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

#include <Patch.hh>

Inheritance diagram for core::chemical::Patch:

Public Member Functions
	Patch ()
	Constructor. More...

	Patch (TypeSetMode res_type_set_mode)
	Constructor with ResidueTypeSet mode. More...

	~Patch () 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 (ResidueTypeBase const &rsd) const
	can I operate on this residue type? More...

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

bool	generates_base_residue_type () const
	Is this a special patch that expands the list of base residue types? More...

virtual MutableResidueTypeOP	apply (ResidueType const &rsd_type, bool const instantiate=true) const
	returns patched residue, 0 if patch failed More...

virtual MutableResidueTypeOP	apply (MutableResidueType const &rsd_type, bool const instantiate=true) 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...

std::string	patched_name (ResidueTypeBase const &rsd) const
	Returns the name of the residueType after applying the patch (Theoretical - doesn't actually check if the patch would be applied.) More...

void	set_selector (ResidueTypeSelector const &selector)

void	set_name (std::string const &name)

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

virtual utility::vector1 < std::string > const &	custom_types () const
	The custom variant types added by this patch. More...

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

virtual void	add_type (core::chemical::VariantType const type)
	Add a VariantType to the list that this patch applies. More...

virtual void	add_custom_type (std::string const &custom_type)
	Add a custom VariantType to the list that this patch applies. More...

void	replaces_residue_type (bool replaces)

utility::vector1< std::string >	adds_atoms (ResidueType const &rsd_in) const
	returns list of added atom names, useful for identifying patches that go with PDB residues More...

utility::vector1< std::string >	deletes_atoms (ResidueType const &rsd_in) const
	returns list of deleted atom names, useful for identifying patches that go with PDB residues More...

utility::vector1< std::string >	adds_properties (ResidueType const &rsd_in) const
	returns list of added property names, useful for identifying patches that go with PDB residues More...

utility::vector1< ResidueProperty >	adds_properties_enums (ResidueType const &rsd_in) const
	Returns list of added properties, by enum. Useful for identifying patches that go with PDB residues. More...

utility::vector1< std::string >	deletes_properties (ResidueType const &rsd_in) const
	returns list of deleted property names, useful for identifying patches that go with PDB residues More...

utility::vector1< ResidueProperty >	deletes_properties_enums (ResidueType const &rsd_in) const
	returns list of deleted property enums, useful for identifying patches that go with PDB residues. More...

utility::vector1< std::string >	deletes_variants (ResidueType const &rsd_in) const
	returns list of deleted variant names, useful for identifying patches that go with PDB residues More...

utility::vector1 < core::chemical::VariantType >	deletes_variants_by_enum (ResidueType const &rsd_type) const
	Returns list of deleted VariantTypes. Doesn't support on-the-fly VariantTypes. More...

bool	changes_connections_on (ResidueType const &rsd_in, std::string const &atom) const
	Does the patch potentially change the connections for the given atom on the ResidueType. More...

void	add_case (PatchCaseOP pcase)
	Add a patch case to this patch. More...

std::string	generates_new_name3 (ResidueType const &rsd_in) const
	returns new name3, if changed. Only one new name3 allowed. More...

std::string	generates_interchangeability_group (ResidueType const &rsd_in) const
	returns new interchangeability_group, if changed. Only one new interchangeability_group allowed. More...

chemical::AA	generates_aa (ResidueType const &rsd_in) const
	returns new AA, if changed. More...

bool	is_metapatch () const
	Is this a metapatch? More...

Private Attributes
TypeSetMode	res_type_set_mode_ = core::chemical::FULL_ATOM_t
	private data More...

std::string	name_ = ""
	name of the patch More...

bool	is_metapatch_ = false
	Is this a metapatch? More...

utility::vector1 < core::chemical::VariantType >	types_
	Variant types created by the patch. More...

utility::vector1< std::string >	custom_types_
	Custom variant types created by this patch. More...

ResidueTypeSelector	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_ = false
	if set this patch will not change the name of the ResidueType and returns true for replaces() More...

bool	generates_base_residue_type_ = false
	If true, this patch adds to the list of base residue types. Note that this increases the initializaton cost and base memory footprint of Rosetta! More...

