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core::chemical::Metapatch Class Reference

A class patching basic ResidueType to create variant types, containing multiple PatchCase. More...

#include <Metapatch.hh>

Inheritance diagram for core::chemical::Metapatch:
Inheritance graph
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Public Member Functions

 Metapatch ()
 
 ~Metapatch () override
 Automatically generated virtual destructor for class deriving directly from VirtualBase. More...
 
void read_file (std::string const &filename)
 constructor from file More...
 
virtual bool applies_to (ResidueType const &rsd) const
 can I operate on this residue type? More...
 
PatchCOP get_one_patch (std::string const &atom_name) const
 
bool meets_requirements (ResidueType const &r, Size i) const
 
virtual std::string const & name () const
 unique name of this patch, eg Nter-simple, Cter-full, Phospho, ... ? More...
 
virtual utility::vector1
< std::string > const & 
types () const
 the variant types created by applying this patch More...
 
utility::vector1< std::string > atoms (ResidueType const &rsd_type) const
 

Private Attributes

std::string name_
 private data More...
 
utility::vector1< std::string > types_
 variant types created by the created patches More...
 
utility::vector1< PatchCaseOPcases_
 different cases to which the derived patches patch will be applied slightly differently, e.g., N-terminus patch to PRO and GLY More...
 
chemical::AtomProperty pertinent_property_
 
utility::vector1< std::string > case_lines_
 
ResidueTypeSelector selector_
 criteria to select ResidueTypes to which the patches are applied More...
 

Detailed Description

A class patching basic ResidueType to create variant types, containing multiple PatchCase.

Constructor & Destructor Documentation

core::chemical::Metapatch::Metapatch ( )
core::chemical::Metapatch::~Metapatch ( )
overridedefault

Automatically generated virtual destructor for class deriving directly from VirtualBase.

Auto-generated virtual destructor

Member Function Documentation

virtual bool core::chemical::Metapatch::applies_to ( ResidueType const &  rsd) const
inlinevirtual

can I operate on this residue type?

References selector_.

utility::vector1< std::string > core::chemical::Metapatch::atoms ( ResidueType const &  rsd_type) const
PatchCOP core::chemical::Metapatch::get_one_patch ( std::string const &  atom_name) const
bool core::chemical::Metapatch::meets_requirements ( ResidueType const &  r,
Size  i 
) const
inline
virtual std::string const& core::chemical::Metapatch::name ( ) const
inlinevirtual

unique name of this patch, eg Nter-simple, Cter-full, Phospho, ... ?

References name_.

void core::chemical::Metapatch::read_file ( std::string const &  filename)

constructor from file

  • first read in all lines from the file, discarding # comment lines
  • parse input lines for Metapatch name and variant types (NAME, TYPES)
  • parse input lines for general ResidueTypeSelector defined for this Patch (BEGIN_SELECTOR, END_SELECTOR)
  • parse input lines to create each case accordingly (BEGIN_CASE, END_CASE)
    Note
    keep the order to avoid triggering parsing errors

References core::chemical::ResidueTypeSelector::add_line(), core::chemical::case_from_lines(), case_lines_, cases_, core::chemical::ResidueTypeSelector::clear(), name_, pertinent_property_, core::chemical::AtomPropertiesManager::property_from_string(), selector_, protocols::hybridization::t, core::chemical::tag_from_line(), core::chemical::tr(), and types_.

virtual utility::vector1< std::string > const& core::chemical::Metapatch::types ( ) const
inlinevirtual

the variant types created by applying this patch

References types_.

Referenced by get_one_patch().

Member Data Documentation

utility::vector1< std::string > core::chemical::Metapatch::case_lines_
private

Referenced by get_one_patch(), and read_file().

utility::vector1< PatchCaseOP > core::chemical::Metapatch::cases_
private

different cases to which the derived patches patch will be applied slightly differently, e.g., N-terminus patch to PRO and GLY

Referenced by read_file().

std::string core::chemical::Metapatch::name_
private

private data

name of the patch

Referenced by get_one_patch(), name(), and read_file().

chemical::AtomProperty core::chemical::Metapatch::pertinent_property_
private

Referenced by meets_requirements(), and read_file().

ResidueTypeSelector core::chemical::Metapatch::selector_
private

criteria to select ResidueTypes to which the patches are applied

Referenced by applies_to(), get_one_patch(), and read_file().

utility::vector1< std::string > core::chemical::Metapatch::types_
private

variant types created by the created patches

Referenced by get_one_patch(), read_file(), and types().


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