binder Namespace Reference

Classes
class	Binder
	Bindings Generator - represent object that can generate binding info for function, class, enum or data variable. More...
class	ClassBinder
class	Config
class	Context
	Module - represent bindings of individual Python module. More...
class	EnumBinder
class	FunctionBinder
class	IncludeSet
class	map_binder
class	vector_binder

Typedefs
typedef std::shared_ptr< Binder >	BinderOP
typedef std::vector< BinderOP >	Binders

Functions
string	template_specialization (clang::CXXRecordDecl const *C)
string	class_name (CXXRecordDecl const *C)
string	python_class_name (CXXRecordDecl const *C)
string	class_qualified_name (CXXRecordDecl const *C)
vector< QualType >	get_type_dependencies (CXXRecordDecl const *C)
bool	is_inherited_from_enable_shared_from_this (CXXRecordDecl const *C)
bool	is_field_assignable (FieldDecl const *f)
bool	is_bindable (FieldDecl *f)
	check if generator can create binding More...
string	bind_data_member (FieldDecl const *d, string const &class_qualified_name)
bool	is_bindable (clang::CXXRecordDecl const *C)
	check if generator can create binding More...
bool	is_binding_requested (clang::CXXRecordDecl const *C, Config const &config)
	check if user requested binding for the given declaration More...
bool	is_skipping_requested (clang::CXXRecordDecl const *C, Config const &config)
	check if user requested skipping for the given declaration More...
void	add_relevant_includes (clang::CXXRecordDecl const *C, IncludeSet &includes, int level)
bool	base_default_default_constructor_available (CXXRecordDecl const *C)
	DEPRECATED Check if all bases have public default constructors. More...
string	binding_public_data_members (CXXRecordDecl const *C)
bool	is_const_overload (CXXMethodDecl *mc)
string	callback_structure_name (CXXRecordDecl const *C)
bool	is_callback_structure_needed (CXXRecordDecl const *C)
bool	is_callback_structure_constructible (CXXRecordDecl const *C)
string	bind_member_functions_for_call_back (CXXRecordDecl const *C, set< string > &binded, int &ret_id, std::vector< clang::FunctionDecl const * > &prefix_includes)
string	binding_public_member_functions (CXXRecordDecl const *C, bool callback_structure, bool callback_structure_constructible, Context &context)
string	binding_template_bases (CXXRecordDecl const *C, bool callback_structure, bool callback_structure_constructible, Context &context)
string	bind_forward_declaration (CXXRecordDecl const *C, Context &context)
	Create forward-binding for given class which consist of only class type without any member, function or constructors. More...
string	bind_constructor (CXXConstructorDecl const *T, pair< string, string > const &constructor_types, uint args_to_bind, bool request_bindings_f, Context &context)
string	bind_constructor (CXXConstructorDecl const *T, pair< string, string > const &constructor_types, Context &context)
std::string	class_name (clang::CXXRecordDecl const *C)
std::string	class_qualified_name (clang::CXXRecordDecl const *C)
std::vector< clang::QualType >	get_type_dependencies (clang::CXXRecordDecl const *C)
std::vector< clang::NamedDecl const * >	get_decl_dependencies (clang::CXXRecordDecl const *C)
std::string	bind_forward_declaration (clang::CXXRecordDecl const *C, Context &)
	Create forward-binding for given class which consist of only class type without any member, function or constructors. More...
std::pair< string, string >	split_in_two (string const &s, string const &error_string)
	Split string in two by ether space or tab character. More...
llvm::raw_ostream &	operator<< (llvm::raw_ostream &os, Binder const &b)
string	generate_include_directives (IncludeSet const &include_set)
string	file_name_prefix_for_binder (BinderOP &b)
	Generate file name where binding for given generator should be stored. More...
void	add_relevant_includes (clang::EnumDecl const *E, IncludeSet &includes, int level)
	extract include needed for this generator and add it to includes vector More...
std::string	bind_enum (std::string const &module, EnumDecl *E)
std::string	bind_enum (std::string const &module, clang::EnumDecl *E)
string	function_arguments (clang::FunctionDecl const *record)
pair< string, string >	function_arguments_for_lambda (clang::FunctionDecl const *record, uint n)
tuple< string, string, string >	function_arguments_for_py_overload (clang::FunctionDecl const *record)
string	template_specialization (FunctionDecl const *F)
string	python_function_name (FunctionDecl const *F)
string	function_pointer_type (FunctionDecl const *F)
string	function_qualified_name (FunctionDecl const *F)
vector< QualType >	get_type_dependencies (FunctionDecl const *F)
bool	is_binding_requested (FunctionDecl const *F, Config const &config)
	check if user requested binding for the given declaration More...
bool	is_skipping_requested (FunctionDecl const *F, Config const &config)
	check if user requested skipping for the given declaration More...
string	bind_function (FunctionDecl const *F, uint args_to_bind, bool request_bindings_f, Context &context)
string	bind_function (string const &module, FunctionDecl const *F, Context &context)
void	add_relevant_includes (FunctionDecl const *F, IncludeSet &includes, int level)
	extract include needed for this generator and add it to includes vector More...
bool	is_bindable (FunctionDecl const *F)
	check if generator can create binding More...
std::string	python_function_name (clang::FunctionDecl const *F)
std::string	function_pointer_type (clang::FunctionDecl const *record)
std::string	function_qualified_name (clang::FunctionDecl const *F)
bool	is_binding_requested (clang::FunctionDecl const *F, Config const &config)
	check if user requested binding for the given declaration More...
bool	is_skipping_requested (clang::FunctionDecl const *F, Config const &config)
	check if user requested skipping for the given declaration More...
std::string	bind_function (std::string const &module, clang::FunctionDecl const *F, Context &)
void	add_relevant_includes (clang::FunctionDecl const *F, IncludeSet &includes, int level)
	extract include needed for this generator and add it to includes vector More...
bool	is_bindable (clang::FunctionDecl const *F)
	check if generator can create binding More...
bool	is_binding_requested (clang::QualType const &qt, Config const &config)
	check if user requested binding for the given QualType More...
bool	is_skipping_requested (QualType const &qt, Config const &config)
string	relevant_include (NamedDecl const *decl)
void	add_relevant_include_for_decl (NamedDecl const *decl, IncludeSet &includes)
void	add_relevant_includes (QualType const &qt, IncludeSet &includes, int level)
	extract include needed for this generator and add it to includes vector More...
bool	is_bindable (QualType const &qt)
void	request_bindings (clang::QualType const &qt, Context &context)
	extract type info from QualType if any and bind relative type More...
string	standard_name (string const &type)
bool	is_python_builtin (NamedDecl const *C)
	check if given class/struct is builtin in Python and therefor should not be binded More...
bool	is_skipping_requested (clang::QualType const &qt, Config const &config)
	check if user requested skipping for the given QualType More...
std::string	relevant_include (clang::NamedDecl const *decl)
void	add_relevant_include_for_decl (clang::NamedDecl const *decl, IncludeSet &includes)
void	add_relevant_includes (clang::QualType const &qt, IncludeSet &includes, int level)
	extract include needed for this generator and add it to includes vector More...
bool	is_bindable (clang::QualType const &qt)
bool	is_python_builtin (clang::NamedDecl const *C)
	check if given class/struct is builtin in Python and therefor should not be binded More...
vector< string >	split (string const &buffer, string const &separator)
	Split string using given separator. More...
void	replace (string &r, string const &from, string const &to)
	Replace all occurrences of string. More...
string	replace_ (string const &s, string const &from, string const &to)
	Replace all occurrences of string and return result as new string. More...
bool	begins_with (std::string const &source, std::string const &prefix)
	check if string begins with given prefix More...
bool	ends_with (std::string const &source, std::string const &prefix)
	check if string ends with given prefix More...
string	indent (std::string const &code, std::string const &indentation)
	indent given code More...
void	update_source_file (std::string const &prefix, std::string const &file_name, std::string const &code)
	Try to read exisitng file and if content does not match to code - write a new version. Also create nested dirs starting from prefix if nessesary. More...
string	namespace_from_named_decl (NamedDecl const *decl)
string	typename_from_type_decl (TypeDecl *decl)
	generate unique string representation of type represented by given declaration More...
string	base_namespace (string const &ns)
	Calculate base (upper) namespace for given one: core::pose::motif –> core::pose. More...
string	last_namespace (string const &ns)
	Calculate last namespace for given one: core::pose::motif –> motif. More...
void	fix_boolean_types (std::string &type)
	replace all _Bool types with bool More...
string	expresion_to_string (clang::Expr *e)
	Generate string representation of given expression. More...
string	template_argument_to_string (clang::TemplateArgument const &)
	Generate string representation of given TemplateArgument. More...
string	line_number (NamedDecl const *decl)
string	mangle_type_name (string const &name, bool mark_template)
string	generate_comment_for_declaration (clang::NamedDecl const *decl)
string	get_text (comments::Comment const *C, SourceManager const &SM, SourceLocation previous)
std::string	generate_documentation_string_for_declaration (clang::Decl const *decl)
std::string	namespace_from_named_decl (clang::NamedDecl const *decl)
	calculate namespace path from given NamedDecl, like: std, core::pose More...
std::string	typename_from_type_decl (clang::TypeDecl *decl)
std::string	line_number (clang::NamedDecl const *decl)
	calcualte line in source file for NamedDecl More...

