helper class for class EnzConstraintParameters, gathers information More...

#include <EnzCstTemplateRes.hh>

Inheritance diagram for protocols::toolbox::match_enzdes_util::EnzCstTemplateRes:

Public Types
typedef std::map< core::chemical::ResidueTypeCOP, utility::vector1< utility::vector1< core::Size > > >	RestypeToTemplateAtomsMap

typedef std::map< core::chemical::ResidueTypeCOP, utility::vector1< utility::vector1< core::Size > > >	AtomIndsForRestypeMap

Public Member Functions
	~EnzCstTemplateRes () override
	Automatically generated virtual destructor for class deriving directly from VirtualBase. More...

	EnzCstTemplateRes (core::chemical::ResidueTypeSetCOP src_restype_set)

	EnzCstTemplateRes (core::chemical::ResidueTypeSetCOP src_restype_set, EnzConstraintParametersCAP src_enzio_param)

	EnzCstTemplateRes (EnzCstTemplateResCOP other, EnzConstraintParametersCAP new_ref_param)
	WARNING: currently doesn't copy the template atoms in the respos map. More...

void	initialize_from_params (std::string const &a1, std::string const &a2, std::string const &a3, utility::vector1< std::string > const &allowed_3res)

void	read_params (std::istringstream &line_stream)
	read and set up the general information for one residue of one pair block in a cstfile More...

void	show_params () const
	show the contents of a particular instance More...

void	get_pose_data (core::pose::Pose &pose) const
	check whether the data gathered from the cst file and the pdbfile/pose is consistent in itself and with one another More...

void	set_enzio_param (EnzConstraintParametersCAP src_enz_io_param)

void	set_param_index (core::Size index)

core::Size	param_index () const

EnzCstTemplateResAtomsCOP	get_template_atoms_at_pos (core::pose::Pose const &pose, core::Size seqpos) const

bool	rb_minimizable () const

bool	is_backbone () const

core::Size	corresponding_res_block () const

bool	find_in_pose_if_missing_from_header (core::pose::Pose &pose)

void	set_external_position (core::Size resnum)

utility::vector1< std::string > const &	allowed_res_types () const

utility::vector1< core::chemical::ResidueTypeCOP > const &	allowed_res_types_pointers () const

RestypeToTemplateAtomsMap::const_iterator	atom_inds_for_restype_begin () const
	Iterator to the map from ResidueType pointers (addresses) to the set of atoms that are used to build from; this returns ResidueTypes in an indeterminant order as they are going to be sorted based on where in memory the ResidueTypes happened to be allocated. More...

RestypeToTemplateAtomsMap::const_iterator	atom_inds_for_restype_end () const
	End iterator to the map from ResidueType pointers to the set of atoms that are used to build from. More...

void	clear_all ()

void	remap_resid (core::id::SequenceMapping const &smap)

bool	compatible_restype (core::chemical::ResidueTypeCOP restype) const

void	determine_atom_inds_for_restype (core::chemical::ResidueTypeCOP restype) const

utility::vector1< core::Size > const &	atom_inds_for_restype (core::Size template_atom, core::chemical::ResidueTypeCOP restype) const

bool	residue_conformations_redundant (core::conformation::Residue const &res1, core::conformation::Residue const &res2) const
	checks whether the distance between any of the template res atoms of res1 and res2 is below a certain cutoff. More...

void	identical_info_consistency_check () const

Private Attributes
utility::vector1< std::string >	atom1_

utility::vector1< std::string >	atom2_

utility::vector1< std::string >	atom3_

std::string	at1_type_

std::string	at2_type_

std::string	at3_type_

utility::vector1< std::string >	allowed_res_types_

utility::vector1< core::chemical::ResidueTypeCOP >	allowed_res_types_pointers_

RestypeToTemplateAtomsMap	atom_inds_for_restype_

bool	rb_minimizable_

bool	is_backbone_

utility::vector1< core::Size >	respos_from_external_

bool	identical_tag_found_

core::Size	corresponding_res_block_

core::Size	corresponding_res_num_in_block_

core::chemical::ResidueTypeSetCOP	restype_set_

EnzConstraintParametersCAP	enz_io_param_

core::Size	param_index_

Detailed Description

helper class for class EnzConstraintParameters, gathers information

from cst input and pdb input

Member Typedef Documentation

◆ AtomIndsForRestypeMap

typedef std::map< core::chemical::ResidueTypeCOP, utility::vector1< utility::vector1< core::Size > > > protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::AtomIndsForRestypeMap

◆ RestypeToTemplateAtomsMap

typedef std::map< core::chemical::ResidueTypeCOP, utility::vector1< utility::vector1< core::Size > > > protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::RestypeToTemplateAtomsMap

Constructor & Destructor Documentation

◆ ~EnzCstTemplateRes()

protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::~EnzCstTemplateRes ( )

overridedefault

Automatically generated virtual destructor for class deriving directly from VirtualBase.

Auto-generated virtual destructor

◆ EnzCstTemplateRes() [1/3]

protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::EnzCstTemplateRes ( core::chemical::ResidueTypeSetCOP src_restype_set )

References clear_all().

◆ EnzCstTemplateRes() [2/3]

protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::EnzCstTemplateRes	(	core::chemical::ResidueTypeSetCOP	src_restype_set,
		EnzConstraintParametersCAP	src_enzio_param
	)

References clear_all().

◆ EnzCstTemplateRes() [3/3]

protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::EnzCstTemplateRes	(	EnzCstTemplateResCOP	other,
		EnzConstraintParametersCAP	new_ref_param
	)

WARNING: currently doesn't copy the template atoms in the respos map.

