phil.hh File Reference

#include <core/types.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/ResidueSelector.hh>
#include <basic/options/util.hh>
#include <basic/basic.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/conformation/Conformation.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/import_pose/import_pose.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/dna/setup.hh>
#include <core/scoring/dna/BasePartner.hh>
#include <numeric/xyzVector.hh>
#include <numeric/xyzMatrix.hh>
#include <numeric/xyz.functions.hh>
#include <numeric/conversions.hh>
#include <utility/vector1.functions.hh>
#include <utility/tools/make_vector1.hh>
#include <utility/tools/make_map.hh>
#include <ObjexxFCL/string.functions.hh>
#include <ObjexxFCL/format.hh>
#include <numeric/random/random.hh>

Typedefs
typedef utility::vector1< std::string >	strings
	from devel/blab/tools.hh: More...
typedef utility::vector1< core::Size >	Sizes
typedef utility::vector1< core::Real >	Reals
typedef utility::vector1< bool >	bools
typedef numeric::xyzMatrix< Real >	Matrix
typedef utility::vector1< Vector >	Vectors

Functions
template<class T >
T const &	random_element (utility::vector1< T > const &v)
std::string	filebase (std::string const &file)
std::string const	CENTROID_DNA ("centroid_dna")
Size	pose_resid_from_PDB (Pose const &pose, int const pdbpos, char const pdbchain)
	put this here since it's going to change w/trunk, update code in one place More...
void	set_chain_end_fold_tree (Pose &pose)
bool	is_small (Real const x)
void	get_mean_sdev (Reals const &vals, Real &mean, Real &sdev)
	helper More...
template<typename T1 , typename T2 >
utility::vector1< T1 >	get_keys (std::map< T1, T2 > const &m)
bool	has_substring (std::string const &full, std::string const &sub)
bool	has_substring (std::string const &full, const char *sub)
char	torsion2big_bin (Real const phi, Real const psi, Real const omega)
std::string	torsion2big_bin_string (Size const pos1, Size const pos2, Pose const &pose, bool const allow_nonprotein=false)
Size	get_jump_to_position (Size const seqpos, Pose const &pose)
Size	chain_begin (Size const ch, Pose const &pose)
Size	chain_end (Size const ch, Pose const &pose)
Size	chain_begin (Pose const &pose, Size const ch)
Size	chain_end (Pose const &pose, Size const ch)
Size	num_chains (Pose const &pose)
void	make_sequence_change (Size const seqpos, AA const &new_aa, pose::Pose &pose, Size const which_his_variant=1)
conformation::ResidueOP	get_vanilla_protein_residue (char const name1)
conformation::ResidueOP	get_vanilla_dna_residue (char const name1)
static Real const	init_phi (-150.0)
static Real const	init_psi (150.0)
static Real const	init_omega (180.0)
bool	init_torsions_still_present (bools const &is_flexible, Pose const &pose)
void	cenpose_from_file (Pose &pose, string const filename)
	read a centroid pose More...
void	cendnapose_from_file (Pose &pose, string const filename)
	read a centroid pose More...
template<class T >
bool	has_element (vector1< T > const &v, T const &t)
template<class T >
bool	has_element (T const &t, vector1< T > const &v)
	never can remember the order... More...
core::chemical::AA	dna_aa_from_oneletter_code (char const c)

Typedef Documentation

bools

typedef utility::vector1< bool > bools

Matrix

typedef numeric::xyzMatrix< Real > Matrix

Reals

typedef utility::vector1< core::Real > Reals

Sizes

typedef utility::vector1< core::Size > Sizes

strings

typedef utility::vector1< std::string > strings

from devel/blab/tools.hh:

Vectors

typedef utility::vector1< Vector > Vectors

Function Documentation

cendnapose_from_file()

void cendnapose_from_file	(	Pose &	pose,
		string const	filename
	)

read a centroid pose

References CENTROID_DNA(), lactamize::filename, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, and basic::options::OptionKeys::in::file::residue_type_set.

cenpose_from_file()

void cenpose_from_file	(	Pose &	pose,
		string const	filename
	)

read a centroid pose

References lactamize::filename, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, and basic::options::OptionKeys::in::file::residue_type_set.

CENTROID_DNA()

std::string const CENTROID_DNA

(

"centroid_dna"

)

Referenced by cendnapose_from_file().

chain_begin() [1/2]

Size chain_begin	(	Pose const &	pose,
		Size const	ch
	)

References beta_nonlocal::pose.

chain_begin() [2/2]

Size chain_begin	(	Size const	ch,
		Pose const &	pose
	)

References beta_nonlocal::pose.

Referenced by zinc1_homodimer_setup::apply(), get_movable_jumps(), abbinding::setup_foldtree(), PhDocking::setup_foldtree(), hbs_creator::setup_pert_foldtree(), zinc1_homodimer_design::setup_rollmoving(), tf_specificity_test(), and transform_pose().

chain_end() [1/2]

Size chain_end	(	Pose const &	pose,
		Size const	ch
	)

References beta_nonlocal::pose.

chain_end() [2/2]

Size chain_end	(	Size const	ch,
		Pose const &	pose
	)

References beta_nonlocal::pose.

