protocols::hydrate Namespace Reference

Classes
class	Hydrate

Typedefs
typedef utility::pointer::shared_ptr< Hydrate >	HydrateOP
typedef utility::pointer::shared_ptr< Hydrate const >	HydrateCOP

Functions
void	read_hyfile (std::string const &hyfile_name, utility::vector1< bool > &enforced_V, utility::vector1< bool > &hydrate_V)
bool	is_inside (pose::Pose const &pose, Vector const &xyz)
bool	atom_is_hydratable (pose::Pose const &pose, core::Size const residue, std::string const &atom)
bool	atom_is_hydratable (pose::Pose const &pose, core::Size const residue, core::Size const atom)
void	hydrate_hyfile (pose::Pose &pose, utility::vector1< bool > const &hydrate_V, std::string const &resfile="default")
void	place_de_novo_wat_at_anchor (pose::Pose &pose)
void	set_water_info_and_add_de_novo_water (pose::Pose &pose, core::scoring::ScoreFunction const &scorefxn)
void	hydrate_cavities (pose::Pose &pose)
void	set_dew_waters_not_to_be_included (pose::Pose &pose, Real const partial_hydrate_dew)
bool	residue_near_water (pose::Pose const &pose, core::Size const ii)
void	set_task_and_movemap (pose::Pose const &pose, std::string const &protein_flexibility, pack::task::PackerTaskOP &task, kinematics::MoveMap &mm, bool const minimize_bb_where_packing)
void	calculate_water_overcoordinated_hb_correction (pose::Pose const &pose, utility::vector1< Real > &hb_correction)
void	remove_high_energy_water_molecules (pose::Pose &pose, core::scoring::ScoreFunction const &scorefxn)
void	enforce_all_waters (pose::Pose &pose)
void	get_ready_for_sew_packing (pose::Pose &pose, pack::task::PackerTaskOP &task)
void	remove_all_anchors_and_ENF (pose::Pose &pose)
void	read_header (core::Size const total_res, std::string const &line, kinematics::MoveMap &mm)
void	read_body (core::Size const total_res, std::string const &line, kinematics::MoveMap &mm)
void	set_bb_movemap (pose::Pose const &pose, std::string const &mini_backbone_file_name, kinematics::MoveMap &mm)
void	remove_non_buried_wat (pose::Pose &pose)
void	add_water_overcoordinated_hb_score (pose::Pose &pose, core::scoring::ScoreFunction &scorefxn)
void	show_water_hb_network (pose::Pose const &pose)
void	water_specific_hbond_energy (pose::Pose &pose, core::scoring::ScoreFunction &scorefxn)
void	set_task_with_de_novo_water_using_resfile (pose::Pose &pose, std::string resfile, pack::task::PackerTaskOP &task)
void	print_residues_near_water (pose::Pose const &pose)
void	append_single_far_away_water (pose::Pose &pose)
void	calculate_water_overcoordinated_hb_correction (core::pose::Pose const &pose, utility::vector1< core::Real > &water_hb_correction)

Typedef Documentation

HydrateCOP

typedef utility::pointer::shared_ptr< Hydrate const > protocols::hydrate::HydrateCOP

HydrateOP

typedef utility::pointer::shared_ptr< Hydrate > protocols::hydrate::HydrateOP

Function Documentation

add_water_overcoordinated_hb_score()

void protocols::hydrate::add_water_overcoordinated_hb_score	(	pose::Pose &	pose,
		core::scoring::ScoreFunction &	scorefxn
	)

References calculate_water_overcoordinated_hb_correction(), core::sequence::end, core::scoring::ScoreFunction::energy_method_options(), protocols::jd2::JobDistributor::get_instance(), core::import_pose::atom_tree_diffs::map_of_weighted_scores(), core::scoring::ScoreFunction::set_energy_method_options(), core::pose::Pose::total_residue(), and protocols::TR().

