core::chemical::io Namespace Reference

Classes
class	MergeAndSplitBehaviorManager

Typedefs
typedef std::map< std::string, std::string >	AtomRenamingMap
typedef std::pair< merge_residue_behavior, io::AtomRenamingMap >	ResidueMergeInstructions
typedef std::map< std::string, ResidueMergeInstructions >	MergeBehaviorMap
typedef std::pair< utility::vector1< std::pair< std::string, std::string > >, utility::vector1< AtomRenamingMap > >	SplitBehaviors
typedef std::map< std::string, SplitBehaviors >	SplitBehaviorsMap
typedef utility::pointer::shared_ptr< MergeAndSplitBehaviorManager >	MergeAndSplitBehaviorManagerOP
typedef utility::pointer::shared_ptr< MergeAndSplitBehaviorManager const >	MergeAndSplitBehaviorManagerCOP

Enumerations
enum	merge_residue_behavior { mrb_do_not_merge , mrb_merge_w_prev , mrb_merge_w_next }
	Per-residue setting for the behavior of each residue from an input file. More...

Functions
AtomRenamingMap	get_atom_renamings (std::string const &instructions)
merge_residue_behavior	mrb_from_name (std::string const &mrb)
MergeBehaviorMap	read_merge_behaviors_from_database_file (std::string const &filename)
	Return a mapping of PDB 3-letter codes to a set of merging instructions. More...
utility::vector1< AtomRenamingMap >	get_groups_of_atom_renamings (utility::vector1< std::string > const &instructions)
SplitBehaviors	get_SplitBehaviors (std::string const &residue_names, std::string const &behavior)
SplitBehaviorsMap	read_split_behaviors_from_database_file (std::string const &filename)
	Return a mapping of PDB 3-letter codes to a set of splitting instructions. More...

Typedef Documentation

AtomRenamingMap

typedef std::map< std::string, std::string > core::chemical::io::AtomRenamingMap

MergeAndSplitBehaviorManagerCOP

typedef utility::pointer::shared_ptr< MergeAndSplitBehaviorManager const > core::chemical::io::MergeAndSplitBehaviorManagerCOP

MergeAndSplitBehaviorManagerOP

typedef utility::pointer::shared_ptr< MergeAndSplitBehaviorManager > core::chemical::io::MergeAndSplitBehaviorManagerOP

MergeBehaviorMap

typedef std::map< std::string, ResidueMergeInstructions > core::chemical::io::MergeBehaviorMap

ResidueMergeInstructions

typedef std::pair< merge_residue_behavior, io::AtomRenamingMap > core::chemical::io::ResidueMergeInstructions

SplitBehaviors

typedef std::pair< utility::vector1< std::pair< std::string, std::string > >, utility::vector1< AtomRenamingMap > > core::chemical::io::SplitBehaviors

SplitBehaviorsMap

typedef std::map< std::string, SplitBehaviors > core::chemical::io::SplitBehaviorsMap

Enumeration Type Documentation

merge_residue_behavior

enum core::chemical::io::merge_residue_behavior

Per-residue setting for the behavior of each residue from an input file.

Enumerator
mrb_do_not_merge
mrb_merge_w_prev
mrb_merge_w_next

Function Documentation

get_atom_renamings()

AtomRenamingMap core::chemical::io::get_atom_renamings

(

std::string const &

instructions

)

Referenced by get_groups_of_atom_renamings(), and read_merge_behaviors_from_database_file().

get_groups_of_atom_renamings()

utility::vector1< AtomRenamingMap > core::chemical::io::get_groups_of_atom_renamings

(

utility::vector1< std::string > const &

instructions

)

References get_atom_renamings().

Referenced by get_SplitBehaviors().

get_SplitBehaviors()

SplitBehaviors core::chemical::io::get_SplitBehaviors	(	std::string const &	residue_names,
		std::string const &	behavior
	)

References protocols::vip::base_name(), and get_groups_of_atom_renamings().

Referenced by read_split_behaviors_from_database_file().

mrb_from_name()

merge_residue_behavior core::chemical::io::mrb_from_name

(

std::string const &

mrb

)

References mrb_do_not_merge, mrb_merge_w_next, and mrb_merge_w_prev.

Referenced by read_merge_behaviors_from_database_file().

read_merge_behaviors_from_database_file()

MergeBehaviorMap core::chemical::io::read_merge_behaviors_from_database_file

(

std::string const &

filename

)

Return a mapping of PDB 3-letter codes to a set of merging instructions.

References protocols::abinitio::filename(), get_atom_renamings(), mrb_from_name(), and core::chemical::TR().

Referenced by core::chemical::io::MergeAndSplitBehaviorManager::MergeAndSplitBehaviorManager().

read_split_behaviors_from_database_file()

SplitBehaviorsMap core::chemical::io::read_split_behaviors_from_database_file

(

std::string const &

filename

)

Return a mapping of PDB 3-letter codes to a set of splitting instructions.

References protocols::abinitio::filename(), get_SplitBehaviors(), and core::chemical::TR().

Referenced by core::chemical::io::MergeAndSplitBehaviorManager::MergeAndSplitBehaviorManager().