Variables
const char *	call_back_function_body_template
char const *	constructor_template = "\tcl.def(\"__init__\", []({2} *self_{0}) {{ new (self_) {2}({1}); }}, \"doc\");"
char const *	constructor_if_template = "\tcl.def(\"__init__\", [cl_type](pybind11::handle self_{0}) {{ if (self_.get_type() == cl_type) new (self_.cast<{2} *>()) {2}({1}); else new (self_.cast<{3} *>()) {3}({1}); }}, \"doc\");"
const char *	main_module_header
const char *	module_header = "\n#include <pybind11/pybind11.h>\n\n{}#ifndef BINDER_PYBIND11_TYPE_CASTER\n\t#define BINDER_PYBIND11_TYPE_CASTER\n\tPYBIND11_DECLARE_HOLDER_TYPE(T, std::shared_ptr<T>);\n#endif\n\n"
const char *	module_function_suffix = "(std::function< pybind11::module &(std::string const &namespace_) > &M)"
static std::map< string, string > const	cpp_python_operator_map

Typedef Documentation

typedef std::shared_ptr< Binder > binder::BinderOP

typedef std::vector<BinderOP> binder::Binders

Function Documentation

void binder::add_relevant_include_for_decl	(	clang::NamedDecl const *	decl,
		IncludeSet &	includes
	)

void binder::add_relevant_include_for_decl	(	NamedDecl const *	decl,
		IncludeSet &	includes
	)

References binder::IncludeSet::add_include(), begins_with(), name, O_annotate_includes, basic::options::OptionKeys::score::fiber_diffraction::p, and relevant_include().