Detailed Description

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

Constructor & Destructor Documentation

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

default

Constructor.

core::chemical::Patch::Patch ( TypeSetMode res_type_set_mode )

Constructor with ResidueTypeSet mode.

Constructor with ResidueTypeSet name.

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

overridedefault

Automatically generated virtual destructor for class deriving directly from VirtualBase.

Auto-generated virtual destructor

Member Function Documentation

void core::chemical::Patch::add_case ( PatchCaseOP pcase )

Add a patch case to this patch.

References cases_, and generates_base_residue_type_.

Referenced by read_file().

void core::chemical::Patch::add_custom_type ( std::string const & custom_type )

virtual

Add a custom VariantType to the list that this patch applies.

Author: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).; Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).; Andy Watkins (amw57.nosp@m.9@st.nosp@m.anfor.nosp@m.d.ed.nosp@m.u)

References custom_types_.

void core::chemical::Patch::add_type ( core::chemical::VariantType const type )

virtual

Add a VariantType to the list that this patch applies.

Author: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).; Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).; Andy Watkins (amw57.nosp@m.9@st.nosp@m.anfor.nosp@m.d.ed.nosp@m.u)

References types_.

utility::vector1< std::string > core::chemical::Patch::adds_atoms ( ResidueType const & rsd_type ) const

returns list of added atom names, useful for identifying patches that go with PDB residues

loop through the cases in this patch and if it is applicable to this ResidueType, compile a list of any atom_names that are added.

References applies_to(), and cases_.

utility::vector1< std::string > core::chemical::Patch::adds_properties ( ResidueType const & rsd_type ) const

returns list of added property names, useful for identifying patches that go with PDB residues

loop through the cases in this patch and if it is applicable to this ResidueType, compile a list of any properties that are added.

References applies_to(), cases_, and update_ResidueType_enum_files::properties.

utility::vector1< ResidueProperty > core::chemical::Patch::adds_properties_enums ( ResidueType const & rsd_type ) const

Returns list of added properties, by enum. Useful for identifying patches that go with PDB residues.

Author: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

loop through the cases in this patch and if it is applicable to this ResidueType, compile a list of any properties that are added, by enum. Faster than string version.

References applies_to(), cases_, and update_ResidueType_enum_files::properties.

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

inlinevirtual

can I operate on this residue type?

References selector_.

Referenced by adds_atoms(), adds_properties(), adds_properties_enums(), apply(), changes_connections_on(), deletes_atoms(), deletes_properties(), deletes_properties_enums(), deletes_variants(), deletes_variants_by_enum(), generates_aa(), generates_interchangeability_group(), generates_new_name3(), and replaces().

MutableResidueTypeOP core::chemical::Patch::apply	(	ResidueType const &	rsd_type,
		bool const	instantiate = `true`
	)		const

virtual

returns patched residue, 0 if patch failed

Referenced by generates_aa().

MutableResidueTypeOP core::chemical::Patch::apply	(	MutableResidueType const &	rsd_type,
		bool const	instantiate = `true`
	)		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. Finally, call finalize() to update all primary and derived data for the new ResidueType.

References applies_to(), cases_, custom_types_, name(), core::chemical::ResidueTypeBase::name(), name_, patched_name(), replaces_residue_type_, core::chemical::tr(), and types_.

bool core::chemical::Patch::changes_connections_on	(	ResidueType const &	rsd_in,
		std::string const &	atom
	)		const

Does the patch potentially change the connections for the given atom on the ResidueType.

References applies_to(), and cases_.

virtual utility::vector1< std::string > const& core::chemical::Patch::custom_types ( ) const

inlinevirtual

The custom variant types added by this patch.

This must be a vector of strings, since the custom types are generated at runtime and can't be enumerated at compile time.

Author: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

References custom_types_.

utility::vector1< std::string > core::chemical::Patch::deletes_atoms ( ResidueType const & rsd_type ) const

returns list of deleted atom names, useful for identifying patches that go with PDB residues

loop through the cases in this patch and if it is applicable to this ResidueType, compile a list of any atom_names that are deleted.