Referenced by protocols::hydrate::Hydrate::apply().

append_single_far_away_water()

void protocols::hydrate::append_single_far_away_water

(

pose::Pose &

pose

)

References core::pose::Pose::append_residue_by_jump(), core::conformation::ResidueFactory::create_residue(), core::pose::Pose::data(), core::chemical::FA_STANDARD, and core::pose::datacache::CacheableDataType::WATER_PACKING_INFO.

atom_is_hydratable() [1/2]

bool protocols::hydrate::atom_is_hydratable	(	pose::Pose const &	pose,
		core::Size const	residue,
		core::Size const	atom
	)

References atom_is_hydratable(), core::conformation::Residue::atom_name(), and core::pose::Pose::residue().

atom_is_hydratable() [2/2]

bool protocols::hydrate::atom_is_hydratable	(	pose::Pose const &	pose,
		core::Size const	residue,
		std::string const &	atom
	)

References core::conformation::Residue::atom_index(), core::conformation::Residue::atom_name(), is_inside(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().

Referenced by atom_is_hydratable(), hydrate_cavities(), and hydrate_hyfile().

calculate_water_overcoordinated_hb_correction() [1/2]

void protocols::hydrate::calculate_water_overcoordinated_hb_correction	(	core::pose::Pose const &	pose,
		utility::vector1< core::Real > &	water_hb_correction
	)

References core::scoring::hbonds::HBond::acc_atm(), core::scoring::hbonds::HBond::acc_atm_is_protein_backbone(), core::scoring::hbonds::HBond::acc_res(), core::conformation::Residue::atom_name(), core::conformation::Residue::atom_type(), core::scoring::hbonds::HBondSet::clear(), core::scoring::hbonds::HBond::don_hatm_is_protein_backbone(), core::scoring::hbonds::HBond::don_res(), core::pose::Pose::energies(), core::scoring::hbonds::HBond::energy(), core::scoring::hbonds::fill_hbond_set(), core::scoring::hbonds::hb_energy(), core::scoring::hbonds::HBondSet::hbond(), core::scoring::hbond_bb_sc, core::scoring::hbond_sc, core::scoring::hbond_wat, core::chemical::AtomType::is_acceptor(), core::conformation::Residue::name(), core::scoring::hbonds::HBondSet::nhbonds(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), core::scoring::hbonds::HBond::weight(), and core::scoring::Energies::weights().

Referenced by add_water_overcoordinated_hb_score(), and remove_high_energy_water_molecules().

calculate_water_overcoordinated_hb_correction() [2/2]

void protocols::hydrate::calculate_water_overcoordinated_hb_correction	(	pose::Pose const &	pose,
		utility::vector1< Real > &	hb_correction
	)

References core::scoring::hbonds::HBond::acc_atm(), core::scoring::hbonds::HBond::acc_atm_is_protein_backbone(), core::scoring::hbonds::HBond::acc_res(), core::conformation::Residue::atom_name(), core::conformation::Residue::atom_type(), core::scoring::hbonds::HBondSet::clear(), core::scoring::hbonds::HBond::don_hatm_is_protein_backbone(), core::scoring::hbonds::HBond::don_res(), core::pose::Pose::energies(), core::scoring::hbonds::HBond::energy(), core::scoring::hbonds::fill_hbond_set(), core::scoring::hbonds::hb_energy(), core::scoring::hbonds::HBondSet::hbond(), core::scoring::hbond_bb_sc, core::scoring::hbond_sc, core::scoring::hbond_wat, core::chemical::AtomType::is_acceptor(), core::conformation::Residue::name(), core::scoring::hbonds::HBondSet::nhbonds(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), core::scoring::hbonds::HBond::weight(), and core::scoring::Energies::weights().

Referenced by add_water_overcoordinated_hb_score(), and remove_high_energy_water_molecules().

enforce_all_waters()

void protocols::hydrate::enforce_all_waters

(

pose::Pose &

pose

)

References core::pose::Pose::data(), core::conformation::Residue::name(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::pose::datacache::CacheableDataType::WATER_PACKING_INFO.