Referenced by add_relevant_includes().

void binder::add_relevant_includes	(	clang::EnumDecl const *	E,
		IncludeSet &	includes,
		int	level
	)

extract include needed for this generator and add it to includes vector

References binder::IncludeSet::add_decl(), and add_relevant_include_for_decl().

void binder::add_relevant_includes	(	clang::QualType const &	qt,
		IncludeSet &	includes,
		int	level
	)

extract include needed for this generator and add it to includes vector

void binder::add_relevant_includes	(	clang::FunctionDecl const *	F,
		IncludeSet &	includes,
		int	level
	)

extract include needed for this generator and add it to includes vector

void binder::add_relevant_includes	(	QualType const &	qt,
		IncludeSet &	includes,
		int	level
	)

extract include needed for this generator and add it to includes vector

References basic::options::OptionKeys::out::level.

void binder::add_relevant_includes	(	clang::CXXRecordDecl const *	C,
		IncludeSet &	includes,
		int	level
	)

References binder::IncludeSet::add_decl(), add_relevant_include_for_decl(), is_bindable(), basic::options::OptionKeys::in::file::t, and test.T850_SubClassing::v.

Referenced by binder::EnumBinder::add_relevant_includes(), binder::FunctionBinder::add_relevant_includes(), binder::ClassBinder::add_relevant_includes(), and add_relevant_includes().

void binder::add_relevant_includes	(	FunctionDecl const *	F,
		IncludeSet &	includes,
		int	level
	)

extract include needed for this generator and add it to includes vector

References binder::IncludeSet::add_decl(), add_relevant_include_for_decl(), add_relevant_includes(), get_type_dependencies(), and basic::options::OptionKeys::in::file::t.

bool binder::base_default_default_constructor_available

(

CXXRecordDecl const *

C

)

DEPRECATED Check if all bases have public default constructors.

References basic::options::OptionKeys::score::fiber_diffraction::b, and basic::options::OptionKeys::in::file::t.

Referenced by binder::ClassBinder::bind().

std::string binder::base_namespace

(

string const &

ns

)

Calculate base (upper) namespace for given one: core::pose::motif –> core::pose.

References demo.D060_Folding::f.

Referenced by binder::Context::create_all_nested_namespaces(), and binder::Context::generate().

bool binder::begins_with	(	std::string const &	source,
		std::string const &	prefix
	)

check if string begins with given prefix

References basic::options::OptionKeys::antibody::prefix.

Referenced by add_relevant_include_for_decl(), file_name_prefix_for_binder(), is_bindable(), binder::Config::is_include_skipping_requested(), binder::Config::is_namespace_binding_requested(), binder::Config::is_namespace_skipping_requested(), and is_python_builtin().

string binder::bind_constructor	(	CXXConstructorDecl const *	T,
		pair< string, string > const &	constructor_types,
		uint	args_to_bind,
		bool	request_bindings_f,
		Context &	context
	)

References app.delta_score_per_mutation::args, constructor_if_template, constructor_template, tools.CppParser::context, fmt::format(), function_arguments(), function_arguments_for_lambda(), basic::options::OptionKeys::dna::specificity::params, and request_bindings().

string binder::bind_constructor	(	CXXConstructorDecl const *	T,
		pair< string, string > const &	constructor_types,
		Context &	context
	)

References tools.CppParser::context.

Referenced by binder::ClassBinder::bind().

string binder::bind_data_member	(	FieldDecl const *	d,
		string const &	class_qualified_name
	)

References class_qualified_name().

Referenced by binding_public_data_members().

std::string binder::bind_enum	(	std::string const &	module,
		clang::EnumDecl *	E
	)

std::string binder::bind_enum	(	std::string const &	module,
		EnumDecl *	E
	)

References generate_documentation_string_for_declaration(), and name.

Referenced by binder::EnumBinder::bind(), and binder::ClassBinder::bind().

std::string binder::bind_forward_declaration	(	clang::CXXRecordDecl const *	C,
		Context &
	)

Create forward-binding for given class which consist of only class type without any member, function or constructors.

string binder::bind_forward_declaration	(	CXXRecordDecl const *	C,
		Context &	context
	)

Create forward-binding for given class which consist of only class type without any member, function or constructors.

References class_qualified_name(), is_inherited_from_enable_shared_from_this(), line_number(), binder::Context::module_variable_name(), namespace_from_named_decl(), python_class_name(), and relevant_include().

std::string binder::bind_function	(	std::string const &	module,
		clang::FunctionDecl const *	F,
		Context &
	)

string binder::bind_function	(	FunctionDecl const *	F,
		uint	args_to_bind,
		bool	request_bindings_f,
		Context &	context
	)

References app.delta_score_per_mutation::args, class_qualified_name(), tools.CppParser::context, ObjexxFCL::format::F(), fix_boolean_types(), function_arguments_for_lambda(), function_pointer_type(), function_qualified_name(), generate_documentation_string_for_declaration(), extract_scores_and_constraints::get, python_function_name(), request_bindings(), standard_name(), and template_specialization().

