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Public Member Functions | Protected Member Functions | Private Attributes | List of all members
protocols::toolbox::match_enzdes_util::EnzdesLoopInfo Class Reference

#include <EnzdesLoopsFile.hh>

Inheritance diagram for protocols::toolbox::match_enzdes_util::EnzdesLoopInfo:
Inheritance graph
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Public Member Functions

 ~EnzdesLoopInfo () override
 Automatically generated virtual destructor for class deriving directly from VirtualBase. 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< ResInteractionsres_interactions_
 
utility::vector1
< CstResInteractions
cstres_interactions_
 

Constructor & Destructor Documentation

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

Automatically generated virtual destructor for class deriving directly from VirtualBase.

Auto-generated virtual destructor

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

Member Function Documentation

bool protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::check_data_consistency ( bool  report = false) const
bool protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::contact_buried_problematic_res ( ) const
inline
utility::vector1< CstResInteractions > const& protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::cst_interactions ( ) const
inline

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.

References max_length_, min_length_, protocols::mean_field::num_elements(), 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

References max_length_.

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

References min_length_.

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

References pdb_numb_.

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

References pose_numb_.

bool protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::preserve_buried_contacts ( ) const
inline
bool protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::read_loops_file_block ( utility::io::izstream &  data)
utility::vector1< ResInteractions > const& protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::res_interactions ( ) const
inline

References res_interactions_.

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

References ss_strings_.

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

References ss_strings_.

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

References loop_start_.

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

References loop_start_pdb_.

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

References loop_start_pdb_chain_.

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

References loop_end_.

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

References loop_end_pdb_.

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

References loop_end_pdb_chain_.

Member Data Documentation

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

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