Referenced by protocols::hydrate::Hydrate::apply().

get_ready_for_sew_packing()

void protocols::hydrate::get_ready_for_sew_packing	(	pose::Pose &	pose,
		pack::task::PackerTaskOP &	task
	)

References core::conformation::ResidueFactory::create_residue(), core::pose::Pose::data(), core::pose::Pose::energies(), core::chemical::FA_STANDARD, core::conformation::Residue::name(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::scoring::Energies::residue_total_energy(), core::pose::Pose::total_residue(), protocols::TR(), core::pose::datacache::CacheableDataType::WATER_PACKING_INFO, and core::conformation::Residue::xyz().

Referenced by protocols::hydrate::Hydrate::apply().

hydrate_cavities()

void protocols::hydrate::hydrate_cavities

(

pose::Pose &

pose

)

References core::conformation::Residue::aa(), core::chemical::ResidueTypeBase::aa(), core::chemical::aa_his, core::scoring::hbonds::HBond::acc_atm(), core::scoring::hbonds::HBond::acc_res(), core::pose::Pose::append_residue_by_jump(), atom_is_hydratable(), core::conformation::Residue::atom_name(), core::conformation::Residue::atom_type(), core::scoring::hbonds::HBondSet::clear(), core::conformation::ResidueFactory::create_residue(), core::pose::Pose::data(), core::scoring::hbonds::HBond::don_hatm(), core::scoring::hbonds::HBond::don_res(), core::scoring::hbonds::HBond::energy(), core::chemical::FA_STANDARD, core::scoring::hbonds::fill_hbond_set(), core::scoring::hbonds::HBondSet::hbond(), core::chemical::AtomType::is_acceptor(), core::chemical::AtomType::is_polar_hydrogen(), core::conformation::Residue::name(), core::conformation::Residue::natoms(), core::scoring::hbonds::HBondSet::nhbonds(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), protocols::TR(), core::conformation::Residue::type(), core::pose::datacache::CacheableDataType::WATER_PACKING_INFO, and core::conformation::Residue::xyz().

Referenced by protocols::hydrate::Hydrate::apply().

hydrate_hyfile()

void protocols::hydrate::hydrate_hyfile	(	pose::Pose &	pose,
		utility::vector1< bool > const &	hydrate_V,
		std::string const &	resfile = "default"
	)

References core::conformation::Residue::aa(), core::chemical::ResidueTypeBase::aa(), core::chemical::aa_his, core::pose::Pose::append_residue_by_jump(), atom_is_hydratable(), core::conformation::Residue::atom_name(), core::conformation::Residue::atom_type(), core::pack::task::TaskFactory::create_packer_task(), core::conformation::ResidueFactory::create_residue(), core::pose::Pose::data(), core::chemical::FA_STANDARD, core::chemical::AtomType::is_acceptor(), core::chemical::AtomType::is_polar_hydrogen(), core::chemical::AtomType::is_virtual(), core::conformation::Residue::name(), core::conformation::Residue::natoms(), core::pack::task::parse_resfile(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), protocols::TR(), core::conformation::Residue::type(), core::pose::datacache::CacheableDataType::WATER_PACKING_INFO, and core::conformation::Residue::xyz().

Referenced by set_water_info_and_add_de_novo_water().

is_inside()

bool protocols::hydrate::is_inside	(	pose::Pose const &	pose,
		Vector const &	xyz
	)

References core::kinematics::distance(), PI, core::pose::Pose::residue(), protocols::sparta::section(), core::pose::Pose::total_residue(), protocols::kinmatch::xyz(), and core::conformation::Residue::xyz().