Member Function Documentation

◆ allowed_res_types()

utility::vector1< std::string > const& protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::allowed_res_types ( ) const

inline

References allowed_res_types_.

◆ allowed_res_types_pointers()

utility::vector1< core::chemical::ResidueTypeCOP > const& protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::allowed_res_types_pointers ( ) const

inline

References allowed_res_types_pointers_.

◆ atom_inds_for_restype()

utility::vector1< core::Size > const & protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::atom_inds_for_restype	(	core::Size	template_atom,
		core::chemical::ResidueTypeCOP	restype
	)		const

References atom_inds_for_restype_, and determine_atom_inds_for_restype().

◆ atom_inds_for_restype_begin()

RestypeToTemplateAtomsMap::const_iterator protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::atom_inds_for_restype_begin ( ) const

inline

Iterator to the map from ResidueType pointers (addresses) to the set of atoms that are used to build from; this returns ResidueTypes in an indeterminant order as they are going to be sorted based on where in memory the ResidueTypes happened to be allocated.

References atom_inds_for_restype_.

◆ atom_inds_for_restype_end()

RestypeToTemplateAtomsMap::const_iterator protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::atom_inds_for_restype_end ( ) const

inline

End iterator to the map from ResidueType pointers to the set of atoms that are used to build from.

References atom_inds_for_restype_.

◆ clear_all()

void protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::clear_all ( )

References allowed_res_types_, allowed_res_types_pointers_, at1_type_, at2_type_, at3_type_, atom1_, atom2_, atom3_, atom_inds_for_restype_, corresponding_res_block_, corresponding_res_num_in_block_, param_index_, and respos_from_external_.

Referenced by EnzCstTemplateRes().

◆ compatible_restype()

bool protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::compatible_restype ( core::chemical::ResidueTypeCOP restype ) const

References atom1_, atom2_, atom3_, core::chemical::DEPROTONATED, and core::chemical::PROTONATED.

◆ corresponding_res_block()

core::Size protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::corresponding_res_block ( ) const

inline

References corresponding_res_block_.

◆ determine_atom_inds_for_restype()

void protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::determine_atom_inds_for_restype ( core::chemical::ResidueTypeCOP restype ) const

References allowed_res_types_pointers_, at1_type_, atom1_, atom2_, atom3_, atom_inds_for_restype_, core::chemical::AtomType::name(), and protocols::toolbox::match_enzdes_util::tr().

Referenced by atom_inds_for_restype(), and get_pose_data().

◆ find_in_pose_if_missing_from_header()

bool protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::find_in_pose_if_missing_from_header ( core::pose::Pose & pose )

References allowed_res_types_, corresponding_res_block_, corresponding_res_num_in_block_, enz_io_param_, protocols::toolbox::match_enzdes_util::get_enzdes_observer(), core::conformation::Residue::name3(), param_index_, core::pose::Pose::residue(), respos_from_external_, core::pose::Pose::size(), and protocols::toolbox::match_enzdes_util::tr().

◆ get_pose_data()

void protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::get_pose_data ( core::pose::Pose & pose ) const

check whether the data gathered from the cst file and the pdbfile/pose is consistent in itself and with one another

References allowed_res_types_, atom_inds_for_restype_, determine_atom_inds_for_restype(), enz_io_param_, protocols::toolbox::match_enzdes_util::get_enzdes_observer(), core::conformation::Residue::name3(), param_index_, core::pose::Pose::residue(), and core::pose::Pose::residue_type_ptr().

◆ get_template_atoms_at_pos()

EnzCstTemplateResAtomsCOP protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::get_template_atoms_at_pos	(	core::pose::Pose const &	pose,
		core::Size	seqpos
	)		const

References enz_io_param_, protocols::toolbox::match_enzdes_util::get_enzdes_observer(), and param_index_.

◆ identical_info_consistency_check()

void protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::identical_info_consistency_check ( ) const

References allowed_res_types_, corresponding_res_block_, corresponding_res_num_in_block_, enz_io_param_, identical_tag_found_, and core::id::to_string().

◆ initialize_from_params()

void protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::initialize_from_params	(	std::string const &	a1,
		std::string const &	a2,
		std::string const &	a3,
		utility::vector1< std::string > const &	allowed_3res
	)

References allowed_res_types_, atom1_, atom2_, atom3_, and restype_set_.

◆ is_backbone()

bool protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::is_backbone ( ) const

inline

References is_backbone_.

◆ param_index()

core::Size protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::param_index ( ) const

inline

References param_index_.

◆ rb_minimizable()

bool protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::rb_minimizable ( ) const

inline

References rb_minimizable_.

◆ read_params()

void protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::read_params ( std::istringstream & line_stream )

read and set up the general information for one residue of one pair block in a cstfile

References core::chemical::aa_from_oneletter_code(), allowed_res_types_, at1_type_, at2_type_, at3_type_, atom1_, atom2_, atom3_, corresponding_res_block_, corresponding_res_num_in_block_, identical_tag_found_, is_backbone_, core::chemical::name_from_aa(), core::chemical::oneletter_code_specifies_aa(), rb_minimizable_, respos_from_external_, and restype_set_.

◆ remap_resid()

void protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::remap_resid ( core::id::SequenceMapping const & smap )

References respos_from_external_.

◆ residue_conformations_redundant()

bool protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::residue_conformations_redundant	(	core::conformation::Residue const &	res1,
		core::conformation::Residue const &	res2
	)		const