Classes
struct	BondData

class	CtabParserBase

class	CtabV2000Parser

class	CtabV3000Parser

class	MolFileIOAtom

class	MolFileIOBond

class	MolFileIOMolecule

class	MolFileIOReader

class	MolWriter

class	SDFParser

Typedefs
typedef utility::pointer::shared_ptr < MolFileIOAtom >	MolFileIOAtomOP

typedef utility::pointer::shared_ptr < MolFileIOBond >	MolFileIOBondOP

typedef utility::pointer::shared_ptr < MolFileIOMolecule >	MolFileIOMoleculeOP

typedef utility::pointer::shared_ptr < const MolFileIOAtom >	MolFileIOAtomCOP

typedef utility::pointer::shared_ptr < const MolFileIOBond >	MolFileIOBondCOP

typedef utility::pointer::shared_ptr < const MolFileIOMolecule >	MolFileIOMoleculeCOP

typedef boost::undirected_graph < MolFileIOAtomOP, MolFileIOBondOP >	MolFileIOGraph

typedef MolFileIOGraph::vertex_descriptor	mioAD

typedef MolFileIOGraph::edge_descriptor	mioBD

typedef core::Size	AtomIndex

typedef core::Size	BondIndex

typedef std::map< std::string, std::string >	StrStrMap

Functions
static basic::Tracer	TR ("core.chemical.sdf.CtabV2000Parser")

static basic::Tracer	TR ("core.chemical.sdf.CtabV3000Parser")

std::set< BondData >	parse_bond_type_data (std::string raw_data)

std::map< core::Size, std::string >	parse_atom_type_data (std::string raw_data)

static basic::Tracer	tr ("core.chemical.sdf.mol_writer")

template<class Input_t >
void	output_residue (std::string const &outfile, Input_t &residue)

template<class Input_t >
void	output_residue (std::ostream &output_stream, Input_t &residue)

static basic::Tracer	TR ("core.io.sdf.MolFileIOData")

void	dump_graph (MolFileIOGraph const &graph)

bool	has (MolFileIOGraph const &graph, mioAD vd)

bool	has (MolFileIOGraph const &graph, mioBD ed)

static basic::Tracer	TR ("core.io.sdf.MolFileIOReader")

MutableResidueTypeOP	convert_to_ResidueType (utility::vector1< MolFileIOMoleculeOP > molfile_data, std::string atom_type_tag="fa_standard", std::string element_type_tag="default", std::string mm_atom_type_tag="fa_standard")
	Convert the vector of MolFileIOMolecules into a single residue type, using multiple entries as rotamers Can return a null pointer if there's something wrong with the underlying data. More...

MutableResidueTypeOP	convert_to_ResidueType (utility::vector1< MolFileIOMoleculeOP > molfile_data, AtomTypeSetCOP atom_types, ElementSetCOP element_types, MMAtomTypeSetCOP mm_atom_types)
	Convert the vector of MolFileIOMolecules into a single residue type, using multiple entries as rotamers Can return a null pointer if there's something wrong with the underlying data. More...

utility::vector1 < MutableResidueTypeOP >	convert_to_ResidueTypes (utility::vector1< MolFileIOMoleculeOP > molfile_data, bool load_rotamers=true, std::string atom_type_tag="fa_standard", std::string element_type_tag="default", std::string mm_atom_type_tag="fa_standard")
	Convert the vector of MolFileIOMolecules into multiple residue types If load_rotamers is false, each will be loaded as a single ResidueType Otherwise, entries with the same name will be loaded as rotamers Will not return results for entries with bad Data. More...

utility::vector1 < MutableResidueTypeOP >	convert_to_ResidueTypes (utility::vector1< MolFileIOMoleculeOP > molfile_data, bool load_rotamers, AtomTypeSetCOP atom_types, ElementSetCOP element_types, MMAtomTypeSetCOP mm_atom_types)
	Convert the vector of MolFileIOMolecules into multiple residue types If load_rotamers is false, each will be loaded as a single ResidueType Otherwise, entries with the same name will be loaded as rotamers Will not return results for entries with bad Data. More...

utility::vector1 < MutableResidueTypeOP >	convert_to_ResidueTypes (std::string const &filename, bool load_rotamers, std::string atom_type_tag, std::string elements_tag, std::string mm_atom_type_tag)
	Load a given file into one or more residue types If load_rotamers is false, each will be loaded as a single ResidueType Otherwise, entries with the same name will be loaded as rotamers. More...

utility::vector1 < MutableResidueTypeOP >	convert_to_ResidueTypes (std::string const &filename, bool load_rotamers, AtomTypeSetCOP atom_types, ElementSetCOP element_types, MMAtomTypeSetCOP mm_atom_types)
	Load a given file into one or more residue types If load_rotamers is false, each will be loaded as a single ResidueType Otherwise, entries with the same name will be loaded as rotamers. More...

static basic::Tracer	TR ("core.chemical.sdf.SDFParser")

Typedef Documentation

typedef core::Size core::chemical::sdf::AtomIndex

typedef core::Size core::chemical::sdf::BondIndex

typedef MolFileIOGraph::vertex_descriptor core::chemical::sdf::mioAD

typedef MolFileIOGraph::edge_descriptor core::chemical::sdf::mioBD

typedef utility::pointer::shared_ptr< const MolFileIOAtom > core::chemical::sdf::MolFileIOAtomCOP

typedef utility::pointer::shared_ptr< MolFileIOAtom > core::chemical::sdf::MolFileIOAtomOP

typedef utility::pointer::shared_ptr< const MolFileIOBond > core::chemical::sdf::MolFileIOBondCOP

typedef utility::pointer::shared_ptr< MolFileIOBond > core::chemical::sdf::MolFileIOBondOP

typedef boost::undirected_graph< MolFileIOAtomOP, MolFileIOBondOP > core::chemical::sdf::MolFileIOGraph

typedef utility::pointer::shared_ptr< const MolFileIOMolecule > core::chemical::sdf::MolFileIOMoleculeCOP

typedef utility::pointer::shared_ptr< MolFileIOMolecule > core::chemical::sdf::MolFileIOMoleculeOP

typedef std::map<std::string, std::string> core::chemical::sdf::StrStrMap

Function Documentation

MutableResidueTypeOP core::chemical::sdf::convert_to_ResidueType	(	utility::vector1< MolFileIOMoleculeOP >	molfile_data,
		std::string	atom_type_tag,
		std::string	elements_tag,
		std::string	mm_atom_type_tag
	)