Referenced by zinc1_homodimer_setup::apply(), LDConverterMover::apply(), derive(), get_movable_jumps(), abbinding::setup_foldtree(), PhDocking::setup_foldtree(), hbs_creator::setup_pert_foldtree(), zinc1_homodimer_design::setup_rollmoving(), and transform_pose().

dna_aa_from_oneletter_code()

core::chemical::AA dna_aa_from_oneletter_code

(

char const

c

)

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, and utility_exit_with_message.

filebase()

std::string filebase

(

std::string const &

file

)

References evaluate_beta_mutants::file.

get_jump_to_position()

Size get_jump_to_position	(	Size const	seqpos,
		Pose const &	pose
	)

References create_a3b_hbs::f, create_a3b_hbs::j, beta_nonlocal::pose, ObjexxFCL::string_of(), and utility_exit_with_message.

get_keys()

template<typename T1 , typename T2 >

utility::vector1< T1 > get_keys

(

std::map< T1, T2 > const &

m

)

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::m.

get_mean_sdev()

void get_mean_sdev	(	Reals const &	vals,
		Real &	mean,
		Real &	sdev
	)

helper

Split a string to a vector1

References basic::options::OptionKeys::ddg::mean.

get_vanilla_dna_residue()

conformation::ResidueOP get_vanilla_dna_residue

(

char const

name1

)

References basic::options::OptionKeys::in::file::residue_type_set, and runtime_assert.

get_vanilla_protein_residue()

conformation::ResidueOP get_vanilla_protein_residue

(

char const

name1

)

References basic::options::OptionKeys::in::file::residue_type_set, and runtime_assert.

has_element() [1/2]

template<class T >

bool has_element	(	T const &	t,
		vector1< T > const &	v
	)

never can remember the order...

References detail::find(), predPRE::t, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

has_element() [2/2]

template<class T >

bool has_element	(	vector1< T > const &	v,
		T const &	t
	)

useful vector1 function

References detail::find(), predPRE::t, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

has_substring() [1/2]

bool has_substring	(	std::string const &	full,
		const char *	sub
	)

has_substring() [2/2]

bool has_substring	(	std::string const &	full,
		std::string const &	sub
	)

init_omega()

static Real const init_omega

(

180.

0

)

Referenced by init_torsions_still_present(), and simple_loop_modeling_test().

init_phi()

static Real const init_phi ( -150.  0 )

static

Referenced by init_torsions_still_present(), and simple_loop_modeling_test().

init_psi()

static Real const init_psi

(

150.

0

)

Referenced by init_torsions_still_present(), and simple_loop_modeling_test().

init_torsions_still_present()

bool init_torsions_still_present	(	bools const &	is_flexible,
		Pose const &	pose
	)

References ObjexxFCL::abs(), gpu_set_args::done, test.T009_Exceptions::e, create_a3b_hbs::i, init_omega(), init_phi(), init_psi(), beta_nonlocal::pose, and basic::subtract_degree_angles().

is_small()

bool is_small

(

Real const

x

)

References ObjexxFCL::abs(), test.T009_Exceptions::e, and x.

make_sequence_change()

void make_sequence_change	(	Size const	seqpos,
		AA const &	new_aa,
		pose::Pose &	pose,
		Size const	which_his_variant = 1
	)

This function will make a sequence mutation while trying to preserve the variants

References errmsg(), beta_nonlocal::pose, basic::options::OptionKeys::in::file::residue_type_set, ObjexxFCL::string_of(), and utility_exit_with_message.

num_chains()

Size num_chains

(

Pose const &

pose

)

References beta_nonlocal::pose.

Referenced by xtal_water_bunsat::apply(), AnchorFinderMover::apply(), IAMover::assign_IA_mover(), calc_RF(), check_single_chain(), dna_chain_check(), dna_io_test(), main(), pep_phipsi_analysis(), pep_rmsd_analysis(), read_in_pdbs(), run_pep_prep(), RunPepSpec(), and test_membrane_fold_tree().

pose_resid_from_PDB()

Size pose_resid_from_PDB ( Pose const &  pose, int const  pdbpos, char const  pdbchain  )

inline

put this here since it's going to change w/trunk, update code in one place

Helper function to remove the leading directory stuff

References beta_nonlocal::pose.

random_element()

template<class T >

T const& random_element

(

utility::vector1< T > const &

v

)

References numeric::random::RandomGenerator::random_element(), numeric::random::rg(), and kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

Referenced by Bola::random_move().

set_chain_end_fold_tree()

void set_chain_end_fold_tree

(

Pose &

pose

)

Useful helper for setting a standard foldtree

References basic::options::OptionKeys::AnchoredDesign::anchor, loops::cutpoint, create_a3b_hbs::f, create_a3b_hbs::i, and beta_nonlocal::pose.

torsion2big_bin()

char torsion2big_bin	(	Real const	phi,
		Real const	psi,
		Real const	omega
	)

References ObjexxFCL::abs(), basic::options::OptionKeys::AnchoredDesign::filters::omega, oop_conformations::phi, and oop_conformations::psi.

Referenced by torsion2big_bin_string().

torsion2big_bin_string()

std::string torsion2big_bin_string	(	Size const	pos1,
		Size const	pos2,
		Pose const &	pose,
		bool const	allow_nonprotein = false
	)

References create_a3b_hbs::i, beta_nonlocal::pose, runtime_assert, torsion2big_bin(), and utility_exit_with_message.