protocols::toolbox::match_enzdes_util::EnzdesLoopInfo Class Reference

#include <EnzdesLoopsFile.hh>

Inheritance diagram for protocols::toolbox::match_enzdes_util::EnzdesLoopInfo:

Collaboration diagram for protocols::toolbox::match_enzdes_util::EnzdesLoopInfo:

Public Member Functions
virtual	~EnzdesLoopInfo ()
	Automatically generated virtual destructor for class deriving directly from ReferenceCount. More...
	EnzdesLoopInfo ()
bool	read_loops_file_block (utility::io::izstream &data)
bool	check_data_consistency (bool report=false) const
bool	ss_strings_specified () const
bool	pdb_numb () const
bool	pose_numb () const
core::Size	start_pdb () const
core::Size	stop_pdb () const
char	start_pdb_chain () const
char	stop_pdb_chain () const
core::Size	start () const
core::Size	stop () const
core::Size	min_length () const
core::Size	max_length () const
utility::vector1< std::string > const &	ss_strings () const
utility::vector1 < ResInteractions > const &	res_interactions () const
utility::vector1 < CstResInteractions > const &	cst_interactions () const
bool	preserve_buried_contacts () const
bool	contact_buried_problematic_res () const

Protected Member Functions
void	generate_ss_strings_from_blueprint (std::string const &ss_blueprint)
	generate all secondary structure strings that correspond to the given blueprint. A blueprint is a string containing a succession of the following substrings: 1 ss-char followed by '(', a number and ')' or 1 ss-char followed by '(', a number, '-', a second number, and ')', i.e. H(3-5)L(2-3)H(8)L(5-10)E(4-5)L(2-3) the function interprets this string to mean a helix of length between 3 and 5, followed by a loop of length 2 or 3, followed by helix of length 8, followed by a loop of length between 5 and 10, followed by a sheet of length 4 or 5, followed by a loop of length 2 or 3. the function then generates one string for every possible combination of secondary structure elements that correspond to this blueprint. in the above example, a total of 3*2*1*6*2*2 = 144 different secondary structure strings will be generated. for every one of these strings, the function checks whether its length is within min_length_ and max_length_, and if this is the case, the string gets saved in the ss_strings_ vector. More...

Private Attributes
core::Size	loop_start_
core::Size	loop_end_
core::Size	loop_start_pdb_
core::Size	loop_end_pdb_
char	loop_start_pdb_chain_
char	loop_end_pdb_chain_
bool	pose_numb_
bool	pdb_numb_
core::Size	min_length_
core::Size	max_length_
utility::vector1< std::string >	ss_strings_
bool	preserve_buried_contacts_
bool	contact_buried_problematic_res_
utility::vector1< ResInteractions >	res_interactions_
utility::vector1 < CstResInteractions >	cstres_interactions_

Detailed Description

Definition at line 179 of file EnzdesLoopsFile.hh.

Constructor & Destructor Documentation

protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::~EnzdesLoopInfo ( )

virtual

Automatically generated virtual destructor for class deriving directly from ReferenceCount.

Auto-generated virtual destructor

Definition at line 44 of file EnzdesLoopsFile.cc.

protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::EnzdesLoopInfo

(

)

Definition at line 344 of file EnzdesLoopsFile.cc.

References cstres_interactions_, res_interactions_, and ss_strings_.

Member Function Documentation

bool protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::check_data_consistency

(

bool

report = false)

const

Definition at line 485 of file EnzdesLoopsFile.cc.

References loop_end_, loop_end_pdb_, loop_start_, loop_start_pdb_, max_length_, min_length_, pdb_numb_, pose_numb_, ss_strings_, and protocols::toolbox::match_enzdes_util::tr().

Referenced by read_loops_file_block().

bool protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::contact_buried_problematic_res ( ) const

inline

Definition at line 259 of file EnzdesLoopsFile.hh.

References contact_buried_problematic_res_.

utility::vector1< CstResInteractions > const& protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::cst_interactions ( ) const

inline

Definition at line 249 of file EnzdesLoopsFile.hh.

References cstres_interactions_.

void protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::generate_ss_strings_from_blueprint ( std::string const &  ss_blueprint)

protected

generate all secondary structure strings that correspond to the given blueprint. A blueprint is a string containing a succession of the following substrings: 1 ss-char followed by '(', a number and ')' or 1 ss-char followed by '(', a number, '-', a second number, and ')', i.e. H(3-5)L(2-3)H(8)L(5-10)E(4-5)L(2-3) the function interprets this string to mean a helix of length between 3 and 5, followed by a loop of length 2 or 3, followed by helix of length 8, followed by a loop of length between 5 and 10, followed by a sheet of length 4 or 5, followed by a loop of length 2 or 3. the function then generates one string for every possible combination of secondary structure elements that correspond to this blueprint. in the above example, a total of 3*2*1*6*2*2 = 144 different secondary structure strings will be generated. for every one of these strings, the function checks whether its length is within min_length_ and max_length_, and if this is the case, the string gets saved in the ss_strings_ vector.

Definition at line 541 of file EnzdesLoopsFile.cc.

References max_length_, min_length_, ss_strings_, and protocols::toolbox::match_enzdes_util::tr().

Referenced by read_loops_file_block().

core::Size protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::max_length ( ) const

inline

Definition at line 236 of file EnzdesLoopsFile.hh.

References max_length_.

core::Size protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::min_length ( ) const

inline

Definition at line 232 of file EnzdesLoopsFile.hh.

