protocols::toolbox::match_enzdes_util::EnzCstTemplateRes Class Reference

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
virtual	~EnzCstTemplateRes ()
	Automatically generated virtual destructor for class deriving directly from ReferenceCount. 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	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

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

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

Constructor & Destructor Documentation

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

virtual

Automatically generated virtual destructor for class deriving directly from ReferenceCount.

Auto-generated virtual destructor

protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::EnzCstTemplateRes

(

core::chemical::ResidueTypeSetCOP

src_restype_set

)

References clear_all().

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

References clear_all().

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

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

inline

References allowed_res_types_.

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

inline

References allowed_res_types_pointers_.

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().

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_.

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_.

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().

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.

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

inline

References corresponding_res_block_.

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().

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().

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::chemical::ResidueType::get_self_ptr(), core::conformation::Residue::name3(), param_index_, core::pose::Pose::residue(), and core::pose::Pose::residue_type().

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_.

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().

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

inline

References is_backbone_.

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

inline

References param_index_.

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

inline

References rb_minimizable_.

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_.

void protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::remap_resid

(

core::id::SequenceMapping const &

smap

)

References respos_from_external_.

bool protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::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.

References core::conformation::Residue::atom(), atom_inds_for_restype_, core::chemical::ResidueType::get_self_ptr(), core::chemical::ResidueType::name(), core::conformation::Residue::type(), and core::conformation::Atom::xyz().

void protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::set_enzio_param ( EnzConstraintParametersCAP  src_enz_io_param )

inline

References enz_io_param_.

void protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::set_external_position

(

core::Size

resnum

)

References respos_from_external_.

void protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::set_param_index ( core::Size  index )

inline

References param_index_.

void protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::show_params

(

)

const

show the contents of a particular instance

References allowed_res_types_, at1_type_, atom1_, atom2_, atom3_, and protocols::toolbox::match_enzdes_util::tr().

Member Data Documentation

utility::vector1< std::string > protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::allowed_res_types_

private

Referenced by allowed_res_types(), clear_all(), find_in_pose_if_missing_from_header(), get_pose_data(), identical_info_consistency_check(), read_params(), and show_params().

utility::vector1< core::chemical::ResidueTypeCOP > protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::allowed_res_types_pointers_

mutableprivate

Referenced by allowed_res_types_pointers(), clear_all(), and determine_atom_inds_for_restype().

std::string protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::at1_type_

private

Referenced by clear_all(), determine_atom_inds_for_restype(), read_params(), and show_params().

std::string protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::at2_type_

private

Referenced by clear_all(), and read_params().

std::string protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::at3_type_

private

Referenced by clear_all(), and read_params().

utility::vector1< std::string > protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::atom1_

private

Referenced by clear_all(), compatible_restype(), determine_atom_inds_for_restype(), read_params(), and show_params().

utility::vector1< std::string > protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::atom2_

private

Referenced by clear_all(), compatible_restype(), determine_atom_inds_for_restype(), read_params(), and show_params().

utility::vector1< std::string > protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::atom3_

private

Referenced by clear_all(), compatible_restype(), determine_atom_inds_for_restype(), read_params(), and show_params().

RestypeToTemplateAtomsMap protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::atom_inds_for_restype_

mutableprivate

Referenced by atom_inds_for_restype(), atom_inds_for_restype_begin(), atom_inds_for_restype_end(), clear_all(), determine_atom_inds_for_restype(), get_pose_data(), and residue_conformations_redundant().

core::Size protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::corresponding_res_block_

private

Referenced by clear_all(), corresponding_res_block(), find_in_pose_if_missing_from_header(), identical_info_consistency_check(), and read_params().

core::Size protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::corresponding_res_num_in_block_

private

Referenced by clear_all(), find_in_pose_if_missing_from_header(), identical_info_consistency_check(), and read_params().

EnzConstraintParametersCAP protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::enz_io_param_

private

Referenced by find_in_pose_if_missing_from_header(), get_pose_data(), get_template_atoms_at_pos(), identical_info_consistency_check(), and set_enzio_param().

bool protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::identical_tag_found_

private

Referenced by identical_info_consistency_check(), and read_params().

bool protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::is_backbone_

private

Referenced by is_backbone(), and read_params().

core::Size protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::param_index_

private

Referenced by clear_all(), find_in_pose_if_missing_from_header(), get_pose_data(), get_template_atoms_at_pos(), param_index(), and set_param_index().

bool protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::rb_minimizable_

private

Referenced by rb_minimizable(), and read_params().

utility::vector1< core::Size > protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::respos_from_external_

private

Referenced by clear_all(), find_in_pose_if_missing_from_header(), read_params(), remap_resid(), and set_external_position().

core::chemical::ResidueTypeSetCOP protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::restype_set_

private

Referenced by read_params().

---

The documentation for this class was generated from the following files:

• src/protocols/toolbox/match_enzdes_util/EnzCstTemplateRes.hh
• src/protocols/toolbox/match_enzdes_util/EnzCstTemplateRes.cc