Referenced by binding_public_member_functions().

string binder::bind_function	(	string const &	module,
		FunctionDecl const *	F,
		Context &	context
	)

References tools.CppParser::context.

Referenced by binder::FunctionBinder::bind().

string binder::bind_member_functions_for_call_back	(	CXXRecordDecl const *	C,
		set< string > &	binded,
		int &	ret_id,
		std::vector< clang::FunctionDecl const * > &	prefix_includes
	)

References app.delta_score_per_mutation::args, basic::options::OptionKeys::score::fiber_diffraction::b, call_back_function_body_template, fix_boolean_types(), fmt::format(), function_arguments_for_py_overload(), extract_scores_and_constraints::get, indent(), is_bindable(), is_const_overload(), is_skipping_requested(), key, basic::options::OptionKeys::stepwise::move, python_function_name(), and utility::to_string().

Referenced by binder::ClassBinder::generate_prefix_code().

string binder::binding_public_data_members

(

CXXRecordDecl const *

C

)

References bind_data_member(), class_qualified_name(), demo.D060_Folding::f, and is_bindable().

Referenced by binder::ClassBinder::bind(), and binding_template_bases().

string binder::binding_public_member_functions	(	CXXRecordDecl const *	C,
		bool	callback_structure,
		bool	callback_structure_constructible,
		Context &	context
	)

References bind_function(), extract_scores_and_constraints::get, is_bindable(), is_const_overload(), and is_skipping_requested().

Referenced by binder::ClassBinder::bind(), and binding_template_bases().

string binder::binding_template_bases	(	CXXRecordDecl const *	C,
		bool	callback_structure,
		bool	callback_structure_constructible,
		Context &	context
	)

References basic::options::OptionKeys::score::fiber_diffraction::b, binding_public_data_members(), binding_public_member_functions(), extract_scores_and_constraints::get, and is_skipping_requested().

Referenced by binder::ClassBinder::bind().

string binder::callback_structure_name ( CXXRecordDecl const *  C )

inline

References python_class_name().

Referenced by binder::ClassBinder::bind(), and binder::ClassBinder::generate_prefix_code().

std::string binder::class_name

(

clang::CXXRecordDecl const *

C

)

string binder::class_name

(

CXXRecordDecl const *

C

)

References standard_name(), and template_specialization().

Referenced by python_class_name().

std::string binder::class_qualified_name

(

clang::CXXRecordDecl const *

C

)

string binder::class_qualified_name

(

CXXRecordDecl const *

C

)

References standard_name(), and template_specialization().

Referenced by binder::Context::add_to_binded(), binder::ClassBinder::bind(), bind_data_member(), bind_forward_declaration(), bind_function(), binder::ClassBinder::bind_repr(), binding_public_data_members(), function_pointer_type(), binder::ClassBinder::generate_prefix_code(), binder::Context::global_insertion_operator(), binder::ClassBinder::id(), is_binding_requested(), binder::Context::is_forward_needed(), is_skipping_requested(), binder::ClassBinder::maybe_base_classes(), and binder::Context::sort_binders().

bool binder::ends_with	(	std::string const &	source,
		std::string const &	prefix
	)

check if string ends with given prefix

References basic::options::OptionKeys::antibody::prefix.

Referenced by is_const_overload().

std::string binder::expresion_to_string

(

clang::Expr *

e

)

Generate string representation of given expression.

References basic::options::OptionKeys::in::file::s.

string binder::file_name_prefix_for_binder

(

BinderOP &

b

)

Generate file name where binding for given generator should be stored.

References begins_with(), namespace_from_named_decl(), relevant_include(), and replace().

Referenced by binder::Context::generate().

void binder::fix_boolean_types

(

string &

type

)

replace all _Bool types with bool

Referenced by bind_function(), bind_member_functions_for_call_back(), binder::ClassBinder::bind_with(), function_arguments(), function_arguments_for_lambda(), function_arguments_for_py_overload(), function_pointer_type(), function_qualified_name(), and template_specialization().

std::string binder::function_arguments

(

clang::FunctionDecl const *

record

)

References fix_boolean_types().

Referenced by binder::FunctionBinder::bind(), bind_constructor(), function_pointer_type(), and function_qualified_name().

std::pair< std::string, std::string > binder::function_arguments_for_lambda	(	clang::FunctionDecl const *	record,
		uint	n
	)

References basic::options::OptionKeys::score::fiber_diffraction::a, fix_boolean_types(), and utility::to_string().

Referenced by bind_constructor(), and bind_function().

std::tuple< std::string, std::string, std::string > binder::function_arguments_for_py_overload

(

clang::FunctionDecl const *

record

)

References basic::options::OptionKeys::score::fiber_diffraction::a, fix_boolean_types(), basic::options::OptionKeys::score::fiber_diffraction::p, and utility::to_string().

Referenced by bind_member_functions_for_call_back().

std::string binder::function_pointer_type

(

clang::FunctionDecl const *

record

)

string binder::function_pointer_type

(

FunctionDecl const *

F

)

References class_qualified_name(), fix_boolean_types(), function_arguments(), basic::options::OptionKeys::antibody::prefix, and standard_name().

