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Classes | Typedefs | Functions
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

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

Function Documentation

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