pose_normal_angle_max(), mp::secstruct(), secstruct(), mp::spanning(), spanning(), mp::termini(), termini(), thickness, mp::thickness(), mp::TMprojection(), TMprojection(), basic::options::OptionKeys::inout::dbms::user, wt_non_helix, mp::wt_non_helix(), wt_secstruct, mp::wt_secstruct(), wt_spanning, mp::wt_spanning(), wt_termini, mp::wt_termini(), wt_TMprojection, mp::wt_TMprojection(), numeric::xyzVector< T >::x(), numeric::xyzVector< T >::y(), and numeric::xyzVector< T >::z().

Referenced by main().

Variable Documentation

center

Vector center

Referenced by add_vrts(), SampleTiltProtocol::apply(), MembraneViewMover::apply(), MPFoldingMover::apply(), LoadMembraneMover::apply(), bk_test(), calc_scores(), check_options(), compute_windowed_rama(), copy_rotamerized_torsions(), main(), make_fragments(), mutate_to_ala(), read_membrane(), setup_symmetric_dimer(), MembraneRelaxMover::show_membrane_position(), and PBPotentialMover::write_APBS_config().

center_delta

Real center_delta

Referenced by check_options(), read_embeddings(), and user_overwrites_options().

center_search_cycles

Real center_search_cycles

Referenced by check_options(), read_embeddings(), and user_overwrites_options().

center_start

Vector center_start

Referenced by check_options(), read_embeddings(), and user_overwrites_options().

chain_normal_angle_max

Real chain_normal_angle_max

Referenced by check_options(), read_embeddings(), and user_overwrites_options().

normal

Vector normal

Referenced by add_vrts(), MembraneViewMover::apply(), MPFoldingMover::apply(), LoadMembraneMover::apply(), check_options(), main(), gaussian-sampling::propose_move(), read_membrane(), and MembraneRelaxMover::show_membrane_position().

normal_angle_delta

Real normal_angle_delta

Referenced by check_options(), read_embeddings(), and user_overwrites_options().

normal_angle_start

Real normal_angle_start

Referenced by check_options(), read_embeddings(), and user_overwrites_options().

normal_search_cycles

Real normal_search_cycles

Referenced by check_options(), read_embeddings(), and user_overwrites_options().

normal_start

Vector normal_start

Referenced by check_options(), read_embeddings(), and user_overwrites_options().

pose_normal_angle_max

Real pose_normal_angle_max

Referenced by check_options(), read_embeddings(), and user_overwrites_options().

thickness

Real thickness

Referenced by MPDomainAssembly::apply(), read_membrane(), read_thickness(), spanfile_for_each_chain(), spanfile_from_pdb(), and user_overwrites_options().

TR

basic::Tracer TR("apps.pilot.jkleman.mp_parameters") ( "apps.pilot.jkleman.mp_parameters"  )

static

Referenced by read_embeddings(), read_membrane(), read_parameters(), and read_penalties().

wt_non_helix

Real wt_non_helix

Referenced by check_options(), read_penalties(), and user_overwrites_options().

wt_secstruct

Real wt_secstruct

Referenced by check_options(), read_penalties(), and user_overwrites_options().

wt_spanning

Real wt_spanning

Referenced by check_options(), read_penalties(), and user_overwrites_options().

wt_termini

Real wt_termini

Referenced by check_options(), read_penalties(), and user_overwrites_options().

wt_TMprojection

Real wt_TMprojection

Referenced by check_options(), read_penalties(), and user_overwrites_options().