Referenced by binder::Context::add_insertion_operator(), and bind_function().

std::string binder::function_qualified_name

(

clang::FunctionDecl const *

F

)

string binder::function_qualified_name

(

FunctionDecl const *

F

)

References fix_boolean_types(), function_arguments(), standard_name(), and template_specialization().

Referenced by bind_function(), binder::FunctionBinder::id(), is_binding_requested(), is_const_overload(), and is_skipping_requested().

std::string binder::generate_comment_for_declaration

(

clang::NamedDecl const *

decl

)

References line_number(), relevant_include(), and standard_name().

Referenced by binder::EnumBinder::bind(), binder::ClassBinder::bind(), binder::ClassBinder::bind_with(), and binder::ClassBinder::generate_prefix_code().

std::string binder::generate_documentation_string_for_declaration

(

clang::Decl const *

decl

)

References get_text(), replace(), and utility::options::OptionKeys::options::table::text.

Referenced by binder::ClassBinder::bind(), bind_enum(), and bind_function().

string binder::generate_include_directives

(

IncludeSet const &

include_set

)

References extract_scores_and_constraints::get, and binder::IncludeSet::includes().

Referenced by binder::Context::generate().

std::vector<clang::NamedDecl const *> binder::get_decl_dependencies

(

clang::CXXRecordDecl const *

C

)

string binder::get_text	(	comments::Comment const *	C,
		SourceManager const &	SM,
		SourceLocation	previous
	)

Referenced by generate_documentation_string_for_declaration().

std::vector<clang::QualType> binder::get_type_dependencies

(

clang::CXXRecordDecl const *

C

)

vector<QualType> binder::get_type_dependencies

(

CXXRecordDecl const *

C

)

References basic::options::OptionKeys::in::file::t.

Referenced by is_binding_requested(), and is_skipping_requested().

vector<QualType> binder::get_type_dependencies

(

FunctionDecl const *

F

)

Referenced by add_relevant_includes(), is_binding_requested(), and is_skipping_requested().

std::string binder::indent	(	string const &	code,
		string const &	indentation
	)

indent given code

References basic::options::OptionKeys::in::file::l, clean_pdb_keep_ligand::lines, and split().

Referenced by binder::ClassBinder::bind(), bind_member_functions_for_call_back(), basic::YamlEmitter::do_indent(), basic::JsonEmitter::do_indent(), basic::YamlEmitter::end_raw(), utility::options::OptionCollection::load_options_from_stream(), basic::Emitter::start_list(), basic::Emitter::start_map(), basic::YamlEmitter::start_raw(), basic::JsonEmitter::start_raw(), and basic::YamlEmitter::write_list_marker().

bool binder::is_bindable

(

clang::QualType const &

qt

)

bool binder::is_bindable

(

clang::FunctionDecl const *

F

)

check if generator can create binding

bool binder::is_bindable

(

FieldDecl *

f

)

check if generator can create binding

References is_field_assignable().

Referenced by binder::FunctionBinder::bindable(), BinderVisitor::VisitCXXRecordDecl(), and BinderVisitor::VisitFunctionDecl().

bool binder::is_bindable

(

clang::CXXRecordDecl const *

C

)

check if generator can create binding

References is_python_builtin(), basic::options::OptionKeys::in::file::t, and test.T850_SubClassing::v.

Referenced by add_relevant_includes(), binder::ClassBinder::bind(), bind_member_functions_for_call_back(), binder::ClassBinder::bindable(), binding_public_data_members(), binding_public_member_functions(), is_callback_structure_constructible(), is_callback_structure_needed(), and binder::ClassBinder::maybe_base_classes().

bool binder::is_bindable

(

QualType const &

qt

)

References begins_with(), and standard_name().

bool binder::is_bindable

(

FunctionDecl const *

F

)

check if generator can create binding

References cpp_python_operator_map, ObjexxFCL::format::F(), and basic::options::OptionKeys::score::fiber_diffraction::p.

bool binder::is_binding_requested	(	clang::QualType const &	qt,
		Config const &	config
	)

check if user requested binding for the given QualType

References basic::options::OptionKeys::frags::scoring::config.

bool binder::is_binding_requested	(	clang::FunctionDecl const *	F,
		Config const &	config
	)

check if user requested binding for the given declaration

bool binder::is_binding_requested	(	FunctionDecl const *	F,
		Config const &	config
	)

check if user requested binding for the given declaration

References function_qualified_name(), get_type_dependencies(), is_binding_requested(), binder::Config::is_function_binding_requested(), binder::Config::is_namespace_binding_requested(), namespace_from_named_decl(), and basic::options::OptionKeys::in::file::t.

Referenced by binder::FunctionBinder::request_bindings_and_skipping().

bool binder::is_binding_requested	(	clang::CXXRecordDecl const *	C,
		Config const &	config
	)

check if user requested binding for the given declaration

References class_qualified_name(), get_type_dependencies(), binder::Config::is_class_binding_requested(), binder::Config::is_namespace_binding_requested(), is_skipping_requested(), namespace_from_named_decl(), standard_name(), and basic::options::OptionKeys::in::file::t.

Referenced by is_binding_requested(), and binder::ClassBinder::request_bindings_and_skipping().

bool binder::is_callback_structure_constructible

(

CXXRecordDecl const *

C

)

References basic::options::OptionKeys::score::fiber_diffraction::b, extract_scores_and_constraints::get, is_bindable(), and is_skipping_requested().