Referenced by atom_is_hydratable(), and remove_non_buried_wat().

place_de_novo_wat_at_anchor()

void protocols::hydrate::place_de_novo_wat_at_anchor

(

pose::Pose &

pose

)

References core::conformation::ResidueFactory::create_residue(), core::pose::Pose::data(), core::chemical::FA_STANDARD, core::conformation::Residue::name(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), core::pose::datacache::CacheableDataType::WATER_PACKING_INFO, and core::conformation::Residue::xyz().

Referenced by set_water_info_and_add_de_novo_water().

print_residues_near_water()

void protocols::hydrate::print_residues_near_water

(

pose::Pose const &

pose

)

References core::conformation::Residue::name(), core::pose::Pose::residue(), residue_near_water(), core::pose::Pose::total_residue(), and protocols::TR().

Referenced by protocols::hydrate::Hydrate::apply().

read_body()

void protocols::hydrate::read_body	(	core::Size const	total_res,
		std::string const &	line,
		kinematics::MoveMap &	mm
	)

References core::kinematics::MoveMap::set_bb(), and protocols::TR().

Referenced by set_bb_movemap().

read_header()

void protocols::hydrate::read_header	(	core::Size const	total_res,
		std::string const &	line,
		kinematics::MoveMap &	mm
	)

References core::kinematics::MoveMap::set_bb(), and protocols::TR().

Referenced by set_bb_movemap().

read_hyfile()

void protocols::hydrate::read_hyfile	(	std::string const &	hyfile_name,
		utility::vector1< bool > &	enforced_V,
		utility::vector1< bool > &	hydrate_V
	)

References core::sequence::end, and protocols::TR().

Referenced by set_water_info_and_add_de_novo_water().

remove_all_anchors_and_ENF()

void protocols::hydrate::remove_all_anchors_and_ENF

(

pose::Pose &

pose

)

References core::pose::Pose::data(), core::conformation::Residue::name(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::pose::datacache::CacheableDataType::WATER_PACKING_INFO.

Referenced by protocols::hydrate::Hydrate::apply().

remove_high_energy_water_molecules()

void protocols::hydrate::remove_high_energy_water_molecules	(	pose::Pose &	pose,
		core::scoring::ScoreFunction const &	scorefxn
	)

References calculate_water_overcoordinated_hb_correction(), core::conformation::Residue::clone(), core::pose::Pose::data(), core::pose::Pose::energies(), core::conformation::Residue::name(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::scoring::Energies::residue_total_energy(), core::pose::Pose::total_residue(), protocols::TR(), and core::pose::datacache::CacheableDataType::WATER_PACKING_INFO.

Referenced by protocols::hydrate::Hydrate::apply().

remove_non_buried_wat()

void protocols::hydrate::remove_non_buried_wat

(

pose::Pose &

pose

)

References core::conformation::Residue::clone(), is_inside(), core::conformation::Residue::name(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), protocols::TR(), and core::conformation::Residue::xyz().

Referenced by protocols::hydrate::Hydrate::apply().

residue_near_water()

bool protocols::hydrate::residue_near_water	(	pose::Pose const &	pose,
		core::Size const	ii
	)

References core::conformation::Residue::name(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().

Referenced by print_residues_near_water(), and set_task_and_movemap().

set_bb_movemap()

void protocols::hydrate::set_bb_movemap	(	pose::Pose const &	pose,
		std::string const &	mini_backbone_file_name,
		kinematics::MoveMap &	mm
	)

References read_body(), read_header(), core::pose::Pose::total_residue(), and protocols::TR().

Referenced by protocols::hydrate::Hydrate::apply().

set_dew_waters_not_to_be_included()

void protocols::hydrate::set_dew_waters_not_to_be_included	(	pose::Pose &	pose,
		Real const	partial_hydrate_dew
	)

References core::conformation::ResidueFactory::create_residue(), core::pose::Pose::data(), core::chemical::FA_STANDARD, core::conformation::Residue::name(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::scoring::rg, core::pose::Pose::total_residue(), protocols::TR(), and core::pose::datacache::CacheableDataType::WATER_PACKING_INFO.

