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

#include <Patch.hh>

Public Member Functions
virtual	~Patch ()
	Automatically generated virtual destructor for class deriving directly from ReferenceCount. 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...

virtual bool	replaces (ResidueType const &rsd) const
	do I replace this residue type? More...

virtual ResidueTypeOP	apply (ResidueType const &rsd_type) const
	returns patched residue, 0 if patch failed More...

virtual std::string const &	name () const
	unique name of this patch, eg Nter-simple, Cter-full, Phospho, ... ? More...

virtual utility::vector1 < VariantType > const &	types () const
	the variant types created by applying this patch More...

Private Attributes
std::string	name_
	private data More...

utility::vector1< VariantType >	types_
	variant types created by the patch More...

ResidueSelector	selector_
	criteria to select ResidueTypes to which the patch is applied More...

utility::vector1< PatchCaseOP >	cases_
	different cases to which the patch is applied slightly differently, e.g., N-terminus patch to PRO and GLY More...

bool	replaces_residue_type_
	if set this patch will not change the name of the ResidueType and returns true for replaces() More...

Detailed Description

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

Constructor & Destructor Documentation

core::chemical::Patch::~Patch ( )

virtual

Automatically generated virtual destructor for class deriving directly from ReferenceCount.

Auto-generated virtual destructor

Member Function Documentation

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

inlinevirtual

can I operate on this residue type?

References selector_.

Referenced by apply(), core::chemical::ResidueTypeSet::apply_patches(), and replaces().

ResidueTypeOP core::chemical::Patch::apply ( ResidueType const & rsd_type ) const

virtual

returns patched residue, 0 if patch failed

loop through the cases in this patch and if it is applicable to this ResidueType, the corresponding patch operations are applied to create a new variant type of the basic ResidueType. The new types's name and its variant type info are updated together with all other primary and derived ResidueType data.

References applies_to(), cases_, core::chemical::ResidueType::name(), name_, core::chemical::patch_linker, replaces_residue_type_, core::chemical::tr, and types_.

Referenced by core::chemical::ResidueTypeSet::apply_patches().

virtual std::string const& core::chemical::Patch::name ( ) const

inlinevirtual

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

References name_.

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

constructor from file

first read in all lines from the file, discarding # comment lines
parse input lines for Patch name and variant types (NAME, TYPES)
parse input lines for general ResidueSelector 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::ResidueSelector::add_line(), core::chemical::case_from_lines(), cases_, core::chemical::ResidueSelector::clear(), getline(), l, name_, replaces_residue_type_, selector_, core::scoring::hbonds::t, tag, core::chemical::tag_from_line(), core::chemical::tr, types_, and utility_exit_with_message.