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

#include <Patch.hh>

Inheritance diagram for core::chemical::Patch:

Collaboration diagram for core::chemical::Patch:

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.

Definition at line 98 of file Patch.hh.

Constructor & Destructor Documentation

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

virtual

Automatically generated virtual destructor for class deriving directly from ReferenceCount.

Auto-generated virtual destructor

Definition at line 180 of file Patch.cc.

Member Function Documentation

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

inlinevirtual

can I operate on this residue type?

Definition at line 109 of file Patch.hh.

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.

Definition at line 355 of file Patch.cc.

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, ... ?

Definition at line 131 of file Patch.hh.

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

Definition at line 268 of file Patch.cc.

References core::chemical::ResidueSelector::add_line(), core::chemical::case_from_lines(), cases_, core::chemical::ResidueSelector::clear(), name_, replaces_residue_type_, selector_, core::scoring::hbonds::t(), core::chemical::tag_from_line(), core::chemical::tr(), and types_.