Rosetta Core  2014.35
Classes | Typedefs | Functions | Variables
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< BondDataparse_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< ResidueTypeOPconvert_to_ResidueType (utility::vector1< MolFileIOMoleculeOP > molfile_data, std::string atom_type_tag, std::string elements_tag, std::string mm_atom_type_tag)
 
utility::vector1< ResidueTypeOPconvert_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 MolFileIOGraph::vertex_descriptor core::chemical::sdf::mioAD
typedef MolFileIOGraph::edge_descriptor core::chemical::sdf::mioBD
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 
)
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
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)
std::set< BondData > core::chemical::sdf::parse_bond_type_data ( std::string  raw_data)

Variable Documentation

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