Referenced by binder::ClassBinder::bind().

bool binder::is_callback_structure_needed

(

CXXRecordDecl const *

C

)

References basic::options::OptionKeys::score::fiber_diffraction::b, and is_bindable().

Referenced by binder::ClassBinder::bind(), and binder::ClassBinder::generate_prefix_code().

bool binder::is_const_overload

(

CXXMethodDecl *

mc

)

References C, ends_with(), function_qualified_name(), and name.

Referenced by bind_member_functions_for_call_back(), and binding_public_member_functions().

bool binder::is_field_assignable

(

FieldDecl const *

f

)

References C.

Referenced by is_bindable().

bool binder::is_inherited_from_enable_shared_from_this

(

CXXRecordDecl const *

C

)

References basic::options::OptionKeys::score::fiber_diffraction::b.

Referenced by binder::ClassBinder::bind(), and bind_forward_declaration().

bool binder::is_python_builtin

(

clang::NamedDecl const *

C

)

check if given class/struct is builtin in Python and therefor should not be binded

bool binder::is_python_builtin

(

NamedDecl const *

C

)

check if given class/struct is builtin in Python and therefor should not be binded

References begins_with(), name, and standard_name().

Referenced by is_bindable(), binder::Binder::is_binded(), binder::Context::is_forward_needed(), and binder::Context::request_bindings().

bool binder::is_skipping_requested	(	clang::QualType const &	qt,
		Config const &	config
	)

check if user requested skipping for the given QualType

bool binder::is_skipping_requested	(	QualType const &	qt,
		Config const &	config
	)

References basic::options::OptionKeys::frags::scoring::config.

Referenced by request_bindings().

bool binder::is_skipping_requested	(	clang::FunctionDecl const *	F,
		Config const &	config
	)

check if user requested skipping for the given declaration

bool binder::is_skipping_requested	(	FunctionDecl const *	F,
		Config const &	config
	)

check if user requested skipping for the given declaration

References C, function_qualified_name(), get_type_dependencies(), binder::Config::is_function_skipping_requested(), binder::Config::is_namespace_skipping_requested(), test.T007_TracerIO::M, name, namespace_from_named_decl(), basic::options::OptionKeys::rescore::skip, standard_name(), and basic::options::OptionKeys::in::file::t.

Referenced by binder::FunctionBinder::request_bindings_and_skipping().

bool binder::is_skipping_requested	(	clang::CXXRecordDecl const *	C,
		Config const &	config
	)

check if user requested skipping for the given declaration

References class_qualified_name(), get_type_dependencies(), binder::Config::is_class_skipping_requested(), binder::Config::is_namespace_skipping_requested(), namespace_from_named_decl(), basic::options::OptionKeys::rescore::skip, standard_name(), and basic::options::OptionKeys::in::file::t.

Referenced by bind_member_functions_for_call_back(), binding_public_member_functions(), binding_template_bases(), is_binding_requested(), is_callback_structure_constructible(), binder::ClassBinder::maybe_base_classes(), and binder::ClassBinder::request_bindings_and_skipping().

std::string binder::last_namespace

(

string const &

ns

)

Calculate last namespace for given one: core::pose::motif –> motif.

References demo.D060_Folding::f.

Referenced by binder::Context::generate().

std::string binder::line_number

(

clang::NamedDecl const *

decl

)

calcualte line in source file for NamedDecl

string binder::line_number

(

NamedDecl const *

decl

)

References utility::to_string().

Referenced by binder::FunctionBinder::bind(), bind_forward_declaration(), and generate_comment_for_declaration().

std::string binder::mangle_type_name	(	string const &	name,
		bool	mark_template
	)

Referenced by binder::ClassBinder::bind_with(), python_class_name(), and python_function_name().

std::string binder::namespace_from_named_decl

(

clang::NamedDecl const *

decl

)

calculate namespace path from given NamedDecl, like: std, core::pose

string binder::namespace_from_named_decl

(

NamedDecl const *

decl

)

References basic::options::OptionKeys::in::path::path, and standard_name().

Referenced by binder::EnumBinder::bind(), binder::FunctionBinder::bind(), binder::ClassBinder::bind(), bind_forward_declaration(), binder::ClassBinder::bind_with(), binder::Context::create_all_nested_namespaces(), file_name_prefix_for_binder(), binder::Context::generate(), is_binding_requested(), is_skipping_requested(), and binder::EnumBinder::request_bindings_and_skipping().

llvm::raw_ostream & binder::operator<<	(	llvm::raw_ostream &	os,
		Binder const &	b
	)

References name, binder::Binder::named_decl(), and basic::options::OptionKeys::in::path::path.

string binder::python_class_name

(

CXXRecordDecl const *

C

)

References class_name(), mangle_type_name(), and name.

Referenced by binder::ClassBinder::bind(), bind_forward_declaration(), and callback_structure_name().

std::string binder::python_function_name

(

clang::FunctionDecl const *

F

)

string binder::python_function_name

(

FunctionDecl const *

F

)

References cpp_python_operator_map, mangle_type_name(), and template_specialization().

Referenced by bind_function(), and bind_member_functions_for_call_back().

std::string binder::relevant_include

(

clang::NamedDecl const *

decl

)

string binder::relevant_include

(

NamedDecl const *

decl

)

References app.delta_score_per_mutation::data.