References min_length_.

bool protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::pdb_numb ( ) const

inline

Definition at line 200 of file EnzdesLoopsFile.hh.

References pdb_numb_.

bool protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::pose_numb ( ) const

inline

Definition at line 204 of file EnzdesLoopsFile.hh.

References pose_numb_.

bool protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::preserve_buried_contacts ( ) const

inline

Definition at line 254 of file EnzdesLoopsFile.hh.

References preserve_buried_contacts_.

bool protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::read_loops_file_block

(

utility::io::izstream &

data)

Definition at line 358 of file EnzdesLoopsFile.cc.

References check_data_consistency(), cstres_interactions_, generate_ss_strings_from_blueprint(), loop_end_, loop_end_pdb_, loop_end_pdb_chain_, loop_start_, loop_start_pdb_, loop_start_pdb_chain_, max_length_, min_length_, pdb_numb_, pose_numb_, res_interactions_, core::io::pdb::split(), ss_strings_, and protocols::toolbox::match_enzdes_util::tr().

utility::vector1< ResInteractions > const& protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::res_interactions ( ) const

inline

Definition at line 245 of file EnzdesLoopsFile.hh.

References res_interactions_.

utility::vector1< std::string > const& protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::ss_strings ( ) const

inline

Definition at line 241 of file EnzdesLoopsFile.hh.

References ss_strings_.

bool protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::ss_strings_specified ( ) const

inline

Definition at line 196 of file EnzdesLoopsFile.hh.

References ss_strings_.

core::Size protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::start ( ) const

inline

Definition at line 224 of file EnzdesLoopsFile.hh.

References loop_start_.

core::Size protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::start_pdb ( ) const

inline

Definition at line 208 of file EnzdesLoopsFile.hh.

References loop_start_pdb_.

char protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::start_pdb_chain ( ) const

inline

Definition at line 216 of file EnzdesLoopsFile.hh.

References loop_start_pdb_chain_.

core::Size protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::stop ( ) const

inline

Definition at line 228 of file EnzdesLoopsFile.hh.

References loop_end_.

core::Size protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::stop_pdb ( ) const

inline

Definition at line 212 of file EnzdesLoopsFile.hh.

References loop_end_pdb_.

char protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::stop_pdb_chain ( ) const

inline

Definition at line 220 of file EnzdesLoopsFile.hh.

References loop_end_pdb_chain_.

Member Data Documentation

bool protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::contact_buried_problematic_res_

private

Definition at line 301 of file EnzdesLoopsFile.hh.

Referenced by contact_buried_problematic_res().

utility::vector1< CstResInteractions > protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::cstres_interactions_

private

Definition at line 305 of file EnzdesLoopsFile.hh.

Referenced by cst_interactions(), EnzdesLoopInfo(), and read_loops_file_block().

core::Size protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::loop_end_

private

Definition at line 287 of file EnzdesLoopsFile.hh.

Referenced by check_data_consistency(), read_loops_file_block(), and stop().

core::Size protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::loop_end_pdb_

private

Definition at line 287 of file EnzdesLoopsFile.hh.

Referenced by check_data_consistency(), read_loops_file_block(), and stop_pdb().

char protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::loop_end_pdb_chain_

private

Definition at line 288 of file EnzdesLoopsFile.hh.

Referenced by read_loops_file_block(), and stop_pdb_chain().

core::Size protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::loop_start_

private

Definition at line 287 of file EnzdesLoopsFile.hh.

Referenced by check_data_consistency(), read_loops_file_block(), and start().

core::Size protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::loop_start_pdb_

private

Definition at line 287 of file EnzdesLoopsFile.hh.

Referenced by check_data_consistency(), read_loops_file_block(), and start_pdb().

char protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::loop_start_pdb_chain_

private

Definition at line 288 of file EnzdesLoopsFile.hh.

Referenced by read_loops_file_block(), and start_pdb_chain().

core::Size protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::max_length_

private

Definition at line 291 of file EnzdesLoopsFile.hh.

Referenced by check_data_consistency(), generate_ss_strings_from_blueprint(), max_length(), and read_loops_file_block().

core::Size protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::min_length_

private

Definition at line 291 of file EnzdesLoopsFile.hh.

Referenced by check_data_consistency(), generate_ss_strings_from_blueprint(), min_length(), and read_loops_file_block().

bool protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::pdb_numb_

private

Definition at line 289 of file EnzdesLoopsFile.hh.

Referenced by check_data_consistency(), pdb_numb(), and read_loops_file_block().

bool protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::pose_numb_

private

Definition at line 289 of file EnzdesLoopsFile.hh.

Referenced by check_data_consistency(), pose_numb(), and read_loops_file_block().

bool protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::preserve_buried_contacts_

private

Definition at line 298 of file EnzdesLoopsFile.hh.

Referenced by preserve_buried_contacts().

utility::vector1< ResInteractions > protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::res_interactions_

private

Definition at line 303 of file EnzdesLoopsFile.hh.

Referenced by EnzdesLoopInfo(), read_loops_file_block(), and res_interactions().

utility::vector1< std::string > protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::ss_strings_

private

Definition at line 295 of file EnzdesLoopsFile.hh.

Referenced by check_data_consistency(), EnzdesLoopInfo(), generate_ss_strings_from_blueprint(), read_loops_file_block(), ss_strings(), and ss_strings_specified().

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

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