Referenced by protocols::hydrate::Hydrate::apply().

set_task_and_movemap()

void protocols::hydrate::set_task_and_movemap	(	pose::Pose const &	pose,
		std::string const &	protein_flexibility,
		pack::task::PackerTaskOP &	task,
		kinematics::MoveMap &	mm,
		bool const	minimize_bb_where_packing
	)

References core::chemical::aa_from_oneletter_code(), core::pack::task::TaskFactory::create_packer_task(), core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), core::conformation::Residue::name(), core::chemical::num_canonical_aas, core::kinematics::FoldTree::num_jump(), core::pack::task::parse_resfile(), core::pose::Pose::residue(), residue_near_water(), core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), core::kinematics::MoveMap::set_jump(), core::pose::Pose::total_residue(), protocols::TR(), and core::conformation::Residue::xyz().

Referenced by protocols::hydrate::Hydrate::apply().

set_task_with_de_novo_water_using_resfile()

void protocols::hydrate::set_task_with_de_novo_water_using_resfile	(	pose::Pose &	pose,
		std::string	resfile,
		pack::task::PackerTaskOP &	task
	)

References core::pack::task::TaskFactory::create_packer_task(), core::conformation::Residue::name(), core::pack::task::parse_resfile(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and protocols::TR().

set_water_info_and_add_de_novo_water()

void protocols::hydrate::set_water_info_and_add_de_novo_water	(	pose::Pose &	pose,
		core::scoring::ScoreFunction const &	scorefxn
	)

References core::pose::Pose::data(), hydrate_hyfile(), core::conformation::Residue::name(), place_de_novo_wat_at_anchor(), read_hyfile(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), protocols::TR(), and core::pose::datacache::CacheableDataType::WATER_PACKING_INFO.

Referenced by protocols::hydrate::Hydrate::apply().

show_water_hb_network()

void protocols::hydrate::show_water_hb_network

(

pose::Pose const &

pose

)

References core::scoring::hbonds::HBond::acc_atm(), core::scoring::hbonds::HBond::acc_atm_is_protein_backbone(), core::scoring::hbonds::HBond::acc_res(), core::scoring::hbonds::HBondSet::clear(), core::scoring::hbonds::HBond::don_hatm(), core::scoring::hbonds::HBond::don_hatm_is_protein_backbone(), core::scoring::hbonds::HBond::don_res(), core::pose::Pose::energies(), core::scoring::hbonds::HBond::energy(), core::scoring::hbonds::fill_hbond_set(), core::scoring::hbonds::HBondSet::hbond(), core::scoring::hbond_bb_sc, core::scoring::hbond_sc, core::scoring::hbond_wat, core::conformation::Residue::name(), core::scoring::hbonds::HBondSet::nhbonds(), core::pose::Pose::residue(), protocols::TR(), core::scoring::hbonds::HBond::weight(), and core::scoring::Energies::weights().

Referenced by protocols::hydrate::Hydrate::apply().

water_specific_hbond_energy()

void protocols::hydrate::water_specific_hbond_energy	(	pose::Pose &	pose,
		core::scoring::ScoreFunction &	scorefxn
	)

References core::conformation::Residue::clone(), core::sequence::end, core::pose::Pose::energies(), core::scoring::ScoreFunction::energy_method_options(), protocols::jd2::JobDistributor::get_instance(), core::scoring::hbond_bb_sc, core::scoring::hbond_sc, core::scoring::hbond_wat, core::import_pose::atom_tree_diffs::map_of_weighted_scores(), core::conformation::Residue::name(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::scoring::ScoreFunction::set_energy_method_options(), core::scoring::Energies::total_energies(), core::pose::Pose::total_residue(), and core::scoring::ScoreFunction::weights().

Referenced by protocols::hydrate::Hydrate::apply().