References applies_to(), and cases_.

utility::vector1< std::string > core::chemical::Patch::deletes_properties ( ResidueType const & rsd_type ) const

returns list of deleted property names, useful for identifying patches that go with PDB residues

loop through the cases in this patch and if it is applicable to this ResidueType, compile a list of any properties that are deleted.

References applies_to(), cases_, and update_ResidueType_enum_files::properties.

utility::vector1< ResidueProperty > core::chemical::Patch::deletes_properties_enums ( ResidueType const & rsd_type ) const

returns list of deleted property enums, useful for identifying patches that go with PDB residues.

Author: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

loop through the cases in this patch and if it is applicable to this ResidueType, compile a list of any properties that are deleted, by enum. Faster than string version.

References applies_to(), cases_, and update_ResidueType_enum_files::properties.

utility::vector1< std::string > core::chemical::Patch::deletes_variants ( ResidueType const & rsd_type ) const

returns list of deleted variant names, useful for identifying patches that go with PDB residues

loop through the cases in this patch and if it is applicable to this ResidueType, compile a list of any variants that are deleted.

References applies_to(), cases_, and update_ResidueType_enum_files::variants.

utility::vector1< core::chemical::VariantType > core::chemical::Patch::deletes_variants_by_enum ( ResidueType const & rsd_type ) const

Returns list of deleted VariantTypes. Doesn't support on-the-fly VariantTypes.

Author: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

loop through the cases in this patch and if it is applicable to this ResidueType, compile a list of any variants that are deleted. This version returns a list of VariantType enums (and does not support on-the-fly types).

References applies_to(), cases_, and update_ResidueType_enum_files::variants.

chemical::AA core::chemical::Patch::generates_aa ( ResidueType const & rsd_type ) const

returns new AA, if changed.

loop through the cases in this patch and if it is applicable to this ResidueType, discover if there is a new name3 generated by the patch.

References protocols::cluster::calibur::aa, core::chemical::ResidueTypeBase::aa(), core::chemical::aa_none, applies_to(), apply(), and cases_.

bool core::chemical::Patch::generates_base_residue_type ( ) const

inline

Is this a special patch that expands the list of base residue types?

References generates_base_residue_type_.

Referenced by patched_name().

std::string core::chemical::Patch::generates_interchangeability_group ( ResidueType const & rsd_type ) const

returns new interchangeability_group, if changed. Only one new interchangeability_group allowed.

loop through the cases in this patch and if it is applicable to this ResidueType, discover if there is a new interchangeability_group generated by the patch.

References applies_to(), and cases_.

std::string core::chemical::Patch::generates_new_name3 ( ResidueType const & rsd_type ) const

returns new name3, if changed. Only one new name3 allowed.

loop through the cases in this patch and if it is applicable to this ResidueType, discover if there is a new name3 generated by the patch.

References applies_to(), and cases_.

bool core::chemical::Patch::is_metapatch ( ) const

inline

Is this a metapatch?

References is_metapatch_.

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

inlinevirtual

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

References name_.

Referenced by apply(), and set_name().

std::string core::chemical::Patch::patched_name ( ResidueTypeBase const & rsd ) const

Returns the name of the residueType after applying the patch (Theoretical - doesn't actually check if the patch would be applied.)

References core::chemical::ResidueTypeBase::base_name(), generates_base_residue_type(), core::chemical::ResidueTypeBase::name(), name_, and core::chemical::PATCH_LINKER.

Referenced by apply().

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 to create each case accordingly (BEGIN_CASE, END_CASE)
Note
keep the order to avoid triggering parsing errors

References add_case(), core::chemical::ResidueTypeSelector::add_line(), core::chemical::case_from_lines(), cases_, core::chemical::ResidueTypeSelector::clear(), custom_types_, core::chemical::ResidueProperties::get_variant_from_string(), is_metapatch_, name_, replaces_residue_type_, res_type_set_mode_, selector_, protocols::hybridization::t, core::chemical::tag_from_line(), core::chemical::tr(), and types_.