Referenced by add_relevant_include_for_decl(), binder::FunctionBinder::bind(), bind_forward_declaration(), file_name_prefix_for_binder(), and generate_comment_for_declaration().

void binder::replace	(	string &	r,
		string const &	from,
		string const &	to
	)

Replace all occurrences of string.

Replace all occurrences of string inplace.

Referenced by tools.DoxygenExtractorPyPP.doxygen_doc_extractor::__call__(), app.pyrosetta_toolkit.modules.prettytable.prettytable.PrettyTable::_get_formatted_html_string(), app.pyrosetta_toolkit.modules.prettytable.prettytable.PrettyTable::_get_simple_html_string(), utility::file::PathName::assign(), utility::file::FileName::assign(), BuildBindings::buildModule_One(), BuildBindings::calculate_source_modification_date(), file_name_prefix_for_binder(), exclude::finalize(), exclude::finalize_old(), generate_documentation_string_for_declaration(), tools.CppParser::generate_monolith_main(), tools.dox_extract.dox_extract::getDoxygenComment(), tools.CppParser.CppClass::getMangledName(), exclude::isFileInScons(), utility::file::PathName::path(), utility::file::FileName::path(), replace_(), self-test::run_test(), standard_name(), and BuildBindings::windows_buildOneNamespace().

std::string binder::replace_	(	string const &	s,
		string const &	from,
		string const &	to
	)

Replace all occurrences of string and return result as new string.

References replace().

Referenced by binder::Context::generate().

void binder::request_bindings	(	clang::QualType const &	qt,
		Context &	context
	)

extract type info from QualType if any and bind relative type

References tools.CppParser::context, extract_scores_and_constraints::get, is_skipping_requested(), binder::Context::request_bindings(), and typename_from_type_decl().

Referenced by bind_constructor(), bind_function(), binder::ClassBinder::maybe_base_classes(), binder::EnumBinder::request_bindings_and_skipping(), binder::FunctionBinder::request_bindings_and_skipping(), and binder::ClassBinder::request_bindings_and_skipping().

std::vector< std::string > binder::split	(	string const &	buffer,
		string const &	separator
	)

Split string using given separator.

References line, and clean_pdb_keep_ligand::lines.

Referenced by app.pyrosetta_toolkit.modules.prettytable.prettytable.PrettyTable::_stringify_row(), BuildBindings::buildModule_All(), BuildBindings::buildModule_One(), app.pyrosetta_toolkit.modules.DesignBreakdown.DesignBreakdown::calculate_results(), BuildBindings::calculate_source_modification_date(), app.pyrosetta_toolkit.window_modules.design.ResfileDesignWindow.ResfileDesignWindow::check_for_residue_existance(), app.pyrosetta_toolkit.modules.tools.output::convert_PDBLIST_to_sqlite3db(), app.pyrosetta_toolkit.modules.ScoreAnalysis.ScoreAnalysis::copy_results(), arls_impl::find_programs(), build::generate_bindings(), build::generate_rosetta_external_cmake_files(), BuildBindings::get_all_rosetta_objs(), BuildBindings::get_compiler_defines(), toolbox.adjust_library_path::get_current_dylib_path(), build::get_rosetta_include_directories(), build::get_rosetta_system_include_directories(), app.pyrosetta_toolkit.modules.tools.interfaces.Antibodies::getContactCDRs(), PhiPsi::hbond_record(), indent(), exclude::isFileInScons(), tools.CppParser.CppClass::isPublicMembersWrappable(), best_ifaceE::main(), get_scores::main(), prune_atdiff_top5pct::main(), BuildBindings::main(), app.pyrosetta_toolkit.window_modules.design.ResfileDesignWindow.ResfileDesignWindow::nextRes(), app.pyrosetta_toolkit.window_modules.ligand_ncaa_ptm_manager.ligand_ncaa_ptm_manager.ligand_ncaa_ptm_manager::open_param_or_patch(), app.pyrosetta_toolkit.modules.tools.output::output_molfile_to_params(), tools.CppParser.GccXML::parse(), app.pyrosetta_toolkit.window_modules.scorefunction.ScoreFxnControl.ScoreFxnControl::populateScoreList(), app.pyrosetta_toolkit.window_modules.design.ResfileDesignWindow.ResfileDesignWindow::prevRes(), app.pyrosetta_toolkit.modules.ScoreAnalysis.ScoreAnalysis::read_FASC(), app.pyrosetta_toolkit.modules.ScoreAnalysis.ScoreAnalysis::read_SC(), register_options(), app.pyrosetta_toolkit.window_modules.design.ResfileDesignWindow.ResfileDesignWindow::remove_from_current_designs_callback(), app.pyrosetta_toolkit.modules.tools.general_tools::renameandsave(), app.pyrosetta_toolkit.modules.calibur.calibur::ret_centers(), app.pyrosetta_toolkit.modules.tools.loops::return_residue_array(), run(), self-test::run_test(), demo.D090_Ala_scan::scanning_analysis(), app.pyrosetta_toolkit.window_main.frames.SimpleAnalysisFrame.SimpleAnalysisFrame::score_loops(), split_in_two(), update_source_file(), app.pyrosetta_toolkit.window_modules.design.ResfileDesignWindow.ResfileDesignWindow::updateInfo(), BuildBindings::windows_buildOneNamespace(), and tools.CppParser::wrapModule().

std::pair<string, string> binder::split_in_two	(	string const &	s,
		string const &	error_string
	)

Split string in two by ether space or tab character.

