core::chemical::sdf Namespace Reference

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::owning_ptr < MolFileIOAtom >	MolFileIOAtomOP
typedef utility::pointer::owning_ptr < MolFileIOBond >	MolFileIOBondOP
typedef utility::pointer::owning_ptr < MolFileIOMolecule >	MolFileIOMoleculeOP
typedef utility::pointer::owning_ptr < const MolFileIOAtom >	MolFileIOAtomCOP
typedef utility::pointer::owning_ptr < const MolFileIOBond >	MolFileIOBondCOP
typedef utility::pointer::owning_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
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)
void	dump_graph (MolFileIOGraph const &graph)
bool	has (MolFileIOGraph const &graph, mioAD vd)
bool	has (MolFileIOGraph const &graph, mioBD ed)
utility::vector1< ResidueTypeOP >	convert_to_ResidueType (utility::vector1< MolFileIOMoleculeOP > molfile_data, std::string atom_type_tag, std::string elements_tag, std::string mm_atom_type_tag)
utility::vector1< ResidueTypeOP >	convert_to_ResidueType (utility::vector1< MolFileIOMoleculeOP > molfile_data, AtomTypeSetCAP atom_types, ElementSetCAP element_type_set, MMAtomTypeSetCAP mm_atom_types)

Variables
static basic::Tracer	TR ("core.chemical.sdf.CtabV2000Parser")
static basic::Tracer	TR ("core.chemical.sdf.CtabV3000Parser")
static basic::Tracer	tr ("core.chemical.sdf.mol_writer")
static basic::Tracer	TR ("core.io.sdf.MolFileIOData")
static basic::Tracer	TR ("core.io.sdf.MolFileIOReader")
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::owning_ptr< const MolFileIOAtom > core::chemical::sdf::MolFileIOAtomCOP

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

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

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

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

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

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

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

Function Documentation

utility::vector1< ResidueTypeOP > 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
	)

References core::chemical::ChemicalManager::atom_type_set(), core::chemical::ChemicalManager::element_set(), core::chemical::ChemicalManager::get_instance(), and core::chemical::ChemicalManager::mm_atom_type_set().

Referenced by core::chemical::ChemicalManager::create_residue_type_set().

utility::vector1< ResidueTypeOP > core::chemical::sdf::convert_to_ResidueType	(	utility::vector1< MolFileIOMoleculeOP >	molfile_data,
		AtomTypeSetCAP	atom_types,
		ElementSetCAP	element_type_set,
		MMAtomTypeSetCAP	mm_atom_types
	)

References core::sequence::end.

void core::chemical::sdf::dump_graph

(

MolFileIOGraph const &

graph

)

References has(), target, 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

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

(

std::string

raw_data

)

References utility::string_split(), and utility::trim().

std::set< BondData > core::chemical::sdf::parse_bond_type_data

(

std::string

raw_data

)

References utility::from_string(), utility::split(), utility::string_split(), and type.

Variable Documentation

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

static

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

static

Referenced by core::chemical::sdf::MolFileIOMolecule::convert_to_ResidueType(), dump_graph(), core::chemical::sdf::SDFParser::parse(), core::chemical::sdf::CtabV2000Parser::parse(), core::chemical::sdf::CtabV2000Parser::parse_atom_line(), core::chemical::sdf::CtabV3000Parser::parse_atom_line(), core::chemical::sdf::CtabV2000Parser::parse_bond_line(), core::chemical::sdf::CtabV3000Parser::parse_bond_line(), core::chemical::sdf::MolFileIOReader::parse_file(), core::chemical::sdf::SDFParser::parse_optional_data(), core::chemical::sdf::CtabV2000Parser::parse_property_line(), and core::chemical::sdf::MolFileIOMolecule::set_from_extra_data().

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

static

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

static

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

static

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

static