Convert the vector of MolFileIOMolecules into a single residue type, using multiple entries as rotamers Can return a null pointer if there's something wrong with the underlying data.

Referenced by core::chemical::GlobalResidueTypeSet::attempt_readin(), and convert_to_ResidueTypes().

MutableResidueTypeOP core::chemical::sdf::convert_to_ResidueType	(	utility::vector1< MolFileIOMoleculeOP >	molfile_data,
		AtomTypeSetCOP	atom_types,
		ElementSetCOP	element_type_set,
		MMAtomTypeSetCOP	mm_atom_types
	)

Convert the vector of MolFileIOMolecules into a single residue type, using multiple entries as rotamers Can return a null pointer if there's something wrong with the underlying data.

References TR().

utility::vector1< MutableResidueTypeOP > core::chemical::sdf::convert_to_ResidueTypes	(	utility::vector1< MolFileIOMoleculeOP >	molfile_data,
		bool	load_rotamers,
		std::string	atom_type_tag,
		std::string	elements_tag,
		std::string	mm_atom_type_tag
	)

Convert the vector of MolFileIOMolecules into multiple residue types If load_rotamers is false, each will be loaded as a single ResidueType Otherwise, entries with the same name will be loaded as rotamers Will not return results for entries with bad Data.

Referenced by convert_to_ResidueTypes(), and core::chemical::GlobalResidueTypeSet::extra_nonparam_restypes_from_commandline().

utility::vector1< MutableResidueTypeOP > core::chemical::sdf::convert_to_ResidueTypes	(	utility::vector1< MolFileIOMoleculeOP >	molfile_data,
		bool	load_rotamers,
		AtomTypeSetCOP	atom_types,
		ElementSetCOP	element_types,
		MMAtomTypeSetCOP	mm_atom_types
	)

Convert the vector of MolFileIOMolecules into multiple residue types If load_rotamers is false, each will be loaded as a single ResidueType Otherwise, entries with the same name will be loaded as rotamers Will not return results for entries with bad Data.

References convert_to_ResidueType(), and TR().

utility::vector1< MutableResidueTypeOP > core::chemical::sdf::convert_to_ResidueTypes	(	std::string const &	filename,
		bool	load_rotamers,
		std::string	atom_type_tag,
		std::string	elements_tag,
		std::string	mm_atom_type_tag
	)

Load a given file into one or more residue types If load_rotamers is false, each will be loaded as a single ResidueType Otherwise, entries with the same name will be loaded as rotamers.

References convert_to_ResidueTypes().

utility::vector1< MutableResidueTypeOP > core::chemical::sdf::convert_to_ResidueTypes	(	std::string const &	filename,
		bool	load_rotamers,
		AtomTypeSetCOP	atom_types,
		ElementSetCOP	element_types,
		MMAtomTypeSetCOP	mm_atom_types
	)

Load a given file into one or more residue types If load_rotamers is false, each will be loaded as a single ResidueType Otherwise, entries with the same name will be loaded as rotamers.

References convert_to_ResidueTypes(), and core::chemical::sdf::MolFileIOReader::parse_file().

void core::chemical::sdf::dump_graph ( MolFileIOGraph const & graph )

References has(), and TR().

bool core::chemical::sdf::has	(	MolFileIOGraph const &	graph,
		mioAD	vd
	)

inline

Referenced by core::chemical::sdf::MolFileIOMolecule::atom_index(), core::chemical::sdf::MolFileIOMolecule::convert_to_ResidueType(), and dump_graph().

bool core::chemical::sdf::has	(	MolFileIOGraph const &	graph,
		mioBD	ed
	)

inline

template<class Input_t >

void core::chemical::sdf::output_residue	(	std::string const &	outfile,
		Input_t &	residue
	)

References core::chemical::sdf::MolWriter::output_residue().

Referenced by core::chemical::gasteiger::assign_gasteiger_atom_types().

template<class Input_t >

void core::chemical::sdf::output_residue	(	std::ostream &	output_stream,
		Input_t &	residue
	)

References core::chemical::sdf::MolWriter::output_residue().

std::map< core::Size, std::string > core::chemical::sdf::parse_atom_type_data ( std::string raw_data )

std::set< BondData > core::chemical::sdf::parse_bond_type_data ( std::string raw_data )

References protocols::sparta::split().

static basic::Tracer core::chemical::sdf::TR ( "core.chemical.sdf.CtabV2000Parser" )

static

static basic::Tracer core::chemical::sdf::TR ( "core.chemical.sdf.CtabV3000Parser" )

static

static basic::Tracer core::chemical::sdf::TR ( "core.io.sdf.MolFileIOReader" )

static

static basic::Tracer core::chemical::sdf::TR ( "core.chemical.sdf.SDFParser" )

static

static basic::Tracer core::chemical::sdf::tr ( "core.chemical.sdf.mol_writer" )

static

static basic::Tracer core::chemical::sdf::TR ( "core.io.sdf.MolFileIOData" )

static

Classes

Typedefs

Functions

Typedef Documentation

Function Documentation