References min(), ObjexxFCL::space(), and split().

Referenced by binder::Config::read().

std::string binder::standard_name

(

string const &

type

)

References basic::options::OptionKeys::score::fiber_diffraction::p, and replace().

Referenced by binder::ClassBinder::bind(), bind_function(), binder::ClassBinder::bind_with(), class_name(), class_qualified_name(), function_pointer_type(), function_qualified_name(), generate_comment_for_declaration(), is_bindable(), is_binding_requested(), is_python_builtin(), is_skipping_requested(), binder::ClassBinder::maybe_base_classes(), namespace_from_named_decl(), template_specialization(), and typename_from_type_decl().

std::string binder::template_argument_to_string

(

clang::TemplateArgument const &

t

)

Generate string representation of given TemplateArgument.

References basic::options::OptionKeys::in::file::s.

Referenced by binder::ClassBinder::bind_with(), and template_specialization().

std::string binder::template_specialization

(

clang::CXXRecordDecl const *

C

)

References fix_boolean_types(), basic::options::OptionKeys::in::file::t, and template_argument_to_string().

Referenced by binder::ClassBinder::bind_with(), class_name(), and class_qualified_name().

string binder::template_specialization

(

FunctionDecl const *

F

)

References fix_boolean_types(), standard_name(), and template_argument_to_string().

Referenced by bind_function(), function_qualified_name(), and python_function_name().

std::string binder::typename_from_type_decl

(

clang::TypeDecl *

decl

)

string binder::typename_from_type_decl

(

TypeDecl *

decl

)

generate unique string representation of type represented by given declaration

References standard_name().

Referenced by binder::Context::add(), and request_bindings().

void binder::update_source_file	(	std::string const &	prefix,
		std::string const &	file_name,
		std::string const &	code
	)

Try to read exisitng file and if content does not match to code - write a new version. Also create nested dirs starting from prefix if nessesary.

References demo.D060_Folding::f, basic::options::OptionKeys::in::path::path, basic::options::OptionKeys::antibody::prefix, and split().

Referenced by binder::Context::generate().

Variable Documentation

const char* binder::call_back_function_body_template

Initial value:

= R"_(
pybind11::gil_scoped_acquire gil;
pybind11::function overload = pybind11::get_overload(this, "{}");
if (overload) return overload.operator()<pybind11::return_value_policy::reference>({}).cast<{}>();
)_"

Referenced by bind_member_functions_for_call_back().

char const* binder::constructor_if_template = "\tcl.def(\"__init__\", [cl_type](pybind11::handle self_{0}) {{ if (self_.get_type() == cl_type) new (self_.cast<{2} *>()) {2}({1}); else new (self_.cast<{3} *>()) {3}({1}); }}, \"doc\");"

Referenced by bind_constructor().

char const* binder::constructor_template = "\tcl.def(\"__init__\", []({2} *self_{0}) {{ new (self_) {2}({1}); }}, \"doc\");"

Referenced by bind_constructor().

std::map<string, string > const binder::cpp_python_operator_map

static

Initial value:

{
  {"operator+", "__add__"},
  {"operator-", "__sub__"},

  
  
  {"operator*=", "__imul__"},
  {"operator/=", "__idiv__"},

  {"operator()", "__call__"},
  {"operator==", "__eq__"},
  {"operator!=", "__ne__"},
  {"operator[]", "__getitem__"},
  {"operator=",  "assign"},
  {"operator++", "plus_plus"},
  {"operator--", "minus_minus"},
}

Referenced by is_bindable(), and python_function_name().

const char* binder::main_module_header

Initial value:

= R"_(#include <map>
#include <memory>
#include <stdexcept>
#include <functional>

#include <pybind11/pybind11.h>

typedef std::function< pybind11::module & (std::string const &) > ModuleGetter;

{0}

PYBIND11_PLUGIN({1}) {{
  std::map <std::string, std::shared_ptr<pybind11::module> > modules;
  ModuleGetter M = [&](std::string const &namespace_) -> pybind11::module & {{
    auto it = modules.find(namespace_);
    if( it == modules.end() ) throw std::runtime_error("Attempt to access pybind11::module for namespace " + namespace_ + " before it was created!!!");
    return * it->second;
  }};

  modules[""] = std::make_shared<pybind11::module>("{1}", "{1} module");

  std::vector< std::pair<std::string, std::string> > sub_modules {{
{2} }};
  for(auto &p : sub_modules ) modules[p.first.size() ? p.first+"::"+p.second : p.second] = std::make_shared<pybind11::module>( modules[p.first]->def_submodule(p.second.c_str(), ("Bindings for " + p.first + "::" + p.second + " namespace").c_str() ) );

{3}
  return modules[""]->ptr();
}}
)_"

Referenced by binder::Context::generate().

const char* binder::module_function_suffix = "(std::function< pybind11::module &(std::string const &namespace_) > &M)"

Referenced by binder::Context::generate().

const char* binder::module_header = "\n#include <pybind11/pybind11.h>\n\n{}#ifndef BINDER_PYBIND11_TYPE_CASTER\n\t#define BINDER_PYBIND11_TYPE_CASTER\n\tPYBIND11_DECLARE_HOLDER_TYPE(T, std::shared_ptr<T>);\n#endif\n\n"

Referenced by binder::Context::generate().